From c4d71da4548fbae89eaaff7f38b33d334b7efbc7 Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Wed, 5 Jul 2023 17:09:49 -0700
Subject: [PATCH 01/99] all the new files for the "new style" build

---
 LICENSE.txt             |  2 +-
 conda_requirements.txt  |  4 +-
 py_gnome/LICENSE.txt    | 30 +++++++++++++++
 py_gnome/README.rst     | 84 +++++++++++++++++++++++++++++++++++++++++
 py_gnome/pyproject.toml |  4 ++
 py_gnome/setup.cfg      | 56 +++++++++++++++++++++++++++
 py_gnome/setup.py       | 69 ++++++++++++++++-----------------
 7 files changed, 212 insertions(+), 37 deletions(-)
 create mode 100644 py_gnome/LICENSE.txt
 create mode 100644 py_gnome/README.rst
 create mode 100644 py_gnome/pyproject.toml
 create mode 100644 py_gnome/setup.cfg

diff --git a/LICENSE.txt b/LICENSE.txt
index eb810dfdf..604a22710 100644
--- a/LICENSE.txt
+++ b/LICENSE.txt
@@ -27,4 +27,4 @@ OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
 ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 OTHER DEALINGS IN THE SOFTWARE.
 
-For more information, please refer to <http://unlicense.org/>
+For more information, please refer to <https://creativecommons.org/share-your-work/public-domain/cc0/>
diff --git a/conda_requirements.txt b/conda_requirements.txt
index ef8417395..d07ee41d8 100644
--- a/conda_requirements.txt
+++ b/conda_requirements.txt
@@ -55,11 +55,11 @@ progressbar
 
 
 # NOAA maintained packages
-gridded=0.5.5
+gridded>=0.5.5
 pynucos
 cell_tree2d
 py_gd=2.*
-# libgd  # this should be brought in by py_gd, but something odd was happening on the CI
+adios_db
 
 
 
diff --git a/py_gnome/LICENSE.txt b/py_gnome/LICENSE.txt
new file mode 100644
index 000000000..604a22710
--- /dev/null
+++ b/py_gnome/LICENSE.txt
@@ -0,0 +1,30 @@
+This work was created by an agency of the United States Federal Government.
+As such, it is released into the Public Domain.
+
+Neither the Federal Government nor NOAA makes any guarantee as to its
+suitability for any purpose.
+
+This is free and unencumbered software released into the public domain.
+
+Anyone is free to copy, modify, publish, use, compile, sell, or
+distribute this software, either in source code form or as a compiled
+binary, for any purpose, commercial or non-commercial, and by any
+means.
+
+In jurisdictions that recognize copyright laws, the author or authors
+of this software dedicate any and all copyright interest in the
+software to the public domain. We make this dedication for the benefit
+of the public at large and to the detriment of our heirs and
+successors. We intend this dedication to be an overt act of
+relinquishment in perpetuity of all present and future rights to this
+software under copyright law.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.
+
+For more information, please refer to <https://creativecommons.org/share-your-work/public-domain/cc0/>
diff --git a/py_gnome/README.rst b/py_gnome/README.rst
new file mode 100644
index 000000000..880302cb5
--- /dev/null
+++ b/py_gnome/README.rst
@@ -0,0 +1,84 @@
+
+.. image:: graphics/new_gnome_icon/GNOME_logo_450px-wide.png
+   :alt: GNOME Logo
+   :align: center
+
+#######
+PyGNOME
+#######
+
+
+Introduction
+============
+
+**GNOME** (General NOAA Operational Modeling Environment) is a modeling tool
+developed by the National Oceanic and Atmospheric Administration (**NOAA**),
+Office of Response and Restoration (**ORR**), Emergency Response Division.
+
+It is designed to support oil and other hazardous material spills in the coastal environment, and is also a ful featured, flexible particle tracking system, that can be used for other oceangraphic transport applications, such as fish larvae, maringe debris, etc.
+
+PyGNOME is a python package that encapsulates GNOME's functionality.
+
+Disclaimer:
+-----------
+
+**This code is under active development**
+
+* It should not be considered an officially endorsed NOAA product.
+* Output produced by this code should not be considered endorsed by NOAA.
+
+Documentation
+=============
+
+`Project Documentation <https://gnome.orr.noaa.gov/doc/pygnome/index.html>`_
+
+`FAQ <https://github.com/NOAA-ORR-ERD/GNOME2/wiki/FAQ---Troubleshoot>`_
+
+
+Installation
+============
+
+We have put some effort into making this package reasonably easy,
+or at least possible, to install in a number of ways on a few different computing platforms:
+
+ - OS-X
+ - Windows
+ - Linux (tested on CentOS 7)
+
+At this time, it must be compiled from the source code.
+
+The "tricky" part is installing the dependencies: details in the following:
+
+`Install using conda <./Installing.rst>`_
+
+The conda package manager is built primarily for scientific, engineering,
+and math applications it is the easiest way to get set up to use ``PyGNOME``, and it what is used in our development and testing process.
+
+If you don't want to / can't use conda -- here are some notes on that:
+
+`Installing Without Conda <./Install_without_conda.rst>`_
+
+
+The WebGNOME Interface:
+=======================
+
+Scripting is the most featureful way to access PyGNOME's capabilities.
+However we have developed a system that allows a user to create and run PyGNOME models from a web browser.
+
+There is a publicly available instance of WebGNOME at:
+
+https://gnome.orr.noaa.gov
+
+If you want to run your own instance of WebGNOME, the code is in the following projects:
+
+- `WebGnomeAPI <https://github.com/NOAA-ORR-ERD/WebGnomeAPI>`_:
+  A web server that implements the PyGNOME interface
+- `WebGnomeClient <https://github.com/NOAA-ORR-ERD/WebGnomeClient>`_:
+  A Web application for setting up and running PyGNOME models
+
+**Fair Warning:**
+
+The WebGNOME system is under active development, and by its very nature does not expose the full capabilities of PyGNOME.
+
+
+
diff --git a/py_gnome/pyproject.toml b/py_gnome/pyproject.toml
new file mode 100644
index 000000000..50636899a
--- /dev/null
+++ b/py_gnome/pyproject.toml
@@ -0,0 +1,4 @@
+
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
diff --git a/py_gnome/setup.cfg b/py_gnome/setup.cfg
new file mode 100644
index 000000000..d7bb24cf4
--- /dev/null
+++ b/py_gnome/setup.cfg
@@ -0,0 +1,56 @@
+[metadata]
+name = pyGnome
+version = attr: gnome.__version__
+author = Gnome team at NOAA/ORR/ERD
+author_email = orr.gnome@noaa.gov
+description = GNOME (General NOAA Operational Modeling Environment)
+              is the modeling tool the Office of Response and
+              Restoration's (OR&R) Emergency Response Division uses to
+              predict the possible route, or trajectory, a pollutant
+              might follow in or on a body of water, such as in an
+              oil spill. It can also be used as a customizable general particle tracking code.
+long_description = file: ./README.rst, ./LICENSE.rst
+keywords = "oilspill, modeling, particle-tracking"
+license = CC0-1.0
+classifiers =
+    Development Status :: 5 - Production/Stable
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: Implementation :: CPython
+    Programming Language :: C++
+    Programming Language :: Cython
+    Intended Audience :: Science/Research
+    License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
+    Natural Language :: English
+    Operating System :: OS Independent
+    Topic :: Scientific/Engineering
+    Topic :: Scientific/Engineering :: Oceanography
+
+
+[options]
+zip_safe = False
+include_package_data = True
+packages = find:
+python_requires = >=3.9
+# install_requires =
+#     requests
+#     importlib-metadata; python_version<"3.8"
+
+[options.package_data]
+gnome = 'data/yeardata/*',
+        'outputters/sample.b64',
+        'weatherers/platforms.json'
+
+[options.entry_points]
+console_scripts =
+    executable-name = my_package.module:function
+
+[options.extras_require]
+pdf = ReportLab>=1.2; RXP
+rest = docutils>=0.3; pack ==1.1, ==1.3
+
+[options.packages.find]
+exclude =
+    examples*
+    tools*
+    docs*
+    my_package.tests*
diff --git a/py_gnome/setup.py b/py_gnome/setup.py
index 745c96476..7c27f76ff 100755
--- a/py_gnome/setup.py
+++ b/py_gnome/setup.py
@@ -588,53 +588,54 @@ def get_conda_includes_win():
                                 language="c",
                                 ))
 
-def get_version():
-    """
-    return the version number from the __init__
-    """
-    for line in open("gnome/__init__.py"):
-        if line.startswith("__version__"):
-            version = line.strip().split('=')[1].strip().strip("'").strip('"')
-            return version
-    raise ValueError("can't find version string in __init__")
+# def get_version():
+#     """
+#     return the version number from the __init__
+#     """
+#     for line in open("gnome/__init__.py"):
+#         if line.startswith("__version__"):
+#             version = line.strip().split('=')[1].strip().strip("'").strip('"')
+#             return version
+#     raise ValueError("can't find version string in __init__")
 
 
 for e in extensions:
     e.cython_directives = {'language_level': "3"}  # all are Python-3
 
-setup(name='pyGnome',
-      version=get_version(),
-      ext_modules=extensions,
-      packages=find_packages(),
-      package_dir={'gnome': 'gnome'},
-      package_data={'gnome': ['data/yeardata/*',
-                              'outputters/sample.b64',
-                              'weatherers/platforms.json'
-                              ]},
+# setup(name='pyGnome',
+      # version=get_version(),
+
+setup(ext_modules=extensions,
+      # packages=find_packages(),
+      # package_dir={'gnome': 'gnome'},
+      # package_data={'gnome': ['data/yeardata/*',
+      #                         'outputters/sample.b64',
+      #                         'weatherers/platforms.json'
+      #                         ]},
       # you are not going to be able to "pip install" this anyway
       # -- no need for requirements
-      requires=[],   # want other packages here?
+#     requires=[],   # want other packages here?
       cmdclass={'build_ext': build_ext,
                 'cleanall': cleanall},
 
       # scripts,
 
       # metadata for upload to PyPI
-      author="Gnome team at NOAA/ORR/ERD",
-      author_email="orr.gnome@noaa.gov",
-      description=("GNOME (General NOAA Operational Modeling Environment) "
-                   "is the modeling tool the Office of Response and "
-                   "Restoration's (OR&R) Emergency Response Division uses to "
-                   "predict the possible route, or trajectory, a pollutant "
-                   "might follow in or on a body of water, such as in an "
-                   "oil spill.  "
-                   "It can also be used as a customizable general particle "
-                   "tracking code. "
-                   "Branch: {} "
-                   "LastUpdate: {}"
-                   .format(branch_name, last_update)),
-      license="Public Domain",
-      keywords="oilspill modeling particle_tracking",
+      # author="Gnome team at NOAA/ORR/ERD",
+      # author_email="orr.gnome@noaa.gov",
+      # description=("GNOME (General NOAA Operational Modeling Environment) "
+      #              "is the modeling tool the Office of Response and "
+      #              "Restoration's (OR&R) Emergency Response Division uses to "
+      #              "predict the possible route, or trajectory, a pollutant "
+      #              "might follow in or on a body of water, such as in an "
+      #              "oil spill.  "
+      #              "It can also be used as a customizable general particle "
+      #              "tracking code. "
+      #              "Branch: {} "
+      #              "LastUpdate: {}"
+      #              .format(branch_name, last_update)),
+      # license="Public Domain",
+      # keywords="oilspill modeling particle_tracking",
       url="https://github.com/NOAA-ORR-ERD/PyGnome"
       )
 

From 3b1d4f15a1326f0ec20db17d0a2b5fa02ce4c535 Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Thu, 6 Jul 2023 16:16:45 -0700
Subject: [PATCH 02/99] moved lib_gnome, and added MANIFEST.in

---
 py_gnome/MANIFEST.in                          |  5 +++
 .../conda_requirements.txt                    |  0
 .../conda_requirements_build.txt              |  2 ++
 .../conda_requirements_docs.txt               |  0
 .../conda_requirements_test.txt               |  0
 .../lib_gnome}/ADCPMover_c.cpp                |  0
 .../lib_gnome}/ADCPMover_c.h                  |  0
 .../lib_gnome}/ADCPTimeValue_c.cpp            |  0
 .../lib_gnome}/ADCPTimeValue_c.h              |  0
 {lib_gnome => py_gnome/lib_gnome}/Basics.h    |  0
 .../lib_gnome}/CATSMover3D_c.cpp              |  0
 .../lib_gnome}/CATSMover3D_c.h                |  0
 .../lib_gnome}/CATSMover_c.cpp                |  0
 .../lib_gnome}/CATSMover_c.h                  |  0
 {lib_gnome => py_gnome/lib_gnome}/CMYLIST.CPP |  0
 {lib_gnome => py_gnome/lib_gnome}/CMYLIST.H   |  0
 {lib_gnome => py_gnome/lib_gnome}/CMap2.cpp   |  0
 {lib_gnome => py_gnome/lib_gnome}/CMap2.h     |  0
 .../lib_gnome}/CMapLayer_c.cpp                |  0
 .../lib_gnome}/ClassID_c.cpp                  |  0
 {lib_gnome => py_gnome/lib_gnome}/ClassID_c.h |  0
 .../lib_gnome}/CompFunctions.cpp              |  0
 .../lib_gnome}/CompFunctions.h                |  0
 .../lib_gnome}/ComponentMover_c.cpp           |  0
 .../lib_gnome}/ComponentMover_c.h             |  0
 .../lib_gnome}/CompoundMap_c.cpp              |  0
 .../lib_gnome}/CompoundMap_c.h                |  0
 .../lib_gnome}/CompoundMover_c.cpp            |  0
 .../lib_gnome}/CompoundMover_c.h              |  0
 .../lib_gnome}/CurrentCycleMover_c.cpp        |  0
 .../lib_gnome}/CurrentCycleMover_c.h          |  0
 .../lib_gnome}/CurrentMover_c.cpp             |  0
 .../lib_gnome}/CurrentMover_c.h               |  0
 {lib_gnome => py_gnome/lib_gnome}/DagStruct.h |  0
 {lib_gnome => py_gnome/lib_gnome}/DagTree.cpp |  0
 {lib_gnome => py_gnome/lib_gnome}/DagTree.h   |  0
 .../lib_gnome}/DagTreeIO.cpp                  |  0
 {lib_gnome => py_gnome/lib_gnome}/DagTreeIO.h |  0
 .../lib_gnome}/ExportSymbols.h                |  0
 {lib_gnome => py_gnome/lib_gnome}/GENDEFS.H   |  0
 .../lib_gnome}/GEOMETR2.CPP                   |  0
 {lib_gnome => py_gnome/lib_gnome}/GEOMETRY.H  |  0
 .../lib_gnome}/GEOMETRY.cpp                   |  0
 .../lib_gnome}/GridCurMover_c.cpp             |  0
 .../lib_gnome}/GridCurMover_c.h               |  0
 .../lib_gnome}/GridCurrentMover_c.cpp         |  0
 .../lib_gnome}/GridCurrentMover_c.h           |  0
 .../lib_gnome}/GridMapUtils.cpp               |  0
 .../lib_gnome}/GridMapUtils.h                 |  0
 .../lib_gnome}/GridMap_c.cpp                  |  0
 {lib_gnome => py_gnome/lib_gnome}/GridMap_c.h |  0
 {lib_gnome => py_gnome/lib_gnome}/GridVel_c.h |  0
 .../lib_gnome}/GridWindMover_c.cpp            |  0
 .../lib_gnome}/GridWindMover_c.h              |  0
 .../lib_gnome}/GridWndMover_c.cpp             |  0
 .../lib_gnome}/GridWndMover_c.h               |  0
 .../lib_gnome}/IceMover_c.cpp                 |  0
 .../lib_gnome}/IceMover_c.h                   |  0
 .../lib_gnome}/IceWindMover_c.cpp             |  0
 .../lib_gnome}/IceWindMover_c.h               |  0
 .../lib_gnome}/LEList_c.cpp                   |  0
 {lib_gnome => py_gnome/lib_gnome}/LEList_c.h  |  0
 .../lib_gnome}/LocaleWizard_c.cpp             |  0
 .../lib_gnome}/LocaleWizard_c.h               |  0
 .../lib_gnome}/MYRANDOM.CPP                   |  0
 {lib_gnome => py_gnome/lib_gnome}/MYRANDOM.H  |  0
 .../lib_gnome}/MakeDagTree.cpp                |  0
 .../lib_gnome}/MakeTriangles.cpp              |  0
 {lib_gnome => py_gnome/lib_gnome}/Map3D_c.cpp |  0
 {lib_gnome => py_gnome/lib_gnome}/Map3D_c.h   |  0
 .../lib_gnome}/MapUtils.cpp                   |  0
 {lib_gnome => py_gnome/lib_gnome}/MapUtils.h  |  0
 {lib_gnome => py_gnome/lib_gnome}/Map_c.cpp   |  0
 {lib_gnome => py_gnome/lib_gnome}/Map_c.h     |  0
 .../lib_gnome}/MemUtils.cpp                   |  0
 {lib_gnome => py_gnome/lib_gnome}/MemUtils.h  |  0
 {lib_gnome => py_gnome/lib_gnome}/Model_c.cpp |  0
 {lib_gnome => py_gnome/lib_gnome}/Model_c.h   |  0
 {lib_gnome => py_gnome/lib_gnome}/Mover_c.cpp |  0
 {lib_gnome => py_gnome/lib_gnome}/Mover_c.h   |  0
 .../lib_gnome}/NetCDFMoverCurv_c.cpp          |  0
 .../lib_gnome}/NetCDFMoverCurv_c.h            |  0
 .../lib_gnome}/NetCDFMoverTri_c.cpp           |  0
 .../lib_gnome}/NetCDFMoverTri_c.h             |  0
 .../lib_gnome}/NetCDFMover_c.cpp              |  0
 .../lib_gnome}/NetCDFMover_c.h                |  0
 .../lib_gnome}/NetCDFWindMoverCurv_c.cpp      |  0
 .../lib_gnome}/NetCDFWindMoverCurv_c.h        |  0
 .../lib_gnome}/NetCDFWindMover_c.cpp          |  0
 .../lib_gnome}/NetCDFWindMover_c.h            |  0
 .../lib_gnome}/OLEList_c.cpp                  |  0
 {lib_gnome => py_gnome/lib_gnome}/OLEList_c.h |  0
 .../lib_gnome}/OSSMTimeValue_c.cpp            |  0
 .../lib_gnome}/OSSMTimeValue_c.h              |  0
 .../lib_gnome}/OSSMWeatherer_c.cpp            |  0
 .../lib_gnome}/OSSMWeatherer_c.h              |  0
 {lib_gnome => py_gnome/lib_gnome}/OUTILS.H    |  0
 {lib_gnome => py_gnome/lib_gnome}/OUTILS.cpp  |  0
 .../lib_gnome}/ObjectUtils.h                  |  0
 .../lib_gnome}/PtCurMap_c.cpp                 |  0
 .../lib_gnome}/PtCurMap_c.h                   |  0
 .../lib_gnome}/PtCurMover_c.cpp               |  0
 .../lib_gnome}/PtCurMover_c.h                 |  0
 .../lib_gnome}/Random3D_c.cpp                 |  0
 .../lib_gnome}/Random3D_c.h                   |  0
 .../lib_gnome}/RandomVertical_c.cpp           |  0
 .../lib_gnome}/RandomVertical_c.h             |  0
 .../lib_gnome}/Random_c.cpp                   |  0
 {lib_gnome => py_gnome/lib_gnome}/Random_c.h  |  0
 .../lib_gnome}/RectGridVeL_c.cpp              |  0
 .../lib_gnome}/RectGridVeL_c.h                |  0
 .../lib_gnome}/RectUtils.cpp                  |  0
 {lib_gnome => py_gnome/lib_gnome}/RectUtils.h |  0
 .../lib_gnome}/Replacements.cpp               |  0
 .../lib_gnome}/Replacements.h                 |  0
 .../lib_gnome}/RiseVelocity_c.cpp             |  0
 .../lib_gnome}/RiseVelocity_c.h               |  0
 {lib_gnome => py_gnome/lib_gnome}/Shio.h      |  0
 .../lib_gnome}/ShioCurrent1.cpp               |  0
 .../lib_gnome}/ShioCurrent2.cpp               |  0
 .../lib_gnome}/ShioHeight.cpp                 |  0
 .../lib_gnome}/ShioTimeValue_c.cpp            |  0
 .../lib_gnome}/ShioTimeValue_c.h              |  0
 .../lib_gnome}/StringFunctions.cpp            |  0
 .../lib_gnome}/StringFunctions.h              |  0
 .../lib_gnome}/TideCurCycleMover_c.cpp        |  0
 .../lib_gnome}/TideCurCycleMover_c.h          |  0
 .../lib_gnome}/TimeGridVel_c.cpp              |  0
 .../lib_gnome}/TimeGridVel_c.h                |  0
 .../lib_gnome}/TimeGridWind_c.cpp             |  0
 .../lib_gnome}/TimeGridWind_c.h               |  0
 .../lib_gnome}/TimeValue_c.cpp                |  0
 .../lib_gnome}/TimeValue_c.h                  |  0
 .../lib_gnome}/TimeValuesIO.cpp               |  0
 .../lib_gnome}/TimeValuesIO.h                 |  0
 .../lib_gnome}/TriCurMover_c.cpp              |  0
 .../lib_gnome}/TriCurMover_c.h                |  0
 .../lib_gnome}/TriGridVel3D_c.cpp             |  0
 .../lib_gnome}/TriGridVel3D_c.h               |  0
 .../lib_gnome}/TriGridVel_c.cpp               |  0
 .../lib_gnome}/TriGridVel_c.h                 |  0
 {lib_gnome => py_gnome/lib_gnome}/TypeDefs.h  |  0
 {lib_gnome => py_gnome/lib_gnome}/Units.h     |  0
 .../lib_gnome}/VectMap_c.cpp                  |  0
 {lib_gnome => py_gnome/lib_gnome}/VectMap_c.h |  0
 .../lib_gnome}/Weatherer_c.cpp                |  0
 .../lib_gnome}/Weatherer_c.h                  |  0
 .../lib_gnome}/Weatherers_c.cpp               |  0
 .../lib_gnome}/Weatherers_c.h                 |  0
 .../lib_gnome}/WindMover_c.cpp                |  0
 .../lib_gnome}/WindMover_c.h                  |  0
 .../lib_gnome}/my_build_list.h                |  0
 py_gnome/setup.cfg                            |  2 +-
 py_gnome/setup.py                             | 33 +++++++++++--------
 154 files changed, 28 insertions(+), 14 deletions(-)
 create mode 100644 py_gnome/MANIFEST.in
 rename conda_requirements.txt => py_gnome/conda_requirements.txt (100%)
 rename conda_requirements_build.txt => py_gnome/conda_requirements_build.txt (92%)
 rename conda_requirements_docs.txt => py_gnome/conda_requirements_docs.txt (100%)
 rename conda_requirements_test.txt => py_gnome/conda_requirements_test.txt (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ADCPMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ADCPMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ADCPTimeValue_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ADCPTimeValue_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Basics.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CATSMover3D_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CATSMover3D_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CATSMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CATSMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CMYLIST.CPP (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CMYLIST.H (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CMap2.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CMap2.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CMapLayer_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ClassID_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ClassID_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CompFunctions.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CompFunctions.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ComponentMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ComponentMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CompoundMap_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CompoundMap_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CompoundMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CompoundMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CurrentCycleMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CurrentCycleMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CurrentMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/CurrentMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/DagStruct.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/DagTree.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/DagTree.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/DagTreeIO.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/DagTreeIO.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ExportSymbols.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GENDEFS.H (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GEOMETR2.CPP (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GEOMETRY.H (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GEOMETRY.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GridCurMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GridCurMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GridCurrentMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GridCurrentMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GridMapUtils.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GridMapUtils.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GridMap_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GridMap_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GridVel_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GridWindMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GridWindMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GridWndMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/GridWndMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/IceMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/IceMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/IceWindMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/IceWindMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/LEList_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/LEList_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/LocaleWizard_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/LocaleWizard_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/MYRANDOM.CPP (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/MYRANDOM.H (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/MakeDagTree.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/MakeTriangles.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Map3D_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Map3D_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/MapUtils.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/MapUtils.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Map_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Map_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/MemUtils.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/MemUtils.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Model_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Model_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Mover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Mover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/NetCDFMoverCurv_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/NetCDFMoverCurv_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/NetCDFMoverTri_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/NetCDFMoverTri_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/NetCDFMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/NetCDFMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/NetCDFWindMoverCurv_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/NetCDFWindMoverCurv_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/NetCDFWindMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/NetCDFWindMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/OLEList_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/OLEList_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/OSSMTimeValue_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/OSSMTimeValue_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/OSSMWeatherer_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/OSSMWeatherer_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/OUTILS.H (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/OUTILS.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ObjectUtils.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/PtCurMap_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/PtCurMap_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/PtCurMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/PtCurMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Random3D_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Random3D_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/RandomVertical_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/RandomVertical_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Random_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Random_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/RectGridVeL_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/RectGridVeL_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/RectUtils.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/RectUtils.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Replacements.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Replacements.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/RiseVelocity_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/RiseVelocity_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Shio.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ShioCurrent1.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ShioCurrent2.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ShioHeight.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ShioTimeValue_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/ShioTimeValue_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/StringFunctions.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/StringFunctions.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TideCurCycleMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TideCurCycleMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TimeGridVel_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TimeGridVel_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TimeGridWind_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TimeGridWind_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TimeValue_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TimeValue_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TimeValuesIO.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TimeValuesIO.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TriCurMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TriCurMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TriGridVel3D_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TriGridVel3D_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TriGridVel_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TriGridVel_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/TypeDefs.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Units.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/VectMap_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/VectMap_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Weatherer_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Weatherer_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Weatherers_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/Weatherers_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/WindMover_c.cpp (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/WindMover_c.h (100%)
 rename {lib_gnome => py_gnome/lib_gnome}/my_build_list.h (100%)

diff --git a/py_gnome/MANIFEST.in b/py_gnome/MANIFEST.in
new file mode 100644
index 000000000..6633ee542
--- /dev/null
+++ b/py_gnome/MANIFEST.in
@@ -0,0 +1,5 @@
+# include of of lib_gnome in the source dist
+graft lib_gnome
+include gnome/cy_gnome/*.pyx
+include gnome/cy_gnome/*.pxd
+
diff --git a/conda_requirements.txt b/py_gnome/conda_requirements.txt
similarity index 100%
rename from conda_requirements.txt
rename to py_gnome/conda_requirements.txt
diff --git a/conda_requirements_build.txt b/py_gnome/conda_requirements_build.txt
similarity index 92%
rename from conda_requirements_build.txt
rename to py_gnome/conda_requirements_build.txt
index c1fe19a37..deb9da4f3 100644
--- a/conda_requirements_build.txt
+++ b/py_gnome/conda_requirements_build.txt
@@ -4,3 +4,5 @@
 cython=0.29.*
 setuptools>=62  # older versions uses different build dirs
 gitpython
+python-build
+
diff --git a/conda_requirements_docs.txt b/py_gnome/conda_requirements_docs.txt
similarity index 100%
rename from conda_requirements_docs.txt
rename to py_gnome/conda_requirements_docs.txt
diff --git a/conda_requirements_test.txt b/py_gnome/conda_requirements_test.txt
similarity index 100%
rename from conda_requirements_test.txt
rename to py_gnome/conda_requirements_test.txt
diff --git a/lib_gnome/ADCPMover_c.cpp b/py_gnome/lib_gnome/ADCPMover_c.cpp
similarity index 100%
rename from lib_gnome/ADCPMover_c.cpp
rename to py_gnome/lib_gnome/ADCPMover_c.cpp
diff --git a/lib_gnome/ADCPMover_c.h b/py_gnome/lib_gnome/ADCPMover_c.h
similarity index 100%
rename from lib_gnome/ADCPMover_c.h
rename to py_gnome/lib_gnome/ADCPMover_c.h
diff --git a/lib_gnome/ADCPTimeValue_c.cpp b/py_gnome/lib_gnome/ADCPTimeValue_c.cpp
similarity index 100%
rename from lib_gnome/ADCPTimeValue_c.cpp
rename to py_gnome/lib_gnome/ADCPTimeValue_c.cpp
diff --git a/lib_gnome/ADCPTimeValue_c.h b/py_gnome/lib_gnome/ADCPTimeValue_c.h
similarity index 100%
rename from lib_gnome/ADCPTimeValue_c.h
rename to py_gnome/lib_gnome/ADCPTimeValue_c.h
diff --git a/lib_gnome/Basics.h b/py_gnome/lib_gnome/Basics.h
similarity index 100%
rename from lib_gnome/Basics.h
rename to py_gnome/lib_gnome/Basics.h
diff --git a/lib_gnome/CATSMover3D_c.cpp b/py_gnome/lib_gnome/CATSMover3D_c.cpp
similarity index 100%
rename from lib_gnome/CATSMover3D_c.cpp
rename to py_gnome/lib_gnome/CATSMover3D_c.cpp
diff --git a/lib_gnome/CATSMover3D_c.h b/py_gnome/lib_gnome/CATSMover3D_c.h
similarity index 100%
rename from lib_gnome/CATSMover3D_c.h
rename to py_gnome/lib_gnome/CATSMover3D_c.h
diff --git a/lib_gnome/CATSMover_c.cpp b/py_gnome/lib_gnome/CATSMover_c.cpp
similarity index 100%
rename from lib_gnome/CATSMover_c.cpp
rename to py_gnome/lib_gnome/CATSMover_c.cpp
diff --git a/lib_gnome/CATSMover_c.h b/py_gnome/lib_gnome/CATSMover_c.h
similarity index 100%
rename from lib_gnome/CATSMover_c.h
rename to py_gnome/lib_gnome/CATSMover_c.h
diff --git a/lib_gnome/CMYLIST.CPP b/py_gnome/lib_gnome/CMYLIST.CPP
similarity index 100%
rename from lib_gnome/CMYLIST.CPP
rename to py_gnome/lib_gnome/CMYLIST.CPP
diff --git a/lib_gnome/CMYLIST.H b/py_gnome/lib_gnome/CMYLIST.H
similarity index 100%
rename from lib_gnome/CMYLIST.H
rename to py_gnome/lib_gnome/CMYLIST.H
diff --git a/lib_gnome/CMap2.cpp b/py_gnome/lib_gnome/CMap2.cpp
similarity index 100%
rename from lib_gnome/CMap2.cpp
rename to py_gnome/lib_gnome/CMap2.cpp
diff --git a/lib_gnome/CMap2.h b/py_gnome/lib_gnome/CMap2.h
similarity index 100%
rename from lib_gnome/CMap2.h
rename to py_gnome/lib_gnome/CMap2.h
diff --git a/lib_gnome/CMapLayer_c.cpp b/py_gnome/lib_gnome/CMapLayer_c.cpp
similarity index 100%
rename from lib_gnome/CMapLayer_c.cpp
rename to py_gnome/lib_gnome/CMapLayer_c.cpp
diff --git a/lib_gnome/ClassID_c.cpp b/py_gnome/lib_gnome/ClassID_c.cpp
similarity index 100%
rename from lib_gnome/ClassID_c.cpp
rename to py_gnome/lib_gnome/ClassID_c.cpp
diff --git a/lib_gnome/ClassID_c.h b/py_gnome/lib_gnome/ClassID_c.h
similarity index 100%
rename from lib_gnome/ClassID_c.h
rename to py_gnome/lib_gnome/ClassID_c.h
diff --git a/lib_gnome/CompFunctions.cpp b/py_gnome/lib_gnome/CompFunctions.cpp
similarity index 100%
rename from lib_gnome/CompFunctions.cpp
rename to py_gnome/lib_gnome/CompFunctions.cpp
diff --git a/lib_gnome/CompFunctions.h b/py_gnome/lib_gnome/CompFunctions.h
similarity index 100%
rename from lib_gnome/CompFunctions.h
rename to py_gnome/lib_gnome/CompFunctions.h
diff --git a/lib_gnome/ComponentMover_c.cpp b/py_gnome/lib_gnome/ComponentMover_c.cpp
similarity index 100%
rename from lib_gnome/ComponentMover_c.cpp
rename to py_gnome/lib_gnome/ComponentMover_c.cpp
diff --git a/lib_gnome/ComponentMover_c.h b/py_gnome/lib_gnome/ComponentMover_c.h
similarity index 100%
rename from lib_gnome/ComponentMover_c.h
rename to py_gnome/lib_gnome/ComponentMover_c.h
diff --git a/lib_gnome/CompoundMap_c.cpp b/py_gnome/lib_gnome/CompoundMap_c.cpp
similarity index 100%
rename from lib_gnome/CompoundMap_c.cpp
rename to py_gnome/lib_gnome/CompoundMap_c.cpp
diff --git a/lib_gnome/CompoundMap_c.h b/py_gnome/lib_gnome/CompoundMap_c.h
similarity index 100%
rename from lib_gnome/CompoundMap_c.h
rename to py_gnome/lib_gnome/CompoundMap_c.h
diff --git a/lib_gnome/CompoundMover_c.cpp b/py_gnome/lib_gnome/CompoundMover_c.cpp
similarity index 100%
rename from lib_gnome/CompoundMover_c.cpp
rename to py_gnome/lib_gnome/CompoundMover_c.cpp
diff --git a/lib_gnome/CompoundMover_c.h b/py_gnome/lib_gnome/CompoundMover_c.h
similarity index 100%
rename from lib_gnome/CompoundMover_c.h
rename to py_gnome/lib_gnome/CompoundMover_c.h
diff --git a/lib_gnome/CurrentCycleMover_c.cpp b/py_gnome/lib_gnome/CurrentCycleMover_c.cpp
similarity index 100%
rename from lib_gnome/CurrentCycleMover_c.cpp
rename to py_gnome/lib_gnome/CurrentCycleMover_c.cpp
diff --git a/lib_gnome/CurrentCycleMover_c.h b/py_gnome/lib_gnome/CurrentCycleMover_c.h
similarity index 100%
rename from lib_gnome/CurrentCycleMover_c.h
rename to py_gnome/lib_gnome/CurrentCycleMover_c.h
diff --git a/lib_gnome/CurrentMover_c.cpp b/py_gnome/lib_gnome/CurrentMover_c.cpp
similarity index 100%
rename from lib_gnome/CurrentMover_c.cpp
rename to py_gnome/lib_gnome/CurrentMover_c.cpp
diff --git a/lib_gnome/CurrentMover_c.h b/py_gnome/lib_gnome/CurrentMover_c.h
similarity index 100%
rename from lib_gnome/CurrentMover_c.h
rename to py_gnome/lib_gnome/CurrentMover_c.h
diff --git a/lib_gnome/DagStruct.h b/py_gnome/lib_gnome/DagStruct.h
similarity index 100%
rename from lib_gnome/DagStruct.h
rename to py_gnome/lib_gnome/DagStruct.h
diff --git a/lib_gnome/DagTree.cpp b/py_gnome/lib_gnome/DagTree.cpp
similarity index 100%
rename from lib_gnome/DagTree.cpp
rename to py_gnome/lib_gnome/DagTree.cpp
diff --git a/lib_gnome/DagTree.h b/py_gnome/lib_gnome/DagTree.h
similarity index 100%
rename from lib_gnome/DagTree.h
rename to py_gnome/lib_gnome/DagTree.h
diff --git a/lib_gnome/DagTreeIO.cpp b/py_gnome/lib_gnome/DagTreeIO.cpp
similarity index 100%
rename from lib_gnome/DagTreeIO.cpp
rename to py_gnome/lib_gnome/DagTreeIO.cpp
diff --git a/lib_gnome/DagTreeIO.h b/py_gnome/lib_gnome/DagTreeIO.h
similarity index 100%
rename from lib_gnome/DagTreeIO.h
rename to py_gnome/lib_gnome/DagTreeIO.h
diff --git a/lib_gnome/ExportSymbols.h b/py_gnome/lib_gnome/ExportSymbols.h
similarity index 100%
rename from lib_gnome/ExportSymbols.h
rename to py_gnome/lib_gnome/ExportSymbols.h
diff --git a/lib_gnome/GENDEFS.H b/py_gnome/lib_gnome/GENDEFS.H
similarity index 100%
rename from lib_gnome/GENDEFS.H
rename to py_gnome/lib_gnome/GENDEFS.H
diff --git a/lib_gnome/GEOMETR2.CPP b/py_gnome/lib_gnome/GEOMETR2.CPP
similarity index 100%
rename from lib_gnome/GEOMETR2.CPP
rename to py_gnome/lib_gnome/GEOMETR2.CPP
diff --git a/lib_gnome/GEOMETRY.H b/py_gnome/lib_gnome/GEOMETRY.H
similarity index 100%
rename from lib_gnome/GEOMETRY.H
rename to py_gnome/lib_gnome/GEOMETRY.H
diff --git a/lib_gnome/GEOMETRY.cpp b/py_gnome/lib_gnome/GEOMETRY.cpp
similarity index 100%
rename from lib_gnome/GEOMETRY.cpp
rename to py_gnome/lib_gnome/GEOMETRY.cpp
diff --git a/lib_gnome/GridCurMover_c.cpp b/py_gnome/lib_gnome/GridCurMover_c.cpp
similarity index 100%
rename from lib_gnome/GridCurMover_c.cpp
rename to py_gnome/lib_gnome/GridCurMover_c.cpp
diff --git a/lib_gnome/GridCurMover_c.h b/py_gnome/lib_gnome/GridCurMover_c.h
similarity index 100%
rename from lib_gnome/GridCurMover_c.h
rename to py_gnome/lib_gnome/GridCurMover_c.h
diff --git a/lib_gnome/GridCurrentMover_c.cpp b/py_gnome/lib_gnome/GridCurrentMover_c.cpp
similarity index 100%
rename from lib_gnome/GridCurrentMover_c.cpp
rename to py_gnome/lib_gnome/GridCurrentMover_c.cpp
diff --git a/lib_gnome/GridCurrentMover_c.h b/py_gnome/lib_gnome/GridCurrentMover_c.h
similarity index 100%
rename from lib_gnome/GridCurrentMover_c.h
rename to py_gnome/lib_gnome/GridCurrentMover_c.h
diff --git a/lib_gnome/GridMapUtils.cpp b/py_gnome/lib_gnome/GridMapUtils.cpp
similarity index 100%
rename from lib_gnome/GridMapUtils.cpp
rename to py_gnome/lib_gnome/GridMapUtils.cpp
diff --git a/lib_gnome/GridMapUtils.h b/py_gnome/lib_gnome/GridMapUtils.h
similarity index 100%
rename from lib_gnome/GridMapUtils.h
rename to py_gnome/lib_gnome/GridMapUtils.h
diff --git a/lib_gnome/GridMap_c.cpp b/py_gnome/lib_gnome/GridMap_c.cpp
similarity index 100%
rename from lib_gnome/GridMap_c.cpp
rename to py_gnome/lib_gnome/GridMap_c.cpp
diff --git a/lib_gnome/GridMap_c.h b/py_gnome/lib_gnome/GridMap_c.h
similarity index 100%
rename from lib_gnome/GridMap_c.h
rename to py_gnome/lib_gnome/GridMap_c.h
diff --git a/lib_gnome/GridVel_c.h b/py_gnome/lib_gnome/GridVel_c.h
similarity index 100%
rename from lib_gnome/GridVel_c.h
rename to py_gnome/lib_gnome/GridVel_c.h
diff --git a/lib_gnome/GridWindMover_c.cpp b/py_gnome/lib_gnome/GridWindMover_c.cpp
similarity index 100%
rename from lib_gnome/GridWindMover_c.cpp
rename to py_gnome/lib_gnome/GridWindMover_c.cpp
diff --git a/lib_gnome/GridWindMover_c.h b/py_gnome/lib_gnome/GridWindMover_c.h
similarity index 100%
rename from lib_gnome/GridWindMover_c.h
rename to py_gnome/lib_gnome/GridWindMover_c.h
diff --git a/lib_gnome/GridWndMover_c.cpp b/py_gnome/lib_gnome/GridWndMover_c.cpp
similarity index 100%
rename from lib_gnome/GridWndMover_c.cpp
rename to py_gnome/lib_gnome/GridWndMover_c.cpp
diff --git a/lib_gnome/GridWndMover_c.h b/py_gnome/lib_gnome/GridWndMover_c.h
similarity index 100%
rename from lib_gnome/GridWndMover_c.h
rename to py_gnome/lib_gnome/GridWndMover_c.h
diff --git a/lib_gnome/IceMover_c.cpp b/py_gnome/lib_gnome/IceMover_c.cpp
similarity index 100%
rename from lib_gnome/IceMover_c.cpp
rename to py_gnome/lib_gnome/IceMover_c.cpp
diff --git a/lib_gnome/IceMover_c.h b/py_gnome/lib_gnome/IceMover_c.h
similarity index 100%
rename from lib_gnome/IceMover_c.h
rename to py_gnome/lib_gnome/IceMover_c.h
diff --git a/lib_gnome/IceWindMover_c.cpp b/py_gnome/lib_gnome/IceWindMover_c.cpp
similarity index 100%
rename from lib_gnome/IceWindMover_c.cpp
rename to py_gnome/lib_gnome/IceWindMover_c.cpp
diff --git a/lib_gnome/IceWindMover_c.h b/py_gnome/lib_gnome/IceWindMover_c.h
similarity index 100%
rename from lib_gnome/IceWindMover_c.h
rename to py_gnome/lib_gnome/IceWindMover_c.h
diff --git a/lib_gnome/LEList_c.cpp b/py_gnome/lib_gnome/LEList_c.cpp
similarity index 100%
rename from lib_gnome/LEList_c.cpp
rename to py_gnome/lib_gnome/LEList_c.cpp
diff --git a/lib_gnome/LEList_c.h b/py_gnome/lib_gnome/LEList_c.h
similarity index 100%
rename from lib_gnome/LEList_c.h
rename to py_gnome/lib_gnome/LEList_c.h
diff --git a/lib_gnome/LocaleWizard_c.cpp b/py_gnome/lib_gnome/LocaleWizard_c.cpp
similarity index 100%
rename from lib_gnome/LocaleWizard_c.cpp
rename to py_gnome/lib_gnome/LocaleWizard_c.cpp
diff --git a/lib_gnome/LocaleWizard_c.h b/py_gnome/lib_gnome/LocaleWizard_c.h
similarity index 100%
rename from lib_gnome/LocaleWizard_c.h
rename to py_gnome/lib_gnome/LocaleWizard_c.h
diff --git a/lib_gnome/MYRANDOM.CPP b/py_gnome/lib_gnome/MYRANDOM.CPP
similarity index 100%
rename from lib_gnome/MYRANDOM.CPP
rename to py_gnome/lib_gnome/MYRANDOM.CPP
diff --git a/lib_gnome/MYRANDOM.H b/py_gnome/lib_gnome/MYRANDOM.H
similarity index 100%
rename from lib_gnome/MYRANDOM.H
rename to py_gnome/lib_gnome/MYRANDOM.H
diff --git a/lib_gnome/MakeDagTree.cpp b/py_gnome/lib_gnome/MakeDagTree.cpp
similarity index 100%
rename from lib_gnome/MakeDagTree.cpp
rename to py_gnome/lib_gnome/MakeDagTree.cpp
diff --git a/lib_gnome/MakeTriangles.cpp b/py_gnome/lib_gnome/MakeTriangles.cpp
similarity index 100%
rename from lib_gnome/MakeTriangles.cpp
rename to py_gnome/lib_gnome/MakeTriangles.cpp
diff --git a/lib_gnome/Map3D_c.cpp b/py_gnome/lib_gnome/Map3D_c.cpp
similarity index 100%
rename from lib_gnome/Map3D_c.cpp
rename to py_gnome/lib_gnome/Map3D_c.cpp
diff --git a/lib_gnome/Map3D_c.h b/py_gnome/lib_gnome/Map3D_c.h
similarity index 100%
rename from lib_gnome/Map3D_c.h
rename to py_gnome/lib_gnome/Map3D_c.h
diff --git a/lib_gnome/MapUtils.cpp b/py_gnome/lib_gnome/MapUtils.cpp
similarity index 100%
rename from lib_gnome/MapUtils.cpp
rename to py_gnome/lib_gnome/MapUtils.cpp
diff --git a/lib_gnome/MapUtils.h b/py_gnome/lib_gnome/MapUtils.h
similarity index 100%
rename from lib_gnome/MapUtils.h
rename to py_gnome/lib_gnome/MapUtils.h
diff --git a/lib_gnome/Map_c.cpp b/py_gnome/lib_gnome/Map_c.cpp
similarity index 100%
rename from lib_gnome/Map_c.cpp
rename to py_gnome/lib_gnome/Map_c.cpp
diff --git a/lib_gnome/Map_c.h b/py_gnome/lib_gnome/Map_c.h
similarity index 100%
rename from lib_gnome/Map_c.h
rename to py_gnome/lib_gnome/Map_c.h
diff --git a/lib_gnome/MemUtils.cpp b/py_gnome/lib_gnome/MemUtils.cpp
similarity index 100%
rename from lib_gnome/MemUtils.cpp
rename to py_gnome/lib_gnome/MemUtils.cpp
diff --git a/lib_gnome/MemUtils.h b/py_gnome/lib_gnome/MemUtils.h
similarity index 100%
rename from lib_gnome/MemUtils.h
rename to py_gnome/lib_gnome/MemUtils.h
diff --git a/lib_gnome/Model_c.cpp b/py_gnome/lib_gnome/Model_c.cpp
similarity index 100%
rename from lib_gnome/Model_c.cpp
rename to py_gnome/lib_gnome/Model_c.cpp
diff --git a/lib_gnome/Model_c.h b/py_gnome/lib_gnome/Model_c.h
similarity index 100%
rename from lib_gnome/Model_c.h
rename to py_gnome/lib_gnome/Model_c.h
diff --git a/lib_gnome/Mover_c.cpp b/py_gnome/lib_gnome/Mover_c.cpp
similarity index 100%
rename from lib_gnome/Mover_c.cpp
rename to py_gnome/lib_gnome/Mover_c.cpp
diff --git a/lib_gnome/Mover_c.h b/py_gnome/lib_gnome/Mover_c.h
similarity index 100%
rename from lib_gnome/Mover_c.h
rename to py_gnome/lib_gnome/Mover_c.h
diff --git a/lib_gnome/NetCDFMoverCurv_c.cpp b/py_gnome/lib_gnome/NetCDFMoverCurv_c.cpp
similarity index 100%
rename from lib_gnome/NetCDFMoverCurv_c.cpp
rename to py_gnome/lib_gnome/NetCDFMoverCurv_c.cpp
diff --git a/lib_gnome/NetCDFMoverCurv_c.h b/py_gnome/lib_gnome/NetCDFMoverCurv_c.h
similarity index 100%
rename from lib_gnome/NetCDFMoverCurv_c.h
rename to py_gnome/lib_gnome/NetCDFMoverCurv_c.h
diff --git a/lib_gnome/NetCDFMoverTri_c.cpp b/py_gnome/lib_gnome/NetCDFMoverTri_c.cpp
similarity index 100%
rename from lib_gnome/NetCDFMoverTri_c.cpp
rename to py_gnome/lib_gnome/NetCDFMoverTri_c.cpp
diff --git a/lib_gnome/NetCDFMoverTri_c.h b/py_gnome/lib_gnome/NetCDFMoverTri_c.h
similarity index 100%
rename from lib_gnome/NetCDFMoverTri_c.h
rename to py_gnome/lib_gnome/NetCDFMoverTri_c.h
diff --git a/lib_gnome/NetCDFMover_c.cpp b/py_gnome/lib_gnome/NetCDFMover_c.cpp
similarity index 100%
rename from lib_gnome/NetCDFMover_c.cpp
rename to py_gnome/lib_gnome/NetCDFMover_c.cpp
diff --git a/lib_gnome/NetCDFMover_c.h b/py_gnome/lib_gnome/NetCDFMover_c.h
similarity index 100%
rename from lib_gnome/NetCDFMover_c.h
rename to py_gnome/lib_gnome/NetCDFMover_c.h
diff --git a/lib_gnome/NetCDFWindMoverCurv_c.cpp b/py_gnome/lib_gnome/NetCDFWindMoverCurv_c.cpp
similarity index 100%
rename from lib_gnome/NetCDFWindMoverCurv_c.cpp
rename to py_gnome/lib_gnome/NetCDFWindMoverCurv_c.cpp
diff --git a/lib_gnome/NetCDFWindMoverCurv_c.h b/py_gnome/lib_gnome/NetCDFWindMoverCurv_c.h
similarity index 100%
rename from lib_gnome/NetCDFWindMoverCurv_c.h
rename to py_gnome/lib_gnome/NetCDFWindMoverCurv_c.h
diff --git a/lib_gnome/NetCDFWindMover_c.cpp b/py_gnome/lib_gnome/NetCDFWindMover_c.cpp
similarity index 100%
rename from lib_gnome/NetCDFWindMover_c.cpp
rename to py_gnome/lib_gnome/NetCDFWindMover_c.cpp
diff --git a/lib_gnome/NetCDFWindMover_c.h b/py_gnome/lib_gnome/NetCDFWindMover_c.h
similarity index 100%
rename from lib_gnome/NetCDFWindMover_c.h
rename to py_gnome/lib_gnome/NetCDFWindMover_c.h
diff --git a/lib_gnome/OLEList_c.cpp b/py_gnome/lib_gnome/OLEList_c.cpp
similarity index 100%
rename from lib_gnome/OLEList_c.cpp
rename to py_gnome/lib_gnome/OLEList_c.cpp
diff --git a/lib_gnome/OLEList_c.h b/py_gnome/lib_gnome/OLEList_c.h
similarity index 100%
rename from lib_gnome/OLEList_c.h
rename to py_gnome/lib_gnome/OLEList_c.h
diff --git a/lib_gnome/OSSMTimeValue_c.cpp b/py_gnome/lib_gnome/OSSMTimeValue_c.cpp
similarity index 100%
rename from lib_gnome/OSSMTimeValue_c.cpp
rename to py_gnome/lib_gnome/OSSMTimeValue_c.cpp
diff --git a/lib_gnome/OSSMTimeValue_c.h b/py_gnome/lib_gnome/OSSMTimeValue_c.h
similarity index 100%
rename from lib_gnome/OSSMTimeValue_c.h
rename to py_gnome/lib_gnome/OSSMTimeValue_c.h
diff --git a/lib_gnome/OSSMWeatherer_c.cpp b/py_gnome/lib_gnome/OSSMWeatherer_c.cpp
similarity index 100%
rename from lib_gnome/OSSMWeatherer_c.cpp
rename to py_gnome/lib_gnome/OSSMWeatherer_c.cpp
diff --git a/lib_gnome/OSSMWeatherer_c.h b/py_gnome/lib_gnome/OSSMWeatherer_c.h
similarity index 100%
rename from lib_gnome/OSSMWeatherer_c.h
rename to py_gnome/lib_gnome/OSSMWeatherer_c.h
diff --git a/lib_gnome/OUTILS.H b/py_gnome/lib_gnome/OUTILS.H
similarity index 100%
rename from lib_gnome/OUTILS.H
rename to py_gnome/lib_gnome/OUTILS.H
diff --git a/lib_gnome/OUTILS.cpp b/py_gnome/lib_gnome/OUTILS.cpp
similarity index 100%
rename from lib_gnome/OUTILS.cpp
rename to py_gnome/lib_gnome/OUTILS.cpp
diff --git a/lib_gnome/ObjectUtils.h b/py_gnome/lib_gnome/ObjectUtils.h
similarity index 100%
rename from lib_gnome/ObjectUtils.h
rename to py_gnome/lib_gnome/ObjectUtils.h
diff --git a/lib_gnome/PtCurMap_c.cpp b/py_gnome/lib_gnome/PtCurMap_c.cpp
similarity index 100%
rename from lib_gnome/PtCurMap_c.cpp
rename to py_gnome/lib_gnome/PtCurMap_c.cpp
diff --git a/lib_gnome/PtCurMap_c.h b/py_gnome/lib_gnome/PtCurMap_c.h
similarity index 100%
rename from lib_gnome/PtCurMap_c.h
rename to py_gnome/lib_gnome/PtCurMap_c.h
diff --git a/lib_gnome/PtCurMover_c.cpp b/py_gnome/lib_gnome/PtCurMover_c.cpp
similarity index 100%
rename from lib_gnome/PtCurMover_c.cpp
rename to py_gnome/lib_gnome/PtCurMover_c.cpp
diff --git a/lib_gnome/PtCurMover_c.h b/py_gnome/lib_gnome/PtCurMover_c.h
similarity index 100%
rename from lib_gnome/PtCurMover_c.h
rename to py_gnome/lib_gnome/PtCurMover_c.h
diff --git a/lib_gnome/Random3D_c.cpp b/py_gnome/lib_gnome/Random3D_c.cpp
similarity index 100%
rename from lib_gnome/Random3D_c.cpp
rename to py_gnome/lib_gnome/Random3D_c.cpp
diff --git a/lib_gnome/Random3D_c.h b/py_gnome/lib_gnome/Random3D_c.h
similarity index 100%
rename from lib_gnome/Random3D_c.h
rename to py_gnome/lib_gnome/Random3D_c.h
diff --git a/lib_gnome/RandomVertical_c.cpp b/py_gnome/lib_gnome/RandomVertical_c.cpp
similarity index 100%
rename from lib_gnome/RandomVertical_c.cpp
rename to py_gnome/lib_gnome/RandomVertical_c.cpp
diff --git a/lib_gnome/RandomVertical_c.h b/py_gnome/lib_gnome/RandomVertical_c.h
similarity index 100%
rename from lib_gnome/RandomVertical_c.h
rename to py_gnome/lib_gnome/RandomVertical_c.h
diff --git a/lib_gnome/Random_c.cpp b/py_gnome/lib_gnome/Random_c.cpp
similarity index 100%
rename from lib_gnome/Random_c.cpp
rename to py_gnome/lib_gnome/Random_c.cpp
diff --git a/lib_gnome/Random_c.h b/py_gnome/lib_gnome/Random_c.h
similarity index 100%
rename from lib_gnome/Random_c.h
rename to py_gnome/lib_gnome/Random_c.h
diff --git a/lib_gnome/RectGridVeL_c.cpp b/py_gnome/lib_gnome/RectGridVeL_c.cpp
similarity index 100%
rename from lib_gnome/RectGridVeL_c.cpp
rename to py_gnome/lib_gnome/RectGridVeL_c.cpp
diff --git a/lib_gnome/RectGridVeL_c.h b/py_gnome/lib_gnome/RectGridVeL_c.h
similarity index 100%
rename from lib_gnome/RectGridVeL_c.h
rename to py_gnome/lib_gnome/RectGridVeL_c.h
diff --git a/lib_gnome/RectUtils.cpp b/py_gnome/lib_gnome/RectUtils.cpp
similarity index 100%
rename from lib_gnome/RectUtils.cpp
rename to py_gnome/lib_gnome/RectUtils.cpp
diff --git a/lib_gnome/RectUtils.h b/py_gnome/lib_gnome/RectUtils.h
similarity index 100%
rename from lib_gnome/RectUtils.h
rename to py_gnome/lib_gnome/RectUtils.h
diff --git a/lib_gnome/Replacements.cpp b/py_gnome/lib_gnome/Replacements.cpp
similarity index 100%
rename from lib_gnome/Replacements.cpp
rename to py_gnome/lib_gnome/Replacements.cpp
diff --git a/lib_gnome/Replacements.h b/py_gnome/lib_gnome/Replacements.h
similarity index 100%
rename from lib_gnome/Replacements.h
rename to py_gnome/lib_gnome/Replacements.h
diff --git a/lib_gnome/RiseVelocity_c.cpp b/py_gnome/lib_gnome/RiseVelocity_c.cpp
similarity index 100%
rename from lib_gnome/RiseVelocity_c.cpp
rename to py_gnome/lib_gnome/RiseVelocity_c.cpp
diff --git a/lib_gnome/RiseVelocity_c.h b/py_gnome/lib_gnome/RiseVelocity_c.h
similarity index 100%
rename from lib_gnome/RiseVelocity_c.h
rename to py_gnome/lib_gnome/RiseVelocity_c.h
diff --git a/lib_gnome/Shio.h b/py_gnome/lib_gnome/Shio.h
similarity index 100%
rename from lib_gnome/Shio.h
rename to py_gnome/lib_gnome/Shio.h
diff --git a/lib_gnome/ShioCurrent1.cpp b/py_gnome/lib_gnome/ShioCurrent1.cpp
similarity index 100%
rename from lib_gnome/ShioCurrent1.cpp
rename to py_gnome/lib_gnome/ShioCurrent1.cpp
diff --git a/lib_gnome/ShioCurrent2.cpp b/py_gnome/lib_gnome/ShioCurrent2.cpp
similarity index 100%
rename from lib_gnome/ShioCurrent2.cpp
rename to py_gnome/lib_gnome/ShioCurrent2.cpp
diff --git a/lib_gnome/ShioHeight.cpp b/py_gnome/lib_gnome/ShioHeight.cpp
similarity index 100%
rename from lib_gnome/ShioHeight.cpp
rename to py_gnome/lib_gnome/ShioHeight.cpp
diff --git a/lib_gnome/ShioTimeValue_c.cpp b/py_gnome/lib_gnome/ShioTimeValue_c.cpp
similarity index 100%
rename from lib_gnome/ShioTimeValue_c.cpp
rename to py_gnome/lib_gnome/ShioTimeValue_c.cpp
diff --git a/lib_gnome/ShioTimeValue_c.h b/py_gnome/lib_gnome/ShioTimeValue_c.h
similarity index 100%
rename from lib_gnome/ShioTimeValue_c.h
rename to py_gnome/lib_gnome/ShioTimeValue_c.h
diff --git a/lib_gnome/StringFunctions.cpp b/py_gnome/lib_gnome/StringFunctions.cpp
similarity index 100%
rename from lib_gnome/StringFunctions.cpp
rename to py_gnome/lib_gnome/StringFunctions.cpp
diff --git a/lib_gnome/StringFunctions.h b/py_gnome/lib_gnome/StringFunctions.h
similarity index 100%
rename from lib_gnome/StringFunctions.h
rename to py_gnome/lib_gnome/StringFunctions.h
diff --git a/lib_gnome/TideCurCycleMover_c.cpp b/py_gnome/lib_gnome/TideCurCycleMover_c.cpp
similarity index 100%
rename from lib_gnome/TideCurCycleMover_c.cpp
rename to py_gnome/lib_gnome/TideCurCycleMover_c.cpp
diff --git a/lib_gnome/TideCurCycleMover_c.h b/py_gnome/lib_gnome/TideCurCycleMover_c.h
similarity index 100%
rename from lib_gnome/TideCurCycleMover_c.h
rename to py_gnome/lib_gnome/TideCurCycleMover_c.h
diff --git a/lib_gnome/TimeGridVel_c.cpp b/py_gnome/lib_gnome/TimeGridVel_c.cpp
similarity index 100%
rename from lib_gnome/TimeGridVel_c.cpp
rename to py_gnome/lib_gnome/TimeGridVel_c.cpp
diff --git a/lib_gnome/TimeGridVel_c.h b/py_gnome/lib_gnome/TimeGridVel_c.h
similarity index 100%
rename from lib_gnome/TimeGridVel_c.h
rename to py_gnome/lib_gnome/TimeGridVel_c.h
diff --git a/lib_gnome/TimeGridWind_c.cpp b/py_gnome/lib_gnome/TimeGridWind_c.cpp
similarity index 100%
rename from lib_gnome/TimeGridWind_c.cpp
rename to py_gnome/lib_gnome/TimeGridWind_c.cpp
diff --git a/lib_gnome/TimeGridWind_c.h b/py_gnome/lib_gnome/TimeGridWind_c.h
similarity index 100%
rename from lib_gnome/TimeGridWind_c.h
rename to py_gnome/lib_gnome/TimeGridWind_c.h
diff --git a/lib_gnome/TimeValue_c.cpp b/py_gnome/lib_gnome/TimeValue_c.cpp
similarity index 100%
rename from lib_gnome/TimeValue_c.cpp
rename to py_gnome/lib_gnome/TimeValue_c.cpp
diff --git a/lib_gnome/TimeValue_c.h b/py_gnome/lib_gnome/TimeValue_c.h
similarity index 100%
rename from lib_gnome/TimeValue_c.h
rename to py_gnome/lib_gnome/TimeValue_c.h
diff --git a/lib_gnome/TimeValuesIO.cpp b/py_gnome/lib_gnome/TimeValuesIO.cpp
similarity index 100%
rename from lib_gnome/TimeValuesIO.cpp
rename to py_gnome/lib_gnome/TimeValuesIO.cpp
diff --git a/lib_gnome/TimeValuesIO.h b/py_gnome/lib_gnome/TimeValuesIO.h
similarity index 100%
rename from lib_gnome/TimeValuesIO.h
rename to py_gnome/lib_gnome/TimeValuesIO.h
diff --git a/lib_gnome/TriCurMover_c.cpp b/py_gnome/lib_gnome/TriCurMover_c.cpp
similarity index 100%
rename from lib_gnome/TriCurMover_c.cpp
rename to py_gnome/lib_gnome/TriCurMover_c.cpp
diff --git a/lib_gnome/TriCurMover_c.h b/py_gnome/lib_gnome/TriCurMover_c.h
similarity index 100%
rename from lib_gnome/TriCurMover_c.h
rename to py_gnome/lib_gnome/TriCurMover_c.h
diff --git a/lib_gnome/TriGridVel3D_c.cpp b/py_gnome/lib_gnome/TriGridVel3D_c.cpp
similarity index 100%
rename from lib_gnome/TriGridVel3D_c.cpp
rename to py_gnome/lib_gnome/TriGridVel3D_c.cpp
diff --git a/lib_gnome/TriGridVel3D_c.h b/py_gnome/lib_gnome/TriGridVel3D_c.h
similarity index 100%
rename from lib_gnome/TriGridVel3D_c.h
rename to py_gnome/lib_gnome/TriGridVel3D_c.h
diff --git a/lib_gnome/TriGridVel_c.cpp b/py_gnome/lib_gnome/TriGridVel_c.cpp
similarity index 100%
rename from lib_gnome/TriGridVel_c.cpp
rename to py_gnome/lib_gnome/TriGridVel_c.cpp
diff --git a/lib_gnome/TriGridVel_c.h b/py_gnome/lib_gnome/TriGridVel_c.h
similarity index 100%
rename from lib_gnome/TriGridVel_c.h
rename to py_gnome/lib_gnome/TriGridVel_c.h
diff --git a/lib_gnome/TypeDefs.h b/py_gnome/lib_gnome/TypeDefs.h
similarity index 100%
rename from lib_gnome/TypeDefs.h
rename to py_gnome/lib_gnome/TypeDefs.h
diff --git a/lib_gnome/Units.h b/py_gnome/lib_gnome/Units.h
similarity index 100%
rename from lib_gnome/Units.h
rename to py_gnome/lib_gnome/Units.h
diff --git a/lib_gnome/VectMap_c.cpp b/py_gnome/lib_gnome/VectMap_c.cpp
similarity index 100%
rename from lib_gnome/VectMap_c.cpp
rename to py_gnome/lib_gnome/VectMap_c.cpp
diff --git a/lib_gnome/VectMap_c.h b/py_gnome/lib_gnome/VectMap_c.h
similarity index 100%
rename from lib_gnome/VectMap_c.h
rename to py_gnome/lib_gnome/VectMap_c.h
diff --git a/lib_gnome/Weatherer_c.cpp b/py_gnome/lib_gnome/Weatherer_c.cpp
similarity index 100%
rename from lib_gnome/Weatherer_c.cpp
rename to py_gnome/lib_gnome/Weatherer_c.cpp
diff --git a/lib_gnome/Weatherer_c.h b/py_gnome/lib_gnome/Weatherer_c.h
similarity index 100%
rename from lib_gnome/Weatherer_c.h
rename to py_gnome/lib_gnome/Weatherer_c.h
diff --git a/lib_gnome/Weatherers_c.cpp b/py_gnome/lib_gnome/Weatherers_c.cpp
similarity index 100%
rename from lib_gnome/Weatherers_c.cpp
rename to py_gnome/lib_gnome/Weatherers_c.cpp
diff --git a/lib_gnome/Weatherers_c.h b/py_gnome/lib_gnome/Weatherers_c.h
similarity index 100%
rename from lib_gnome/Weatherers_c.h
rename to py_gnome/lib_gnome/Weatherers_c.h
diff --git a/lib_gnome/WindMover_c.cpp b/py_gnome/lib_gnome/WindMover_c.cpp
similarity index 100%
rename from lib_gnome/WindMover_c.cpp
rename to py_gnome/lib_gnome/WindMover_c.cpp
diff --git a/lib_gnome/WindMover_c.h b/py_gnome/lib_gnome/WindMover_c.h
similarity index 100%
rename from lib_gnome/WindMover_c.h
rename to py_gnome/lib_gnome/WindMover_c.h
diff --git a/lib_gnome/my_build_list.h b/py_gnome/lib_gnome/my_build_list.h
similarity index 100%
rename from lib_gnome/my_build_list.h
rename to py_gnome/lib_gnome/my_build_list.h
diff --git a/py_gnome/setup.cfg b/py_gnome/setup.cfg
index d7bb24cf4..96b6644ff 100644
--- a/py_gnome/setup.cfg
+++ b/py_gnome/setup.cfg
@@ -9,7 +9,7 @@ description = GNOME (General NOAA Operational Modeling Environment)
               predict the possible route, or trajectory, a pollutant
               might follow in or on a body of water, such as in an
               oil spill. It can also be used as a customizable general particle tracking code.
-long_description = file: ./README.rst, ./LICENSE.rst
+long_description = file: README.rst, LICENSE.txt
 keywords = "oilspill, modeling, particle-tracking"
 license = CC0-1.0
 classifiers =
diff --git a/py_gnome/setup.py b/py_gnome/setup.py
index 7c27f76ff..f27662ab0 100755
--- a/py_gnome/setup.py
+++ b/py_gnome/setup.py
@@ -12,42 +12,45 @@
 (which happens in the gnome.__init__.py file)
 """
 
-import os
-import sys
-import sysconfig
+import datetime
 import importlib
 import glob
+import os
+from pathlib import Path
+import platform
 import shutil
-import datetime
+import sys
+import sysconfig
+
 
 # to support "develop" mode:
 import setuptools
-from setuptools import setup, find_packages
+from setuptools import setup
+
 from distutils.command.clean import clean
 
 from distutils.extension import Extension
 from Cython.Distutils import build_ext
 
-import platform
 from git import Repo
 
 import numpy as np
 
-# could run setup from anywhere
+# could run setup from anywhere (though not really??)
 SETUP_PATH = os.path.dirname(os.path.abspath(__file__))
+#SETUP_PATH = Path(__file__).parent
 
 # the extension used for compiled modules
-# # why is this so ugly?!? on py2?
+# does this not work ??
 # comp_modules_ext = sysconfig.get_config_var('EXT_SUFFIX')
 # if comp_modules_ext is None:
 #     comp_modules_ext = '.lib' if 'win' in sys.platform else ".so"
-if sys.version_info.major == 3:
+if sys.version_info.major < 3 or sys.version_info.minor < 9:
+    raise NotImplementedError("PyGNOME can only be built with Python 3.9 or above")
+else:
     py_impl = ['.'] + [c.lower() for c in platform.python_implementation() if c.isupper()]
     py_impl = py_impl + sysconfig.get_python_version().split('.') + ['-'] + [sysconfig.get_platform().replace('-','_')]
     win_comp_modules_ext = ''.join(py_impl) + '.lib'
-else:
-    win_comp_modules_ext = '.lib'
-
 
 # cd to SETUP_PATH, run develop or install, then cd back
 CWD = os.getcwd()
@@ -355,9 +358,13 @@ def get_conda_includes_win():
              ]
 
 
-cpp_code_dir = os.path.join('..', 'lib_gnome')
+# cpp_code_dir = (SETUP_PATH / 'lib_gnome').relative_to(SETUP_PATH)
+# cpp_files = [str(cpp_code_dir / f) for f in cpp_files]
+cpp_code_dir = os.path.join('.', 'lib_gnome')
+# cpp_code_dir = './lib_gnome'
 cpp_files = [os.path.join(cpp_code_dir, f) for f in cpp_files]
 
+print(cpp_files)
 
 # setting the "pyGNOME" define so that conditional compilation
 # in the cpp files is done right.

From 7b3d56f1dd7d90afc8f4b7b300d1c65a12ab6774 Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Mon, 10 Jul 2023 15:52:28 -0700
Subject: [PATCH 03/99] pyproject.toml almost working

---
 py_gnome/MANIFEST.in                          |  15 ++++-
 py_gnome/conda_requirements_build.txt         |   1 +
 .../file_formats/sample_gnome_output.nc       | Bin 0 -> 66554 bytes
 py_gnome/gnome/__init__.py                    |   2 +-
 py_gnome/pyproject.toml                       |  53 ++++++++++++++++-
 py_gnome/setup.cfg                            |  56 ------------------
 6 files changed, 68 insertions(+), 59 deletions(-)
 create mode 100644 py_gnome/documentation/source/file_formats/sample_gnome_output.nc
 delete mode 100644 py_gnome/setup.cfg

diff --git a/py_gnome/MANIFEST.in b/py_gnome/MANIFEST.in
index 6633ee542..85382fc8b 100644
--- a/py_gnome/MANIFEST.in
+++ b/py_gnome/MANIFEST.in
@@ -1,5 +1,18 @@
-# include of of lib_gnome in the source dist
+# include all of lib_gnome in the source dist
 graft lib_gnome
+
+# all the Cython files
 include gnome/cy_gnome/*.pyx
 include gnome/cy_gnome/*.pxd
 
+# conda requirements
+conda_requirements.txt
+conda_requirements_build.txt
+conda_requirements_docs.txt
+
+# tests and scripts
+graft tests
+graft scripts
+
+# documentation
+graft documentation
diff --git a/py_gnome/conda_requirements_build.txt b/py_gnome/conda_requirements_build.txt
index deb9da4f3..b8ab70a78 100644
--- a/py_gnome/conda_requirements_build.txt
+++ b/py_gnome/conda_requirements_build.txt
@@ -3,6 +3,7 @@
 
 cython=0.29.*
 setuptools>=62  # older versions uses different build dirs
+setuptools-scm>=6.2
 gitpython
 python-build
 
diff --git a/py_gnome/documentation/source/file_formats/sample_gnome_output.nc b/py_gnome/documentation/source/file_formats/sample_gnome_output.nc
new file mode 100644
index 0000000000000000000000000000000000000000..01ceb2f5c3d2072253bebc15e3235bf1b69dcfa0
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zcSh>5bt;b@yLA&T7v?PKlX3pQM*XQzW$Inl+_-T=5N-^g9M?)s33^#W3V*+>s#Ip>
z`pnPUVp_j@J(;c)({kH}rrtLe|Nh1Cte}Yv)gf!{d~{4Wym|SjYk$1)l5za_n|a@l
z?6YSh{;3Mj>9zfKc9!Cv*|cU%_x$Yl+N+DVMUHeY@@fzm)ndhO0j<tWD_PfM!Qm2?
zy4R!`b8-d-`R+>}a%W=Pu+k0jGsl>}n?3yCw7vaJdDfRh#`V?O6Q}te-B}p7a^wdu
z8Pi8MSBG3Z8*BY3`_j?%9bXFjrqx%=eO7nfnGs^A!#9VP2|}N#qZiKp$47_1Dirtj
zTX*Hg|90B-&i@?S|F0{(6SA^THIK40L?t3GdU4<JXO0&Y&&ar_43@k?`(QB~?=RCm
LkC5xDug>{D%-cKm

literal 0
HcmV?d00001

diff --git a/py_gnome/gnome/__init__.py b/py_gnome/gnome/__init__.py
index 791eea519..b3a11f379 100644
--- a/py_gnome/gnome/__init__.py
+++ b/py_gnome/gnome/__init__.py
@@ -25,7 +25,7 @@
 # just so it will be in the namespace.
 from .gnomeobject import GnomeId, AddLogger
 
-__version__ = '1.1.6'
+__version__ = '1.1.7'
 
 
 # a few imports so that the basic stuff is there
diff --git a/py_gnome/pyproject.toml b/py_gnome/pyproject.toml
index 50636899a..83c9a19c1 100644
--- a/py_gnome/pyproject.toml
+++ b/py_gnome/pyproject.toml
@@ -1,4 +1,55 @@
 
 [build-system]
-requires = ["setuptools"]
+requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyGNOME"
+version = "0.0.0"
+authors = [
+    {name = "Gnome team at NOAA/ORR/ERD", email = "orr.gnome@noaa.gov"},
+]
+description = "Particle tracking code with features specifically for oil spill modeling."
+requires-python = ">=3.9"
+keywords = ["oilspill", "modeling", "particle-tracking"]
+license = {text = "CC0-1.0"}
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: C++",
+    "Programming Language :: Cython",
+    "Intended Audience :: Science/Research",
+    "License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Oceanography",
+]
+
+# dynamic = ["version", "readme"]
+
+# dependencies = [
+#     "requests",
+#     'importlib-metadata; python_version<"3.8"',
+# ]
+
+#[tool.setuptools_scm]
+# write_to = "gnome/_version.py"
+
+[tool.setuptools]
+zip-safe = false
+
+# [tool.setuptools.packages.find]
+[tool.setuptools.packages.find]
+where = ["gnome"]  # list of folders that contain the packages (["."] by default)
+include = ["gnome*"]  # package names should match these glob patterns (["*"] by default)
+# exclude = ["my_package.tests*"]  # exclude packages matching these glob patterns (empty by default)
+namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
+
+
+[tool.setuptools.dynamic]
+# version = {attr = "gnome.__version__"}
+readme = {file = ["README.rst"]}
+
+# [project.optional-dependencies]
diff --git a/py_gnome/setup.cfg b/py_gnome/setup.cfg
deleted file mode 100644
index 96b6644ff..000000000
--- a/py_gnome/setup.cfg
+++ /dev/null
@@ -1,56 +0,0 @@
-[metadata]
-name = pyGnome
-version = attr: gnome.__version__
-author = Gnome team at NOAA/ORR/ERD
-author_email = orr.gnome@noaa.gov
-description = GNOME (General NOAA Operational Modeling Environment)
-              is the modeling tool the Office of Response and
-              Restoration's (OR&R) Emergency Response Division uses to
-              predict the possible route, or trajectory, a pollutant
-              might follow in or on a body of water, such as in an
-              oil spill. It can also be used as a customizable general particle tracking code.
-long_description = file: README.rst, LICENSE.txt
-keywords = "oilspill, modeling, particle-tracking"
-license = CC0-1.0
-classifiers =
-    Development Status :: 5 - Production/Stable
-    Programming Language :: Python :: 3 :: Only
-    Programming Language :: Python :: Implementation :: CPython
-    Programming Language :: C++
-    Programming Language :: Cython
-    Intended Audience :: Science/Research
-    License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
-    Natural Language :: English
-    Operating System :: OS Independent
-    Topic :: Scientific/Engineering
-    Topic :: Scientific/Engineering :: Oceanography
-
-
-[options]
-zip_safe = False
-include_package_data = True
-packages = find:
-python_requires = >=3.9
-# install_requires =
-#     requests
-#     importlib-metadata; python_version<"3.8"
-
-[options.package_data]
-gnome = 'data/yeardata/*',
-        'outputters/sample.b64',
-        'weatherers/platforms.json'
-
-[options.entry_points]
-console_scripts =
-    executable-name = my_package.module:function
-
-[options.extras_require]
-pdf = ReportLab>=1.2; RXP
-rest = docutils>=0.3; pack ==1.1, ==1.3
-
-[options.packages.find]
-exclude =
-    examples*
-    tools*
-    docs*
-    my_package.tests*

From 17c2a45d4650b927fd8564393a275f0968d3a975 Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Mon, 10 Jul 2023 17:59:52 -0700
Subject: [PATCH 04/99] first pyproject.toml file working!

---
 py_gnome/MANIFEST.in    | 19 +------------------
 py_gnome/pyproject.toml | 14 ++++++++------
 2 files changed, 9 insertions(+), 24 deletions(-)

diff --git a/py_gnome/MANIFEST.in b/py_gnome/MANIFEST.in
index 85382fc8b..6fa8c3d19 100644
--- a/py_gnome/MANIFEST.in
+++ b/py_gnome/MANIFEST.in
@@ -1,18 +1 @@
-# include all of lib_gnome in the source dist
-graft lib_gnome
-
-# all the Cython files
-include gnome/cy_gnome/*.pyx
-include gnome/cy_gnome/*.pxd
-
-# conda requirements
-conda_requirements.txt
-conda_requirements_build.txt
-conda_requirements_docs.txt
-
-# tests and scripts
-graft tests
-graft scripts
-
-# documentation
-graft documentation
+prune utility_scripts
diff --git a/py_gnome/pyproject.toml b/py_gnome/pyproject.toml
index 83c9a19c1..9133b889d 100644
--- a/py_gnome/pyproject.toml
+++ b/py_gnome/pyproject.toml
@@ -1,11 +1,12 @@
 
 [build-system]
+# note: using setuptools_scm for file finding, not versioning
+#       we should probably do versioning later, but it requires tagging the git repo properly
 requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "pyGNOME"
-version = "0.0.0"
 authors = [
     {name = "Gnome team at NOAA/ORR/ERD", email = "orr.gnome@noaa.gov"},
 ]
@@ -27,20 +28,21 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Oceanography",
 ]
 
-# dynamic = ["version", "readme"]
+dynamic = ["version", "readme"]
 
+# really hard to do with conda compatibility :-)
 # dependencies = [
 #     "requests",
 #     'importlib-metadata; python_version<"3.8"',
 # ]
 
-#[tool.setuptools_scm]
-# write_to = "gnome/_version.py"
+[tool.setuptools_scm]
+root = ".."
+# write_to = "py_gnome/gnome/_version.py"
 
 [tool.setuptools]
 zip-safe = false
 
-# [tool.setuptools.packages.find]
 [tool.setuptools.packages.find]
 where = ["gnome"]  # list of folders that contain the packages (["."] by default)
 include = ["gnome*"]  # package names should match these glob patterns (["*"] by default)
@@ -49,7 +51,7 @@ namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
 
 [tool.setuptools.dynamic]
-# version = {attr = "gnome.__version__"}
+version = {attr = "gnome.__version__"}
 readme = {file = ["README.rst"]}
 
 # [project.optional-dependencies]

From df0bb5523339a9294ca50c234667167ea4d0898f Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Mon, 10 Jul 2023 20:26:03 -0700
Subject: [PATCH 05/99] update CI to use pip install (new build setup)

---
 .gitlab-ci.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c67a8107b..b5aba69a2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -50,7 +50,7 @@ compile_pygnome:
     - pip install oil_database/adios_db/
 
     - cd ./py_gnome
-    - python setup.py install
+    - pip install --no-build-isolation ./
 
     - cd ../  # make sure that it won't find the source gnome package.
     - python -c "import gnome"  # make sure that it imports
@@ -76,6 +76,8 @@ test_pygnome:
   script:
     - conda install -y --file conda_requirements_test.txt
     - cd ./py_gnome/tests/unit_tests && pytest --runslow
+
+    # save the package list if tests pass
     - conda list > conda_packages.txt
 
 # Ideally, all the scripts in "testing_scripts" should run without errors,

From e568dd14801331ffffb975aacee47c83a91afd9a Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Tue, 11 Jul 2023 09:32:47 -0700
Subject: [PATCH 06/99] CI to new  location of conda_requirements

---
 .gitlab-ci.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b5aba69a2..81ba58499 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -42,21 +42,21 @@ compile_pygnome:
 
     # get the adios_db code: needed for tests and requirements
     - git clone --depth 1 -b develop https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
+    - cd ./py_gnome
     - conda install -y python=$PYTHON_VER --file conda_requirements.txt
                                           --file conda_requirements_build.txt
                                           --file oil_database/adios_db/conda_requirements.txt
 
     # install adios_db
-    - pip install oil_database/adios_db/
+    - pip install ../oil_database/adios_db/
 
-    - cd ./py_gnome
     - pip install --no-build-isolation ./
 
     - cd ../  # make sure that it won't find the source gnome package.
     - python -c "import gnome"  # make sure that it imports
 
     # need extra requirements for the docs
-    - conda install -y --file conda_requirements_docs.txt
+    - conda install -y --file py_gnome/conda_requirements_docs.txt
     - cd py_gnome/documentation && make html  # build the docs
   artifacts:
     when: always
@@ -74,7 +74,7 @@ test_pygnome:
   allow_failure: false
   image: registry.orr.noaa.gov/erd/centos-conda/centos7-python$PYTHON_VER
   script:
-    - conda install -y --file conda_requirements_test.txt
+    - conda install -y --file py_gnome/conda_requirements_test.txt
     - cd ./py_gnome/tests/unit_tests && pytest --runslow
 
     # save the package list if tests pass
@@ -135,14 +135,14 @@ test_pygnome_windows:
     - git clone --depth 1 -b develop https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
 
     - conda install -y python=$PYTHON_VER mamba
+    - cd ./py_gnome
     - echo "Setting up conda environment"
     - mamba install -y python=$PYTHON_VER --file conda_requirements.txt
                                           --file conda_requirements_build.txt
                                           --file conda_requirements_test.txt
-                                          --file oil_database/adios_db/conda_requirements.txt
+                                          --file ../oil_database/adios_db/conda_requirements.txt
 
     - echo "Building PyGNOME"
-    - cd ./py_gnome
     - python setup.py install
 
     # Make sure that it imports from some folder other than the

From cc0fc505b5917cc5f38961905d3ad44900212848 Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Wed, 12 Jul 2023 15:57:28 -0700
Subject: [PATCH 07/99] fixed one more path to requirements file

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 81ba58499..794ab0e4c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -45,7 +45,7 @@ compile_pygnome:
     - cd ./py_gnome
     - conda install -y python=$PYTHON_VER --file conda_requirements.txt
                                           --file conda_requirements_build.txt
-                                          --file oil_database/adios_db/conda_requirements.txt
+                                          --file ../oil_database/adios_db/conda_requirements.txt
 
     # install adios_db
     - pip install ../oil_database/adios_db/

From 8df1aff95e8c79558eaeac83e0aca75db08c401f Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Thu, 13 Jul 2023 15:28:45 -0700
Subject: [PATCH 08/99] removed print of cpp file list.

---
 py_gnome/setup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/py_gnome/setup.py b/py_gnome/setup.py
index f27662ab0..692ff2fd1 100755
--- a/py_gnome/setup.py
+++ b/py_gnome/setup.py
@@ -364,7 +364,6 @@ def get_conda_includes_win():
 # cpp_code_dir = './lib_gnome'
 cpp_files = [os.path.join(cpp_code_dir, f) for f in cpp_files]
 
-print(cpp_files)
 
 # setting the "pyGNOME" define so that conditional compilation
 # in the cpp files is done right.

From fd28ed496bfb0114e3c8f212827c5402e8da4eab Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Sun, 16 Jul 2023 13:03:50 -0700
Subject: [PATCH 09/99] updated to use scikit build / CMake

---
 py_gnome/CMakeLists.txt         | 114 +++++++++++++++++++++++++++
 py_gnome/cmake/FindNetCDF.cmake | 131 ++++++++++++++++++++++++++++++++
 py_gnome/cmake/Readme.txt       |  10 +++
 py_gnome/pyproject.toml         |  15 ++--
 4 files changed, 262 insertions(+), 8 deletions(-)
 create mode 100644 py_gnome/CMakeLists.txt
 create mode 100644 py_gnome/cmake/FindNetCDF.cmake
 create mode 100644 py_gnome/cmake/Readme.txt

diff --git a/py_gnome/CMakeLists.txt b/py_gnome/CMakeLists.txt
new file mode 100644
index 000000000..b38be5dfb
--- /dev/null
+++ b/py_gnome/CMakeLists.txt
@@ -0,0 +1,114 @@
+# to jcfr@github henryiii
+
+
+cmake_minimum_required(VERSION 3.15...3.26)
+project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
+
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+
+find_package(NetCDF REQUIRED MODULE)
+
+find_package(
+  Python
+  COMPONENTS Interpreter Development.Module NumPy
+  REQUIRED)
+
+find_program(CYTHON "cython")
+
+set (EXT_NAMES cy_mover
+                   cy_helpers
+                   cy_wind_mover
+                   cy_current_mover
+                   cy_cats_mover
+                   cy_component_mover
+                   cy_gridcurrent_mover
+                   cy_gridwind_mover
+                   cy_ice_mover
+                   cy_ice_wind_mover
+                   cy_currentcycle_mover
+                   cy_ossm_time
+                   cy_random_mover
+                   cy_random_mover_3d
+                   cy_rise_velocity_mover
+                   cy_land_check
+                   cy_grid_map
+                   cy_shio_time
+                   cy_grid
+                   cy_grid_rect
+                   cy_grid_curv
+                   cy_weatherers
+                   )
+
+set( CPP_FILES RectGridVeL_c.cpp
+             MemUtils.cpp
+             Mover_c.cpp
+             Replacements.cpp
+             ClassID_c.cpp
+             Random_c.cpp
+             TimeValuesIO.cpp
+             GEOMETRY.cpp
+             OSSMTimeValue_c.cpp
+             TimeValue_c.cpp
+             RectUtils.cpp
+             WindMover_c.cpp
+             CompFunctions.cpp
+             StringFunctions.cpp
+             OUTILS.cpp
+             CATSMover_c.cpp
+             CurrentMover_c.cpp
+             ComponentMover_c.cpp
+             ShioTimeValue_c.cpp
+             ShioHeight.cpp
+             TriGridVel_c.cpp
+             DagTree.cpp
+             DagTreeIO.cpp
+             ShioCurrent1.cpp
+             ShioCurrent2.cpp
+             GridCurrentMover_c.cpp
+             GridWindMover_c.cpp
+             IceMover_c.cpp
+             IceWindMover_c.cpp
+             CurrentCycleMover_c.cpp
+             TimeGridVel_c.cpp
+             TimeGridWind_c.cpp
+             MakeTriangles.cpp
+             MakeDagTree.cpp
+             GridMap_c.cpp
+             GridMapUtils.cpp
+             RandomVertical_c.cpp
+             RiseVelocity_c.cpp
+             Weatherers_c.cpp
+             )
+
+list(TRANSFORM CPP_FILES PREPEND "lib_gnome/")
+
+add_library(gnome SHARED ${CPP_FILES})
+
+target_link_libraries(gnome PRIVATE NetCDF::NetCDF)
+
+target_compile_definitions(gnome PUBLIC pyGNOME=1)
+
+target_include_directories(gnome PUBLIC lib_gnome)
+
+foreach(ext IN LISTS EXT_NAMES)
+
+    add_custom_command(
+      OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/gnome/cy_gnome/${ext}.cpp"
+      DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/gnome/cy_gnome/${ext}.pyx"
+      VERBATIM
+      COMMAND "${CYTHON}" --cplus -3
+              "${CMAKE_CURRENT_SOURCE_DIR}/gnome/cy_gnome/${ext}.pyx"
+              --output-file
+              "${CMAKE_CURRENT_BINARY_DIR}/gnome/cy_gnome/${ext}.cpp")
+    
+    python_add_library(${ext} MODULE "${CMAKE_CURRENT_BINARY_DIR}/gnome/cy_gnome/${ext}.cpp"
+                   WITH_SOABI)
+
+    target_link_libraries(${ext} PRIVATE gnome Python::NumPy)
+
+    install(TARGETS ${ext} DESTINATION gnome/cy_gnome)
+
+endforeach()
+
+install(TARGETS gnome DESTINATION gnome/cy_gnome)
+
diff --git a/py_gnome/cmake/FindNetCDF.cmake b/py_gnome/cmake/FindNetCDF.cmake
new file mode 100644
index 000000000..194b1a0d3
--- /dev/null
+++ b/py_gnome/cmake/FindNetCDF.cmake
@@ -0,0 +1,131 @@
+#[==[
+Provides the following variables:
+
+  * `NetCDF_FOUND`: Whether NetCDF was found or not.
+  * `NetCDF_INCLUDE_DIRS`: Include directories necessary to use NetCDF.
+  * `NetCDF_LIBRARIES`: Libraries necessary to use NetCDF.
+  * `NetCDF_VERSION`: The version of NetCDF found.
+  * `NetCDF::NetCDF`: A target to use with `target_link_libraries`.
+  * `NetCDF_HAS_PARALLEL`: Whether or not NetCDF was found with parallel IO support.
+#]==]
+
+function(FindNetCDF_get_is_parallel_aware include_dir)
+  file(STRINGS "${include_dir}/netcdf_meta.h" _netcdf_lines
+    REGEX "#define[ \t]+NC_HAS_PARALLEL[ \t]")
+  string(REGEX REPLACE ".*NC_HAS_PARALLEL[ \t]*([0-1]+).*" "\\1" _netcdf_has_parallel "${_netcdf_lines}")
+  if (_netcdf_has_parallel)
+    set(NetCDF_HAS_PARALLEL TRUE PARENT_SCOPE)
+  else()
+    set(NetCDF_HAS_PARALLEL FALSE PARENT_SCOPE)
+  endif()
+endfunction()
+
+# Try to find a CMake-built NetCDF.
+find_package(netCDF CONFIG QUIET)
+if (netCDF_FOUND)
+  # Forward the variables in a consistent way.
+  set(NetCDF_FOUND "${netCDF_FOUND}")
+  set(NetCDF_INCLUDE_DIRS "${netCDF_INCLUDE_DIR}")
+  set(NetCDF_LIBRARIES "${netCDF_LIBRARIES}")
+  set(NetCDF_VERSION "${NetCDFVersion}")
+
+  include(FindPackageHandleStandardArgs)
+  find_package_handle_standard_args(NetCDF
+    REQUIRED_VARS NetCDF_INCLUDE_DIRS NetCDF_LIBRARIES
+    VERSION_VAR NetCDF_VERSION)
+
+  if (NOT TARGET NetCDF::NetCDF)
+    add_library(NetCDF::NetCDF INTERFACE IMPORTED)
+    if (TARGET "netCDF::netcdf")
+      # 4.7.3
+      set_target_properties(NetCDF::NetCDF PROPERTIES
+        INTERFACE_LINK_LIBRARIES "netCDF::netcdf")
+    elseif (TARGET "netcdf")
+      set_target_properties(NetCDF::NetCDF PROPERTIES
+        INTERFACE_LINK_LIBRARIES "netcdf")
+    else ()
+      set_target_properties(NetCDF::NetCDF PROPERTIES
+        INTERFACE_LINK_LIBRARIES "${netCDF_LIBRARIES}")
+    endif ()
+  endif ()
+
+  FindNetCDF_get_is_parallel_aware("${NetCDF_INCLUDE_DIRS}")
+  # Skip the rest of the logic in this file.
+  return ()
+endif ()
+
+find_package(PkgConfig QUIET)
+if (PkgConfig_FOUND)
+  pkg_check_modules(_NetCDF QUIET netcdf IMPORTED_TARGET)
+  if (_NetCDF_FOUND)
+    # Forward the variables in a consistent way.
+    set(NetCDF_FOUND "${_NetCDF_FOUND}")
+    set(NetCDF_INCLUDE_DIRS "${_NetCDF_INCLUDE_DIRS}")
+    set(NetCDF_LIBRARIES "${_NetCDF_LIBRARIES}")
+    set(NetCDF_VERSION "${_NetCDF_VERSION}")
+
+    include(FindPackageHandleStandardArgs)
+    find_package_handle_standard_args(NetCDF
+      REQUIRED_VARS NetCDF_LIBRARIES
+      # This is not required because system-default include paths are not
+      # reported by `FindPkgConfig`, so this might be empty. Assume that if we
+      # have a library, the include directories are fine (if any) since
+      # PkgConfig reported that the package was found.
+      # NetCDF_INCLUDE_DIRS
+      VERSION_VAR NetCDF_VERSION)
+
+    if (NOT TARGET NetCDF::NetCDF)
+      add_library(NetCDF::NetCDF INTERFACE IMPORTED)
+      set_target_properties(NetCDF::NetCDF PROPERTIES
+        INTERFACE_LINK_LIBRARIES "PkgConfig::_NetCDF")
+    endif ()
+
+    FindNetCDF_get_is_parallel_aware("${_NetCDF_INCLUDEDIR}")
+    # Skip the rest of the logic in this file.
+    return ()
+  endif ()
+endif ()
+
+find_path(NetCDF_INCLUDE_DIR
+  NAMES netcdf.h
+  DOC "netcdf include directories")
+mark_as_advanced(NetCDF_INCLUDE_DIR)
+
+find_library(NetCDF_LIBRARY
+  NAMES netcdf
+  DOC "netcdf library")
+mark_as_advanced(NetCDF_LIBRARY)
+
+if (NetCDF_INCLUDE_DIR)
+  file(STRINGS "${NetCDF_INCLUDE_DIR}/netcdf_meta.h" _netcdf_version_lines
+    REGEX "#define[ \t]+NC_VERSION_(MAJOR|MINOR|PATCH|NOTE)")
+  string(REGEX REPLACE ".*NC_VERSION_MAJOR *\([0-9]*\).*" "\\1" _netcdf_version_major "${_netcdf_version_lines}")
+  string(REGEX REPLACE ".*NC_VERSION_MINOR *\([0-9]*\).*" "\\1" _netcdf_version_minor "${_netcdf_version_lines}")
+  string(REGEX REPLACE ".*NC_VERSION_PATCH *\([0-9]*\).*" "\\1" _netcdf_version_patch "${_netcdf_version_lines}")
+  string(REGEX REPLACE ".*NC_VERSION_NOTE *\"\([^\"]*\)\".*" "\\1" _netcdf_version_note "${_netcdf_version_lines}")
+  set(NetCDF_VERSION "${_netcdf_version_major}.${_netcdf_version_minor}.${_netcdf_version_patch}${_netcdf_version_note}")
+  unset(_netcdf_version_major)
+  unset(_netcdf_version_minor)
+  unset(_netcdf_version_patch)
+  unset(_netcdf_version_note)
+  unset(_netcdf_version_lines)
+
+  FindNetCDF_get_is_parallel_aware("${NetCDF_INCLUDE_DIR}")
+endif ()
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(NetCDF
+  REQUIRED_VARS NetCDF_LIBRARY NetCDF_INCLUDE_DIR
+  VERSION_VAR NetCDF_VERSION)
+
+if (NetCDF_FOUND)
+  set(NetCDF_INCLUDE_DIRS "${NetCDF_INCLUDE_DIR}")
+  set(NetCDF_LIBRARIES "${NetCDF_LIBRARY}")
+
+  if (NOT TARGET NetCDF::NetCDF)
+    add_library(NetCDF::NetCDF UNKNOWN IMPORTED)
+    set_target_properties(NetCDF::NetCDF PROPERTIES
+      IMPORTED_LOCATION "${NetCDF_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${NetCDF_INCLUDE_DIR}")
+  endif ()
+endif ()
diff --git a/py_gnome/cmake/Readme.txt b/py_gnome/cmake/Readme.txt
new file mode 100644
index 000000000..dacff88b6
--- /dev/null
+++ b/py_gnome/cmake/Readme.txt
@@ -0,0 +1,10 @@
+Assortedstuff needed by CMake
+
+At the moment:
+
+The netcdf libfinder from kitware / VTK:
+
+https://github.com/Kitware/VTK/blob/master/CMake/FindNetCDF.cmake
+
+This should get included in scikit build at some point.
+
diff --git a/py_gnome/pyproject.toml b/py_gnome/pyproject.toml
index 9133b889d..35d131eb8 100644
--- a/py_gnome/pyproject.toml
+++ b/py_gnome/pyproject.toml
@@ -2,11 +2,11 @@
 [build-system]
 # note: using setuptools_scm for file finding, not versioning
 #       we should probably do versioning later, but it requires tagging the git repo properly
-requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
-build-backend = "setuptools.build_meta"
+requires = ["scikit-build-core", "cython", "numpy"]
+build-backend = "scikit_build_core.build"
 
 [project]
-name = "pyGNOME"
+name = "gnome"
 authors = [
     {name = "Gnome team at NOAA/ORR/ERD", email = "orr.gnome@noaa.gov"},
 ]
@@ -28,7 +28,10 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Oceanography",
 ]
 
-dynamic = ["version", "readme"]
+version = "1.1.7dev"
+readme = "README.rst"
+
+# dynamic = ["version", "readme"]
 
 # really hard to do with conda compatibility :-)
 # dependencies = [
@@ -50,8 +53,4 @@ include = ["gnome*"]  # package names should match these glob patterns (["*"] by
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
 
-[tool.setuptools.dynamic]
-version = {attr = "gnome.__version__"}
-readme = {file = ["README.rst"]}
-
 # [project.optional-dependencies]

From 763982a60fe8a9d4e0149b981d807c3ad0088e03 Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Sun, 16 Jul 2023 13:45:25 -0700
Subject: [PATCH 10/99] getting closer, @rpath wrong

---
 py_gnome/CMakeLists.txt               | 9 +++++++++
 py_gnome/conda_requirements_build.txt | 2 ++
 2 files changed, 11 insertions(+)

diff --git a/py_gnome/CMakeLists.txt b/py_gnome/CMakeLists.txt
index b38be5dfb..a3900c15f 100644
--- a/py_gnome/CMakeLists.txt
+++ b/py_gnome/CMakeLists.txt
@@ -106,9 +106,18 @@ foreach(ext IN LISTS EXT_NAMES)
 
     target_link_libraries(${ext} PRIVATE gnome Python::NumPy)
 
+
+    #if(APPLE)
+      set_target_properties(${ext} PROPERTIES INSTALL_RPATH "@loader_path/.")
+    #elseif(UNIX)
+    #  set_target_properties(${ext} PROPERTIES INSTALL_RPATH "$ORIGIN/.")
+    #endif()
+
     install(TARGETS ${ext} DESTINATION gnome/cy_gnome)
 
+
 endforeach()
 
 install(TARGETS gnome DESTINATION gnome/cy_gnome)
 
+
diff --git a/py_gnome/conda_requirements_build.txt b/py_gnome/conda_requirements_build.txt
index b8ab70a78..9f0b303f8 100644
--- a/py_gnome/conda_requirements_build.txt
+++ b/py_gnome/conda_requirements_build.txt
@@ -6,4 +6,6 @@ setuptools>=62  # older versions uses different build dirs
 setuptools-scm>=6.2
 gitpython
 python-build
+cmake
+ninja
 

From ba73e6f8b5c3d6131be4e5ef7a02ac153a23ad65 Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Tue, 18 Jul 2023 13:50:53 -0700
Subject: [PATCH 11/99] adding basic_types extension

---
 py_gnome/CMakeLists.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/py_gnome/CMakeLists.txt b/py_gnome/CMakeLists.txt
index a3900c15f..f0c46e662 100644
--- a/py_gnome/CMakeLists.txt
+++ b/py_gnome/CMakeLists.txt
@@ -15,7 +15,8 @@ find_package(
 
 find_program(CYTHON "cython")
 
-set (EXT_NAMES cy_mover
+set (EXT_NAMES cy_basic_types
+                   cy_mover
                    cy_helpers
                    cy_wind_mover
                    cy_current_mover

From 926691911fac4193eff5da525d95e404965f04d9 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Tue, 30 Jan 2024 15:19:01 -0800
Subject: [PATCH 12/99] New build based on scikit-build-core seems to be
 working ok now.

---
 .gitlab-ci.yml                        |   3 +-
 dockerfile                            |   2 +-
 py_gnome/CMakeLists.txt               | 164 +++++++++++++-------------
 py_gnome/conda_requirements_build.txt |   4 +-
 py_gnome/setup.py                     |  68 +----------
 5 files changed, 94 insertions(+), 147 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 794ab0e4c..3d050d8e7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -49,8 +49,7 @@ compile_pygnome:
 
     # install adios_db
     - pip install ../oil_database/adios_db/
-
-    - pip install --no-build-isolation ./
+    - pip install ./
 
     - cd ../  # make sure that it won't find the source gnome package.
     - python -c "import gnome"  # make sure that it imports
diff --git a/dockerfile b/dockerfile
index 8646d8016..e66d4a786 100644
--- a/dockerfile
+++ b/dockerfile
@@ -27,8 +27,8 @@ RUN conda list
 # adios_db requirements should already be there from the deploy_requirements file
 # RUN cd pygnome/oil_database/adios_db && conda install --file conda_requirements.txt
 
-RUN cd pygnome/py_gnome && python setup.py install
 RUN cd pygnome/oil_database/adios_db && python -m pip install ./
+RUN cd pygnome/py_gnome && pip install ./
 
 # to check if they got installed properly
 RUN python -c "import adios_db"
diff --git a/py_gnome/CMakeLists.txt b/py_gnome/CMakeLists.txt
index f0c46e662..a4e3fe514 100644
--- a/py_gnome/CMakeLists.txt
+++ b/py_gnome/CMakeLists.txt
@@ -9,77 +9,80 @@ list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 find_package(NetCDF REQUIRED MODULE)
 
 find_package(
-  Python
-  COMPONENTS Interpreter Development.Module NumPy
-  REQUIRED)
+    Python
+    COMPONENTS Interpreter Development.Module NumPy
+    REQUIRED
+)
 
 find_program(CYTHON "cython")
 
-set (EXT_NAMES cy_basic_types
-                   cy_mover
-                   cy_helpers
-                   cy_wind_mover
-                   cy_current_mover
-                   cy_cats_mover
-                   cy_component_mover
-                   cy_gridcurrent_mover
-                   cy_gridwind_mover
-                   cy_ice_mover
-                   cy_ice_wind_mover
-                   cy_currentcycle_mover
-                   cy_ossm_time
-                   cy_random_mover
-                   cy_random_mover_3d
-                   cy_rise_velocity_mover
-                   cy_land_check
-                   cy_grid_map
-                   cy_shio_time
-                   cy_grid
-                   cy_grid_rect
-                   cy_grid_curv
-                   cy_weatherers
-                   )
-
-set( CPP_FILES RectGridVeL_c.cpp
-             MemUtils.cpp
-             Mover_c.cpp
-             Replacements.cpp
-             ClassID_c.cpp
-             Random_c.cpp
-             TimeValuesIO.cpp
-             GEOMETRY.cpp
-             OSSMTimeValue_c.cpp
-             TimeValue_c.cpp
-             RectUtils.cpp
-             WindMover_c.cpp
-             CompFunctions.cpp
-             StringFunctions.cpp
-             OUTILS.cpp
-             CATSMover_c.cpp
-             CurrentMover_c.cpp
-             ComponentMover_c.cpp
-             ShioTimeValue_c.cpp
-             ShioHeight.cpp
-             TriGridVel_c.cpp
-             DagTree.cpp
-             DagTreeIO.cpp
-             ShioCurrent1.cpp
-             ShioCurrent2.cpp
-             GridCurrentMover_c.cpp
-             GridWindMover_c.cpp
-             IceMover_c.cpp
-             IceWindMover_c.cpp
-             CurrentCycleMover_c.cpp
-             TimeGridVel_c.cpp
-             TimeGridWind_c.cpp
-             MakeTriangles.cpp
-             MakeDagTree.cpp
-             GridMap_c.cpp
-             GridMapUtils.cpp
-             RandomVertical_c.cpp
-             RiseVelocity_c.cpp
-             Weatherers_c.cpp
-             )
+set(EXT_NAMES
+    cy_basic_types
+    cy_mover
+    cy_helpers
+    cy_wind_mover
+    cy_current_mover
+    cy_cats_mover
+    cy_component_mover
+    cy_gridcurrent_mover
+    cy_gridwind_mover
+    cy_ice_mover
+    cy_ice_wind_mover
+    cy_currentcycle_mover
+    cy_ossm_time
+    cy_random_mover
+    cy_random_mover_3d
+    cy_rise_velocity_mover
+    cy_land_check
+    cy_grid_map
+    cy_shio_time
+    cy_grid
+    cy_grid_rect
+    cy_grid_curv
+    cy_weatherers
+)
+
+set(CPP_FILES
+    RectGridVeL_c.cpp
+    MemUtils.cpp
+    Mover_c.cpp
+    Replacements.cpp
+    ClassID_c.cpp
+    Random_c.cpp
+    TimeValuesIO.cpp
+    GEOMETRY.cpp
+    OSSMTimeValue_c.cpp
+    TimeValue_c.cpp
+    RectUtils.cpp
+    WindMover_c.cpp
+    CompFunctions.cpp
+    StringFunctions.cpp
+    OUTILS.cpp
+    CATSMover_c.cpp
+    CurrentMover_c.cpp
+    ComponentMover_c.cpp
+    ShioTimeValue_c.cpp
+    ShioHeight.cpp
+    TriGridVel_c.cpp
+    DagTree.cpp
+    DagTreeIO.cpp
+    ShioCurrent1.cpp
+    ShioCurrent2.cpp
+    GridCurrentMover_c.cpp
+    GridWindMover_c.cpp
+    IceMover_c.cpp
+    IceWindMover_c.cpp
+    CurrentCycleMover_c.cpp
+    TimeGridVel_c.cpp
+    TimeGridWind_c.cpp
+    MakeTriangles.cpp
+    MakeDagTree.cpp
+    GridMap_c.cpp
+    GridMapUtils.cpp
+    RandomVertical_c.cpp
+    RiseVelocity_c.cpp
+    Weatherers_c.cpp
+)
 
 list(TRANSFORM CPP_FILES PREPEND "lib_gnome/")
 
@@ -94,16 +97,20 @@ target_include_directories(gnome PUBLIC lib_gnome)
 foreach(ext IN LISTS EXT_NAMES)
 
     add_custom_command(
-      OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/gnome/cy_gnome/${ext}.cpp"
-      DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/gnome/cy_gnome/${ext}.pyx"
-      VERBATIM
-      COMMAND "${CYTHON}" --cplus -3
-              "${CMAKE_CURRENT_SOURCE_DIR}/gnome/cy_gnome/${ext}.pyx"
-              --output-file
-              "${CMAKE_CURRENT_BINARY_DIR}/gnome/cy_gnome/${ext}.cpp")
+        OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/gnome/cy_gnome/${ext}.cpp"
+        DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/gnome/cy_gnome/${ext}.pyx"
+        VERBATIM
+        COMMAND "${CYTHON}" --cplus -3
+                "${CMAKE_CURRENT_SOURCE_DIR}/gnome/cy_gnome/${ext}.pyx"
+                --output-file
+                "${CMAKE_CURRENT_BINARY_DIR}/gnome/cy_gnome/${ext}.cpp"
+    )
     
-    python_add_library(${ext} MODULE "${CMAKE_CURRENT_BINARY_DIR}/gnome/cy_gnome/${ext}.cpp"
-                   WITH_SOABI)
+    python_add_library(
+        ${ext}
+        MODULE "${CMAKE_CURRENT_BINARY_DIR}/gnome/cy_gnome/${ext}.cpp"
+        WITH_SOABI
+    )
 
     target_link_libraries(${ext} PRIVATE gnome Python::NumPy)
 
@@ -116,9 +123,6 @@ foreach(ext IN LISTS EXT_NAMES)
 
     install(TARGETS ${ext} DESTINATION gnome/cy_gnome)
 
-
 endforeach()
 
 install(TARGETS gnome DESTINATION gnome/cy_gnome)
-
-
diff --git a/py_gnome/conda_requirements_build.txt b/py_gnome/conda_requirements_build.txt
index 9f0b303f8..9289fbfb9 100644
--- a/py_gnome/conda_requirements_build.txt
+++ b/py_gnome/conda_requirements_build.txt
@@ -1,11 +1,11 @@
 # Required to build PyGNOME
 # NOTE: you also need a compiler set up to build Python extensions
 
-cython=0.29.*
+cython=3.0.*
 setuptools>=62  # older versions uses different build dirs
 setuptools-scm>=6.2
 gitpython
 python-build
 cmake
 ninja
-
+scikit-build-core>=0.7.*
diff --git a/py_gnome/setup.py b/py_gnome/setup.py
index 692ff2fd1..8e080a8a1 100755
--- a/py_gnome/setup.py
+++ b/py_gnome/setup.py
@@ -38,7 +38,6 @@
 
 # could run setup from anywhere (though not really??)
 SETUP_PATH = os.path.dirname(os.path.abspath(__file__))
-#SETUP_PATH = Path(__file__).parent
 
 # the extension used for compiled modules
 # does this not work ??
@@ -60,8 +59,6 @@
     repo = Repo('../.')
     branch_name = repo.active_branch.name
     last_update = next(repo.iter_commits()).committed_datetime.isoformat(),
-    # except TypeError:
-    #     branch_name = 'no-branch'
 except:  # anything goes wrong -- we want to keep moving
     branch_name = 'no-branch'
     last_update = datetime.datetime.now().isoformat()
@@ -199,8 +196,6 @@ def get_netcdf_libs():
         include_dir = include_dir.decode("ASCII").strip()
         lib_dir = lib_dir.decode("ASCII")
         libs = [l.decode("ASCII") for l in libs]
-        # print("found netcdf install:")
-        # print([lib_dir, libs, include_dir])
         return lib_dir, libs, include_dir
     except OSError:
         raise NotImplementedError("this setup.py needs nc-config "
@@ -221,10 +216,8 @@ def get_conda_includes_win():
 # maybe this will work with Windows, too" at least with conda?
 if sys.platform.startswith("linux") or sys.platform == "darwin":
     netcdf_base, netcdf_libs, netcdf_inc = get_netcdf_libs()
-    # print("netcdf include dir (line 188)", netcdf_inc)
     netcdf_lib_files = []
 elif sys.platform in ("win32"):  # but for now, still using our shipped libs.
-# elif sys.platform in ("darwin", "win32"):
     third_party_dir = os.path.join('..', 'third_party_lib')
     if 'CONDA_PREFIX' in os.environ:
         netcdf_libs, netcdf_inc, netcdf_dll = get_conda_includes_win()
@@ -235,7 +228,6 @@ def get_conda_includes_win():
         netcdf_lib_files = [os.path.join(netcdf_libs, libfile.format(l))
                             for l in netcdf_names]
     else:
-
         # the netCDF environment
         netcdf_base = os.path.join(third_party_dir, 'netcdf-4.3',
                                 sys.platform, architecture)
@@ -358,10 +350,7 @@ def get_conda_includes_win():
              ]
 
 
-# cpp_code_dir = (SETUP_PATH / 'lib_gnome').relative_to(SETUP_PATH)
-# cpp_files = [str(cpp_code_dir / f) for f in cpp_files]
 cpp_code_dir = os.path.join('.', 'lib_gnome')
-# cpp_code_dir = './lib_gnome'
 cpp_files = [os.path.join(cpp_code_dir, f) for f in cpp_files]
 
 
@@ -372,9 +361,10 @@ def get_conda_includes_win():
 # Build the extension objects
 
 # suppressing certain warnings
-compile_args = ["-Wno-unused-function",  # unused function - cython creates a lot
-                "-stdlib=libc++",  # to use the "correct" C++ libs
-                ]
+compile_args = [
+    "-Wno-unused-function",  # unused function - cython creates a lot
+    "-stdlib=libc++",  # to use the "correct" C++ libs
+]
 
 extensions = []
 
@@ -400,11 +390,10 @@ def get_conda_includes_win():
 #           conda netcdf...
 
 if sys.platform == "darwin":
-    # on the mac, the libgnome code is linked into the cy_basic_types
+    # On the mac, the libgnome code is linked into the cy_basic_types
     #    extension -- which makes it available to all the other extensions
     #.   as long as it's imported first.
     # This is being done in the gnome/cy_gnome/__init__.py
-
     basic_types_ext = Extension('gnome.cy_gnome.cy_basic_types',
                                 ['gnome/cy_gnome/cy_basic_types.pyx'] + cpp_files,
                                 language='c++',
@@ -417,7 +406,6 @@ def get_conda_includes_win():
 
     extensions.append(basic_types_ext)
     static_lib_files = []
-
 elif sys.platform == "win32":
     # On windows, the
     # build our compile arguments
@@ -448,7 +436,7 @@ def get_conda_includes_win():
 
     # we will reference this library when building all other extensions
     # fixme: Where is this getting built??
-    #        That filename needs to be dynamically determined with code somehat like:
+    #        That filename needs to be dynamically determined with code somewhat like:
     # if sys.version_info.major > 2:
     #     suffix = importlib.machinery.EXTENSION_SUFFIXES[0]
     #     libname = 'gnome' + suffix
@@ -490,7 +478,6 @@ def get_conda_includes_win():
                                  language='c++',
                                  define_macros=macros,
                                  libraries=['netcdf'],
-                                 # include_dirs=[cpp_code_dir],
                                  include_dirs=include_dirs,
                                  )])
 
@@ -551,7 +538,6 @@ def get_conda_includes_win():
 for mod_name in extension_names:
     cy_file = os.path.join("gnome/cy_gnome", mod_name + ".pyx")
     print("setting up cython extensions")
-    # print("include_dirs:", include_dirs)
     extensions.append(Extension('gnome.cy_gnome.' + mod_name,
                                 [cy_file],
                                 language="c++",
@@ -594,54 +580,12 @@ def get_conda_includes_win():
                                 language="c",
                                 ))
 
-# def get_version():
-#     """
-#     return the version number from the __init__
-#     """
-#     for line in open("gnome/__init__.py"):
-#         if line.startswith("__version__"):
-#             version = line.strip().split('=')[1].strip().strip("'").strip('"')
-#             return version
-#     raise ValueError("can't find version string in __init__")
-
-
 for e in extensions:
     e.cython_directives = {'language_level': "3"}  # all are Python-3
 
-# setup(name='pyGnome',
-      # version=get_version(),
-
 setup(ext_modules=extensions,
-      # packages=find_packages(),
-      # package_dir={'gnome': 'gnome'},
-      # package_data={'gnome': ['data/yeardata/*',
-      #                         'outputters/sample.b64',
-      #                         'weatherers/platforms.json'
-      #                         ]},
-      # you are not going to be able to "pip install" this anyway
-      # -- no need for requirements
-#     requires=[],   # want other packages here?
       cmdclass={'build_ext': build_ext,
                 'cleanall': cleanall},
-
-      # scripts,
-
-      # metadata for upload to PyPI
-      # author="Gnome team at NOAA/ORR/ERD",
-      # author_email="orr.gnome@noaa.gov",
-      # description=("GNOME (General NOAA Operational Modeling Environment) "
-      #              "is the modeling tool the Office of Response and "
-      #              "Restoration's (OR&R) Emergency Response Division uses to "
-      #              "predict the possible route, or trajectory, a pollutant "
-      #              "might follow in or on a body of water, such as in an "
-      #              "oil spill.  "
-      #              "It can also be used as a customizable general particle "
-      #              "tracking code. "
-      #              "Branch: {} "
-      #              "LastUpdate: {}"
-      #              .format(branch_name, last_update)),
-      # license="Public Domain",
-      # keywords="oilspill modeling particle_tracking",
       url="https://github.com/NOAA-ORR-ERD/PyGnome"
       )
 

From 3a5be5c0690f8e106c0746ef6e9577874c794c40 Mon Sep 17 00:00:00 2001
From: Rachael Mueller <Rachael.Mueller@noaa.gov>
Date: Wed, 31 Jan 2024 13:26:37 -0800
Subject: [PATCH 13/99] Fixing my mistake to add doc file to main

---
 .../source/file_formats/WCOFS_netcdf.rst      | 155 ------------------
 1 file changed, 155 deletions(-)
 delete mode 100644 py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst

diff --git a/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst b/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst
deleted file mode 100644
index b5191978f..000000000
--- a/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst
+++ /dev/null
@@ -1,155 +0,0 @@
-.. _WCOFS_netcd:
-
-WCOFS NetCDF formats
-======================
-
-This document provides information on the ROMS output variables required and/or used in 2D and 3D GNOME model applications.  It's organized in three sections to highlight the required outputs for:
-- different purposes (e.g. advection and weathering)
-- 2D applications
-- 3D applications
-
-ROMS output requirements by purpose/utility
--------------
-
-**Advection/transport (required for all cases)**
-
-  lon-psi
-
-  lat-psi
-  
-  angle (necessary unless grid perfectly aligned with N/S, E/W).  No error is thrown but the results won't be right. 
-  
-  u (horizontal movers)
-  
-  v
-  
-  ocean_time
-
-**Advection/transport (optional)**
-
-  wet/dry 
-  
-  masks (this will affect code in ways that are a bit "off-roading")
-  
-  vertical diffusivities (vertical random mover)
-
-**Advection/transport (required for 3D cases)**
-
-  w (vertical mover)
-
-  stretching params:
-       		1. Cs_r,
-    		2. Cs_w,
-      		3. s_rho,
-        	4. S_w,
-         	5. hc,
-          	6. Vtransform,
-          	7. zeta (used to calculate sigma-levels), and
-          	8. h
-
-**Weathering**
-
-  temp
-
-  salt
-
-  u10, eastward_wind, or wind_u
-
-  v10, westward_wind, or wind_v
-
-  [**future**] zeta (for 3D applications but not currently used)
-
-  [**future**] sediment
-
-**Visualization**
-
-  lon-rho, -u, -v, -psi
-
-  lat-rho, -u, -v, -psi
-
-  mask-rho, -u, -v, -psi
-
-2D case WCOFS output requirements 
--------------
-
-**Current transport file**
-
-  ocean_time
-
-  u 
-
-  v
-
-  horizontal diffusivities (random movers)
-
-  temp
-
-  salt
-
-**The following 4 list items can be in a separate grid file or included in the current transport file**
-
-  lon-rho, -u, -v, -psi (only psi required to run model.  The rest are for graphical display)
-
-  lat-rho, -u, -v, -psi
-
-  mask-rho, -u, -v, -psi
-
-  angle (necessary unless grid perfectly aligned with N/S, E/W).  No error is thrown but the results won't be right. 
-
-**wind forcing file**
-
-  u10, eastward_wind, or wind_u
-
-  v10, westward_wind, or wind_v
-
-3D case WCOFS output requirements
--------------
-
-**Current transport file**
-
-  ocean_time
-
-  u 
-
-  v
-
-  w (vertical mover)
-
-  vertical/horizontal diffusivities (random movers)
-
-  temp
-
-  salt
-
-**The following 5 list items (through all stretching params) can be in a separate grid file or together with current transport file**
-  
-  lon-rho, -u, -v, -psi (only psi required to run model.  The rest are for graphical display)
-
-  lat-rho, -u, -v, -psi
-
-  mask-rho, -u, -v, -psi
-
-  angle (necessary unless grid perfectly aligned with N/S, E/W).  No error is thrown but the results won't be right.
-
-  stretching params:
-   1. Cs_r,
-   2. Cs_w,
-   3. s_rho,
-   4. S_w,
-   5. hc,
-   6. Vtransform,
-   7. zeta (used to calculate sigma-levels), and
-   8. h
-
-**winds forcing file**
-
-  u10, eastward_wind, or wind_u
-
-  v10, westward_wind, or wind_v
-
-.. NOTE: this was auto-built into the docstring of the:
-..       gnome/environment/names.py file -- it would be
-..       nice to auto-update, but this is start
-
-.. and we should be able to link to the docstring ...
-

From 48abf9b0f76c9f35b81f8ea9b376ab7d35bb57ff Mon Sep 17 00:00:00 2001
From: Rachael Mueller <Rachael.Mueller@noaa.gov>
Date: Wed, 31 Jan 2024 13:36:12 -0800
Subject: [PATCH 14/99] adding WCOFS doc to my doc dev branch

---
 .../source/file_formats/WCOFS_netcdf.rst      | 155 ++++++++++++++++++
 1 file changed, 155 insertions(+)
 create mode 100644 py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst

diff --git a/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst b/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst
new file mode 100644
index 000000000..b5191978f
--- /dev/null
+++ b/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst
@@ -0,0 +1,155 @@
+.. _WCOFS_netcd:
+
+WCOFS NetCDF formats
+======================
+
+This document provides information on the ROMS output variables required and/or used in 2D and 3D GNOME model applications.  It's organized in three sections to highlight the required outputs for:
+- different purposes (e.g. advection and weathering)
+- 2D applications
+- 3D applications
+
+ROMS output requirements by purpose/utility
+-------------
+
+**Advection/transport (required for all cases)**
+
+  lon-psi
+
+  lat-psi
+  
+  angle (necessary unless grid perfectly aligned with N/S, E/W).  No error is thrown but the results won't be right. 
+  
+  u (horizontal movers)
+  
+  v
+  
+  ocean_time
+
+**Advection/transport (optional)**
+
+  wet/dry 
+  
+  masks (this will affect code in ways that are a bit "off-roading")
+  
+  vertical diffusivities (vertical random mover)
+
+**Advection/transport (required for 3D cases)**
+
+  w (vertical mover)
+
+  stretching params:
+       		1. Cs_r,
+    		2. Cs_w,
+      		3. s_rho,
+        	4. S_w,
+         	5. hc,
+          	6. Vtransform,
+          	7. zeta (used to calculate sigma-levels), and
+          	8. h
+
+**Weathering**
+
+  temp
+
+  salt
+
+  u10, eastward_wind, or wind_u
+
+  v10, westward_wind, or wind_v
+
+  [**future**] zeta (for 3D applications but not currently used)
+
+  [**future**] sediment
+
+**Visualization**
+
+  lon-rho, -u, -v, -psi
+
+  lat-rho, -u, -v, -psi
+
+  mask-rho, -u, -v, -psi
+
+2D case WCOFS output requirements 
+-------------
+
+**Current transport file**
+
+  ocean_time
+
+  u 
+
+  v
+
+  horizontal diffusivities (random movers)
+
+  temp
+
+  salt
+
+**The following 4 list items can be in a separate grid file or included in the current transport file**
+
+  lon-rho, -u, -v, -psi (only psi required to run model.  The rest are for graphical display)
+
+  lat-rho, -u, -v, -psi
+
+  mask-rho, -u, -v, -psi
+
+  angle (necessary unless grid perfectly aligned with N/S, E/W).  No error is thrown but the results won't be right. 
+
+**wind forcing file**
+
+  u10, eastward_wind, or wind_u
+
+  v10, westward_wind, or wind_v
+
+3D case WCOFS output requirements
+-------------
+
+**Current transport file**
+
+  ocean_time
+
+  u 
+
+  v
+
+  w (vertical mover)
+
+  vertical/horizontal diffusivities (random movers)
+
+  temp
+
+  salt
+
+**The following 5 list items (through all stretching params) can be in a separate grid file or together with current transport file**
+  
+  lon-rho, -u, -v, -psi (only psi required to run model.  The rest are for graphical display)
+
+  lat-rho, -u, -v, -psi
+
+  mask-rho, -u, -v, -psi
+
+  angle (necessary unless grid perfectly aligned with N/S, E/W).  No error is thrown but the results won't be right.
+
+  stretching params:
+   1. Cs_r,
+   2. Cs_w,
+   3. s_rho,
+   4. S_w,
+   5. hc,
+   6. Vtransform,
+   7. zeta (used to calculate sigma-levels), and
+   8. h
+
+**winds forcing file**
+
+  u10, eastward_wind, or wind_u
+
+  v10, westward_wind, or wind_v
+
+.. NOTE: this was auto-built into the docstring of the:
+..       gnome/environment/names.py file -- it would be
+..       nice to auto-update, but this is start
+
+.. and we should be able to link to the docstring ...
+

From 7e14d1abcadc317ed1f9428e7d2a46235e9321f7 Mon Sep 17 00:00:00 2001
From: Rachael Mueller <Rachael.Mueller@noaa.gov>
Date: Wed, 31 Jan 2024 14:33:29 -0800
Subject: [PATCH 15/99] First attempt with doc update.  Lots of warnings to
 address

---
 py_gnome/documentation/source/file_formats/index.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/py_gnome/documentation/source/file_formats/index.rst b/py_gnome/documentation/source/file_formats/index.rst
index 0ec34e25f..70336c19a 100644
--- a/py_gnome/documentation/source/file_formats/index.rst
+++ b/py_gnome/documentation/source/file_formats/index.rst
@@ -8,6 +8,7 @@ GNOME File Formats
    maps
    winds
    netcdf
+   WCOFS_netcdf
    noaa_specific_currents
    scaling_current_patterns
    output_formats

From db0ef266826130eac3ffc738e82b883b029321f0 Mon Sep 17 00:00:00 2001
From: Rachael Mueller <rachael.mueller@noaa.gov>
Date: Thu, 1 Feb 2024 00:59:11 +0000
Subject: [PATCH 16/99] fixed title

---
 py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst b/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst
index b5191978f..8f6edf534 100644
--- a/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst
+++ b/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst
@@ -1,4 +1,4 @@
-.. _WCOFS_netcd:
+.. _WCOFS_netcdf:
 
 WCOFS NetCDF formats
 ======================

From ade5655dde1c163c0b647e27788fb479fd2858f4 Mon Sep 17 00:00:00 2001
From: Rachael Mueller <rachael.mueller@noaa.gov>
Date: Thu, 1 Feb 2024 01:02:30 +0000
Subject: [PATCH 17/99] addressed: title underline too short

---
 py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst b/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst
index 8f6edf534..5a6a34bb1 100644
--- a/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst
+++ b/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst
@@ -9,7 +9,7 @@ This document provides information on the ROMS output variables required and/or
 - 3D applications
 
 ROMS output requirements by purpose/utility
--------------
+-------------------------------------------
 
 **Advection/transport (required for all cases)**
 
@@ -70,7 +70,7 @@ ROMS output requirements by purpose/utility
   mask-rho, -u, -v, -psi
 
 2D case WCOFS output requirements 
--------------
+---------------------------------
 
 **Current transport file**
 
@@ -103,7 +103,7 @@ ROMS output requirements by purpose/utility
   v10, westward_wind, or wind_v
 
 3D case WCOFS output requirements
--------------
+---------------------------------
 
 **Current transport file**
 

From 54dcfc42cd68f6601b905fed1e058ba2f7301fcc Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Thu, 1 Feb 2024 15:48:42 -0800
Subject: [PATCH 18/99] reformatting of ROMS netcdf requirements -- only
 started

---
 .../source/file_formats/WCOFS_netcdf.rst      | 56 +++++++++++++++++--
 1 file changed, 52 insertions(+), 4 deletions(-)

diff --git a/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst b/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst
index 5a6a34bb1..c8dc8f426 100644
--- a/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst
+++ b/py_gnome/documentation/source/file_formats/WCOFS_netcdf.rst
@@ -1,17 +1,65 @@
-.. _WCOFS_netcdf:
+.. _ROMS_netcdf:
 
-WCOFS NetCDF formats
-======================
+ROMS Model: NetCDF output
+=========================
 
 This document provides information on the ROMS output variables required and/or used in 2D and 3D GNOME model applications.  It's organized in three sections to highlight the required outputs for:
 - different purposes (e.g. advection and weathering)
 - 2D applications
 - 3D applications
 
+
 ROMS output requirements by purpose/utility
 -------------------------------------------
 
-**Advection/transport (required for all cases)**
+ROMS uses a "Staggered Grid", and PYGNOME seeks to be compliant with the SGRID conversion:
+
+https://sgrid.github.io/sgrid/
+
+However, many ROMS output files are not compliant with that convension,
+so PyGNOME is designed to read ROMS specific files.
+But the concepts are helpful, so ROMS has been described in that context here.
+
+Grid definition
+...............
+
+ROMS is an Arakawa C-grid model -- the full grid definition is required in order to properly interpret the results.
+
+**Required grid variables:**
+
+
+.. +------------------------+------------+----------+----------+
+.. | Header row, column 1   | Header 2   | Header 3 | Header 4 |
+.. | (header rows optional) |            |          |          |
+.. +========================+============+==========+==========+
+.. | body row 1, column 1   | column 2   | column 3 | column 4 |
+.. +------------------------+------------+----------+----------+
+.. | body row 2             | ...        | ...      |          |
+.. +------------------------+------------+----------+----------+
+
++-----------------------+----------------+---------------------------------------+
+| CF/SGRID concept      | ROMS name      | Usual ROMS Variables                  |
++=======================+================+=======================================+
+| node_coordinates      | psi points     | ``lon_psi``, ``lat_psi``, ``mask_psi``|
++-----------------------+----------------+---------------------------------------+
+| face_coordinate       | rho points     | ``lon_rho``, ``lat_rho``, ``mask_rho``|
++-----------------------+----------------+---------------------------------------+
+|          time         |  time          |         ``time`` or ``ocean_time``    |
++-----------------------+----------------+---------------------------------------+
+| **Three dimensions**  |                |                                       |
++-----------------------+----------------+---------------------------------------+
+|           depth       |      ???       |                                       |
++-----------------------+----------------+---------------------------------------+
+|                       |                |                                       |
++-----------------------+----------------+---------------------------------------+
+|                       |                |                                       |
++-----------------------+----------------+---------------------------------------+
+
+
+.. note:: ROMS output often includes the 'u' and 'v' locations: the cneters of the cell edges. These are not used by PyGNOME **IS THIS TRUE??**
+
+
+**Advection/transport**
 
   lon-psi
 

From ac7cf16748262d7853ac64bdda5e72a49d43e55a Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Wed, 7 Feb 2024 13:20:22 -0800
Subject: [PATCH 19/99] CI: We test our package in the test jobs, not the
 compile jobs.

---
 .gitlab-ci.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3d050d8e7..944f9dda8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -51,9 +51,6 @@ compile_pygnome:
     - pip install ../oil_database/adios_db/
     - pip install ./
 
-    - cd ../  # make sure that it won't find the source gnome package.
-    - python -c "import gnome"  # make sure that it imports
-
     # need extra requirements for the docs
     - conda install -y --file py_gnome/conda_requirements_docs.txt
     - cd py_gnome/documentation && make html  # build the docs

From c0f197c065311d03da85b646feaa66c00513b0bd Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Wed, 7 Feb 2024 13:31:50 -0800
Subject: [PATCH 20/99] CI: failed compiling the docs, path to files was not
 updated.

---
 .gitlab-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 944f9dda8..9aef81a07 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -52,8 +52,8 @@ compile_pygnome:
     - pip install ./
 
     # need extra requirements for the docs
-    - conda install -y --file py_gnome/conda_requirements_docs.txt
-    - cd py_gnome/documentation && make html  # build the docs
+    - conda install -y --file conda_requirements_docs.txt
+    - cd documentation && make html  # build the docs
   artifacts:
     when: always
     expire_in: 15 days

From 36d04f50d51ea2a7dfa9e828066c9afa2c98545f Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Wed, 7 Feb 2024 13:44:46 -0800
Subject: [PATCH 21/99] CI: Put the build stage before the test so we have a
 docker image to look at.

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9aef81a07..0013fb8e6 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -3,8 +3,8 @@ variables:
 
 stages:
   - compile
-  - test
   - build
+  - test
 
 cache:
   paths:

From 2797d40f086dab9bd5f27d98fe95e362172e3373 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Wed, 7 Feb 2024 14:49:02 -0800
Subject: [PATCH 22/99] CI: Temporarily allow building the develop docker image
 in the new_build branch.

---
 .gitlab-ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0013fb8e6..c0732645e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -154,6 +154,7 @@ build_develop:
   stage: build
   only:
     - develop
+    - new_build
   tags:
     - shell
     - build

From c3c513875caa2d1ea4effc502ff3542b972608e1 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Wed, 7 Feb 2024 15:32:32 -0800
Subject: [PATCH 23/99] CI: Added workdir to the dockerfile to simplify the
 commands a bit.

---
 dockerfile | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/dockerfile b/dockerfile
index e66d4a786..fa167a0c0 100644
--- a/dockerfile
+++ b/dockerfile
@@ -2,35 +2,35 @@ ARG PYTHON_VER
 
 FROM registry.orr.noaa.gov/erd/centos-conda/centos7-python$PYTHON_VER
 
+# Args declared before the FROM need to be redeclared, don't delete this
+ARG PYTHON_VER
+
 RUN yum install -y wget gcc make bzip2 gcc-c++ ca-certificates \
     libglib2.0-0 libxext6 libsm6 libxrender1 \
     git mercurial subversion tar
 
 COPY ./ /pygnome/
+WORKDIR /pygnome/
 
-RUN cd pygnome && conda install python=$PYTHON_VER \
-                                --file conda_requirements.txt \
-                                --file conda_requirements_build.txt \
-                                --file oil_database/adios_db/conda_requirements.txt
+RUN cd py_gnome && conda install python=$PYTHON_VER \
+    --file conda_requirements.txt \
+    --file conda_requirements_build.txt \
+    --file oil_database/adios_db/conda_requirements.txt
 
 # this was pinning things down too much for the webapi step
 # RUN cd pygnome && conda install -y --file deploy_requirements.txt
 
-RUN conda list
-
 # this kludge should no longer be required
 # RUN conda update -y libgd
 
 # only because this was giving us problems
 # RUN python -c "import py_gd"
 
-# adios_db requirements should already be there from the deploy_requirements file
-# RUN cd pygnome/oil_database/adios_db && conda install --file conda_requirements.txt
+RUN cd oil_database/adios_db && conda install --file conda_requirements.txt
+RUN cd oil_database/adios_db && python -m pip install ./
 
-RUN cd pygnome/oil_database/adios_db && python -m pip install ./
-RUN cd pygnome/py_gnome && pip install ./
+RUN cd py_gnome && pip install ./
 
 # to check if they got installed properly
-RUN python -c "import adios_db"
-RUN python -c "import gnome"
-
+#RUN python -c "import adios_db"
+#RUN python -c "import gnome"

From a2d8ddc645d411849a45e4e607b4ca15285a9420 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Wed, 7 Feb 2024 15:47:00 -0800
Subject: [PATCH 24/99] CI: Wrong paths specified in the conda install command.

---
 dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/dockerfile b/dockerfile
index fa167a0c0..3d4661f4c 100644
--- a/dockerfile
+++ b/dockerfile
@@ -12,9 +12,9 @@ RUN yum install -y wget gcc make bzip2 gcc-c++ ca-certificates \
 COPY ./ /pygnome/
 WORKDIR /pygnome/
 
-RUN cd py_gnome && conda install python=$PYTHON_VER \
-    --file conda_requirements.txt \
-    --file conda_requirements_build.txt \
+RUN conda install python=$PYTHON_VER \
+    --file py_gnome/conda_requirements.txt \
+    --file py_gnome/conda_requirements_build.txt \
     --file oil_database/adios_db/conda_requirements.txt
 
 # this was pinning things down too much for the webapi step

From 9accc7c08b114ae58bc8c4bd2369cd55584383c4 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 22 Feb 2024 12:17:06 -0800
Subject: [PATCH 25/99] CI: Dynamically name the docker image tag in the
 build_develop task.

---
 .gitlab-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c0732645e..04128258c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -167,8 +167,8 @@ build_develop:
 
     # build the py_gnome image
     - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
-    - docker build . --build-arg PYTHON_VER=$PYTHON_VER -t registry.orr.noaa.gov/gnome/pygnome:develop
-    - docker push registry.orr.noaa.gov/gnome/pygnome:develop
+    - docker build . --build-arg PYTHON_VER=$PYTHON_VER -t registry.orr.noaa.gov/gnome/pygnome:$CI_COMMIT_BRANCH
+    - docker push registry.orr.noaa.gov/gnome/pygnome:$CI_COMMIT_BRANCH
 
 build_main:
   stage: build

From 2179e05a2cd1c74e22dbad82da3beff8ccacf7a6 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Fri, 23 Feb 2024 17:40:37 -0800
Subject: [PATCH 26/99] CI: Our target python version is wrong, should be 3.10.

---
 .gitlab-ci.yml                             |  2 +-
 py_gnome/gnome/cy_gnome/__init__.py        |  7 +------
 py_gnome/gnome/cy_gnome/cy_basic_types.pyx | 15 +--------------
 3 files changed, 3 insertions(+), 21 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 04128258c..546552c24 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,5 +1,5 @@
 variables:
-  PYTHON_VER: "3.9"
+  PYTHON_VER: "3.10"
 
 stages:
   - compile
diff --git a/py_gnome/gnome/cy_gnome/__init__.py b/py_gnome/gnome/cy_gnome/__init__.py
index ed5e86075..522e20d57 100644
--- a/py_gnome/gnome/cy_gnome/__init__.py
+++ b/py_gnome/gnome/cy_gnome/__init__.py
@@ -2,9 +2,4 @@
 __init__.py for the gnome/cy_gnome package
 
 """
-
-
-
-
-
-#from . import cy_basic_types  # make sure it's imported, for the C++ lib
+from . import cy_basic_types  # make sure it's imported, for the C++ lib
diff --git a/py_gnome/gnome/cy_gnome/cy_basic_types.pyx b/py_gnome/gnome/cy_gnome/cy_basic_types.pyx
index c4edcbd3b..6dc140848 100644
--- a/py_gnome/gnome/cy_gnome/cy_basic_types.pyx
+++ b/py_gnome/gnome/cy_gnome/cy_basic_types.pyx
@@ -39,7 +39,6 @@ def enum(**enums):
 """
 LE Status as an enum type
 """
-
 class oil_status(IntEnum):
     """
     maps to the C enum
@@ -53,15 +52,6 @@ class oil_status(IntEnum):
     on_tideflat = OILSTAT_ON_TIDEFLAT
 
 
-# oil_status = dict(not_released=OILSTAT_NOTRELEASED,
-#                   in_water=OILSTAT_INWATER,
-#                   on_land=OILSTAT_ONLAND,
-#                   off_maps=OILSTAT_OFFMAPS,
-#                   evaporated=OILSTAT_EVAPORATED,
-#                   to_be_removed=OILSTAT_TO_BE_REMOVED,
-#                   on_tideflat=OILSTAT_ON_TIDEFLAT,
-#                   )
-
 class numerical_methods(IntEnum):
     euler = EULER,
     rk4 = RK4
@@ -79,6 +69,7 @@ disperse status as an enum type
 #                    remove = REMOVE,
 #                    have_removed = HAVE_REMOVED)
 #
+
 """
 SpillType {FORECAST_LE = 1, UNCERTAINTY_LE = 2};
 """
@@ -117,7 +108,3 @@ class ts_format(IntEnum):
 
 cdef Seconds temp
 seconds = type(temp)
-
-
-
-

From c1112977335c382ca2da0282961f71779d2f7fbb Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Fri, 23 Feb 2024 21:16:58 -0800
Subject: [PATCH 27/99] CI: Added the installation of the chrpath utility to
 the dockerfile so we can debug some shared libraries.

---
 dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/dockerfile b/dockerfile
index 3d4661f4c..f85d10a21 100644
--- a/dockerfile
+++ b/dockerfile
@@ -5,9 +5,9 @@ FROM registry.orr.noaa.gov/erd/centos-conda/centos7-python$PYTHON_VER
 # Args declared before the FROM need to be redeclared, don't delete this
 ARG PYTHON_VER
 
-RUN yum install -y wget gcc make bzip2 gcc-c++ ca-certificates \
-    libglib2.0-0 libxext6 libsm6 libxrender1 \
-    git mercurial subversion tar
+RUN yum install -y libglib2.0-0 libxext6 libsm6 libxrender1 \
+    wget gcc make bzip2 gcc-c++ chrpath \
+    ca-certificates git mercurial subversion tar
 
 COPY ./ /pygnome/
 WORKDIR /pygnome/

From f93703a9e2d6791d01926b02966b09b752e2a547 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Sat, 24 Feb 2024 00:31:48 -0800
Subject: [PATCH 28/99] CI: Added the installation of the patchelf utility to
 the dockerfile so we can debug some shared libraries.

---
 dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dockerfile b/dockerfile
index f85d10a21..b0868f6eb 100644
--- a/dockerfile
+++ b/dockerfile
@@ -6,7 +6,7 @@ FROM registry.orr.noaa.gov/erd/centos-conda/centos7-python$PYTHON_VER
 ARG PYTHON_VER
 
 RUN yum install -y libglib2.0-0 libxext6 libsm6 libxrender1 \
-    wget gcc make bzip2 gcc-c++ chrpath \
+    wget gcc make bzip2 gcc-c++ chrpath patchelf \
     ca-certificates git mercurial subversion tar
 
 COPY ./ /pygnome/

From d162847f9a628cf876f427a1e28aba5d344bf46e Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Sun, 25 Feb 2024 00:05:48 -0800
Subject: [PATCH 29/99] Prepping the cmakelists.txt file to start compiling the
 point_in_polygons extension.

---
 py_gnome/CMakeLists.txt                    | 20 ++++++++-----
 py_gnome/gnome/utilities/geometry/setup.py | 33 +++++++++++-----------
 2 files changed, 30 insertions(+), 23 deletions(-)

diff --git a/py_gnome/CMakeLists.txt b/py_gnome/CMakeLists.txt
index a4e3fe514..d2a344bd8 100644
--- a/py_gnome/CMakeLists.txt
+++ b/py_gnome/CMakeLists.txt
@@ -42,7 +42,7 @@ set(EXT_NAMES
     cy_weatherers
 )
 
-set(CPP_FILES
+set(LIBGNOME_CPP_FILES
     RectGridVeL_c.cpp
     MemUtils.cpp
     Mover_c.cpp
@@ -84,9 +84,15 @@ set(CPP_FILES
     Weatherers_c.cpp
 )
 
-list(TRANSFORM CPP_FILES PREPEND "lib_gnome/")
+set(CY_POINT_IN_POLY_CPP_FILES
+    cy_point_in_polygon.pyx
+    c_point_in_polygon.c
+)
+
+list(TRANSFORM LIBGNOME_CPP_FILES PREPEND "lib_gnome/")
+list(TRANSFORM CY_POINT_IN_POLY_CPP_FILES PREPEND "gnome/utilities/geometry")
 
-add_library(gnome SHARED ${CPP_FILES})
+add_library(gnome SHARED ${LIBGNOME_CPP_FILES})
 
 target_link_libraries(gnome PRIVATE NetCDF::NetCDF)
 
@@ -115,11 +121,11 @@ foreach(ext IN LISTS EXT_NAMES)
     target_link_libraries(${ext} PRIVATE gnome Python::NumPy)
 
 
-    #if(APPLE)
+    if(APPLE)
       set_target_properties(${ext} PROPERTIES INSTALL_RPATH "@loader_path/.")
-    #elseif(UNIX)
-    #  set_target_properties(${ext} PROPERTIES INSTALL_RPATH "$ORIGIN/.")
-    #endif()
+    elseif(UNIX)
+      set_target_properties(${ext} PROPERTIES INSTALL_RPATH "$ORIGIN/.")
+    endif()
 
     install(TARGETS ${ext} DESTINATION gnome/cy_gnome)
 
diff --git a/py_gnome/gnome/utilities/geometry/setup.py b/py_gnome/gnome/utilities/geometry/setup.py
index 032447ad8..9db13a651 100644
--- a/py_gnome/gnome/utilities/geometry/setup.py
+++ b/py_gnome/gnome/utilities/geometry/setup.py
@@ -3,16 +3,17 @@
 """
 setup.py for geometry package
 
-It's now built with the main gnome setup.py, but kept this here for easier testing in place...
-only useful now for "develop" mode
+It's now built with the main gnome setup.py, but kept this here for
+easier testing in place...
+Only useful now for "develop" mode
 """
 
-#from distutils.core import setup
-from setuptools import setup # to support "develop" mode
+# from distutils.core import setup
+from setuptools import setup  # to support "develop" mode
 from distutils.extension import Extension
 from Cython.Distutils import build_ext
 
-import numpy # for the includes for the Cython code
+import numpy  # for the includes for the Cython code
 
 
 ext_modules = [Extension("cy_point_in_polygon",
@@ -22,19 +23,19 @@
                ]
 
 setup(
-    name = "geometry",
-    version = "0.03",
-    author = "Chris Barker",
-    author_email = "Chris.Barker@noaa.gov",
-    description = ("some geometry for GNOME"),
-#    long_description=read('README'),
+    name="geometry",
+    version="0.03",
+    author="Chris Barker",
+    author_email="Chris.Barker@noaa.gov",
+    description=("some geometry for GNOME"),
+    # long_description=read('README'),
     classifiers=[
         "Development Status :: 3 - Alpha",
         "Topic :: Utilities",
         ],
-    cmdclass = {'build_ext': build_ext},
-#    packages = ["geometry"],
-    ext_modules = ext_modules,
-#    modules = ["BBox.py",]
-    scripts = [],
+    cmdclass={'build_ext': build_ext},
+    # packages=["geometry"],
+    ext_modules=ext_modules,
+    # modules=["BBox.py",]
+    scripts=[],
     )

From ffd7219d5178606aee651615571ad6defaa6fa2b Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Tue, 27 Feb 2024 10:12:29 -0800
Subject: [PATCH 30/99] scikit-build-core: building cy_point_in_polygon now
 seems to work on mac osx.

---
 py_gnome/CMakeLists.txt | 56 +++++++++++++++++++++++++++++++++++------
 1 file changed, 48 insertions(+), 8 deletions(-)

diff --git a/py_gnome/CMakeLists.txt b/py_gnome/CMakeLists.txt
index d2a344bd8..a71aa545d 100644
--- a/py_gnome/CMakeLists.txt
+++ b/py_gnome/CMakeLists.txt
@@ -2,7 +2,7 @@
 
 
 cmake_minimum_required(VERSION 3.15...3.26)
-project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
+project(${SKBUILD_PROJECT_NAME} LANGUAGES C CXX)
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
@@ -84,13 +84,7 @@ set(LIBGNOME_CPP_FILES
     Weatherers_c.cpp
 )
 
-set(CY_POINT_IN_POLY_CPP_FILES
-    cy_point_in_polygon.pyx
-    c_point_in_polygon.c
-)
-
 list(TRANSFORM LIBGNOME_CPP_FILES PREPEND "lib_gnome/")
-list(TRANSFORM CY_POINT_IN_POLY_CPP_FILES PREPEND "gnome/utilities/geometry")
 
 add_library(gnome SHARED ${LIBGNOME_CPP_FILES})
 
@@ -100,6 +94,8 @@ target_compile_definitions(gnome PUBLIC pyGNOME=1)
 
 target_include_directories(gnome PUBLIC lib_gnome)
 
+install(TARGETS gnome DESTINATION gnome/cy_gnome)
+
 foreach(ext IN LISTS EXT_NAMES)
 
     add_custom_command(
@@ -131,4 +127,48 @@ foreach(ext IN LISTS EXT_NAMES)
 
 endforeach()
 
-install(TARGETS gnome DESTINATION gnome/cy_gnome)
+
+#
+# Extension: cy_point_in_polygon
+#
+
+# Now we make the c_point_in_polygon.c file into a library
+# This will have to do until we figure out how to make a .pyx extension with
+# additional .c files
+# No need to make it dynamic since it
+set(POINT_IN_POLY_C_FILES
+    c_point_in_polygon.c
+)
+
+list(TRANSFORM POINT_IN_POLY_C_FILES PREPEND "gnome/utilities/geometry/")
+
+add_library(point_in_polygon SHARED ${POINT_IN_POLY_C_FILES})
+
+install(TARGETS point_in_polygon DESTINATION gnome/utilities/geometry)
+
+# now we make the cy_point_in_polygon extension
+add_custom_command(
+  OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/gnome/utilities/geometry/cy_point_in_polygon.c"
+  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/gnome/utilities/geometry/cy_point_in_polygon.pyx"
+  VERBATIM
+  COMMAND "${CYTHON}" -3 -v
+          "${CMAKE_CURRENT_SOURCE_DIR}/gnome/utilities/geometry/cy_point_in_polygon.pyx"
+          --output-file
+          "${CMAKE_CURRENT_BINARY_DIR}/gnome/utilities/geometry/cy_point_in_polygon.c"
+)
+
+python_add_library(
+    cy_point_in_polygon
+    MODULE "${CMAKE_CURRENT_BINARY_DIR}/gnome/utilities/geometry/cy_point_in_polygon.c"
+    WITH_SOABI
+)
+
+target_link_libraries(cy_point_in_polygon PRIVATE point_in_polygon Python::NumPy)
+
+if(APPLE)
+    set_target_properties(cy_point_in_polygon PROPERTIES INSTALL_RPATH "@loader_path/.")
+elseif(UNIX)
+    set_target_properties(cy_point_in_polygon PROPERTIES INSTALL_RPATH "$ORIGIN/.")
+endif()
+
+install(TARGETS cy_point_in_polygon DESTINATION gnome/utilities/geometry)

From 3f83125f0b904101a0d00bd640c7f1317718bcee Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Tue, 27 Feb 2024 13:18:37 -0800
Subject: [PATCH 31/99] CI: dockerfile wasn't finding the py_gnome requirements
 files.

---
 dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dockerfile b/dockerfile
index c242c82a9..851d58cba 100644
--- a/dockerfile
+++ b/dockerfile
@@ -12,8 +12,8 @@ COPY ./ /pygnome/
 WORKDIR /pygnome/
 
 RUN conda install python=$PYTHON_VER \
-        --file conda_requirements.txt \
-        --file conda_requirements_build.txt \
+        --file py_gnome/conda_requirements.txt \
+        --file py_gnome/conda_requirements_build.txt \
         --file oil_database/adios_db/conda_requirements.txt
 
 RUN cd oil_database/adios_db && python -m pip install ./

From b5aa260816fccb3e6302545770e8abb035dde633 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Wed, 28 Feb 2024 21:39:46 -0800
Subject: [PATCH 32/99] CI: Find out where conda is installed on the Windows
 runner.  I don't think it's where we think it is.

---
 .gitlab-ci.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 82ceccfd1..7e11fb274 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -108,8 +108,12 @@ test_pygnome_windows:
     - visual-studio-22
   allow_failure: true
   before_script:
+    # where are we?
     - Get-Location
-    - dir
+
+    # where is our conda installation?
+    - Get-ChildItem -Path 'C:\' -Recurse -Filter "*conda*"
+
     # make sure conda is on the path first in the path
     - $Env:Path = 'C:\ProgramData\Miniconda3\Library\bin;' + $Env:Path
     - $Env:Path = 'C:\ProgramData\Miniconda3\;' + $Env:Path

From b20d11038ee0abe729e2986b9f17f375031d43e6 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 29 Feb 2024 09:33:05 -0800
Subject: [PATCH 33/99] CI: Finding conda on the Windows runner, the filter
 list was way too big.

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7e11fb274..fc2872e36 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -112,7 +112,7 @@ test_pygnome_windows:
     - Get-Location
 
     # where is our conda installation?
-    - Get-ChildItem -Path 'C:\' -Recurse -Filter "*conda*"
+    - Get-ChildItem -Path 'C:\' -Recurse -Filter "*conda*" -Exclude "*econdary*" -Exclude "*IconDark*"
 
     # make sure conda is on the path first in the path
     - $Env:Path = 'C:\ProgramData\Miniconda3\Library\bin;' + $Env:Path

From e52a39a05d80d2bbe49b8b056a5fcea3fdb3a289 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 29 Feb 2024 10:08:58 -0800
Subject: [PATCH 34/99] CI: Get-ChildItem wrong syntax

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index fc2872e36..7e504b80e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -112,7 +112,7 @@ test_pygnome_windows:
     - Get-Location
 
     # where is our conda installation?
-    - Get-ChildItem -Path 'C:\' -Recurse -Filter "*conda*" -Exclude "*econdary*" -Exclude "*IconDark*"
+    - Get-ChildItem -Path 'C:\' -Recurse -Filter "*conda*" -Exclude "*econdary*", "*IconDark*"
 
     # make sure conda is on the path first in the path
     - $Env:Path = 'C:\ProgramData\Miniconda3\Library\bin;' + $Env:Path

From a5846494bd86a1abadab976bddc8ab264afa1b8b Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 29 Feb 2024 10:57:29 -0800
Subject: [PATCH 35/99] CI: conda.py seems to exist, but what is the full path?

---
 .gitlab-ci.yml | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7e504b80e..d938ac51d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -112,7 +112,7 @@ test_pygnome_windows:
     - Get-Location
 
     # where is our conda installation?
-    - Get-ChildItem -Path 'C:\' -Recurse -Filter "*conda*" -Exclude "*econdary*", "*IconDark*"
+    - Get-ChildItem -Path 'C:\' -Recurse -Filter "conda.py" | % { $_.FullName }
 
     # make sure conda is on the path first in the path
     - $Env:Path = 'C:\ProgramData\Miniconda3\Library\bin;' + $Env:Path
@@ -120,7 +120,10 @@ test_pygnome_windows:
     - $Env:Path = 'C:\ProgramData\Miniconda3\Scripts;' + $Env:Path
 
     - echo "Our environemt vars:"
-    - $Env:Path
+    - $Env:Path -split ';'
+
+    - echo "Python is running from:"
+    - python -c "import sys; print(sys.executable)"
 
     - echo $CI_PIPELINE_ID
     - conda activate ./$CI_PIPELINE_ID
@@ -131,17 +134,6 @@ test_pygnome_windows:
   script:
     - echo "Building and testing PyGNOME"
 
-    # # make sure our conda package is first in the path
-    # - $Env:Path = 'C:\ProgramData\Miniconda3\Library\bin;' + $Env:Path
-    # - $Env:Path = 'C:\ProgramData\Miniconda3\;' + $Env:Path
-    # - $Env:Path = 'C:\ProgramData\Miniconda3\Scripts;' + $Env:Path
-
-    - echo "Our environemt vars:"
-    - $Env:Path
-
-    - echo "Python is running from:"
-    - python -c "import sys; print(sys.executable)"
-
     # get the adios_db code: needed for tests and requirements
     - git clone --depth 1 -b develop https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
 

From b9cbd263382808084322c8dd3221fd7c2e270083 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 29 Feb 2024 11:46:13 -0800
Subject: [PATCH 36/99] CI: Found where conda is installed, setting the path
 accordingly.

---
 .gitlab-ci.yml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d938ac51d..6f8957b75 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -111,13 +111,14 @@ test_pygnome_windows:
     # where are we?
     - Get-Location
 
-    # where is our conda installation?
-    - Get-ChildItem -Path 'C:\' -Recurse -Filter "conda.py" | % { $_.FullName }
+    # Where is our conda installation?
+    # This will tell us where python is installed.  This could change periodically
+    #- Get-ChildItem -Path 'C:\' -Recurse -Filter "conda.py" | % { $_.FullName }
 
     # make sure conda is on the path first in the path
-    - $Env:Path = 'C:\ProgramData\Miniconda3\Library\bin;' + $Env:Path
-    - $Env:Path = 'C:\ProgramData\Miniconda3\;' + $Env:Path
-    - $Env:Path = 'C:\ProgramData\Miniconda3\Scripts;' + $Env:Path
+    - $Env:Path = 'C:\Python310\Library\bin;' + $Env:Path
+    - $Env:Path = 'C:\Python310\;' + $Env:Path
+    - $Env:Path = 'C:\Python310\Scripts;' + $Env:Path
 
     - echo "Our environemt vars:"
     - $Env:Path -split ';'

From 14fc7b670825c9cb10f07764b76054bc5b33ec4d Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 29 Feb 2024 12:17:19 -0800
Subject: [PATCH 37/99] CI: conda command still not recognized.  Look in the
 python installation for the executable.

---
 .gitlab-ci.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6f8957b75..31cf3c52b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -114,6 +114,9 @@ test_pygnome_windows:
     # Where is our conda installation?
     # This will tell us where python is installed.  This could change periodically
     #- Get-ChildItem -Path 'C:\' -Recurse -Filter "conda.py" | % { $_.FullName }
+    - Get-ChildItem -Path 'C:\Python310' | % { $_.FullName }
+    - Get-ChildItem -Path 'C:\Python310\Scripts' | % { $_.FullName }
+    - Get-ChildItem -Path 'C:\Python310\Library\bin' | % { $_.FullName }
 
     # make sure conda is on the path first in the path
     - $Env:Path = 'C:\Python310\Library\bin;' + $Env:Path

From 89e289835ac2a59a7321c1adba9bf738484a3368 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 29 Feb 2024 13:18:47 -0800
Subject: [PATCH 38/99] CI: Library folder doesn't exist.  Lib does though, so
 we will check it.

---
 .gitlab-ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 31cf3c52b..ba1b760ac 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -116,10 +116,10 @@ test_pygnome_windows:
     #- Get-ChildItem -Path 'C:\' -Recurse -Filter "conda.py" | % { $_.FullName }
     - Get-ChildItem -Path 'C:\Python310' | % { $_.FullName }
     - Get-ChildItem -Path 'C:\Python310\Scripts' | % { $_.FullName }
-    - Get-ChildItem -Path 'C:\Python310\Library\bin' | % { $_.FullName }
+    - Get-ChildItem -Path 'C:\Python310\Lib' | % { $_.FullName }
 
     # make sure conda is on the path first in the path
-    - $Env:Path = 'C:\Python310\Library\bin;' + $Env:Path
+    - $Env:Path = 'C:\Python310\Lib\bin;' + $Env:Path
     - $Env:Path = 'C:\Python310\;' + $Env:Path
     - $Env:Path = 'C:\Python310\Scripts;' + $Env:Path
 

From e3d1e5affb9e2d2ea35ffa69ad2ee4a3613af9e9 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 29 Feb 2024 13:58:18 -0800
Subject: [PATCH 39/99] CI: Let's just search for *conda* in our installation.

---
 .gitlab-ci.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ba1b760ac..99ed790d6 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -114,9 +114,7 @@ test_pygnome_windows:
     # Where is our conda installation?
     # This will tell us where python is installed.  This could change periodically
     #- Get-ChildItem -Path 'C:\' -Recurse -Filter "conda.py" | % { $_.FullName }
-    - Get-ChildItem -Path 'C:\Python310' | % { $_.FullName }
-    - Get-ChildItem -Path 'C:\Python310\Scripts' | % { $_.FullName }
-    - Get-ChildItem -Path 'C:\Python310\Lib' | % { $_.FullName }
+    - Get-ChildItem -Path 'C:\Python310' -Recurse -Filter "*conda*" | % { $_.FullName }
 
     # make sure conda is on the path first in the path
     - $Env:Path = 'C:\Python310\Lib\bin;' + $Env:Path

From 70cae9d6465d29cc60702aaffb17268b72643dc2 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Tue, 5 Mar 2024 13:02:28 -0800
Subject: [PATCH 40/99] CI: For the windows runner, I think we need to
 initialize conda to use powershell.

---
 .gitlab-ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 99ed790d6..8374c2f0d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -128,6 +128,7 @@ test_pygnome_windows:
     - python -c "import sys; print(sys.executable)"
 
     - echo $CI_PIPELINE_ID
+    - conda init powershell
     - conda activate ./$CI_PIPELINE_ID
     - conda config --add channels defaults
     - conda config --add channels conda-forge

From f41e179231632005a7769106a4a36b6ed7712752 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Tue, 5 Mar 2024 14:23:31 -0800
Subject: [PATCH 41/99] CI: conda looks like it is installed in a different
 place than c:\Python310.  This could be a problem if we are setting the path.

---
 .gitlab-ci.yml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8374c2f0d..a392f53c4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -110,16 +110,17 @@ test_pygnome_windows:
   before_script:
     # where are we?
     - Get-Location
+    - Get-ChildItem | % { $_.FullName }  # this should list the current folder
 
     # Where is our conda installation?
     # This will tell us where python is installed.  This could change periodically
-    #- Get-ChildItem -Path 'C:\' -Recurse -Filter "conda.py" | % { $_.FullName }
-    - Get-ChildItem -Path 'C:\Python310' -Recurse -Filter "*conda*" | % { $_.FullName }
+    #- Get-ChildItem -Path 'C:\' -Recurse -Include "conda.exe" | % { $_.FullName }
+    - Get-ChildItem -Path 'C:\' -Recurse -Include "python.exe", "conda.exe" | % { $_.FullName }
 
     # make sure conda is on the path first in the path
-    - $Env:Path = 'C:\Python310\Lib\bin;' + $Env:Path
-    - $Env:Path = 'C:\Python310\;' + $Env:Path
-    - $Env:Path = 'C:\Python310\Scripts;' + $Env:Path
+    #- $Env:Path = 'C:\Python310\Lib\bin;' + $Env:Path
+    #- $Env:Path = 'C:\Python310\;' + $Env:Path
+    #- $Env:Path = 'C:\Python310\Scripts;' + $Env:Path
 
     - echo "Our environemt vars:"
     - $Env:Path -split ';'

From 4839f572508dd3a89275c2d5930c13035d8c85a6 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 7 Mar 2024 10:27:29 -0800
Subject: [PATCH 42/99] CI: The conda command exists apparently at
 c:\ProgramData, but python.exe exists at c:\Python310.  Look for them.

---
 .gitlab-ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a392f53c4..8deaa8c4c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -115,7 +115,8 @@ test_pygnome_windows:
     # Where is our conda installation?
     # This will tell us where python is installed.  This could change periodically
     #- Get-ChildItem -Path 'C:\' -Recurse -Include "conda.exe" | % { $_.FullName }
-    - Get-ChildItem -Path 'C:\' -Recurse -Include "python.exe", "conda.exe" | % { $_.FullName }
+    - Get-ChildItem -Path 'C:\Python310' -Recurse -Include "python.exe", "conda.exe" | % { $_.FullName }
+    - Get-ChildItem -Path 'C:\ProgramData' -Recurse -Include "python.exe", "conda.exe" | % { $_.FullName }
 
     # make sure conda is on the path first in the path
     #- $Env:Path = 'C:\Python310\Lib\bin;' + $Env:Path

From bed13d01f5437522ff87e5c1a511097bf9e9f849 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 7 Mar 2024 12:26:34 -0800
Subject: [PATCH 43/99] CI: Found python.exe & conda.exe in
 c:\ProgramData\miniforge3.  Setting our path.

---
 .gitlab-ci.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8deaa8c4c..3ddd9f3c6 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -116,12 +116,12 @@ test_pygnome_windows:
     # This will tell us where python is installed.  This could change periodically
     #- Get-ChildItem -Path 'C:\' -Recurse -Include "conda.exe" | % { $_.FullName }
     - Get-ChildItem -Path 'C:\Python310' -Recurse -Include "python.exe", "conda.exe" | % { $_.FullName }
-    - Get-ChildItem -Path 'C:\ProgramData' -Recurse -Include "python.exe", "conda.exe" | % { $_.FullName }
+    - Get-ChildItem -Path 'C:\ProgramData\miniforge3' -Recurse -Include "python.exe", "conda.exe" | % { $_.FullName }
 
     # make sure conda is on the path first in the path
-    #- $Env:Path = 'C:\Python310\Lib\bin;' + $Env:Path
-    #- $Env:Path = 'C:\Python310\;' + $Env:Path
-    #- $Env:Path = 'C:\Python310\Scripts;' + $Env:Path
+    - $Env:Path = 'C:\ProgramData\miniforge3\;' + $Env:Path
+    - $Env:Path = 'C:\ProgramData\miniforge3\Scripts;' + $Env:Path
+    - $Env:Path = 'C:\ProgramData\miniforge3\Lib\bin;' + $Env:Path
 
     - echo "Our environemt vars:"
     - $Env:Path -split ';'

From 9c9431900120410db48a77a821c66dd23dbe3c76 Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Mon, 11 Mar 2024 17:16:50 -0700
Subject: [PATCH 44/99] CI: Remove and then create the conda environment
 `pygnome` in test_pygnome_windows.

---
 .gitlab-ci.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3ddd9f3c6..881d8093a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -108,6 +108,8 @@ test_pygnome_windows:
     - visual-studio-22
   allow_failure: true
   before_script:
+    - echo $CI_PIPELINE_ID
+
     # where are we?
     - Get-Location
     - Get-ChildItem | % { $_.FullName }  # this should list the current folder
@@ -129,13 +131,14 @@ test_pygnome_windows:
     - echo "Python is running from:"
     - python -c "import sys; print(sys.executable)"
 
-    - echo $CI_PIPELINE_ID
-    - conda init powershell
-    - conda activate ./$CI_PIPELINE_ID
     - conda config --add channels defaults
     - conda config --add channels conda-forge
     - conda config --get channels
     - conda config --set channel_priority strict
+
+    - conda remove -y --name pygnome --all  # This seems to always return True, so no failure to deal with
+    - conda create -y -n pygnome python=$PYTHON_VER
+    - conda activate pygnome
   script:
     - echo "Building and testing PyGNOME"
 

From f9ebbf68b86acce2f9b8f1a1500bfe033f6dd7a4 Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Mon, 11 Mar 2024 19:55:20 -0700
Subject: [PATCH 45/99] CI: `conda init` changes don't become active until the
 shell is restarted.  Try to init in the current shell.

---
 .gitlab-ci.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 881d8093a..d43a1c92f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -131,6 +131,8 @@ test_pygnome_windows:
     - echo "Python is running from:"
     - python -c "import sys; print(sys.executable)"
 
+    - Invoke-Expression "conda shell.powershell hook"
+
     - conda config --add channels defaults
     - conda config --add channels conda-forge
     - conda config --get channels

From 3fa22324b7826251595ca790c0b8a167cb7a1cf3 Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Mon, 11 Mar 2024 22:04:29 -0700
Subject: [PATCH 46/99] CI: Run the conda powershell init right before the
 conda activate.

---
 .gitlab-ci.yml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d43a1c92f..6cc2f0443 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -140,6 +140,7 @@ test_pygnome_windows:
 
     - conda remove -y --name pygnome --all  # This seems to always return True, so no failure to deal with
     - conda create -y -n pygnome python=$PYTHON_VER
+    - Invoke-Expression "conda shell.powershell hook"
     - conda activate pygnome
   script:
     - echo "Building and testing PyGNOME"
@@ -157,14 +158,8 @@ test_pygnome_windows:
 
     - echo "Building PyGNOME"
     - cd ./py_gnome
-    # - python setup.py install
     - python setup.py develop
 
-    # Make sure that it imports from some folder other than the
-    # gnome package folder.
-    # - cd ../
-    # - python -c "import gnome"
-
     - cd ./tests/unit_tests
     - pytest --runslow
     - cd ../../..

From e1298ecfa371c6860dacb4d9bbda97f1df1e896b Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Mon, 18 Mar 2024 18:51:33 -0700
Subject: [PATCH 47/99] CI: Test Windows: Create a local path conda environment
 and then switch the $Path env.

---
 .gitlab-ci.yml | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6cc2f0443..0fb7f3b63 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -113,19 +113,19 @@ test_pygnome_windows:
     # where are we?
     - Get-Location
     - Get-ChildItem | % { $_.FullName }  # this should list the current folder
-
+   - $Env:PathOrig = $Env:Path
+ 
     # Where is our conda installation?
     # This will tell us where python is installed.  This could change periodically
-    #- Get-ChildItem -Path 'C:\' -Recurse -Include "conda.exe" | % { $_.FullName }
-    - Get-ChildItem -Path 'C:\Python310' -Recurse -Include "python.exe", "conda.exe" | % { $_.FullName }
-    - Get-ChildItem -Path 'C:\ProgramData\miniforge3' -Recurse -Include "python.exe", "conda.exe" | % { $_.FullName }
+    #- Get-ChildItem -Path 'C:\Python310' -Recurse -Include "python.exe", "conda.exe" | % { $_.FullName }
+    #- Get-ChildItem -Path 'C:\ProgramData\miniforge3' -Recurse -Include "python.exe", "conda.exe" | % { $_.FullName }
 
     # make sure conda is on the path first in the path
-    - $Env:Path = 'C:\ProgramData\miniforge3\;' + $Env:Path
-    - $Env:Path = 'C:\ProgramData\miniforge3\Scripts;' + $Env:Path
-    - $Env:Path = 'C:\ProgramData\miniforge3\Lib\bin;' + $Env:Path
-
-    - echo "Our environemt vars:"
+    - $Env:Path = 'C:\ProgramData\miniforge3\;' +
+                  'C:\ProgramData\miniforge3\Scripts;' +
+                  'C:\ProgramData\miniforge3\Lib\bin;' +
+                  $Env:PathOrig
+    - echo "Our $Path:"
     - $Env:Path -split ';'
 
     - echo "Python is running from:"
@@ -138,10 +138,14 @@ test_pygnome_windows:
     - conda config --get channels
     - conda config --set channel_priority strict
 
-    - conda remove -y --name pygnome --all  # This seems to always return True, so no failure to deal with
-    - conda create -y -n pygnome python=$PYTHON_VER
-    - Invoke-Expression "conda shell.powershell hook"
-    - conda activate pygnome
+    - conda create -y -p ./pygnome python=$PYTHON_VER
+
+    - echo $Get-Location + '\pygnome'
+    - $Env:Path = $Get-Location + '\pygnome\;' +
+                  $Get-Location + '\pygnome\Scripts\;' +
+                  $Get-Location + '\pygnome\Lib\bin\;' +
+                  $Env:PathOrig
+    - conda activate ./pygnome
   script:
     - echo "Building and testing PyGNOME"
 

From 2b6076efa45d7b88ba46a8aca5f63ae9054a8403 Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Mon, 18 Mar 2024 18:59:02 -0700
Subject: [PATCH 48/99] CI: Test Windows: Typo: Bad indentation.

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0fb7f3b63..a43448b5f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -113,7 +113,7 @@ test_pygnome_windows:
     # where are we?
     - Get-Location
     - Get-ChildItem | % { $_.FullName }  # this should list the current folder
-   - $Env:PathOrig = $Env:Path
+    - $Env:PathOrig = $Env:Path
  
     # Where is our conda installation?
     # This will tell us where python is installed.  This could change periodically

From 5b24386e50bd3e58c246179c9010768e2285d9ad Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Wed, 27 Mar 2024 12:47:11 -0700
Subject: [PATCH 49/99] scikit-build: some minor changes to save.

---
 .gitlab-ci.yml                  | 3 +++
 py_gnome/conda_requirements.txt | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a43448b5f..db1e34f5e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -51,6 +51,9 @@ compile_pygnome:
 
     # install adios_db
     - pip install ../oil_database/adios_db/
+
+    # install pygnome
+    #python -m build --no-isolation
     - pip install ./
 
     # need extra requirements for the docs
diff --git a/py_gnome/conda_requirements.txt b/py_gnome/conda_requirements.txt
index e25594cf5..c887a3d1e 100644
--- a/py_gnome/conda_requirements.txt
+++ b/py_gnome/conda_requirements.txt
@@ -24,7 +24,7 @@
 
 # it'll probably work with 3.9 -- 3.11, but CI is testing with 3.10
 
-python>=3.9,<3.12
+python>=3.9,<=3.12
 
 
 # for SpatialRelease

From 8f6e457ec0a5b90d6a8f1745469047ca815c4169 Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Tue, 16 Apr 2024 09:15:43 -0700
Subject: [PATCH 50/99] scikit-build-core can now build on Windows.

---
 .gitlab-ci.yml          |  3 ++-
 py_gnome/CMakeLists.txt | 12 ++++++++++--
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index db1e34f5e..dd079bc57 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -165,7 +165,8 @@ test_pygnome_windows:
 
     - echo "Building PyGNOME"
     - cd ./py_gnome
-    - python setup.py develop
+    #python -m build --no-isolation --config-setting cmake.verbose=true
+    - pip install ./
 
     - cd ./tests/unit_tests
     - pytest --runslow
diff --git a/py_gnome/CMakeLists.txt b/py_gnome/CMakeLists.txt
index a71aa545d..23cea4177 100644
--- a/py_gnome/CMakeLists.txt
+++ b/py_gnome/CMakeLists.txt
@@ -1,7 +1,7 @@
 # to jcfr@github henryiii
 
 
-cmake_minimum_required(VERSION 3.15...3.26)
+cmake_minimum_required(VERSION 3.15...3.28)
 project(${SKBUILD_PROJECT_NAME} LANGUAGES C CXX)
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
@@ -16,6 +16,14 @@ find_package(
 
 find_program(CYTHON "cython")
 
+# On Windows, we need to set these environmental variables so that the linker
+# can properly find the .lib file associated with a dynamic library (.dll).
+# And they must be set before any add_library() commands
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+    set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
+    set(BUILD_SHARED_LIBS TRUE)
+endif()
+
 set(EXT_NAMES
     cy_basic_types
     cy_mover
@@ -94,7 +102,7 @@ target_compile_definitions(gnome PUBLIC pyGNOME=1)
 
 target_include_directories(gnome PUBLIC lib_gnome)
 
-install(TARGETS gnome DESTINATION gnome/cy_gnome)
+install(TARGETS gnome LIBRARY DESTINATION gnome/cy_gnome)
 
 foreach(ext IN LISTS EXT_NAMES)
 

From 50df11d7ee78c64fa2b11a1f522464433c6244ae Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Tue, 16 Apr 2024 11:43:57 -0700
Subject: [PATCH 51/99] A bit of cleanup with the scikit-build method & the CI.

---
 .gitlab-ci.yml          | 4 +++-
 py_gnome/CMakeLists.txt | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index dd079bc57..a8fee6ff5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -165,7 +165,9 @@ test_pygnome_windows:
 
     - echo "Building PyGNOME"
     - cd ./py_gnome
-    #python -m build --no-isolation --config-setting cmake.verbose=true
+    # If you want verbose output including the compiler/linker commands,
+    # run the following command:
+    #   python -m build --no-isolation --config-setting cmake.verbose=true
     - pip install ./
 
     - cd ./tests/unit_tests
diff --git a/py_gnome/CMakeLists.txt b/py_gnome/CMakeLists.txt
index 23cea4177..f7ef9c1e4 100644
--- a/py_gnome/CMakeLists.txt
+++ b/py_gnome/CMakeLists.txt
@@ -20,7 +20,7 @@ find_program(CYTHON "cython")
 # can properly find the .lib file associated with a dynamic library (.dll).
 # And they must be set before any add_library() commands
 if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
-    set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
+    set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
     set(BUILD_SHARED_LIBS TRUE)
 endif()
 

From 7e187d1be04fbc8036635bb3863f1ccf9744dc2d Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Wed, 17 Apr 2024 16:45:50 -0700
Subject: [PATCH 52/99] CI: run pip inside python so venv location is
 recognized.

---
 .gitlab-ci.yml          |  3 +--
 py_gnome/CMakeLists.txt | 12 ++++++------
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a8fee6ff5..2361630a8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -164,11 +164,10 @@ test_pygnome_windows:
                                           --file ../oil_database/adios_db/conda_requirements.txt
 
     - echo "Building PyGNOME"
-    - cd ./py_gnome
     # If you want verbose output including the compiler/linker commands,
     # run the following command:
     #   python -m build --no-isolation --config-setting cmake.verbose=true
-    - pip install ./
+    - python -m pip install ./
 
     - cd ./tests/unit_tests
     - pytest --runslow
diff --git a/py_gnome/CMakeLists.txt b/py_gnome/CMakeLists.txt
index f7ef9c1e4..aeb2ffde5 100644
--- a/py_gnome/CMakeLists.txt
+++ b/py_gnome/CMakeLists.txt
@@ -94,15 +94,15 @@ set(LIBGNOME_CPP_FILES
 
 list(TRANSFORM LIBGNOME_CPP_FILES PREPEND "lib_gnome/")
 
-add_library(gnome SHARED ${LIBGNOME_CPP_FILES})
+add_library(lib_gnome SHARED ${LIBGNOME_CPP_FILES})
 
-target_link_libraries(gnome PRIVATE NetCDF::NetCDF)
+target_link_libraries(lib_gnome PRIVATE NetCDF::NetCDF)
 
-target_compile_definitions(gnome PUBLIC pyGNOME=1)
+target_compile_definitions(lib_gnome PUBLIC pyGNOME=1)
 
-target_include_directories(gnome PUBLIC lib_gnome)
+target_include_directories(lib_gnome PUBLIC lib_gnome)
 
-install(TARGETS gnome LIBRARY DESTINATION gnome/cy_gnome)
+install(TARGETS lib_gnome LIBRARY DESTINATION gnome/cy_gnome)
 
 foreach(ext IN LISTS EXT_NAMES)
 
@@ -122,7 +122,7 @@ foreach(ext IN LISTS EXT_NAMES)
         WITH_SOABI
     )
 
-    target_link_libraries(${ext} PRIVATE gnome Python::NumPy)
+    target_link_libraries(${ext} PRIVATE lib_gnome Python::NumPy)
 
 
     if(APPLE)

From 0206c036cca912e5aec012cba382c28faf83c201 Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Thu, 18 Apr 2024 09:27:46 -0700
Subject: [PATCH 53/99] On Windows, we need to make the path to lib_gnome.dll
 available.

---
 py_gnome/gnome/__init__.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/py_gnome/gnome/__init__.py b/py_gnome/gnome/__init__.py
index 5238f7c80..c90b57174 100644
--- a/py_gnome/gnome/__init__.py
+++ b/py_gnome/gnome/__init__.py
@@ -7,8 +7,9 @@
 
   set up the logger to dump to console.
 """
-
 import sys
+import os
+import pathlib
 
 import logging
 import json
@@ -24,7 +25,16 @@
 __version__ = '1.1.7'
 
 
-# a few imports so that the basic stuff is there
+if os.name == 'nt':
+    # In Windows, we need to add the location of our lib_gnome.dll to the
+    # .dll search path.
+    os.add_dll_directory(
+        pathlib.Path(sys._stdlib_dir) / 'site-packages' / 'bin'
+    )
+
+#
+# A few imports so that the basic stuff is there
+#
 
 def check_dependency_versions():
     """

From c2ef2d0c9fb7a9149d826d0fd51c0de8aa9c5a2b Mon Sep 17 00:00:00 2001
From: Caitlin O'Connor <caitlin.oconnor@noaa.gov>
Date: Fri, 26 Apr 2024 13:54:30 -0700
Subject: [PATCH 54/99] added run_backwards flag

---
 py_gnome/gnome/model.py                       | 59 ++++++++++++++++---
 py_gnome/gnome/outputters/outputter.py        | 23 ++++----
 py_gnome/gnome/spill_container.py             |  5 +-
 py_gnome/gnome/spills/release.py              |  3 +
 py_gnome/tests/unit_tests/test_model.py       |  1 +
 .../test_outputters/test_outputter.py         | 31 +++++-----
 6 files changed, 84 insertions(+), 38 deletions(-)

diff --git a/py_gnome/gnome/model.py b/py_gnome/gnome/model.py
index 2d9ba0d2c..f36dfade7 100644
--- a/py_gnome/gnome/model.py
+++ b/py_gnome/gnome/model.py
@@ -152,6 +152,7 @@ class ModelSchema(ObjTypeSchema):
     #manual_weathering = SchemaNode(Bool(), save=False, update=True, test_equal=False, missing=drop)
     weathering_activated = SchemaNode(Bool(), save=True, update=True, test_equal=False, missing=drop)
 
+    run_backwards = SchemaNode(Bool())
 
 class Model(GnomeId):
     '''
@@ -207,6 +208,7 @@ def __init__(self,
                  uncertain_spills=[],
                  #manual_weathering=False,
                  weathering_activated=False,
+                 run_backwards=False,
                  **kwargs):
         '''
         Initializes a model.
@@ -286,6 +288,15 @@ def __init__(self,
             self.time_step = time_step  # this calls rewind() !
         self._reset_num_time_steps()
 
+        # for backwards run set duration and time_step to be negative
+        self._run_backwards = run_backwards
+        if self._run_backwards is True:
+            if self.duration.total_seconds() > 0:
+                self._duration = timedelta(seconds = -self._duration.total_seconds())
+            if self.time_step is not None and self.time_step > 0:
+                self.time_step = -self.time_step
+
+
         # default is to zip save file
         self.zipsave = True
 
@@ -484,6 +495,33 @@ def uncertain(self, uncertain_value):
     def uncertain_spills(self):
         return self.spills.to_dict().get('uncertain_spills', [])
 
+    @property
+    def run_backwards(self):
+        '''
+        Run backwards attribute of the model. If flag is toggled, rewind model
+        '''
+        return self._run_backwards
+
+    @run_backwards.setter
+    def run_backwards(self, run_backwards):
+        '''
+        Run backwards attribute of the model
+        if gets toggled change sign of time and duration
+        '''
+        if self._run_backwards != run_backwards:
+            self._run_backwards = run_backwards  # update run_backwards
+            if self._run_backwards is True:
+                if self.duration.total_seconds() > 0:
+                    self._duration = timedelta(seconds = -self._duration.total_seconds())
+                if self.time_step is not None and self.time_step > 0:
+                    self.time_step = -self.time_step
+            else:
+                if self.duration.total_seconds() < 0:
+                    self._duration = timedelta(seconds = abs(self._duration.total_seconds()))
+                if self.time_step is not None and self.time_step < 0:
+                    self.time_step = abs(self.time_step)
+            self.rewind()
+
     @property
     def cache_enabled(self):
         '''
@@ -1570,6 +1608,7 @@ def check_inputs(self):
         (msgs, isValid) = self.validate()
 
         someSpillIntersectsModel = False
+        isWeatherable = False
         num_spills = len(self.spills)
         if num_spills == 0:
             msg = '{0} contains no spills'.format(self.name)
@@ -1624,8 +1663,14 @@ def check_inputs(self):
 
                         msgs.append(self._warn_pre + msg)
 
-                if spill.release_time < self.start_time + self.duration:
-                    someSpillIntersectsModel = True
+
+
+                if not self.run_backwards:
+                    if spill.release_time < self.start_time + self.duration:
+                        someSpillIntersectsModel = True
+                else:
+                    if spill.release_time > self.start_time + self.duration:
+                        someSpillIntersectsModel = True
 
                 if ((spill.release_time > self.start_time and self.time_step > 0)
                       or (spill.release_time < self.start_time and self.time_step < 0)):
@@ -1654,6 +1699,7 @@ def check_inputs(self):
 
 
                 if spill.substance.is_weatherable:
+                    isWeatherable = True
                     pour_point = spill.substance.pour_point
 
                     if spill.substance.water is not None:
@@ -1714,22 +1760,17 @@ def check_inputs(self):
                 msg = ('Time step and duration must have the same sign: time step = {0} duration = {1} '
                        'To run backwards they must both be negative.'
                         .format(self.time_step,self.duration.total_seconds()))
-                #self.logger.warning(msg)  # for now make this a warning
-                #msgs.append('warning: ' + self.__class__.__name__ + ': ' + msg)
                 isValid = False
                 raise GnomeRuntimeError(msg)
             if self.duration.total_seconds() > 0:
                 msg = ('Time step and duration must have the same sign: time step = {0} duration = {1} '
                        'To run backwards they must both be negative.'
                         .format(self.time_step,self.duration.total_seconds()))
-                #self.logger.warning(msg)  # for now make this a warning
-                #msgs.append('warning: ' + self.__class__.__name__ + ': ' + msg)
                 isValid = False
-            if self.has_weathering:
+            if self.has_weathering and isWeatherable:
+            #if self.weathering_activated: # might have a better check for weathering
                 msg = ('Backwards run is not valid for weathering. '
                        'Turn off weathering to model a backwards trajectory.')
-                #self.logger.warning(msg)  # for now make this a warning
-                #msgs.append('warning: ' + self.__class__.__name__ + ': ' + msg)
                 isValid = False
                 raise GnomeRuntimeError(msg)
 
diff --git a/py_gnome/gnome/outputters/outputter.py b/py_gnome/gnome/outputters/outputter.py
index bbd38ad52..484f3a863 100644
--- a/py_gnome/gnome/outputters/outputter.py
+++ b/py_gnome/gnome/outputters/outputter.py
@@ -174,10 +174,10 @@ def output_timestep(self, value):
         if value is None:
             self._output_timestep = None
         else:
-            if value == timedelta(0):
-                raise ValueError("output_timestep cannot be zero")
-            #if value <= timedelta(0):
-                #raise ValueError("output_timestep must be positive")
+            #if value == timedelta(0):
+                #raise ValueError("output_timestep cannot be zero")
+            if value <= timedelta(0):
+                raise ValueError("output_timestep must be positive")
             self._output_timestep = int(value.total_seconds())
 
     def prepare_for_model_run(self,
@@ -232,12 +232,12 @@ def prepare_for_model_run(self,
         self.sc_pair = spills
 
         if self._output_timestep is not None:
-            if self._output_timestep < 0 and model_time_step > 0:
-                warnings.warn(f"Outputter output timestep {self.output_timestep} is less than "
-                              f"zero.", RuntimeWarning)
-            if self._output_timestep > 0 and model_time_step < 0:
-                warnings.warn(f"Outputter output timestep {self.output_timestep} is greater than "
-                              f"zero.", RuntimeWarning)
+#             if self._output_timestep < 0 and model_time_step > 0:
+#                 warnings.warn(f"Outputter output timestep {self.output_timestep} is less than "
+#                               f"zero.", RuntimeWarning)
+#             if self._output_timestep > 0 and model_time_step < 0:
+#                 warnings.warn(f"Outputter output timestep {self.output_timestep} is greater than "
+#                               f"zero.", RuntimeWarning)
             if abs(self._output_timestep) < abs(model_time_step):
                 warnings.warn(f"Outputter output timestep {self.output_timestep} is less than "
                               f"model time step: {model_time_step} seconds. "
@@ -302,7 +302,8 @@ def prepare_for_model_step(self, time_step, model_time):
                     self._is_first_output = False
                     return
 
-                if model_time + d > self.output_start_time:
+                if ((model_time + d > self.output_start_time and time_step > 0) or
+                    (model_time + d < self.output_start_time and time_step < 0)):
                     if self._is_first_output:
                         self._write_step = True
                         self._is_first_output = False
diff --git a/py_gnome/gnome/spill_container.py b/py_gnome/gnome/spill_container.py
index 5674f9e9c..74e95fb63 100644
--- a/py_gnome/gnome/spill_container.py
+++ b/py_gnome/gnome/spill_container.py
@@ -445,7 +445,7 @@ def _set_substancespills(self):
                                      "trying to add :{}\n"
                                      "These are the substances in the on spills:\n"
                                      "{}".format(substance, subs))
-                                     
+
         # set the number of oil components
         # fixme: with only one substance this could be determined elsewhere
         if hasattr(substance, 'num_components'):
@@ -815,7 +815,8 @@ def prepare_for_model_run(self, array_types=None, time_step=300):
 
         #self._append_initializer_array_types(array_types)
         for s in self.spills:
-            s.prepare_for_model_run(time_step)
+            if s.on:
+                s.prepare_for_model_run(time_step)
         ats = default_array_types.copy()
         ats.update(array_types)
         self._array_types = ats
diff --git a/py_gnome/gnome/spills/release.py b/py_gnome/gnome/spills/release.py
index 090c7b00d..a9bf23982 100644
--- a/py_gnome/gnome/spills/release.py
+++ b/py_gnome/gnome/spills/release.py
@@ -350,6 +350,9 @@ def prepare_for_model_run(self, ts):
         '''
         if self._prepared:
             self.rewind()
+        if ts < 1 and (self.end_release_time != self.release_time):
+            raise ValueError('Backwards run is not valid for continuous releases.  \
+                Use an instantaneous release or run forwards.')
         if self.LE_timestep_ratio(ts) < 1:
             raise ValueError('Not enough LEs: Number of LEs must at least \
                 be equal to the number of timesteps in the release')
diff --git a/py_gnome/tests/unit_tests/test_model.py b/py_gnome/tests/unit_tests/test_model.py
index 1196dcd33..da9d296b9 100644
--- a/py_gnome/tests/unit_tests/test_model.py
+++ b/py_gnome/tests/unit_tests/test_model.py
@@ -60,6 +60,7 @@ def test_exceptions():
     wind = constant_wind(10, 270, units='knots')
     water = Water()
     model.weatherers += Evaporation(water, wind)
+    model.spills += Spill(Release(release_time=model.start_time), substance=test_oil)
     with raises(GnomeRuntimeError):
         model.check_inputs()
 
diff --git a/py_gnome/tests/unit_tests/test_outputters/test_outputter.py b/py_gnome/tests/unit_tests/test_outputters/test_outputter.py
index 05f4722c2..94dc88027 100644
--- a/py_gnome/tests/unit_tests/test_outputters/test_outputter.py
+++ b/py_gnome/tests/unit_tests/test_outputters/test_outputter.py
@@ -155,8 +155,7 @@ def test_output_timestep(model, model_ts, output_ts):
 
 def test_bad_output_timestep():
     """
-    output timestep can never be zero
-    output timestep should match sign of model_time_step
+    output timestep can never be less than zero
     """
     # on init:
     with pytest.raises(ValueError):
@@ -164,23 +163,23 @@ def test_bad_output_timestep():
 
     # changing it later
     out = Outputter(output_timestep=gs.hours(3))
-    # allowing negative timestep for backwards run
-    #with pytest.raises(ValueError):
-        #out.output_timestep = gs.hours(-1)
 
-    assert out.output_timestep == gs.hours(3)
-
-    out.output_timestep = gs.hours(-1)
-    with pytest.warns(RuntimeWarning, match="is less than zero") as warning:
-        out.prepare_for_model_run(model_start_time=datetime.now(),model_time_step=900)
-
-    assert out.output_timestep == gs.hours(-1)
+    with pytest.raises(ValueError):
+        out.output_timestep = gs.hours(-1)
 
-    out.output_timestep = gs.hours(1)
-    with pytest.warns(RuntimeWarning, match="is greater than zero") as warning:
-        out.prepare_for_model_run(model_start_time=datetime.now(),model_time_step=-900)
+    assert out.output_timestep == gs.hours(3)
 
-    assert out.output_timestep == gs.hours(1)
+#     out.output_timestep = gs.hours(-1)
+#     with pytest.warns(RuntimeWarning, match="is less than zero") as warning:
+#         out.prepare_for_model_run(model_start_time=datetime.now(),model_time_step=900)
+#
+#     assert out.output_timestep == gs.hours(-1)
+#
+#     out.output_timestep = gs.hours(1)
+#     with pytest.warns(RuntimeWarning, match="is greater than zero") as warning:
+#         out.prepare_for_model_run(model_start_time=datetime.now(),model_time_step=-900)
+#
+#     assert out.output_timestep == gs.hours(1)
 
 
 def test_too_small_output_timestep(model):

From 0ee0c98785eeb221f46761265204a949a254dc94 Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Thu, 2 May 2024 14:59:03 -0700
Subject: [PATCH 55/99] Updated .rst documentation for building with
 scikit-build-core.

---
 Installing.rst | 299 +++++++++++++++++++++++++++++--------------------
 README.rst     |  35 +++---
 2 files changed, 194 insertions(+), 140 deletions(-)

diff --git a/Installing.rst b/Installing.rst
index d328b4c52..c5fa241a1 100644
--- a/Installing.rst
+++ b/Installing.rst
@@ -32,9 +32,7 @@ Activate the gnome environment::
 Build the gnome package::
 
     > cd py_gnome
-    > python setup.py develop
-
-.. warning:: when you run this command, you will get a warning from ``setuptools`` that running ``setup.py`` directly is deprecated. That is expected, and the build system will be updated before it stops working altogether.
+    > python -m pip install ./
 
 You now should be good to go, but to make sure:
 
@@ -43,7 +41,8 @@ Run the tests::
     > cd tests/unit_tests
     > pytest --runslow
 
-NOTE: the "runslow" tests requiring downloading data for the tests -- you can eliminate that flag to get most of the tests to run without that delay.
+NOTE: *the "runslow" tests requiring downloading data for the tests -- you can
+eliminate that flag to get most of the tests to run without that delay.*
 
 All the details
 ===============
@@ -51,37 +50,59 @@ All the details
 `Anaconda <https://store.continuum.io/cshop/anaconda/>`__ is a Python
 distribution that has most of the difficult-to-build packages that
 PyGNOME needs already built in. Thus it's a nice target for running
-GNOME on your own system. "conda" is the packaging manager used to manage the system.
-
-PyGNOME CAN be used with any Python distribution, but you will need to find or build a number of packages that are not easy to manage. If you are familiar with complex python packaging, then you can probably make it work. But conda makes it much easier, and that's what we use ourselves, and support that use.
+GNOME on your own system. "conda" is the packaging manager used to
+manage the system.
+
+PyGNOME can "in theory" be used with any Python distribution, and if you are
+familiar with complex python packaging, then you might be able to make it work.
+But you will need to find or build a number of dependent packages that are not
+easy to manage.  Additionally, for compiling our C/C++ components, we have
+moved to a build system called 
+`scikit-build-core <https://scikit-build-core.readthedocs.io/en/latest/>`__.
+And it **will be quite difficult** to replicate the steps that are built into
+this package.  In short, we don't recommend it.
 
 Anaconda vs miniconda vs miniforge:
 -----------------------------------
 
-`Anaconda <https://store.continuum.io/cshop/anaconda/>`__ provides a fairly complete python system for computational programming -- it is a large install, but comes with a lot of nice stuff pre-packaged that all works together.
+`Anaconda <https://store.continuum.io/cshop/anaconda/>`__ provides a fairly
+complete python system for computational programming -- it is a large install,
+but comes with a lot of nice stuff pre-packaged that all works together.
 
-`miniconda <http://conda.pydata.org/miniconda.html>`__ is a much smaller install -- it provides only Python and the conda package management system. You can install miniconda, and then install only the packages you need to run PyGNOME.
+`miniconda <http://conda.pydata.org/miniconda.html>`__ is a much smaller
+install -- it provides only Python and the conda package management system.
+You can install miniconda, and then install only the packages you need
+to run PyGNOME.
 
-`miniforge <https://github.com/conda-forge/miniforge>`__ is similar to miniconda, but designed to work primarily with the conda-forge packages. As everything required for PyGNOME is available via conda-forge, and many are not available anywhere else, miniforge is the easiest way to get PyGNOME up and running. You can install miniforge, and then install only the packages you need to run PyGNOME.
+`miniforge <https://github.com/conda-forge/miniforge>`__ is similar to
+miniconda, but designed to work primarily with the conda-forge packages.
+As everything required for PyGNOME is available via conda-forge, and many
+are not available anywhere else, miniforge is the easiest way to get PyGNOME
+up and running. You can install miniforge, and then install only the packages
+you need to run PyGNOME.
 
-Either of these should work fine with PyGNOME, as long as you create an independent environment for it.
+Either of these should work fine with PyGNOME, as long as you create an
+independent environment for it.
 
 **NOTES:**
 
-PyGNOME requires Python version 3.9 or greater (currently 3.10 is currently used operationally -- 3.11 should work, but it not well tested)
+PyGNOME requires Python version 3.9 or greater (version 3.10 is currently used
+operationally -- 3.11 should work, but it not well tested)
 
 Anaconda (and miniconda) can be installed in either single-user or multi-user mode:
 
 https://docs.continuum.io/anaconda/install
 
-We (and Anaconda) recommend single-user mode (Select an install for “Just Me”) -- that way, administrator privileges are not required for either initial installation or maintaining the system.
+We (and Anaconda) recommend single-user mode (Select an install for “Just Me”)
+-- that way, administrator privileges are not required for either initial
+installation or maintaining the system.
 
 Windows:
 ........
 
-You need the Windows 64 bit Python 3 version. Installing with the
-defaults works fine. You probably want to let it set the PATH for you --
-that's a pain to do by hand.
+You need the Windows 64 bit Python 3 version. Installing with the defaults
+works fine. You probably want to let it set the PATH for you -- that's a pain
+to do by hand.
 
 
 OS-X:
@@ -97,54 +118,57 @@ Linux:
 
 The Linux 64bit-python3.10 is the one to use.
 
-We do not support 32 bit on any platform.
+*NOTE: We do not support 32 bit on any platform.*
 
 conda
 -----
 
-`conda <http://conda.pydata.org/docs/intro.html>`__ is the package
-manager that Anaconda is built on. So when working with Anaconda, you
-use the conda package manager for installing conda packages. ``pip``
-can also be used within conda, but it's best to use use conda for as much as you can.
+`conda <http://conda.pydata.org/docs/intro.html>`__ is the package manager
+that Anaconda is built on. So when working with Anaconda, you use the conda
+package manager for installing conda packages. ``pip`` can also be used
+within conda, but it's best to use use conda for as much as you can.
 
-As a rule, if you need a new package, you should try to conda install it, and then, if there is not conda package available, you can pip install it.
+As a rule, if you need a new package, you should try to conda install it,
+and then, if there is not conda package available, you can pip install it.
 
 We have made sure that every package you need for PyGNOME is available for conda.
 
 conda-forge
 ...........
 
-Conda-Forge (https://conda-forge.org/) is a community  project that supplies a huge number of packages for the conda package manager. We have tried to assure that everything you need to run PyGNOME is available via the conda-forge channel.
+`Conda-Forge <https://conda-forge.org/>`__ is a community  project that supplies
+a huge number of packages for the conda package manager. We have tried to
+assure that everything you need to run PyGNOME is available via the
+conda-forge channel.
 
 Setting up
 ..........
 
 Install: `Anaconda <https://www.continuum.io/downloads>`__
-
 or alternatively: `Miniconda <http://conda.pydata.org/miniconda.html>`__
 or `Miniforge <https://github.com/conda-forge/miniforge>`_
 
-Once you have Anaconda, Miniconda, or Miniforge installed, the rest of the instructions should be the same.
+Once you have Anaconda, Miniconda, or Miniforge installed, the rest of the
+instructions should be the same.
 
 
 Update your (new) system
 ........................
 
-Once you have a conda system installed, you should start by
-getting everything up to date, as sometimes packages have been updated
-since the installer was built.
-
-First, update the conda package manager itself:
+Once you have a conda system installed, you should start by getting everything
+up to date, as sometimes packages have been updated since the installer was built.
 
-Enter the following on the command-line::
+First, update the conda package manager itself.  Enter the following on the command-line::
 
     > conda update conda
 
 Setting up anaconda.org channels
 ................................
 
-`anaconda.org <http://anaconda.org>`__ is a web service for hosting conda packages for download.
-The way this is done is through anaconda "channels", which can be thought of simply as places on ``anaconda.org`` where collections of packages are bundled together by the people hosting them.
+`anaconda.org <http://anaconda.org>`__ is a web service for hosting
+conda packages for download.  The way this is done is through anaconda
+"channels", which can be thought of simply as places on ``anaconda.org``
+where collections of packages are bundled together by the people hosting them.
 
 Many of the dependencies that PyGNOME requires come out of the box
 with Anaconda (or the conda "defaults" channel), but a few important
@@ -152,18 +176,16 @@ ones don't.
 
 **The "conda-forge" project:**
 
-https://conda-forge.github.io/
-
-Is a community project to build a wide variety of packages for conda --
-it should support everything that PyGNOME needs.
+`conda-forge <https://conda-forge.github.io/>`__ is a community project to
+build and make available a wide variety of packages for conda -- it should
+support everything that PyGNOME needs.
 
 
 Adding another channel to conda:
 ................................
 
-To make it easy for your install to find conda-forge packages, it should be added to your conda configuration:
-
-Add the conda-forge channel::
+In order to find packages available on conda-forge, it should be added to your
+conda channel configuration:
 
     > conda config --add channels conda-forge
 
@@ -186,7 +208,8 @@ You need to set the channel prioroty to "strict"::
 
   > conda config --set channel_priority strict
 
-This will assure that you will get packages from conda-forge, even if there are newer ones available in the defaults channel.
+This will assure that you will get packages from conda-forge, even if there are
+newer ones available in the defaults channel.
 
 conda environments
 ------------------
@@ -197,18 +220,23 @@ For more information see:
 
 http://conda.pydata.org/docs/using/envs.html
 
-NOTE: We highly recommend that you use a conda environment for GNOME.
+*NOTE: We highly recommend that you use a conda environment for GNOME.*
 
-If you are only going to use Python / conda for PyGNOME, then you could use the base environment.
-However, PyGNOME needs a number of specific package versions, so it is best to keep it separate from any other work you are doing.
+If you are only going to use Python / conda for PyGNOME, then you could use
+the base environment.  However, there are a number of packages that PyGNOME
+needs to be at specific versions, so it is best to keep it separate from
+any other work you are doing.
 
-(NOTE: you can do these steps with the Anaconda Navigator GUI if you have that installed)
+*NOTE: You can do these steps with the Anaconda Navigator GUI if you have that
+installed*
 
 Create an environment for PyGNOME::
 
     > conda create -n gnome python=3.10 --file conda_requirements.txt --file conda_requirements_build.txt --file conda_requirements_test.txt
 
-This will create an environment called "gnome" with Python itself and everything that it needs to be built, run, and tested -- it will be quite a bit, so it may take a while.
+This will create an environment called "gnome" with Python itself and
+everything that it needs to be built, run, and tested -- it will be quite a bit,
+so it may take a while.
 
 To use that environment, you activate it with::
 
@@ -219,23 +247,23 @@ and when you are done, you can deactivate it with::
 
     > conda deactivate
 
-
 After activating the environment, you can proceed with these instructions,
-and all the packages PyGNOME needs will be installed into that environment and kept separate from your main Anaconda install.
+and all the packages PyGNOME needs will be installed into that environment
+and kept separate from your main Anaconda install.
 
 You will need to activate the environment any time you want to work with
 PyGNOME in the future
 
-
 Download the PyGNOME Code
 -------------------------
 
-PyGNOME is not currently available as a conda package, as it is under active development, and many users will need access to the source code.
+PyGNOME is not currently available as a conda package, as it is under active
+development, and many users will need access to the source code.
 
 Once you have a conda environment set up, you can compile and install PyGNOME.
 
-You will need the files from the PyGNOME sources. If you
-have not downloaded it yet, it is available here:
+You will need the files from the PyGNOME sources. If you have not downloaded
+it yet, it is available here:
 
 https://github.com/NOAA-ORR-ERD/PyGNOME
 
@@ -252,7 +280,10 @@ zip and tar archives of the PyGNOME source code can be found here:
 
 https://github.com/NOAA-ORR-ERD/PyGNOME/releases
 
-This will get you the entire source archive of a given release, which is a fine way to work with PyGNOME. However, if you want to be able to quickly include changes as we update the code, you may want to work with a git "clone" of the source code instead.
+This will get you the entire source archive of a given release, which is a
+fine way to work with PyGNOME. However, if you want to be able to quickly
+include changes as we update the code, you may want to work with a git "clone"
+of the source code instead.
 
 Cloning the PyGNOME git repository
 ----------------------------------
@@ -262,20 +293,17 @@ git
 
 You will need a git client:
 
-Linux:
-  it should be available from your package manager::
+On Linux, it should be available from your package manager::
 
     > apt_get install git
     or
     > yum install git
 
-OS-X:
-  git comes with the XCode command line tools:
+On OS-X, git comes with the XCode command line tools:
 
   http://osxdaily.com/2014/02/12/install-command-line-tools-mac-os-x/
 
-Windows:
-  The "official" git for Windows installer is a good bet:
+On Windows, the "official" git for Windows installer is a good bet:
 
   https://git-for-windows.github.io/
 
@@ -286,13 +314,15 @@ Once you have the client, it's as easy as::
 This will create a PyGNOME directory with all the code in it.
 
 git branches:
-  git supports a number of different "branches" or versions of the code. You will most likley want to use the "main" branch (the default) unless you specifically want to experiment with a new feature.
-
+  git supports a number of different "branches" or versions of the code.
+  You will most likley want to use the "main" branch (the default) unless you
+  specifically want to experiment with a new feature.
 
 Setting up conda
 ----------------
 
-If you have not already created an environment in which to run PyGNOME, follow the instructions above.
+If you have not already created an environment in which to run PyGNOME,
+follow the instructions above.
 
 To use the gnome environment you created, it needs to be activated with::
 
@@ -302,26 +332,31 @@ and when you are done, you can deactivate it with::
 
     > conda deactivate
 
-If you don't want to create an environment (or already have one), you can install what PyGNOME needs into an existing environment:
-
-::
+If you don't want to create an environment (or already have one), you can
+install what PyGNOME needs into an existing environment:
 
     > cd PyGNOME  # or wherever you put the PyGNOME project
     > conda install --file conda_requirements.txt --file conda_requirements_build.txt --file conda_requirements_test.txt
 
-NOTE: PyGNOME has a lot of specific dependencies -- it can be very hard for conda to resolve them with an large installed package base. If you have trouble, it's easiest to make a new environment just for PyGNOME.
+*NOTE: PyGNOME has a lot of specific dependencies -- it can be very hard
+for conda to resolve them with an large installed package base.
+If you have trouble, it's easiest to make a new environment just for PyGNOME.*
 
 This should install all the packages required by PyGNOME.
 
-(make sure you are in the correct conda environment, and you have the
-conda-forge channel enabled)
+(*make sure you are in the correct conda environment, and you have the
+conda-forge channel enabled*)
 
 If installing the conda_requirements.txt fails:
 ...............................................
 
-If you get an error about a particular package not being able to be installed, then conda will not install ANY of the packages in the file. We try hard to make sure everything is available on conda-forge. If however, a package of that particular version is missing, you can try:
+If you get an error about a particular package not being able to be installed,
+then conda will not install ANY of the packages in the file. We try hard
+to make sure everything is available on conda-forge. If however, a package
+of that particular version is missing, here are some things you can try.
 
-Edit the conda_requirements.txt file and comment out the offending package by putting a "#" at the start of the line::
+Edit the conda_requirements.txt file and comment out the offending package
+by putting a "#" at the start of the line::
 
     ...
     scipy>=0.17
@@ -330,9 +365,11 @@ Edit the conda_requirements.txt file and comment out the offending package by pu
     gsw>=3.0.3
     ...
 
-That will disable that particular package, and hopefully everything else will install.
+That will disable that particular package, and hopefully everything else
+will install.
 
-You can then try installing the offending package without a version specification::
+You can then try installing the offending package without a version
+specification::
 
     > conda install libgd
 
@@ -342,32 +379,38 @@ And it may work for you.
 The ADIOS Oil Database
 ----------------------
 
-If you want to use PyGNOME with "real oil", rather than inert particles, you will need NOAA's ``adios_db`` package from the ADIOS Oil Database Project:
+If you want to use PyGNOME with "real oil", rather than inert particles,
+you will need NOAA's ``adios_db`` package from the ADIOS Oil Database Project:
 
 https://github.com/NOAA-ORR-ERD/adios_oil_database
 
-This will allow you to use the JSON oil data format downloadable from NOAA's ADIOS Oil Database web app:
+This will allow you to use the JSON oil data format downloadable from NOAA's
+ADIOS Oil Database web app:
 
 https://adios.orr.noaa.gov/
 
-The ``adios_db`` package is available on conda-forge, and should have been installed by the process above. If not, it can be installed with ::
+The ``adios_db`` package is available on conda-forge, and should have been
+installed by the process above. If not, it can be installed with ::
 
   > conda install adios_db
 
-However, the adios_db package is also under active development along with PyGNOME, so if you are working with the develop branch of PyGNOME, you may need the latest version of adios_db as well. In which case, you are best off downloading the sources from GitHub and installing it from source -- similar to PyGNOME.
+However, the adios_db package is also under active development along with
+PyGNOME, so if you are working with the develop branch of PyGNOME,
+you may need the latest version of adios_db as well. In which case,
+you are best off downloading the sources from GitHub and installing it
+from source -- similar to PyGNOME.
 
 The latest releases (of the same branch) of each should be compatible.
 
-cloning the repository ::
+To clone the repository::
 
   > git clone https://github.com/NOAA-ORR-ERD/adios_oil_database.git
 
-Installing its dependencies::
+To install its dependencies::
 
   > cd adios_db
   > conda install --file conda_requirements.txt
 
-
 Installing the package::
 
   > pip install ./
@@ -376,7 +419,9 @@ Installing the package::
 
 Testing the adios_db install.
 
-If you run the PyGNOME tests after having installed ``adios_db``, it will run a few additional tests that require the ``adios_db``. It should not need independent testing.
+If you run the PyGNOME tests after having installed ``adios_db``, it will run
+a few additional tests that require the ``adios_db``. It should not need
+independent testing.
 
 But if you want to test it directly, you will need additional requirements::
 
@@ -400,10 +445,9 @@ The system compiler for OS-X is XCode. It can be installed from the App
 Store.
 
 Apple has changed the XCode install process a number of times over the years.
-
-Rather than providing out of date information:
-
-You need the "Xcode Command Line Tools" -- look for Apple's documentation for how to install those.
+Rather than providing out-of-date information, we will simply state that you
+need the "Xcode Command Line Tools" -- look for Apple's documentation for
+how to install those.
 
 Once the command line tools are installed, you should be able to build
 PyGNOME as described below.
@@ -412,19 +456,32 @@ PyGNOME as described below.
 Windows
 .......
 
-For compiling python extensions on Windows with python3 it is best to use the Microsoft the Visual Studio 2019 (or later) Build Tools. They should be available here:
+For compiling python extensions on Windows with python3 it is best to use
+the Microsoft the Visual Studio 2019 (or later) Build Tools. They should be
+available here:
 
 https://visualstudio.microsoft.com/downloads/
 
 The free "Community" version should be fine.
 
-Once installed, you will want to use one of the  "Visual Studio Developer Command Prompts" provided to actually build PyGNOME -- it sets up the compiler for you.
-
-.. warning:: On some locked down systems, such as those at NOAA, the standard way to use the MS compiler will not work for a user that does not have administration privileges.
-  If you get errors about not being able to run the ``vcvarsall.bat`` script, then the compiler must be run as an administrator.
-  If you have access to the NOAA/ORR GitLab server, a work around is supplied here: `Building Python extensions on Windows <https://gitlab.orr.noaa.gov/erd/programmers/-/blob/main/tech_notes/compiling_py3_C_extensions.md?ref_type=heads>`_.
-  If you have this issue and are not from NOAA, ask for help on Python fora or as an issue in the PyGNOME gitHub project.
-
+Once Visual Studio is installed, a number of
+"Visual Studio Developer Command Prompt" applications will be made available
+on the Windows toolbar.  ``Scikit-build-core`` claims that it can intelligently
+configure its environment to correctly build your package, but to be on the
+safe side, you will want to open up the one with a name that looks something
+similar to **"x64 Native Tools Command Prompt (for VS 20XX)"** in order to
+build PyGNOME -- this is to make sure the compiler is setup for building
+x64 targets.
+
+.. warning:: On some locked down systems, such as those at NOAA, the
+  standard way to use the MS compiler will not work for a user that does not
+  have administration privileges.  If you get errors about not being able to
+  run the ``vcvarsall.bat`` script, then the compiler must be run as an
+  administrator.  If you have access to the NOAA/ORR GitLab server, a
+  work around is supplied here:
+  `Building Python extensions on Windows <https://gitlab.orr.noaa.gov/erd/programmers/-/blob/main/tech_notes/compiling_py3_C_extensions.md?ref_type=heads>`__.
+  If you have this issue and are not from NOAA, ask for help on the Python
+  forum or as an issue in the PyGNOME gitHub project.
 
 Linux
 .....
@@ -441,45 +498,41 @@ system, use your system package manager to get it.
 Building PyGNOME
 ................
 
-At this point you should have all the necessary third-party
-tools in place.
-
-And it is probably best to build the "develop" target for your PyGNOME package if you plan on developing or debugging the PyGNOME source code
-(or updating the source code from GitHub).
-
-Building the "develop" target allows changes in the python code
-to be immediately available in your python environment without re-installing.
+At this point you should have all the necessary third-party tools in place,
+and you can build the PyGNOME package itself.  But How you build the package
+depends on how you plan to use it.
 
-Of course if you plan on simply using the package, you may certainly
-build with the "install" target. Just keep in mind that any updates to
-the project will need to be rebuilt and re-installed in order for
-changes to take effect.
+Most people will likely want to simply use the package for building and running
+simulations.  For this, run the following:
 
-There are a number of options for building:
+    > cd <your_pygnome_git_repo>/py_gnome
+    > python -m pip install ./
 
-::
-
-    > python setup.py develop
+Just keep in mind that any updates to the project will need to be
+rebuilt and re-installed in order for changes to take effect.
 
-builds and installs the ``gnome`` package in "development" (editable) mode.
-
-::
+*NOTE: You may have noticed that we run the pip module inside python instead of
+running the `pip` executable directly.  We have noticed on some platforms
+(Windows) that conda virtual environments, when activated, sometimes don't
+properly update the $Path environmental variable, causing pip to be run from
+the base conda environment instead of the current one.  The result is that
+PyGNOME gets installed there instead of our current conda environment.
+Running pip as a module ensures we are referencing the correct environment
+for installation*
 
-    > python setup.py install
-
-builds and installs the ``gnome`` package into your Python install.
-
-::
+If you are planning to develop or debug the PyGNOME source code itself,
+then you may want to perform a "develop" install.  A "develop" install allows
+changes in the python code to be immediately available in your python
+environment without re-installing.
 
-    > python setup.py cleanall
+For this, run the following:
 
-cleans files generated by the build as well as files auto-generated by
-cython. It is a good idea to run ``cleanall`` after updating from the
-gitHub repo -- particularly if strange errors are occurring.
+    > cd <your_pygnome_git_repo>/py_gnome
+    > python -m pip install --editable ./
 
-You will need to re-run ``develop`` or ``install`` after running ``cleanall``
+If you would like or need to uninstall the package, run the following:
 
-NOTE: PyGNOME is not currently configured to be built with pip -- you need to call ``setup.py`` directly.
+    > python -m pip uninstall gnome
 
 
 Testing PyGNOME
@@ -490,7 +543,7 @@ PyGNOME is working properly.
 
 To run the tests::
 
-    > cd py_gnome/tests/unit_tests
+    > cd <your_pygnome_git_repo>/py_gnome/tests/unit_tests
     > pytest
 
 and if those pass, you can run::
diff --git a/README.rst b/README.rst
index 8e59789d8..1dfb07ab3 100644
--- a/README.rst
+++ b/README.rst
@@ -15,7 +15,10 @@ Introduction
 developed by the National Oceanic and Atmospheric Administration (**NOAA**),
 Office of Response and Restoration (**ORR**), Emergency Response Division.
 
-It is designed to support oil and other hazardous material spills in the coastal environment, and is also a full featured, flexible particle tracking system, that can be used for other oceanographic transport applications, such as fish larvae, marine debris, etc.
+It is designed to support oil and other hazardous material spills in the
+coastal environment, and is also a full featured, flexible particle tracking
+system, that can be used for other oceanographic transport applications,
+such as fish larvae, marine debris, etc.
 
 PyGNOME is a python package that encapsulates GNOME's functionality.
 
@@ -39,37 +42,34 @@ Installation
 ============
 
 We have put some effort into making this package reasonably easy,
-or at least possible, to install in a number of ways on a few different computing platforms:
+or at least possible, to install on a few different computing platforms:
 
  - OS-X
  - Windows
  - Linux (tested on CentOS 7)
 
-At this time, it must be compiled from the source code.
-
-The "tricky" part is installing the dependencies: details in the following:
-
-`Install using conda <./Installing.rst>`_
-
-The conda package manager is built primarily for scientific, engineering,
-and math applications it is the easiest way to get set up to use ``PyGNOME``, and it is used in our development and testing process.
-
-If you don't want to / can't use conda -- here are some notes on that:
-
-`Installing Without Conda <./Install_without_conda.rst>`_
+This package contains modules written in C/C++, and they must be
+compiled for this package to function, and we primarily use the Anaconda
+distribution of Python for installation.  Anaconda is built primarily for
+scientific, engineering, and math applications.
+It is now the only supported way to get set up to use ``PyGNOME``,
+and it is used in our development and testing process.
 
+`Install using Anaconda <./Installing.rst>`_
 
 The WebGNOME Interface:
 =======================
 
 Scripting is the most featurefull way to access PyGNOME's capabilities.
-However we have developed a system that allows a user to create and run PyGNOME models from a web browser.
+However we have developed a system that allows a user to create and run
+PyGNOME models from a web browser.
 
 There is a publicly available instance of WebGNOME at:
 
 https://gnome.orr.noaa.gov
 
-If you want to run your own instance of WebGNOME, the code is in the following projects:
+If you want to run your own instance of WebGNOME, the code is in the
+following projects:
 
 - `WebGnomeAPI <https://github.com/NOAA-ORR-ERD/WebGnomeAPI>`_:
   A web server that implements the PyGNOME interface
@@ -78,4 +78,5 @@ If you want to run your own instance of WebGNOME, the code is in the following p
 
 **Fair Warning:**
 
-The WebGNOME system is under active development, and by its very nature does not expose the full capabilities of PyGNOME.
+The WebGNOME system is under active development, and by its very nature
+does not expose the full capabilities of PyGNOME.

From 9c4813f783be347e3b9a90f4f0f864be46f82988 Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Fri, 3 May 2024 19:26:44 -0700
Subject: [PATCH 56/99] 2nd pass cleaning up the .rst documentation.

---
 Installing.rst | 131 ++++++++++++++++++++++++++-----------------------
 1 file changed, 69 insertions(+), 62 deletions(-)

diff --git a/Installing.rst b/Installing.rst
index c5fa241a1..0d1063f7c 100644
--- a/Installing.rst
+++ b/Installing.rst
@@ -41,7 +41,7 @@ Run the tests::
     > cd tests/unit_tests
     > pytest --runslow
 
-NOTE: *the "runslow" tests requiring downloading data for the tests -- you can
+NOTE: *The "runslow" tests requiring downloading data for the tests -- you can
 eliminate that flag to get most of the tests to run without that delay.*
 
 All the details
@@ -118,7 +118,7 @@ Linux:
 
 The Linux 64bit-python3.10 is the one to use.
 
-*NOTE: We do not support 32 bit on any platform.*
+NOTE: *We do not support 32 bit on any platform.*
 
 conda
 -----
@@ -129,7 +129,7 @@ package manager for installing conda packages. ``pip`` can also be used
 within conda, but it's best to use use conda for as much as you can.
 
 As a rule, if you need a new package, you should try to conda install it,
-and then, if there is not conda package available, you can pip install it.
+and then, if there is no conda package available, you can pip install it.
 
 We have made sure that every package you need for PyGNOME is available for conda.
 
@@ -185,7 +185,7 @@ Adding another channel to conda:
 ................................
 
 In order to find packages available on conda-forge, it should be added to your
-conda channel configuration:
+conda channel configuration::
 
     > conda config --add channels conda-forge
 
@@ -206,7 +206,7 @@ In that order -- the order is important
 
 You need to set the channel prioroty to "strict"::
 
-  > conda config --set channel_priority strict
+    > conda config --set channel_priority strict
 
 This will assure that you will get packages from conda-forge, even if there are
 newer ones available in the defaults channel.
@@ -268,9 +268,7 @@ it yet, it is available here:
 https://github.com/NOAA-ORR-ERD/PyGNOME
 
 You can either download a zip file of all the sources and unpack it, or
-you can "clone" the git repository. If you clone the repository, you will
-be able to update the code with the latest version with a simple command,
-rather than having to re-download the whole package.
+you can "clone" the git repository. Either choice is valid.
 
 
 Downloading a single release
@@ -281,29 +279,35 @@ zip and tar archives of the PyGNOME source code can be found here:
 https://github.com/NOAA-ORR-ERD/PyGNOME/releases
 
 This will get you the entire source archive of a given release, which is a
-fine way to work with PyGNOME. However, if you want to be able to quickly
-include changes as we update the code, you may want to work with a git "clone"
-of the source code instead.
+fine way to work with PyGNOME.  However if, in the future, you want to use any
+new changes that have been made to the code, you will need to re-download the
+new release in its entirety.
 
-Cloning the PyGNOME git repository
+Cloning the PyGNOME Git repository
 ----------------------------------
 
-git
-...
-
-You will need a git client:
+If you clone the repository, you will be able to update the code with the
+latest version with a simple command (`git pull`).  This will download only
+the files that have changed and requires no archive extraction, so it will
+not only be a faster operation, but we think you will find it is also more
+convenient.
 
-On Linux, it should be available from your package manager::
+First you will need a Git client.  On Linux, it should be available from your
+package manager using one of the following commands::
 
-    > apt_get install git
+    > apt_get install git  # Debian & Linux Mint
     or
-    > yum install git
+    > yum install git  # CentOS & Red Hat Enterprise Linux
 
-On OS-X, git comes with the XCode command line tools:
+NOTE: *There are a few other Linux package managers out there.  Look at this
+`exhaustive list <https://en.wikipedia.org/wiki/List_of_software_package_management_systems#Linux>`__
+to find the one your Linux distribution uses*
+
+On OS-X, Git comes with the XCode command line tools:
 
   http://osxdaily.com/2014/02/12/install-command-line-tools-mac-os-x/
 
-On Windows, the "official" git for Windows installer is a good bet:
+On Windows, the "official" Git for Windows installer is a good bet:
 
   https://git-for-windows.github.io/
 
@@ -311,7 +315,7 @@ Once you have the client, it's as easy as::
 
   > git clone https://github.com/NOAA-ORR-ERD/PyGNOME.git
 
-This will create a PyGNOME directory with all the code in it.
+This will create a `./pygnome` directory with all the code in it.
 
 git branches:
   git supports a number of different "branches" or versions of the code.
@@ -328,17 +332,13 @@ To use the gnome environment you created, it needs to be activated with::
 
     > conda activate gnome
 
-and when you are done, you can deactivate it with::
-
-    > conda deactivate
-
 If you don't want to create an environment (or already have one), you can
-install what PyGNOME needs into an existing environment:
+install what PyGNOME needs into an existing environment::
 
-    > cd PyGNOME  # or wherever you put the PyGNOME project
+    > cd ./pygnome  # or wherever you put the PyGNOME project
     > conda install --file conda_requirements.txt --file conda_requirements_build.txt --file conda_requirements_test.txt
 
-*NOTE: PyGNOME has a lot of specific dependencies -- it can be very hard
+NOTE: *PyGNOME has a lot of specific dependencies -- it can be very hard
 for conda to resolve them with an large installed package base.
 If you have trouble, it's easiest to make a new environment just for PyGNOME.*
 
@@ -404,20 +404,21 @@ The latest releases (of the same branch) of each should be compatible.
 
 To clone the repository::
 
-  > git clone https://github.com/NOAA-ORR-ERD/adios_oil_database.git
+    > git clone https://github.com/NOAA-ORR-ERD/adios_oil_database.git
 
 To install its dependencies::
 
-  > cd adios_db
-  > conda install --file conda_requirements.txt
+    > cd ./oil_database/adios_db
+    > conda install --file conda_requirements.txt
 
 Installing the package::
 
-  > pip install ./
+    > pip install ./
 
 (or ``pip install -e ./`` to get an "editable" version)
 
-Testing the adios_db install.
+Testing the adios_db install
+............................
 
 If you run the PyGNOME tests after having installed ``adios_db``, it will run
 a few additional tests that require the ``adios_db``. It should not need
@@ -427,11 +428,10 @@ But if you want to test it directly, you will need additional requirements::
 
   > conda install --file conda_requirements_test.txt
 
-And then you can run the tests:
+And then you can run the tests::
 
   > pytest --pyargs adios_db
 
-
 Compilers
 ---------
 
@@ -473,7 +473,8 @@ similar to **"x64 Native Tools Command Prompt (for VS 20XX)"** in order to
 build PyGNOME -- this is to make sure the compiler is setup for building
 x64 targets.
 
-.. warning:: On some locked down systems, such as those at NOAA, the
+Warning:
+  On some locked down systems, such as those at NOAA, the
   standard way to use the MS compiler will not work for a user that does not
   have administration privileges.  If you get errors about not being able to
   run the ``vcvarsall.bat`` script, then the compiler must be run as an
@@ -489,11 +490,9 @@ Linux
 Linux uses the GNU gcc compiler. If it is not already installed on your
 system, use your system package manager to get it.
 
--  apt for Ubuntu and Linux Mint
--  rpm for Red Hat
--  dpkg for Debian
+-  apt for Debian based distros (Ubuntu, Mint, Kali, ...)
 -  yum for CentOS
--  ??? for other distros
+-  `... <https://en.wikipedia.org/wiki/List_of_software_package_management_systems#Linux>`__
 
 Building PyGNOME
 ................
@@ -503,7 +502,7 @@ and you can build the PyGNOME package itself.  But How you build the package
 depends on how you plan to use it.
 
 Most people will likely want to simply use the package for building and running
-simulations.  For this, run the following:
+simulations.  For this, run the following::
 
     > cd <your_pygnome_git_repo>/py_gnome
     > python -m pip install ./
@@ -525,12 +524,12 @@ then you may want to perform a "develop" install.  A "develop" install allows
 changes in the python code to be immediately available in your python
 environment without re-installing.
 
-For this, run the following:
+For this, run the following::
 
     > cd <your_pygnome_git_repo>/py_gnome
     > python -m pip install --editable ./
 
-If you would like or need to uninstall the package, run the following:
+If you would like or need to uninstall the package, run the following::
 
     > python -m pip uninstall gnome
 
@@ -561,10 +560,18 @@ runs.
 What if some tests fail?
 ........................
 
-We do our best to keep all tests passing on release versions of the package. But sometimes tests will fail due to the setup of the machine they are being run on -- package versions, etc. So the first thing to do is to make sure you have installed the dependencies as specified.
+We do our best to keep all tests passing on release versions of the package.
+But sometimes tests will fail due to the setup of the machine they are being
+run on -- package versions, etc. So the first thing to do is to make sure you
+have installed the dependencies as specified.
 
-But ``gnome`` is large package -- hardly anyone is going to use all of it. So while we'd like all tests to pass, a given test failure may not be an issue for any given use case.
-It's a bit hard to know whether a given test failure will affect your use case, but if you look at the name of the tests that fail, you might get a hint. For example, if any of the tests fail under ``test_weathering``, and you are not doing any oil weathering modeling, you don't need to worry about it.
+But ``gnome`` is large package -- hardly anyone is going to use all of it.
+So while we'd like all tests to pass, a given test failure may not be an issue
+for any given use case.  It's a bit hard to know whether a given test failure
+will affect your use case, but if you look at the name of the tests that fail,
+you might get a hint. For example, if any of the tests fail under
+``test_weathering``, and you are not doing any oil weathering modeling,
+you don't need to worry about it.
 
 In any case, you can try to run your use case, and see what happens.
 
@@ -575,21 +582,24 @@ Running scripts
 
 There are a number of scripts in the ``scripts`` directory.
 
-In ``example_scripts`` you will find examples of using the ``gnome`` package for various tasks.
+In ``example_scripts`` you will find examples of using the ``gnome`` package
+for various tasks.
 
-In ``testing_scripts`` you will find scripts that have been developed to test various features of the model. There are many more of these, so do look to see if they have what you need. But they are generally written in a less compact way as they are designed to exercise particular features.
+In ``testing_scripts`` you will find scripts that have been developed to
+test various features of the model. There are many more of these, so do look
+to see if they have what you need. But they are generally written in a
+less compact way as they are designed to exercise particular features.
 
-You should be able to run these scripts in the same way as any Python script (with an IDE such as Spyder or PyCharm, or at the command line).
+You should be able to run these scripts in the same way as any Python script
+(with an IDE such as Spyder or PyCharm, or at the command line).
 
 
-To run a script on the command line:
-
-::
+To run a script on the command line::
 
     > cd py_gnome/scripts/example_scripts
 
 
-If you are using a conda environment:
+If you are using a conda environment::
 
     > conda activate gnome
 
@@ -597,16 +607,13 @@ Run the script::
 
     > python example_script.py
 
-Each of the scripts exercises different features of PyGNOME -- they are hopefully well commented to see how they work.
+Each of the scripts exercises different features of PyGNOME -- they are
+hopefully well commented to see how they work.
 
-In the ``testing_scripts`` dir, there is a ``run_all.py`` script that will run all the testing scripts -- primarily to make sure they all can still run as we update the model.
+In the ``testing_scripts`` dir, there is a ``run_all.py`` script that will
+run all the testing scripts -- primarily to make sure they all can still run
+as we update the model.
 
 For further documentation of PyGNOME, see:
 
 https://gnome.orr.noaa.gov/doc/PyGNOME/index.html
-
-
-
-
-
-

From 39b21569818405de75b4aabd1db5da1247c2df22 Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Fri, 3 May 2024 20:46:00 -0700
Subject: [PATCH 57/99] CI: test_pygnome_windows: conda powershell hook might
 be changing our current directory.  Comment it out.

---
 .gitlab-ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 2361630a8..5bd656a21 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -128,13 +128,13 @@ test_pygnome_windows:
                   'C:\ProgramData\miniforge3\Scripts;' +
                   'C:\ProgramData\miniforge3\Lib\bin;' +
                   $Env:PathOrig
-    - echo "Our $Path:"
     - $Env:Path -split ';'
 
-    - echo "Python is running from:"
     - python -c "import sys; print(sys.executable)"
 
-    - Invoke-Expression "conda shell.powershell hook"
+    # This might be changing our current directory.  It only needs to be run
+    # one time anyway, so we will comment it out.
+    #- Invoke-Expression "conda shell.powershell hook"
 
     - conda config --add channels defaults
     - conda config --add channels conda-forge

From 8a88ad5fe110c517b8ac9d763c58a3311d952d90 Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Fri, 3 May 2024 22:43:18 -0700
Subject: [PATCH 58/99] CI: test_pygnome_windows: incorrect powershell syntax
 for setting the path.

---
 .gitlab-ci.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5bd656a21..955bb5385 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -143,10 +143,10 @@ test_pygnome_windows:
 
     - conda create -y -p ./pygnome python=$PYTHON_VER
 
-    - echo $Get-Location + '\pygnome'
-    - $Env:Path = $Get-Location + '\pygnome\;' +
-                  $Get-Location + '\pygnome\Scripts\;' +
-                  $Get-Location + '\pygnome\Lib\bin\;' +
+    - $Env:Path = '' +
+                  (Get-Location) + '\pygnome\;' +
+                  (Get-Location) + '\pygnome\Scripts\;' +
+                  (Get-Location) + '\pygnome\Lib\bin\;' +
                   $Env:PathOrig
     - conda activate ./pygnome
   script:

From d3931474f55b4a54fc2c36474fe91ef117067843 Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Mon, 6 May 2024 12:10:48 -0700
Subject: [PATCH 59/99] CI: test_pygnome_windows: run the powershell hooks, but
 re-establish the current dir afterwards.

---
 .gitlab-ci.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 955bb5385..17611efa2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -117,6 +117,7 @@ test_pygnome_windows:
     - Get-Location
     - Get-ChildItem | % { $_.FullName }  # this should list the current folder
     - $Env:PathOrig = $Env:Path
+    - $Env:CurrDir = Get-Location
  
     # Where is our conda installation?
     # This will tell us where python is installed.  This could change periodically
@@ -132,9 +133,10 @@ test_pygnome_windows:
 
     - python -c "import sys; print(sys.executable)"
 
-    # This might be changing our current directory.  It only needs to be run
-    # one time anyway, so we will comment it out.
-    #- Invoke-Expression "conda shell.powershell hook"
+    # This might be changing our current directory, so we re-establish it
+    # after initializing the powershell hooks.
+    - Invoke-Expression "conda shell.powershell hook"
+    - cd $Env:CurrDir
 
     - conda config --add channels defaults
     - conda config --add channels conda-forge

From ce675f95340310e6c35cc32428984364626e467d Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Mon, 6 May 2024 13:03:49 -0700
Subject: [PATCH 60/99] CI: test_pygnome_windows: Can't activate conda env. 
 Try the full powershell path to env.

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 17611efa2..31707fc35 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -150,7 +150,7 @@ test_pygnome_windows:
                   (Get-Location) + '\pygnome\Scripts\;' +
                   (Get-Location) + '\pygnome\Lib\bin\;' +
                   $Env:PathOrig
-    - conda activate ./pygnome
+    - conda activate '' + (Get-Location) + '\pygnome'
   script:
     - echo "Building and testing PyGNOME"
 

From b9e955ca2932092316185099fdaacbb5aaa4dfaf Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Mon, 6 May 2024 15:12:00 -0700
Subject: [PATCH 61/99] CI: test_pygnome_windows: Trying conda init powershell.
  Docs say the shell needs to be restarted, but we will try it.

---
 .gitlab-ci.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 31707fc35..117152a71 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -133,10 +133,10 @@ test_pygnome_windows:
 
     - python -c "import sys; print(sys.executable)"
 
-    # This might be changing our current directory, so we re-establish it
-    # after initializing the powershell hooks.
-    - Invoke-Expression "conda shell.powershell hook"
-    - cd $Env:CurrDir
+    # This might be changing our current directory.  It only needs to be run
+    # one time anyway, so we will comment it out.
+    #- Invoke-Expression "conda shell.powershell hook"
+    - conda init powershell
 
     - conda config --add channels defaults
     - conda config --add channels conda-forge
@@ -150,7 +150,7 @@ test_pygnome_windows:
                   (Get-Location) + '\pygnome\Scripts\;' +
                   (Get-Location) + '\pygnome\Lib\bin\;' +
                   $Env:PathOrig
-    - conda activate '' + (Get-Location) + '\pygnome'
+    - conda activate ./pygnome
   script:
     - echo "Building and testing PyGNOME"
 

From 3abcd0ad036c5183c5f5346ffcabf358ed8da366 Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Tue, 7 May 2024 09:13:29 -0700
Subject: [PATCH 62/99] CI: test_pygnome_windows: conda env already set.  Maybe
 we don't need to update our $path.

---
 .gitlab-ci.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 117152a71..9b300b550 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -145,11 +145,11 @@ test_pygnome_windows:
 
     - conda create -y -p ./pygnome python=$PYTHON_VER
 
-    - $Env:Path = '' +
-                  (Get-Location) + '\pygnome\;' +
-                  (Get-Location) + '\pygnome\Scripts\;' +
-                  (Get-Location) + '\pygnome\Lib\bin\;' +
-                  $Env:PathOrig
+    #- $Env:Path = '' +
+    #              (Get-Location) + '\pygnome\;' +
+    #              (Get-Location) + '\pygnome\Scripts\;' +
+    #              (Get-Location) + '\pygnome\Lib\bin\;' +
+    #              $Env:PathOrig
     - conda activate ./pygnome
   script:
     - echo "Building and testing PyGNOME"

From ddd055eb13f897975218b8b7037e81d237e678be Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Tue, 7 May 2024 12:14:46 -0700
Subject: [PATCH 63/99] CI: test_pygnome_windows: On SO, it was suggested that
 this would perform a `conda init` without needing to restart PowerShell.  So
 we will test it.

---
 .gitlab-ci.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9b300b550..50e19ae9a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -136,7 +136,11 @@ test_pygnome_windows:
     # This might be changing our current directory.  It only needs to be run
     # one time anyway, so we will comment it out.
     #- Invoke-Expression "conda shell.powershell hook"
-    - conda init powershell
+    #- conda init powershell
+
+    # On SO, it was suggested that this would perform a `conda init`
+    # without needing to restart PowerShell.  So we will test it.
+    - C:\ProgramData\miniforge3\shell\condabin\conda-hook.ps1
 
     - conda config --add channels defaults
     - conda config --add channels conda-forge

From 328e112575607bb47e9569398ab7821a87047cd9 Mon Sep 17 00:00:00 2001
From: "James L. Makela" <james.makela@noaa.gov>
Date: Thu, 9 May 2024 09:54:06 -0700
Subject: [PATCH 64/99] Windows: sometimes the _stdlib_dir is not available. 
 Use os.__file__ instead in those cases.

---
 py_gnome/gnome/__init__.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/py_gnome/gnome/__init__.py b/py_gnome/gnome/__init__.py
index c90b57174..addfca8f6 100644
--- a/py_gnome/gnome/__init__.py
+++ b/py_gnome/gnome/__init__.py
@@ -28,9 +28,14 @@
 if os.name == 'nt':
     # In Windows, we need to add the location of our lib_gnome.dll to the
     # .dll search path.
-    os.add_dll_directory(
-        pathlib.Path(sys._stdlib_dir) / 'site-packages' / 'bin'
-    )
+    here = getattr(sys, '_stdlib_dir', None)
+    if not here and hasattr(os, '__file__'):
+        here = os.path.dirname(os.__file__)
+
+    if here:
+        os.add_dll_directory(
+            pathlib.Path(here) / 'site-packages' / 'bin'
+        )
 
 #
 # A few imports so that the basic stuff is there

From d99098f3738ab36e0232bc103b6713981b98427e Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Thu, 9 May 2024 12:33:12 -0700
Subject: [PATCH 65/99] typo in docstring fixed

---
 py_gnome/gnome/utilities/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/py_gnome/gnome/utilities/__init__.py b/py_gnome/gnome/utilities/__init__.py
index bb8f1ccee..c2d38703d 100644
--- a/py_gnome/gnome/utilities/__init__.py
+++ b/py_gnome/gnome/utilities/__init__.py
@@ -40,7 +40,7 @@ def convert_longitude(lon, coord_system='-180--180'):
     -180 converts to 180
 
     It should be safe to call this on any coords -- if they are already
-    in the expected format, they will not be changes, except for the
+    in the expected format, they will not be changed, except for the
     normalization above.
     """
 

From ab15af46e7d62862de5be3dcb80b6a4325c2f045 Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Thu, 9 May 2024 13:08:24 -0700
Subject: [PATCH 66/99] bumped version, and required version for adios_db

---
 py_gnome/gnome/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/py_gnome/gnome/__init__.py b/py_gnome/gnome/__init__.py
index 5238f7c80..8b00aacfe 100644
--- a/py_gnome/gnome/__init__.py
+++ b/py_gnome/gnome/__init__.py
@@ -21,7 +21,7 @@
 # just so it will be in the namespace.
 from .gnomeobject import GnomeId, AddLogger
 
-__version__ = '1.1.7'
+__version__ = '1.1.8'
 
 
 # a few imports so that the basic stuff is there
@@ -54,7 +54,7 @@ def ver_check(required, installed):
     libs = [('gridded', '0.6.5', ''),
             ('nucos', '3.2.0', ''),
             ('py_gd', '2.2.0', ''),
-            ('adios_db', '1.1.1', 'Only required to use the ADIOS Database '
+            ('adios_db', '1.2.0', 'Only required to use the ADIOS Database '
                                   'JSON format for oil data.')
             ]
 

From 30c1c355abe4e8407fe4e7c66dae6b5ef32a63fb Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Mon, 13 May 2024 01:12:25 -0500
Subject: [PATCH 67/99] updated the scripting section of the docs

---
 .../source/scripting/sample_scripts.rst       | 32 ++++++++++++++++++-
 .../source/scripting/scripting_examples.rst   | 10 +++---
 .../source/scripting/weatherers.rst           |  8 +++++
 .../scripts/example_scripts/gridded_script.py |  7 +++-
 4 files changed, 50 insertions(+), 7 deletions(-)

diff --git a/py_gnome/documentation/source/scripting/sample_scripts.rst b/py_gnome/documentation/source/scripting/sample_scripts.rst
index 48d571d6d..36f474cb1 100644
--- a/py_gnome/documentation/source/scripting/sample_scripts.rst
+++ b/py_gnome/documentation/source/scripting/sample_scripts.rst
@@ -3,7 +3,6 @@
 Sample Scripts Included with PyGNOME
 ####################################
 
-
 A good way to learn to use PyGNOME is to find an example script that uses similar components to what you need, and use that as a starting point.
 
 There are two sets of scripts included with PyGNOME:
@@ -14,6 +13,37 @@ There are two sets of scripts included with PyGNOME:
 * ``py_gnome/scripts/testing_scripts``: scripts set up to test particular aspects of PyGNOME
 
 
+Example Scripts
+===============
+
+The scripts in the example dir may require data found in the ``example_files`` directory.
+
+``simple_script.py``
+--------------------
+
+The very simplest script one can write with PyGNOME. Discussed in:
+:ref:`scripting_overview`
+
+
+``weathering_script.py``
+------------------------
+
+An example of a simple weathering run -- weathering is described more in:
+:ref:`scripting_weathering`
+
+
+``gridded_script.py``
+---------------------
+
+A script that demonstrates how to use gridded currents and winds from netcdf files.
+
+
+``current_uncertainty_example.py``
+----------------------------------
+
+Demonstration of adding uncertainty to a model, and adjusting the uncertainty parameters of a current mover.
+
+
 Testing Scripts
 ===============
 
diff --git a/py_gnome/documentation/source/scripting/scripting_examples.rst b/py_gnome/documentation/source/scripting/scripting_examples.rst
index 6848cf0d8..b1328cfb1 100644
--- a/py_gnome/documentation/source/scripting/scripting_examples.rst
+++ b/py_gnome/documentation/source/scripting/scripting_examples.rst
@@ -1,13 +1,13 @@
 Examples
 ========
 
-Examples of solving various problems with PyGNOME.
+.. Examples of solving various problems with PyGNOME.
 
-To be written:
+.. To be written:
 
-* How to run PyGNOME Backwards
-* How to use multiple files for currents
-* How to model a non-oil floating object (e.g. debris)
+.. * How to run PyGNOME Backwards
+.. * How to use multiple files for currents
+.. * How to model a non-oil floating object (e.g. debris)
 
 
 .. toctree::
diff --git a/py_gnome/documentation/source/scripting/weatherers.rst b/py_gnome/documentation/source/scripting/weatherers.rst
index e8794b9d7..43686cb80 100644
--- a/py_gnome/documentation/source/scripting/weatherers.rst
+++ b/py_gnome/documentation/source/scripting/weatherers.rst
@@ -1,3 +1,5 @@
+.. _scripting_weathering:
+
 Weatherers
 ==========
 
@@ -19,8 +21,14 @@ You can find a documented simple example script in:
 
 ``pygnome/py_gnome/scripts/example_scripts/weathering_script.py``
 
+Or download it here:
+:download:`weathering_script.py <../../../scripts/example_scripts/weathering_script.py>`
+
 It is well commented.
 
+You will also need an oil definition JSON file, such as:
+:download:`alaska-north-slope_AD00020.json <../../../scripts/example_scripts/example_files/alaska-north-slope_AD00020.json>`
+
 
 
 Oil Definitions
diff --git a/py_gnome/scripts/example_scripts/gridded_script.py b/py_gnome/scripts/example_scripts/gridded_script.py
index 3c1b6831b..dcbd66087 100644
--- a/py_gnome/scripts/example_scripts/gridded_script.py
+++ b/py_gnome/scripts/example_scripts/gridded_script.py
@@ -36,11 +36,16 @@
                        output_timestep=gs.hours(6),
                        # set part of map to view
                        viewport=((-125.5, 47.5),
-                                 (-124.0, 48.5))
+                                 (-124.0, 48.5)),
+                       formats=['gif']
                        )
 
 model.outputters += renderer
 
+kmzout = gs.KMZOutput('output/gridded_example.kmz')
+print("adding KMZ outputter")
+model.outputters += kmzout
+
 print("running the model: see output in the output dir")
 
 model.full_run()

From dfdcbd90bc146f254d5b7aa078f3f9386405a777 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Mon, 13 May 2024 03:38:41 -0700
Subject: [PATCH 68/99] Added github actions for building & testing pygnome
 package.

---
 .github/workflows/conda_test.yml | 63 ++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 .github/workflows/conda_test.yml

diff --git a/.github/workflows/conda_test.yml b/.github/workflows/conda_test.yml
new file mode 100644
index 000000000..5416ee94d
--- /dev/null
+++ b/.github/workflows/conda_test.yml
@@ -0,0 +1,63 @@
+name: Run tests with miniconda
+on: [push]
+
+jobs:
+  test:
+    name: Miniconda ${{ matrix.os }} Py${{ matrix.pyver }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        matrix:
+            os: ["ubuntu-latest", "windows-latest","macos-latest"]
+            pyver: ["3.8", "3.9", "3.10", "3.11"]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: test
+#          environment-file: environment.yml
+          python-version: ${{ matrix.pyver }}
+          auto-activate-base: false
+      - shell: bash -l {0}
+        run: |
+          conda config --add channels conda-forge
+      - name: Setup environment
+        shell: bash -l {0}
+        run: |
+            git clone --depth 1 -b develop https://github.com/NOAA-ORR-ERD/adios_oil_database.git
+            conda install -y python=$PYTHON_VER mamba
+            cd ./py_gnome
+            echo "Setting up conda environment"
+            mamba install -y python=$PYTHON_VER --file conda_requirements.txt
+                                                --file conda_requirements_build.txt
+                                                --file conda_requirements_test.txt
+                                                --file ../oil_database/adios_db/conda_requirements.txt
+      - name: Build Our Packages
+        shell: bash -l {0}
+        run: |
+            pip install ./oil_database/adios_db/
+            cd ./py_gnome
+            python -m pip install ./
+      - name: Run pytest
+        shell: bash -l {0}
+        run: |
+            cd ./py_gnome/tests/unit_tests
+            pytest --runslow
+
+  lint:
+    name: Flake8 linting
+    runs-on: "ubuntu-latest"
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: lint
+          python-version: 3.9
+          auto-activate-base: false
+      - shell: bash -l {0}
+        run: |
+          conda config --add channels conda-forge
+      - name: Lint
+        shell: bash -l {0}
+        run: |
+            conda install flake8
+            python -m flake8  --exit-zero --statistics py_gnome/gnome/

From 1c09432e67338ea5dbe77a339027611767553aa7 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Mon, 13 May 2024 03:52:12 -0700
Subject: [PATCH 69/99] No python version specified if we are running a matrix
 of envs.

---
 .github/workflows/conda_test.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/conda_test.yml b/.github/workflows/conda_test.yml
index 5416ee94d..580682b0b 100644
--- a/.github/workflows/conda_test.yml
+++ b/.github/workflows/conda_test.yml
@@ -24,13 +24,13 @@ jobs:
         shell: bash -l {0}
         run: |
             git clone --depth 1 -b develop https://github.com/NOAA-ORR-ERD/adios_oil_database.git
-            conda install -y python=$PYTHON_VER mamba
+            conda install -y mamba
             cd ./py_gnome
             echo "Setting up conda environment"
-            mamba install -y python=$PYTHON_VER --file conda_requirements.txt
-                                                --file conda_requirements_build.txt
-                                                --file conda_requirements_test.txt
-                                                --file ../oil_database/adios_db/conda_requirements.txt
+            mamba install -y --file conda_requirements.txt
+                             --file conda_requirements_build.txt
+                             --file conda_requirements_test.txt
+                             --file ../oil_database/adios_db/conda_requirements.txt
       - name: Build Our Packages
         shell: bash -l {0}
         run: |

From 736213593dc9229c02e4ef9325fdab169480de39 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Mon, 13 May 2024 04:05:53 -0700
Subject: [PATCH 70/99] New version of actions/checkout.

---
 .github/workflows/conda_test.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/conda_test.yml b/.github/workflows/conda_test.yml
index 580682b0b..630e22363 100644
--- a/.github/workflows/conda_test.yml
+++ b/.github/workflows/conda_test.yml
@@ -10,11 +10,11 @@ jobs:
             os: ["ubuntu-latest", "windows-latest","macos-latest"]
             pyver: ["3.8", "3.9", "3.10", "3.11"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: test
-#          environment-file: environment.yml
+          # environment-file: environment.yml
           python-version: ${{ matrix.pyver }}
           auto-activate-base: false
       - shell: bash -l {0}
@@ -47,7 +47,7 @@ jobs:
     name: Flake8 linting
     runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: lint

From 72b8386a57589ce0e8084f015ce870a711a472b0 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Mon, 13 May 2024 04:17:32 -0700
Subject: [PATCH 71/99] Test if multi-line commands work in the github
 workflows.

---
 .github/workflows/conda_test.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/conda_test.yml b/.github/workflows/conda_test.yml
index 630e22363..1f8a496b9 100644
--- a/.github/workflows/conda_test.yml
+++ b/.github/workflows/conda_test.yml
@@ -27,10 +27,10 @@ jobs:
             conda install -y mamba
             cd ./py_gnome
             echo "Setting up conda environment"
-            mamba install -y --file conda_requirements.txt
-                             --file conda_requirements_build.txt
-                             --file conda_requirements_test.txt
-                             --file ../oil_database/adios_db/conda_requirements.txt
+            #mamba install -y --file conda_requirements.txt
+            #                 --file conda_requirements_build.txt
+            #                 --file conda_requirements_test.txt
+            #                 --file ../oil_database/adios_db/conda_requirements.txt
       - name: Build Our Packages
         shell: bash -l {0}
         run: |

From dbf4e66e08bcbd87c85f8960e5da6a0775e4cab8 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Mon, 13 May 2024 04:26:11 -0700
Subject: [PATCH 72/99] re-add multi-line commands, some diagnostic because our
 oil_database install is failing.

---
 .github/workflows/conda_test.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/conda_test.yml b/.github/workflows/conda_test.yml
index 1f8a496b9..e0f1494f2 100644
--- a/.github/workflows/conda_test.yml
+++ b/.github/workflows/conda_test.yml
@@ -27,13 +27,15 @@ jobs:
             conda install -y mamba
             cd ./py_gnome
             echo "Setting up conda environment"
-            #mamba install -y --file conda_requirements.txt
-            #                 --file conda_requirements_build.txt
-            #                 --file conda_requirements_test.txt
-            #                 --file ../oil_database/adios_db/conda_requirements.txt
+            mamba install -y --file conda_requirements.txt
+                             --file conda_requirements_build.txt
+                             --file conda_requirements_test.txt
+                             --file ../oil_database/adios_db/conda_requirements.txt
       - name: Build Our Packages
         shell: bash -l {0}
         run: |
+            pwd
+            ls -la
             pip install ./oil_database/adios_db/
             cd ./py_gnome
             python -m pip install ./

From 52ea656aeb62d215848905c9c2ba7e11aab2da33 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Mon, 13 May 2024 04:35:04 -0700
Subject: [PATCH 73/99] We won't test python 3.8, and multi-line commands are
 failing.

---
 .github/workflows/conda_test.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/conda_test.yml b/.github/workflows/conda_test.yml
index e0f1494f2..5deb39985 100644
--- a/.github/workflows/conda_test.yml
+++ b/.github/workflows/conda_test.yml
@@ -8,7 +8,7 @@ jobs:
     strategy:
         matrix:
             os: ["ubuntu-latest", "windows-latest","macos-latest"]
-            pyver: ["3.8", "3.9", "3.10", "3.11"]
+            pyver: ["3.9", "3.10", "3.11"]
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
@@ -27,9 +27,9 @@ jobs:
             conda install -y mamba
             cd ./py_gnome
             echo "Setting up conda environment"
-            mamba install -y --file conda_requirements.txt
-                             --file conda_requirements_build.txt
-                             --file conda_requirements_test.txt
+            mamba install -y --file conda_requirements.txt \
+                             --file conda_requirements_build.txt \
+                             --file conda_requirements_test.txt \
                              --file ../oil_database/adios_db/conda_requirements.txt
       - name: Build Our Packages
         shell: bash -l {0}

From 324e96373ab907ea1c510014b3a727c6b035363c Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Mon, 13 May 2024 04:46:47 -0700
Subject: [PATCH 74/99] Fix the name of the folder that the oil_database repo
 is cloned into.

---
 .github/workflows/conda_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/conda_test.yml b/.github/workflows/conda_test.yml
index 5deb39985..87eaeb829 100644
--- a/.github/workflows/conda_test.yml
+++ b/.github/workflows/conda_test.yml
@@ -23,7 +23,7 @@ jobs:
       - name: Setup environment
         shell: bash -l {0}
         run: |
-            git clone --depth 1 -b develop https://github.com/NOAA-ORR-ERD/adios_oil_database.git
+            git clone --depth 1 -b develop https://github.com/NOAA-ORR-ERD/adios_oil_database.git oil_database
             conda install -y mamba
             cd ./py_gnome
             echo "Setting up conda environment"

From 88f55bf65ca76a239ef75bdc9f6f1dd4778094a9 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Mon, 13 May 2024 04:55:34 -0700
Subject: [PATCH 75/99] Don't test Ubuntu in the matrix yet.

---
 .github/workflows/conda_test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/conda_test.yml b/.github/workflows/conda_test.yml
index 87eaeb829..3a6a6f134 100644
--- a/.github/workflows/conda_test.yml
+++ b/.github/workflows/conda_test.yml
@@ -7,7 +7,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
         matrix:
-            os: ["ubuntu-latest", "windows-latest","macos-latest"]
+            #os: ["ubuntu-latest", "windows-latest","macos-latest"]
+            os: ["windows-latest","macos-latest"]
             pyver: ["3.9", "3.10", "3.11"]
     steps:
       - uses: actions/checkout@v4

From be535a47d8ae692480a744ae59ed5efed6417b08 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Tue, 14 May 2024 12:38:42 -0700
Subject: [PATCH 76/99] CI: test_pygnome_windows: install oil_database package
 as a prerequisite.

---
 .gitlab-ci.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 50e19ae9a..632fb8bab 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -169,6 +169,9 @@ test_pygnome_windows:
                                           --file conda_requirements_test.txt
                                           --file ../oil_database/adios_db/conda_requirements.txt
 
+    # install adios_db
+    - pip install ../oil_database/adios_db/
+
     - echo "Building PyGNOME"
     # If you want verbose output including the compiler/linker commands,
     # run the following command:

From 1adb07fdf73c816e067615807d7d9ee0c7b15d3d Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 16 May 2024 11:59:50 -0700
Subject: [PATCH 77/99] CI: Build a wheel file that is tagged generally to
 python 3.x.  This will be flexible enough to match our requirements of
 python>=3.9,<=3.12

---
 .gitlab-ci.yml          | 18 ++++++++++++++----
 py_gnome/pyproject.toml |  2 ++
 2 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 632fb8bab..27da77adb 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -52,9 +52,15 @@ compile_pygnome:
     # install adios_db
     - pip install ../oil_database/adios_db/
 
-    # install pygnome
-    #python -m build --no-isolation
-    - pip install ./
+    # Install pygnome
+    # If you want verbose output including the compiler/linker commands,
+    # run the following command:
+    #   python -m build --no-isolation --config-setting cmake.verbose=true
+    #
+    # And there may be times we want to build a wheel file (.whl)
+    # The following command will build a wheel in the current directory:
+    #   python -m pip wheel ./
+    - python -m pip install ./
 
     # need extra requirements for the docs
     - conda install -y --file conda_requirements_docs.txt
@@ -172,10 +178,14 @@ test_pygnome_windows:
     # install adios_db
     - pip install ../oil_database/adios_db/
 
-    - echo "Building PyGNOME"
+    # Install pygnome
     # If you want verbose output including the compiler/linker commands,
     # run the following command:
     #   python -m build --no-isolation --config-setting cmake.verbose=true
+    #
+    # And there may be times we want to build a wheel file (.whl)
+    # The following command will build a wheel in the current directory:
+    #   python -m pip wheel ./
     - python -m pip install ./
 
     - cd ./tests/unit_tests
diff --git a/py_gnome/pyproject.toml b/py_gnome/pyproject.toml
index 35d131eb8..c48d4366b 100644
--- a/py_gnome/pyproject.toml
+++ b/py_gnome/pyproject.toml
@@ -52,5 +52,7 @@ include = ["gnome*"]  # package names should match these glob patterns (["*"] by
 # exclude = ["my_package.tests*"]  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
+[tool.scikit-build]
+wheel.py-api = "py3"
 
 # [project.optional-dependencies]

From 22a4ebf339e274be0c7c2e26109a4a7fad4021dc Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 16 May 2024 13:17:08 -0700
Subject: [PATCH 78/99] GitHub: Try to save a wheel file as a downloadable
 artifact.

---
 .github/workflows/conda_test.yml | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/.github/workflows/conda_test.yml b/.github/workflows/conda_test.yml
index 3a6a6f134..249c00527 100644
--- a/.github/workflows/conda_test.yml
+++ b/.github/workflows/conda_test.yml
@@ -45,6 +45,22 @@ jobs:
         run: |
             cd ./py_gnome/tests/unit_tests
             pytest --runslow
+      - name: Build wheel file
+        shell: bash -l {0}
+        run: |
+            cd ./py_gnome
+            python -m pip wheel ./
+      - name: Copy files to artifact folder
+        shell: bash -l {0}
+        run: |
+            mkdir installable_wheel
+            cp ./py_gnome/*.whl installable_wheel
+            cp ./py_gnome/conda_requirements.txt installable_wheel
+      - name: Upload Artifact
+        uses: actions/upload-artifact@v4
+        with: 
+          name: installable-wheel
+          path: installable_wheel
 
   lint:
     name: Flake8 linting

From 0f7ffdcd22f5f5fa088aaeeed854813320b20c4d Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 16 May 2024 13:29:42 -0700
Subject: [PATCH 79/99] GitHub: downloadable artifact name needs to be unique
 to our actions matrix.

---
 .github/workflows/conda_test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/conda_test.yml b/.github/workflows/conda_test.yml
index 249c00527..d2176d21b 100644
--- a/.github/workflows/conda_test.yml
+++ b/.github/workflows/conda_test.yml
@@ -59,8 +59,8 @@ jobs:
       - name: Upload Artifact
         uses: actions/upload-artifact@v4
         with: 
-          name: installable-wheel
-          path: installable_wheel
+          name: installable-wheel-${{ matrix.os }}-Py${{ matrix.pyver }}
+          path: installable_wheel_${{ matrix.os }}_Py${{ matrix.pyver }}
 
   lint:
     name: Flake8 linting

From 0cc0e973c0052e0e810c144832b961f2ccb8a5d8 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 16 May 2024 13:43:50 -0700
Subject: [PATCH 80/99] GitHub: bug: Artifact directory name not consistently
 named.

---
 .github/workflows/conda_test.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/conda_test.yml b/.github/workflows/conda_test.yml
index d2176d21b..6abc2b5bc 100644
--- a/.github/workflows/conda_test.yml
+++ b/.github/workflows/conda_test.yml
@@ -53,9 +53,9 @@ jobs:
       - name: Copy files to artifact folder
         shell: bash -l {0}
         run: |
-            mkdir installable_wheel
-            cp ./py_gnome/*.whl installable_wheel
-            cp ./py_gnome/conda_requirements.txt installable_wheel
+            mkdir installable_wheel_${{ matrix.os }}_Py${{ matrix.pyver }}
+            cp ./py_gnome/*.whl installable_wheel_${{ matrix.os }}_Py${{ matrix.pyver }}
+            cp ./py_gnome/conda_requirements.txt installable_wheel_${{ matrix.os }}_Py${{ matrix.pyver }}
       - name: Upload Artifact
         uses: actions/upload-artifact@v4
         with: 

From fd5bb89462c5b5642a782935d3126ee2f1d1b54a Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 16 May 2024 13:48:17 -0700
Subject: [PATCH 81/99] GitHub: bug: Make sure python version isn't getting
 clobbered setting up the environment.

---
 .github/workflows/conda_test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/conda_test.yml b/.github/workflows/conda_test.yml
index 6abc2b5bc..4b29ef4ce 100644
--- a/.github/workflows/conda_test.yml
+++ b/.github/workflows/conda_test.yml
@@ -28,7 +28,8 @@ jobs:
             conda install -y mamba
             cd ./py_gnome
             echo "Setting up conda environment"
-            mamba install -y --file conda_requirements.txt \
+            mamba install -y python=${{ matrix.pyver }}  \
+                             --file conda_requirements.txt \
                              --file conda_requirements_build.txt \
                              --file conda_requirements_test.txt \
                              --file ../oil_database/adios_db/conda_requirements.txt

From 183e6dacdfefd2340cdde91e3122687cfba88796 Mon Sep 17 00:00:00 2001
From: Caitlin O'Connor <caitlin.oconnor@noaa.gov>
Date: Mon, 20 May 2024 13:11:03 -0700
Subject: [PATCH 82/99] error message for invalid cats ref pt

---
 lib_gnome/CATSMover_c.cpp       |  1 +
 py_gnome/gnome/movers/movers.py | 27 +++++++++++++++++----------
 2 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/lib_gnome/CATSMover_c.cpp b/lib_gnome/CATSMover_c.cpp
index e96aa352c..44bc63a93 100644
--- a/lib_gnome/CATSMover_c.cpp
+++ b/lib_gnome/CATSMover_c.cpp
@@ -303,6 +303,7 @@ OSErr CATSMover_c::PrepareForModelStep(const Seconds &model_time,
 	err = this->ComputeVelocityScale(model_time);
 	if (err)
 		printError("An error occurred in TCATSMover::PrepareForModelStep");
+		return err;
 
 	// in m/s
 	//note: DIVIDED by timestep because this is later multiplied by the timestep
diff --git a/py_gnome/gnome/movers/movers.py b/py_gnome/gnome/movers/movers.py
index d8ee62d4f..5e55a78ba 100644
--- a/py_gnome/gnome/movers/movers.py
+++ b/py_gnome/gnome/movers/movers.py
@@ -359,16 +359,23 @@ def prepare_for_model_step(self, sc, time_step, model_time_datetime):
                                                   uncertain_spill_count,
                                                   uncertain_spill_size)
             except OSError as e:
-                msg = ('No available data in the time interval '
-                       'that is being modeled\n'
-                       '\tModel time: {}\n'
-                       '\tData available from {} to {}\n'
-                       '\tMover: {} of type {}\n'
-                       '\tError: {}'
-                       .format(model_time_datetime,
-                               self.data_start, self.data_stop,
-                               self.name, self.__class__,
-                               str(e)))
+                if "reference point" in str(e):
+                    msg = ('Reference point not valid '
+                           '\tMover: {} of type {}\n'
+                           '\tError: {}'
+                           .format(self.name, self.__class__,
+                                   str(e)))
+                else:
+                    msg = ('No available data in the time interval '
+                           'that is being modeled\n'
+                           '\tModel time: {}\n'
+                           '\tData available from {} to {}\n'
+                           '\tMover: {} of type {}\n'
+                           '\tError: {}'
+                           .format(model_time_datetime,
+                                   self.data_start, self.data_stop,
+                                   self.name, self.__class__,
+                                   str(e)))
 
                 self.logger.error(msg)
                 raise RuntimeError(msg)

From bdd204864324d1315c9826a3b827de0cc33114ca Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Wed, 22 May 2024 14:39:34 -0700
Subject: [PATCH 83/99] CI: test_pygnome_windows: disable cache for this task.

---
 .gitlab-ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 27da77adb..7cd95f98b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -116,6 +116,7 @@ test_pygnome_windows:
     - windows
     - visual-studio-22
   allow_failure: true
+  cache: []
   before_script:
     - echo $CI_PIPELINE_ID
 

From f9e9659f96c200e3f9845d0838f18aa45dd736c6 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 23 May 2024 10:46:44 -0700
Subject: [PATCH 84/99] Code cleanup on the hull utility module.

---
 py_gnome/gnome/utilities/hull.py | 65 ++++++++++++++++++++------------
 1 file changed, 40 insertions(+), 25 deletions(-)

diff --git a/py_gnome/gnome/utilities/hull.py b/py_gnome/gnome/utilities/hull.py
index 7b96f5072..405b0a4a6 100644
--- a/py_gnome/gnome/utilities/hull.py
+++ b/py_gnome/gnome/utilities/hull.py
@@ -1,46 +1,55 @@
 import geopandas as gpd
-import pandas as pd
-import numpy as np
 from shapely.geometry import Polygon, MultiPolygon, Point, MultiPoint, LineString
-from shapely import concave_hull, union_all, buffer
+from shapely import concave_hull, union_all
+
 
 # Buffer by a number of meters
 def buffer_hull(this_hull, buffer_distance=1):
-    schema = {'geometry':[this_hull]}
-    geodataframe = gpd.GeoDataFrame(schema, crs='epsg:4326', geometry='geometry')
+    schema = {'geometry': [this_hull]}
+    geodataframe = gpd.GeoDataFrame(schema, crs='epsg:4326',
+                                    geometry='geometry')
     geodataframe_3857 = geodataframe.to_crs(epsg=3857)
     geodataframe_3857_buffered = geodataframe_3857.buffer(buffer_distance)
     geodataframe_3857_buffered_back_to_4326 = geodataframe_3857_buffered.to_crs(epsg=4326)
     return geodataframe_3857_buffered_back_to_4326[0]
 
+
 def calculate_hull(spill_container, ratio=0.5, allow_holes=False,
                    separate_by_spill=False):
     hulls_found = []
     if separate_by_spill:
         # Make a dataframe
-        schema = {'positions':[Point(point) for point in spill_container['positions']],
-                  'spill_num':spill_container['spill_num']}
-        data_frame = gpd.GeoDataFrame(schema, crs='epsg:4326', geometry='positions')
+        schema = {'positions': [Point(point)
+                                for point in spill_container['positions']],
+                  'spill_num': spill_container['spill_num']}
+        data_frame = gpd.GeoDataFrame(schema, crs='epsg:4326',
+                                      geometry='positions')
         spill_nums = data_frame['spill_num'].unique()
         for spill_num in spill_nums:
             this_spill = data_frame[data_frame['spill_num'] == spill_num]
-            this_mpt = MultiPoint([Point(point) for point in this_spill['positions']])
-            this_hull = concave_hull(this_mpt, ratio=ratio, allow_holes=allow_holes)
-            if (isinstance(this_hull, Point) or isinstance(this_hull, LineString)):
+            this_mpt = MultiPoint([Point(point)
+                                   for point in this_spill['positions']])
+            this_hull = concave_hull(this_mpt, ratio=ratio,
+                                     allow_holes=allow_holes)
+            if (isinstance(this_hull, Point) or
+                    isinstance(this_hull, LineString)):
                 this_hull = buffer_hull(this_hull)
             if (isinstance(this_hull, Polygon) or
-                isinstance(this_hull, MultiPolygon)):
+                    isinstance(this_hull, MultiPolygon)):
                 hulls_found.append(this_hull)
     else:
         # We want a hull around everything
-        schema = {'positions':[Point(point) for point in spill_container['positions']]}
+        schema = {'positions': [Point(point)
+                                for point in spill_container['positions']]}
         data_frame = gpd.GeoDataFrame(schema, crs='epsg:4326')
-        this_mpt = MultiPoint([Point(point) for point in spill_container['positions']])
-        this_hull = concave_hull(this_mpt, ratio=ratio, allow_holes=allow_holes)
+        this_mpt = MultiPoint([Point(point)
+                               for point in spill_container['positions']])
+        this_hull = concave_hull(this_mpt, ratio=ratio,
+                                 allow_holes=allow_holes)
         if (isinstance(this_hull, Point) or isinstance(this_hull, LineString)):
             this_hull = buffer_hull(this_hull)
         if (isinstance(this_hull, Polygon) or
-            isinstance(this_hull, MultiPolygon)):
+                isinstance(this_hull, MultiPolygon)):
             hulls_found.append(this_hull)
     final_geom = union_all(hulls_found)
     return final_geom if (isinstance(final_geom, Polygon) or
@@ -48,7 +57,7 @@ def calculate_hull(spill_container, ratio=0.5, allow_holes=False,
 
 
 # Cutoffs defined in a structure like the following (by spill_num):
-#cutoff_struct = {1: {'param': 'mass',
+# cutoff_struct = {1: {'param': 'mass',
 #                     'cutoffs': [{'cutoff': 100,
 #                                  'label': 'low'},
 #                                 {'cutoff': 500,
@@ -75,8 +84,9 @@ def calculate_contours(spill_container, cutoff_struct=None,
     # The spills requested are the keys
     spills = cutoff_struct.keys()
     # Make a dataframe
-    schema = {'positions':[Point(point) for point in spill_container['positions']],
-              'spill_num':spill_container['spill_num'],
+    schema = {'positions': [Point(point)
+                            for point in spill_container['positions']],
+              'spill_num': spill_container['spill_num'],
               'mass': spill_container['mass'],
               'age': spill_container['age'],
               'status_codes': spill_container['status_codes']}
@@ -89,7 +99,8 @@ def calculate_contours(spill_container, cutoff_struct=None,
         schema['frac_water'] = spill_container['frac_water']
     if 'density' in spill_container:
         schema['density'] = spill_container['density']
-    data_frame = gpd.GeoDataFrame(schema, crs='epsg:4326', geometry='positions')
+    data_frame = gpd.GeoDataFrame(schema, crs='epsg:4326',
+                                  geometry='positions')
     for spill_num in spills:
         this_spill = data_frame[data_frame['spill_num'] == spill_num]
         this_struct = cutoff_struct[spill_num]
@@ -99,19 +110,23 @@ def calculate_contours(spill_container, cutoff_struct=None,
                 # First one... we just do anything less than the current cutoff
                 this_contour_set = this_spill[this_spill[param] <= cutoff['cutoff']]
             elif idx == len(this_struct['cutoffs'])-1:
-                # Last one... we just do anything greater than the previous cutoff
+                # Last one... we just do anything greater than the
+                # previous cutoff
                 this_contour_set = this_spill[this_spill[param] >= this_struct['cutoffs'][idx-1]['cutoff']]
             else:
                 # Else we bracket it...
                 this_contour_set = this_spill[this_spill[param] <= cutoff['cutoff']]
                 this_contour_set = this_contour_set[this_contour_set[param] >= this_struct['cutoffs'][idx-1]['cutoff']]
             if len(this_contour_set['positions']) > 0:
-                this_contour_mpt = MultiPoint([Point(point) for point in this_contour_set['positions']])
-                this_hull = concave_hull(this_contour_mpt, ratio=ratio, allow_holes=allow_holes)
-                if (isinstance(this_hull, Point) or isinstance(this_hull, LineString)):
+                this_contour_mpt = MultiPoint([Point(point) for point in
+                                               this_contour_set['positions']])
+                this_hull = concave_hull(this_contour_mpt, ratio=ratio,
+                                         allow_holes=allow_holes)
+                if (isinstance(this_hull, Point)
+                        or isinstance(this_hull, LineString)):
                     this_hull = buffer_hull(this_hull)
                 if (isinstance(this_hull, Polygon) or
-                    isinstance(this_hull, MultiPolygon)):
+                        isinstance(this_hull, MultiPolygon)):
                     contours_found.append({'spill_num': spill_num,
                                            'cutoff': cutoff['cutoff'],
                                            'cutoff_id': cutoff['cutoff_id'],

From 6ff7ddc1ef41d40263556405476fc6485d321212 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 23 May 2024 10:47:14 -0700
Subject: [PATCH 85/99] CI: new_build is no longer a side branch.

---
 .gitlab-ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7cd95f98b..82f315976 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -197,7 +197,6 @@ build_develop:
   stage: build
   only:
     - develop
-    - new_build
   tags:
     - shell
     - build

From 014640e80528a8b7f63f122da84bd850ed3976b6 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 23 May 2024 12:01:51 -0700
Subject: [PATCH 86/99] Code cleanup on a number of utility modules.

---
 py_gnome/gnome/utilities/rand.py              |  26 ++-
 py_gnome/gnome/utilities/save_updater.py      | 103 +++++++-----
 py_gnome/gnome/utilities/schema_decorator.py  |   9 +-
 .../utilities/serializable_demo_objects.py    |  37 +++--
 py_gnome/gnome/utilities/shapefile_builder.py | 155 +++++++++++-------
 .../gnome/utilities/surface_concentration.py  |  42 +++--
 py_gnome/gnome/utilities/time_utils.py        |   1 -
 py_gnome/gnome/utilities/transforms.py        |  40 ++---
 8 files changed, 230 insertions(+), 183 deletions(-)

diff --git a/py_gnome/gnome/utilities/rand.py b/py_gnome/gnome/utilities/rand.py
index 64e7c9b83..6603ff9ce 100644
--- a/py_gnome/gnome/utilities/rand.py
+++ b/py_gnome/gnome/utilities/rand.py
@@ -11,13 +11,10 @@
 import random
 
 
-def random_with_persistance(
-    low,
-    high,
-    array=None,  # update this array, if provided
-    persistence=None,
-    time_step=1.,
-    ):
+def random_with_persistance(low, high,
+                            array=None,  # update this array, if provided
+                            persistence=None,
+                            time_step=1.):
     """
     Used by gnome to generate a randomness between low and high, which is
     persistent for duration time_step
@@ -45,7 +42,6 @@ def random_with_persistance(
           should also be the same length array, list or tuple. Give
           all 3 parameters for each element of the array.
     """
-
     # make copies since we don't want to change the original arrays
     low = np.copy(low)
     high = np.copy(high)
@@ -55,7 +51,7 @@ def random_with_persistance(
     else:
         if not isinstance(array, np.ndarray):
             raise ValueError("If an 'array' is provided for computed values,"
-                    " it must be a numpy array")
+                             " it must be a numpy array")
 
     # exceptions
     len_msg = ("Length of 'low', 'high' and 'persistence' arrays"
@@ -71,7 +67,8 @@ def random_with_persistance(
 
     if np.any(high < low):
         raise ValueError('The lower bound for random_with_persistance must be '
-                         'less than or equal to upper bound for all array elements')
+                         'less than or equal to upper bound '
+                         'for all array elements')
 
     if np.all(low == high):
         array[:] = low[:]
@@ -90,8 +87,8 @@ def random_with_persistance(
         assume any persistence greater than 1 hour is meant to be infinite
         interface should only allow 15 minute or infinite
         """
-        #u_mask = (persistence > 0) # update mask for values to be changed
-        u_mask = (persistence > 0) & (persistence <= 900) # update mask for values to be changed
+        # update mask for values to be changed
+        u_mask = (persistence > 0) & (persistence <= 900)
 
         if np.any(u_mask):
             if np.any(persistence[u_mask] != abs(time_step)):
@@ -104,7 +101,9 @@ def random_with_persistance(
                 readable.
                 """
                 orig = high[u_mask] - low[u_mask]
-                l__range = orig * np.sqrt(persistence[u_mask] / float(abs(time_step)))
+                l__range = orig * np.sqrt(
+                    persistence[u_mask] / float(abs(time_step))
+                )
                 mean = (high[u_mask] + low[u_mask]) / 2.
 
                 # update the bounds for generating the random number
@@ -123,7 +122,6 @@ def seed(seed=1):
     :param seed: Random number generator should be seeded by this value.
         Default is 1
     """
-
     cy_helpers.srand(seed)
     random.seed(seed)
     np.random.seed(seed)
diff --git a/py_gnome/gnome/utilities/save_updater.py b/py_gnome/gnome/utilities/save_updater.py
index e26775892..5087ba6d1 100644
--- a/py_gnome/gnome/utilities/save_updater.py
+++ b/py_gnome/gnome/utilities/save_updater.py
@@ -1,13 +1,15 @@
-# Updates a save loaded using pygnome.Model to the latest version
-# !!!!Update the version number in gnome.gnomeobject to be consistent with versioning here
-
-import json
-import logging
-import glob
-import sys
-import contextlib
+"""
+Updates a save loaded using pygnome.Model to the latest version
+!!!!Update the version number in gnome.gnomeobject to be consistent
+with versioning here
+"""
 import os
+import sys
 import re
+import glob
+import logging
+import contextlib
+import json
 import zipfile
 from pathlib import Path
 
@@ -20,14 +22,14 @@
 ]
 
 NON_WEATHERING_DICT = {
- "obj_type": "gnome.spill.substance.NonWeatheringSubstance",
- "id": "dummy-id-from-save_updater",
- "name": "NonWeatheringSubstance_99",
- "initializers": [
-  "InitWindages_99.json"
- ],
- "is_weatherable": False,
- "standard_density": 1000.0
+    "obj_type": "gnome.spill.substance.NonWeatheringSubstance",
+    "id": "dummy-id-from-save_updater",
+    "name": "NonWeatheringSubstance_99",
+    "initializers": [
+        "InitWindages_99.json"
+    ],
+    "is_weatherable": False,
+    "standard_density": 1000.0
 }
 
 # if needed:
@@ -42,6 +44,7 @@
 #  "name": "InitWindages_99"
 # }
 
+
 @contextlib.contextmanager
 def remember_cwd(new_wd):
     curdir = os.getcwd()
@@ -54,9 +57,10 @@ def remember_cwd(new_wd):
 
 def update_savefile(save_directory):
 
-    if not isinstance(save_directory, str) or not os.path.isdir(save_directory):
-        raise ValueError('Must unzip save to directory in order to upgrade it to '
-                         'the latest version')
+    if (not isinstance(save_directory, str) or
+            not os.path.isdir(save_directory)):
+        raise ValueError('Must unzip save to directory in order to upgrade it '
+                         'to the latest version')
 
     messages = []
     errors = []
@@ -88,9 +92,9 @@ def update_savefile(save_directory):
 
 def v0tov1(messages, errors):
     '''
-    Takes a zipfile containing no version.txt and up-converts it to 'version 1'.
-    This functions purpose is to upgrade save files to maintain compatibility
-    after the SpillRefactor upgrades.
+    Takes a zipfile containing no version.txt and up-converts it
+    to 'version 1'.  This function's purpose is to upgrade save files to
+    maintain compatibility after the SpillRefactor upgrades.
     '''
     def Substance_from_ElementType(et_json, water):
         '''
@@ -103,8 +107,9 @@ def Substance_from_ElementType(et_json, water):
                 init['obj_type'] = init['obj_type'].replace('.elements.', '.')
         if 'substance' not in et_json:
             '''
-            Note the id of the new cstructs. The ID IS required at this stage, because
-            the load process will use it later to establish references between objects
+            Note the id of the new cstructs. The ID IS required at this stage,
+            because the load process will use it later to establish references
+            between objects
             '''
             substance = NON_WEATHERING_DICT
             substance["initializers"] = inits
@@ -212,9 +217,14 @@ def v1tov2(messages, errors):
                     oils.append(fname)
                     # See if it can be used with the current GnomeOil
                     try:
+                        # I don't know if this is absolutely necessary,
+                        # but we import this locally so as to not have a
+                        # global dependency on any external oil packages.
+                        from gnome.spills.gnome_oil import GnomeOil
                         GnomeOil(**json_)
                     except Exception:
-                        # can't be used with GnomeOIl: replace with NonWeathering
+                        # Can't be used with GnomeOIl: replace with
+                        # NonWeathering
                         log.info(f"Oil: {json_['name']} is not longer valid\n"
                                  "You will need re-load an oil, which can be "
                                  "obtained from The ADIOS Oil Database:\n"
@@ -237,7 +247,8 @@ def v1tov2(messages, errors):
                     if "InitWindages" in init_js["obj_type"]:
                         json_['windage_range'] = init_js['windage_range']
                         json_['windage_persist'] = init_js['windage_persist']
-                        json.dump(json_, open(fname, 'w', encoding='utf-8'), indent=4)
+                        json.dump(json_, open(fname, 'w', encoding='utf-8'),
+                                  indent=4)
                         files_to_remove.append(wind_init)
 
     with open('version.txt', 'w', encoding='utf-8') as vers_file:
@@ -249,6 +260,7 @@ def v1tov2(messages, errors):
     messages.append('**Update from v1 to v2 successful**')
     return messages, errors
 
+
 def v2tov3(messages, errors):
     '''
     Takes a zipfile containing version 2 and up-converts it
@@ -267,7 +279,7 @@ def v2tov3(messages, errors):
     spills = []  # things with a "gnome.spill" in the path
     movers = []  # current_movers, CurrentMover
     wind_movers = []  # wind_movers, WindMover
-    srs = [] # SpatialRelease
+    srs = []  # SpatialRelease
     for fname in jsonfiles:
         with open(fname, 'r', encoding='utf-8') as fn:
             json_ = json.load(fn)
@@ -282,12 +294,14 @@ def v2tov3(messages, errors):
                     srs.append((fname, json_))
 
     for fn, sp in spills:
-        sp['obj_type'] = sp['obj_type'].replace('gnome.spill.', 'gnome.spills.')
+        sp['obj_type'] = sp['obj_type'].replace('gnome.spill.',
+                                                'gnome.spills.')
         with open(fn, 'w', encoding='utf-8') as fp:
             json.dump(sp, fp, indent=4)
 
     for fn, sr in srs:
-        sr['obj_type'] = sr['obj_type'].replace('SpatialRelease', 'PolygonRelease')
+        sr['obj_type'] = sr['obj_type'].replace('SpatialRelease',
+                                                'PolygonRelease')
         with open(fn, 'w', encoding='utf-8') as fp:
             json.dump(sr, fp, indent=4)
 
@@ -330,13 +344,14 @@ def v3tov4(messages, errors):
 
     files_to_remove = []
 
-    # search for files which have weathering_data object, added to the files_to_remove list
+    # search for files which have weathering_data object, added to the
+    # files_to_remove list
     for fname in jsonfiles:
             with open(fname, 'r', encoding='utf-8') as fn:
                 json_ = json.load(fn)
                 if 'obj_type' in json_:
-                   if json_['obj_type'] == "gnome.weatherers.weathering_data.WeatheringData":
-                      files_to_remove.append(fname)
+                    if json_['obj_type'] == "gnome.weatherers.weathering_data.WeatheringData":
+                        files_to_remove.append(fname)
 
     # remove weathering_data reference from model file
     for fname in jsonfiles:
@@ -346,7 +361,7 @@ def v3tov4(messages, errors):
                     # this is assuming only one
                     for item in json_['weatherers']:
                         if item in files_to_remove:
-                             json_['weatherers'].remove(item)
+                            json_['weatherers'].remove(item)
                 json.dump(json_, open(fname, 'w', encoding='utf-8'), indent=4)
 
     # remove targeted files
@@ -356,6 +371,7 @@ def v3tov4(messages, errors):
     messages.append('**Update from v3 to v4 successful**')
     return messages, errors
 
+
 def v4tov5(messages, errors):
     '''
     Takes a zipfile containing version 4 and up-converts it
@@ -371,11 +387,10 @@ def v4tov5(messages, errors):
 
     jsonfiles = glob.glob('*.json')
 
-
     # updating the name of spills
     movers = []  # PyCurrentMover --> CurrentMover
-    wind_movers = []  #PyWindMover --> WindMover
-    point_wind_movers = [] #WindMover  --> PointWindMover
+    wind_movers = []  # PyWindMover --> WindMover
+    point_wind_movers = []  # WindMover  --> PointWindMover
     for fname in jsonfiles:
         with open(fname, 'r', encoding='utf-8') as fn:
             json_ = json.load(fn)
@@ -398,7 +413,7 @@ def v4tov5(messages, errors):
                                                 'WindMover')
         with open(fn, 'w', encoding='utf-8') as fp:
             json.dump(mv, fp, indent=4)
-            
+
     for fn, mv in point_wind_movers:
         mv['obj_type'] = mv['obj_type'].replace('WindMover',
                                                 'PointWindMover')
@@ -409,10 +424,10 @@ def v4tov5(messages, errors):
         vers_file.write('5\n')
 
     messages.append('**Update from v4 to v5 successful**')
-    
+
     return messages, errors
-    
-    
+
+
 def extract_zipfile(zip_file, to_folder='.'):
     def work(zf):
         folders = [name for name in zf.namelist()
@@ -441,8 +456,8 @@ def work(zf):
             log.info('Save file contained invalid names. '
                      'Editing extracted json to maintain save file integrity.')
             for jsonfile in glob.glob(os.path.join(to_folder, '*.json')):
-                # if any file name edits were made, references may need to be updated too
-                # otherwise the .json file won't be found
+                # if any file name edits were made, references may need
+                # to be updated too otherwise the .json file won't be found
                 contents = None
                 replaced = False
                 with open(jsonfile, 'r', encoding='utf-8') as jf:
@@ -469,12 +484,12 @@ def sanitize_filename(fname):
     NOTE: this looks a lot like html sanitization
           do we need to remove "<" and ">" from filenames?
 
-          and/or should we replace with a placeholder, rather than simply remove?
+          and/or should we replace with a placeholder,
+          rather than simply remove?
     Also -- maybe replace spaces with underscores ...
     '''
     return re.sub(r'[\\\\/*?:"<>|]', "", fname)
     # return re.sub(r'[\\\\/*?:"<>|]', "", fname).replace(" ", "_")
 
 
-
 all_update_steps = [v0tov1, v1tov2, v2tov3, v3tov4, v4tov5]
diff --git a/py_gnome/gnome/utilities/schema_decorator.py b/py_gnome/gnome/utilities/schema_decorator.py
index 9e9d462a5..541416ce1 100644
--- a/py_gnome/gnome/utilities/schema_decorator.py
+++ b/py_gnome/gnome/utilities/schema_decorator.py
@@ -6,14 +6,11 @@
       for GNOME_ID ?
 """
 
-
-
-
-
 # from future import standard_library
 # standard_library.install_aliases()
 # from builtins import *
 
+
 def serializable(cls):
     """
     make a class serializable
@@ -24,7 +21,5 @@ def serializable(cls):
     print(cls.__name__)
     type("Schema")
     Schema(base_schema.ObjTypeSchema)
-    for attr in cls.__dict__:
+    for _attr in cls.__dict__:
         pass
-
-
diff --git a/py_gnome/gnome/utilities/serializable_demo_objects.py b/py_gnome/gnome/utilities/serializable_demo_objects.py
index 5e50e931b..483f75e6d 100644
--- a/py_gnome/gnome/utilities/serializable_demo_objects.py
+++ b/py_gnome/gnome/utilities/serializable_demo_objects.py
@@ -1,9 +1,16 @@
+'''
+This file is documentation and a demonstration of how to use Schema objects to
+allow Gnome objects to do the following tasks:
+    Save the object to a zip file
+    Load the object from a zip file
+    Get a serialization of the object (JSON)
+    Deserialize a JSON structure into an instance
+    Apply a JSON structure as an update
+'''
+import datetime as dt
 
 import numpy as np
-
 import colander
-import datetime as dt
-
 
 from gnome.persist import base_schema
 from gnome.persist.extend_colander import FilenameSchema
@@ -15,15 +22,6 @@
                                                        TimeseriesData)
 from gnome.gnomeobject import GnomeId
 
-'''
-This file is documentation and a demonstration of how to use Schema objects to
-allow Gnome objects to do the following tasks:
-    Save the object to a zip file
-    Load the object from a zip file
-    Get a serialization of the object (JSON)
-    Deserialize a JSON structure into an instance
-    Apply a JSON structure as an update
-'''
 
 def dates():
     return np.array([dt.datetime(2000, 1, 1, 0),
@@ -32,11 +30,13 @@ def dates():
                      dt.datetime(2000, 1, 1, 6),
                      dt.datetime(2000, 1, 1, 8), ])
 
+
 def series_data():
-    return np.array([1,3,6,10,15])
+    return np.array([1, 3, 6, 10, 15])
+
 
 def series_data2():
-    return np.array([2,6,12,20,30])
+    return np.array([2, 6, 12, 20, 30])
 
 
 class DemoObjSchema(base_schema.ObjTypeSchema):
@@ -80,17 +80,19 @@ class DemoObj(GnomeId):
 
     _schema = DemoObjSchema
 
-    def __init__(self, filename=None, foo_float=None, foo_float_array=None, variable=None, variables=None, **kwargs):
+    def __init__(self, filename=None, foo_float=None, foo_float_array=None,
+                 variable=None, variables=None, **kwargs):
         self.filename = filename
         self.foo_float = 42.0
-        self.foo_float_array = [42.0,84.0]
+        self.foo_float_array = [42.0, 84.0]
         self.variable = variable
         self.variables = variables
         super(DemoObj, self).__init__(**kwargs)
 
     @property
     def timeseries(self):
-        return [(t, self.variable.variables[0].data[i]) for i, t in enumerate(self.variable.time)]
+        return [(t, self.variable.variables[0].data[i])
+                for i, t in enumerate(self.variable.time)]
 
     @classmethod
     def demo(cls):
@@ -102,4 +104,3 @@ def demo(cls):
         )
 
         return DemoObj(variable=tsv, variables=[tsv, tsv.variables[0]])
-
diff --git a/py_gnome/gnome/utilities/shapefile_builder.py b/py_gnome/gnome/utilities/shapefile_builder.py
index e90e86918..9d7ae0fdc 100644
--- a/py_gnome/gnome/utilities/shapefile_builder.py
+++ b/py_gnome/gnome/utilities/shapefile_builder.py
@@ -1,15 +1,12 @@
 """Shapefile Builder"""
 
-import geopandas as gpd
-import os
-import pandas as pd
 import pathlib
-import pyogrio
-from shapely.geometry import Point
 import shutil
-import time
 import warnings
-import zipfile
+
+import geopandas as gpd
+import pandas as pd
+from shapely.geometry import Point
 
 from gnome.utilities.hull import calculate_hull, calculate_contours
 
@@ -17,6 +14,7 @@
 warnings.filterwarnings('ignore', message='.*Possibly due to too larger',
                         category=RuntimeWarning, module='pyogrio')
 
+
 class ShapefileBuilder(object):
     def __init__(self, filename, zip_output=True, **kwargs):
         '''
@@ -54,38 +52,47 @@ def write(self):
             shz_name = self.fullfilename.with_suffix('.shz')
             # Write out the zipped shapefile
             full_gdf.to_file(shz_name, driver='ESRI Shapefile',
-                             engine="pyogrio", geometry_type=self.geometry_type)
+                             engine="pyogrio",
+                             geometry_type=self.geometry_type)
             shutil.move(shz_name, self.fullfilename)
         else:
             # Write out the raw shapefile
             full_gdf.to_file(self.fullfilename, driver='ESRI Shapefile',
-                             engine="pyogrio", geometry_type=self.geometry_type)
+                             engine="pyogrio",
+                             geometry_type=self.geometry_type)
         return self.fullfilename
 
     @property
     def filename(self):
         return self.fullfilename
 
+
 class ParticleShapefileBuilder(ShapefileBuilder):
     def __init__(self, filename, zip_output=True, **kwargs):
         '''
         :param filename: Full path and basename of the shape file.
         :param zip: If we should zip the final shapefile results.
         '''
-        super(ParticleShapefileBuilder, self).__init__(filename, zip_output, **kwargs)
+        super(ParticleShapefileBuilder, self).__init__(filename, zip_output,
+                                                       **kwargs)
 
     def append(self, sc):
-        """Given a spill container, write out the current particle data to a data frame"""
+        """
+        Given a spill container, write out the current particle data to a
+        data frame
+        """
         super(ParticleShapefileBuilder, self).append(sc)
-        frame_data = {'LE_id': sc['id'],
-                      'Spill_id': sc['spill_num'],
-                      'Depth': [pos[2] for pos in sc['positions']],
-                      'Mass': sc['mass'],
-                      'Age': sc['age'],
-                      'StatusCode': sc['status_codes'],
-                      'Time': sc.current_time_stamp.strftime('%Y-%m-%dT%H:%M:%S'),
-                      'Position': [Point(pt) for pt in sc['positions']]
+        frame_data = {
+            'LE_id': sc['id'],
+            'Spill_id': sc['spill_num'],
+            'Depth': [pos[2] for pos in sc['positions']],
+            'Mass': sc['mass'],
+            'Age': sc['age'],
+            'StatusCode': sc['status_codes'],
+            'Time': sc.current_time_stamp.strftime('%Y-%m-%dT%H:%M:%S'),
+            'Position': [Point(pt) for pt in sc['positions']]
         }
+
         # Some elements are optional... check those here:
         if 'surface_concentration' in sc and not sc.uncertain:
             frame_data['Surf_Conc'] = sc['surface_concentration']
@@ -95,7 +102,8 @@ def append(self, sc):
             frame_data['FracWater'] = sc['frac_water']
         if 'density' in sc:
             frame_data['Density'] = sc['density']
-        gdf = gpd.GeoDataFrame(frame_data, crs='epsg:4326', geometry='Position')
+        gdf = gpd.GeoDataFrame(frame_data, crs='epsg:4326',
+                               geometry='Position')
         # If we have surface concentration sort by it...
         if 'surface_concentration' in sc and not sc.uncertain:
             gdf = gdf.loc[gdf['Surf_Conc'].sort_values().index]
@@ -111,33 +119,46 @@ def write(self):
             self.geometry_type = 'Point'
         super(ParticleShapefileBuilder, self).write()
 
+
 def area_in_meters(this_hull):
-    schema = {'geometry':[this_hull]}
-    geodataframe = gpd.GeoDataFrame(schema, crs='epsg:4326', geometry='geometry')
+    schema = {'geometry': [this_hull]}
+    geodataframe = gpd.GeoDataFrame(schema, crs='epsg:4326',
+                                    geometry='geometry')
     geodataframe_3857 = geodataframe.to_crs(epsg=3857)
     return geodataframe_3857.area[0]
 
+
 class BoundaryShapefileBuilder(ShapefileBuilder):
     def __init__(self, filename, zip_output=True, **kwargs):
         '''
         :param filename: Full path and basename of the shape file.
         :param zip: If we should zip the final shapefile results.
         '''
-        super(BoundaryShapefileBuilder, self).__init__(filename, zip_output, **kwargs)
-
-    def append(self, sc, separate_by_spill=True, hull_ratio=0.5, hull_allow_holes=False):
-        """Given a spill container, write out the current boundary data to a data frame"""
+        super(BoundaryShapefileBuilder, self).__init__(filename, zip_output,
+                                                       **kwargs)
+
+    def append(self, sc, separate_by_spill=True, hull_ratio=0.5,
+               hull_allow_holes=False):
+        """
+        Given a spill container, write out the current boundary data to a
+        data frame
+        """
         super(BoundaryShapefileBuilder, self).append(sc)
         # Calculate a concave hull
-        hull = calculate_hull(sc, separate_by_spill=separate_by_spill, ratio=hull_ratio,
+        hull = calculate_hull(sc, separate_by_spill=separate_by_spill,
+                              ratio=hull_ratio,
                               allow_holes=hull_allow_holes)
-        # Only process it if we get a hull back.  There are cases where the hull is not
-        # a polygon, and we skip those.
+        # Only process it if we get a hull back.
+        # There are cases where the hull is not a polygon, and we skip those.
         if hull:
-            frame_data = {'geometry': [hull],
-                          'area': [area_in_meters(hull)],
-                          'time': sc.current_time_stamp.strftime('%Y-%m-%dT%H:%M:%S')}
-            gdf = gpd.GeoDataFrame(frame_data, crs='epsg:4326', geometry='geometry')
+            frame_data = {
+                'geometry': [hull],
+                'area': [area_in_meters(hull)],
+                'time': sc.current_time_stamp.strftime('%Y-%m-%dT%H:%M:%S')
+            }
+
+            gdf = gpd.GeoDataFrame(frame_data, crs='epsg:4326',
+                                   geometry='geometry')
             self.data_frames.append(gdf)
 
     def write(self):
@@ -150,33 +171,39 @@ def write(self):
             self.geometry_type = 'Polygon'
         super(BoundaryShapefileBuilder, self).write()
 
+
 class ContourShapefileBuilder(ShapefileBuilder):
     def __init__(self, filename, zip_output=True, **kwargs):
         '''
         :param filename: Full path and basename of the shape file.
         :param zip: If we should zip the final shapefile results.
         '''
-        super(ContourShapefileBuilder, self).__init__(filename, zip_output, **kwargs)
-
-    def append(self, sc, cutoff_struct=None, hull_ratio=0.5, hull_allow_holes=False):
-        """Given a spill container, write out the contours based on the cutoffs provided"""
+        super(ContourShapefileBuilder, self).__init__(filename, zip_output,
+                                                      **kwargs)
+
+    def append(self, sc, cutoff_struct=None, hull_ratio=0.5,
+               hull_allow_holes=False):
+        """
+        Given a spill container, write out the contours based on the
+        cutoffs provided
+        """
         # Cutoffs defined in a structure like the following (by spill_num):
-        #cutoff_struct = {1: {'param': 'mass',
-        #                     'cutoffs': [{'cutoff': 100,
-        #                                  'label': 'low'},
-        #                                 {'cutoff': 500,
-        #                                  'label': 'medium'},
-        #                                 {'cutoff': 1000,
-        #                                  'label': 'heavy'}]},
-        #                 2: {'param': 'surf_conc',
-        #                     'cutoffs': [{'cutoff': 0.3,
-        #                                  'label': 'low'},
-        #                                 {'cutoff': 0.5,
-        #                                  'label': 'medium'},
-        #                                 {'cutoff': 1.0,
-        #                                  'label': 'high'}]
-        #                     }
-        #                 }
+        # cutoff_struct = {1: {'param': 'mass',
+        #                      'cutoffs': [{'cutoff': 100,
+        #                                   'label': 'low'},
+        #                                  {'cutoff': 500,
+        #                                   'label': 'medium'},
+        #                                  {'cutoff': 1000,
+        #                                   'label': 'heavy'}]},
+        #                  2: {'param': 'surf_conc',
+        #                      'cutoffs': [{'cutoff': 0.3,
+        #                                   'label': 'low'},
+        #                                  {'cutoff': 0.5,
+        #                                   'label': 'medium'},
+        #                                  {'cutoff': 1.0,
+        #                                   'label': 'high'}]
+        #                      }
+        #                  }
         # The cutoffs are ordered array... low to high
         # First "low" bin is always [data] < cutoffs[current]
         # Middle bins are cutoffs[previous] < [data] < cutoffs[current]
@@ -186,7 +213,8 @@ def append(self, sc, cutoff_struct=None, hull_ratio=0.5, hull_allow_holes=False)
         # Look in the spill container and get a list of spills
         # Make sure they are defined in the cutoffs_per_spill
         # If they are, we loop through each spill
-        #   In each spill we loop through the cutoffs and create subsets of the data
+        #   In each spill we loop through the cutoffs and create subsets
+        #   of the data.
         #   Make a hull around each subset
         #   Create a geodataframe based on the array of generated hulls
         #   Append to the data_frames
@@ -196,14 +224,17 @@ def append(self, sc, cutoff_struct=None, hull_ratio=0.5, hull_allow_holes=False)
                                       ratio=hull_ratio,
                                       allow_holes=hull_allow_holes)
         if contours:
-            frame_data = {'geometry': [c['contour'] for c in contours],
-                          'spill_num': [c['spill_num'] for c in contours],
-                          'cutoff': [c['cutoff'] for c in contours],
-                          'cutoff_id': [c['cutoff_id'] for c in contours],
-                          'color': [c['color'] for c in contours],
-                          'label': [c['label'] for c in contours],
-                          'time': sc.current_time_stamp.strftime('%Y-%m-%dT%H:%M:%S')}
-            gdf = gpd.GeoDataFrame(frame_data, crs='epsg:4326', geometry='geometry')
+            frame_data = {
+                'geometry': [c['contour'] for c in contours],
+                'spill_num': [c['spill_num'] for c in contours],
+                'cutoff': [c['cutoff'] for c in contours],
+                'cutoff_id': [c['cutoff_id'] for c in contours],
+                'color': [c['color'] for c in contours],
+                'label': [c['label'] for c in contours],
+                'time': sc.current_time_stamp.strftime('%Y-%m-%dT%H:%M:%S')
+            }
+            gdf = gpd.GeoDataFrame(frame_data, crs='epsg:4326',
+                                   geometry='geometry')
             self.data_frames.append(gdf)
 
     def write(self):
diff --git a/py_gnome/gnome/utilities/surface_concentration.py b/py_gnome/gnome/utilities/surface_concentration.py
index 55ab9137d..1cb0f8ecc 100644
--- a/py_gnome/gnome/utilities/surface_concentration.py
+++ b/py_gnome/gnome/utilities/surface_concentration.py
@@ -1,16 +1,10 @@
 #!/usr/bin/env python
-
 """
 Code to compute surface surface_concentration from particles
 
 Ultimatley, there may be multiple versions of this
 -- with Cython optimizationas and all that.
 """
-
-
-
-
-
 import warnings
 import numpy as np
 from scipy.stats import gaussian_kde
@@ -30,8 +24,8 @@ def compute_surface_concentration(sc, algorithm):
     if algorithm == 'kde':
         surface_conc_kde(sc)
     else:
-        raise ValueError('the only surface concentration algorithm currently supported'
-                         'is "kde"')
+        raise ValueError('the only surface concentration algorithm '
+                         'currently supported is "kde"')
 
 
 def surface_conc_kde(sc):
@@ -49,7 +43,7 @@ def surface_conc_kde(sc):
     spill_num = sc['spill_num']
     sc['surface_concentration'] = np.zeros(spill_num.shape[0],)
     for s in np.unique(spill_num):
-        sid = np.where(spill_num==s)
+        sid = np.where(spill_num == s)
         positions = sc['positions'][sid]
         mass = sc['mass'][sid]
         age = sc['age'][sid]
@@ -57,19 +51,27 @@ def surface_conc_kde(sc):
         lon = positions[:, 0]
         lat = positions[:, 1]
 
-        bin_length = 1*3600 #kde will be calculated on particles 0-6hrs, 6-12hrs,...
+        # kde will be calculated on particles 0-6hrs, 6-12hrs,...
+        bin_length = 1 * 3600
+
         t = age.min()
         max_age = age.max()
 
-        while t<=max_age:
-            id = np.where((age<t+bin_length))[0] #we use all particles < t + bin_length for kernel
+        while t <= max_age:
+            # we use all particles < t + bin_length for kernel
+            id = np.where((age < t + bin_length))[0]
+
             lon_for_kernel = lon[id]
             lat_for_kernel = lat[id]
             age_for_kernel = age[id]
             mass_for_kernel = mass[id]
-            id_bin = np.where(age_for_kernel>=t)[0] #we only calculate pdf for particles in bin
 
-            if len(np.unique(lat_for_kernel))>2 and len(np.unique(lon_for_kernel))>2: # can't compute a kde for less than 3 unique points!
+            # we only calculate pdf for particles in bin
+            id_bin = np.where(age_for_kernel >= t)[0]
+
+            # can't compute a kde for less than 3 unique points!
+            if (len(np.unique(lat_for_kernel)) > 2 and
+                    len(np.unique(lon_for_kernel)) > 2):
                 try:
                     lon0, lat0 = min(lon_for_kernel), min(lat_for_kernel)
                     # FIXME: should use projection code to get this right.
@@ -77,15 +79,19 @@ def surface_conc_kde(sc):
                     y = (lat_for_kernel - lat0) * 111325
                     xy = np.vstack([x, y])
                     if len(np.unique(mass_for_kernel)) > 1:
-                        kernel = gaussian_kde(xy,weights=mass_for_kernel/mass_for_kernel.sum())
+                        kernel = gaussian_kde(
+                            xy,
+                            weights=mass_for_kernel / mass_for_kernel.sum()
+                        )
                     else:
                         kernel = gaussian_kde(xy)
                     if mass_for_kernel.sum() > 0:
-                        c[id[id_bin]] = kernel(xy[:,id_bin]) * mass_for_kernel.sum()
+                        c[id[id_bin]] = kernel(xy[:, id_bin]) * mass_for_kernel.sum()
                     else:
-                        c[id[id_bin]] = kernel(xy[:,id_bin]) * len(mass_for_kernel)
+                        c[id[id_bin]] = kernel(xy[:, id_bin]) * len(mass_for_kernel)
                 except np.linalg.LinAlgError:
-                    warnings.warn("LinAlg error occurred in surface concentration calculations.")
+                    warnings.warn('LinAlg error occurred in '
+                                  'surface concentration calculations.')
             t = t + bin_length
 
         sc['surface_concentration'][sid] = c
diff --git a/py_gnome/gnome/utilities/time_utils.py b/py_gnome/gnome/utilities/time_utils.py
index fa608484c..944872b41 100644
--- a/py_gnome/gnome/utilities/time_utils.py
+++ b/py_gnome/gnome/utilities/time_utils.py
@@ -99,7 +99,6 @@ def date_to_sec(date_times):
         date_times = [date_times.astype(datetime)]
 
     if not isinstance(date_times[0], (datetime, cftime.datetime)):
-    # if not isinstance(date_times[0], datetime):
         raise TypeError('date_to_sec only works on datetime and datetime64 '
                         'objects. Got a: {}'.format(type(date_times[0])))
 
diff --git a/py_gnome/gnome/utilities/transforms.py b/py_gnome/gnome/utilities/transforms.py
index 13f2a66ab..fdd6a0180 100644
--- a/py_gnome/gnome/utilities/transforms.py
+++ b/py_gnome/gnome/utilities/transforms.py
@@ -1,6 +1,7 @@
 
 import numpy as np
 
+
 def r_theta_to_uv_current(r_theta):
     """
     Converts array of current values given with magnitude, direction into
@@ -9,7 +10,8 @@ def r_theta_to_uv_current(r_theta):
     the direction the current moves towards.
 
     :param r_theta: NX2 numpy array containing r = r_theta[:,0],
-                    theta = r_theta[:,1]. Theta is in degrees between 0 and 360.
+                    theta = r_theta[:,1]. Theta is in degrees between
+                    0 and 360.
 
     :returns: NX2 numpy array containing the corresponding uv Cartesian
               velocity vector
@@ -21,8 +23,9 @@ def r_theta_to_uv_current(r_theta):
 
 def uv_to_r_theta_current(uv):
     """
-    Converts array of current values given with (u,v) current values to magnitude,
-    direction. Current from 0 deg is (u,v) = (0,1), from 45 deg (u,v) =
+    Converts array of current values given with (u,v) current values to
+    magnitude, direction.
+    Current from 0 deg is (u,v) = (0,1), from 45 deg (u,v) =
     (1,1) i.e. rotate clockwise from North. In addition, (u,v) represents
     the direction the current blows towards
 
@@ -38,25 +41,25 @@ def uv_to_r_theta_current(uv):
 
 def r_theta_to_uv_wind(r_theta):
     """
-    Converts array of wind values given with magnitude, direction into(u,v) wind
-    values. Wind from 0 deg is (u,v) = (0,-1), from 45 deg (u,v) =
+    Converts array of wind values given with magnitude, direction into(u,v)
+    wind values. Wind from 0 deg is (u,v) = (0,-1), from 45 deg (u,v) =
     (-1,-1) i.e. rotate clockwise from North. In addition,
     (u,v) represents the direction the wind blows towards
 
     :param r_theta: NX2 numpy array containing r = r_theta[:,0],
-                    theta = r_theta[:,1]. Theta is in degrees between 0 and 360.
-    :returns: NX2 numpy array containing the corresponding uv Cartesian velocity
-              vector
+                    theta = r_theta[:,1]. Theta is in degrees between
+                    0 and 360.
+    :returns: NX2 numpy array containing the corresponding uv Cartesian
+              velocity vector
     """
-
     r_theta = np.asarray(r_theta, dtype=np.float64).reshape(-1, 2)
     if np.any(r_theta[:, 1] > 360) or np.any(r_theta[:, 1] < 0):
-        raise ValueError('input angle in r_theta[:,1] must be between 0 and 360'
-                         )
+        raise ValueError('input angle in r_theta[:,1] must be '
+                         'between 0 and 360')
 
     if np.any(r_theta[:, 0] < 0):
-        raise ValueError('input magnitude in r_theta[:,0] must be greater than, equal to 0'
-                         )
+        raise ValueError('input magnitude in r_theta[:,0] must be '
+                         'greater than, equal to 0')
 
     rq = np.array(r_theta)
     rq[:, 1] = np.deg2rad(rq[:, 1])
@@ -88,13 +91,12 @@ def uv_to_r_theta_wind(uv):
     r_theta = np.zeros_like(uv)
     r_theta[:, 0] = np.apply_along_axis(np.linalg.norm, 1, uv)
 
-    # NOTE: Since desired angle is different from the angle that arctan2 outputs;
-    #      the uv array is transformed (multiply by -1) and atan2 is called with (u,v)
-    #      Only to ensure we get the angle per the Wind convention
+    # NOTE: Since desired angle is different from the angle that
+    #       arctan2 outputs; the uv array is transformed (multiply by -1)
+    #       and atan2 is called with (u,v)
+    #       Only to ensure we get the angle per the Wind convention
 
     uv = -1 * uv  # create new uv object
-    r_theta[:, 1] = (np.rad2deg(np.arctan2(uv[:, 0], uv[:, 1])) + 360) % 360  # 0 to 360
+    r_theta[:, 1] = (np.rad2deg(np.arctan2(uv[:, 0], uv[:, 1])) + 360) % 360
 
     return r_theta
-
-

From d186bda3759939043cb59986c339fa23ba7a59db Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Thu, 23 May 2024 13:39:59 -0700
Subject: [PATCH 87/99] Code cleanup on some more utility modules.

---
 py_gnome/gnome/utilities/orderedcollection.py | 67 +++++++++----------
 py_gnome/gnome/utilities/plume.py             |  5 +-
 py_gnome/gnome/utilities/profiledeco.py       |  4 +-
 py_gnome/gnome/utilities/projections.py       | 11 +--
 4 files changed, 37 insertions(+), 50 deletions(-)

diff --git a/py_gnome/gnome/utilities/orderedcollection.py b/py_gnome/gnome/utilities/orderedcollection.py
index 6a2b90ccb..0bfc136da 100644
--- a/py_gnome/gnome/utilities/orderedcollection.py
+++ b/py_gnome/gnome/utilities/orderedcollection.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 
+
 class OrderedCollection(object):
     '''
     Generalized Container for a set of objects of a particular type which
@@ -14,22 +15,22 @@ class OrderedCollection(object):
 
     def __init__(self, elems=None, dtype=None):
         if elems and not isinstance(elems, list):
-            raise TypeError('%s: needs a list of objects'
-                            % self.__class__.__name__)
+            raise TypeError(f'{self.__class__.__name__}: '
+                            'needs a list of objects')
         if not elems:
             elems = []
 
         if not dtype and len(elems) == 0:
-            raise TypeError('%s: specify a data type if list is empty'
-                            % self.__class__.__name__)
+            raise TypeError(f'{self.__class__.__name__}: '
+                            'specify a data type if list is empty')
         elif not dtype:
             self.dtype = type(elems[0])
         else:
             self.dtype = dtype
 
         if not all([isinstance(e, self.dtype) for e in elems]):
-            raise TypeError('%s: needs a list of %s'
-                            % (self.__class__.__name__, self.dtype))
+            raise TypeError(f'{self.__class__.__name__}: '
+                            f'needs a list of {self.dtype}')
 
         # a bunch of Gnome classes have an id property defined, which we will
         # prefer
@@ -38,7 +39,8 @@ def __init__(self, elems=None, dtype=None):
         # is hard to reference as a key
 
         self._elems = elems[:]
-        self._d_index = {self._s_id(elem): idx for idx, elem in enumerate(self._elems)}
+        self._d_index = {self._s_id(elem): idx
+                         for idx, elem in enumerate(self._elems)}
 
         self.callbacks = []
 
@@ -88,20 +90,15 @@ def add(self, elem):
             try:
                 for e in elem:
                     if not isinstance(e, self.dtype):
-                        raise TypeError('{0}:\n'
-                                        'Expected: {1!r}\n'
-                                        'Got: {2!r}\n of type: {3}'.format(self.__class__.__name__,
-                                                                           self.dtype,
-                                                                           e,
-                                                                           type(e)))
+                        raise TypeError(f'{self.__class__.__name__}:\n'
+                                        f'Expected: {self.dtype!r}\n'
+                                        f'Got: {e!r}\n of type: {type(e)}')
                     self.add(e)
             except TypeError:
-                raise TypeError('{0}:\n'
-                                'Expected: {1!r} or an iterable of {1}.\n'
-                                'Got: {2!r}\n of type: {3}'.format(self.__class__.__name__,
-                                                                   self.dtype,
-                                                                   elem,
-                                                                   type(elem)))
+                raise TypeError(f'{self.__class__.__name__}:\n'
+                                f'Expected: {self.dtype!r} '
+                                f'or an iterable of {self.dtype}.\n'
+                                f'Got: {elem!r}\n of type: {type(elem)}')
 
     def append(self, elem):
         self.add(elem)
@@ -136,10 +133,8 @@ def replace(self, ident, new_elem):
         raise exception if 'id' is not found.
         '''
         if not isinstance(new_elem, self.dtype):
-            raise TypeError('{0}: expected {1}, '
-                            'got {2}'.format(self.__class__.__name__,
-                                             self.dtype,
-                                             type(new_elem)))
+            raise TypeError(f'{self.__class__.__name__}: '
+                            f'expected {self.dtype}, got {type(new_elem)}')
 
         if isinstance(ident, int):
             l__key = self._s_id(self._elems[ident])
@@ -173,8 +168,7 @@ def index(self, elem):
                 try:
                     idx = self._d_index[idx]
                 except KeyError:
-                    raise ValueError('{0} is not in OrderedCollection'
-                                    .format(elem))
+                    raise ValueError(f'{elem} is not in OrderedCollection')
             else:
                 idx = self._d_index[elem]
         except KeyError:
@@ -183,8 +177,7 @@ def index(self, elem):
             try:
                 idx = self._d_index[ident]
             except KeyError:
-                raise ValueError('{0} is not in OrderedCollection'
-                                 .format(elem))
+                raise ValueError(f'{elem} is not in OrderedCollection')
 
         return sorted(self._d_index.values()).index(idx)
 
@@ -248,7 +241,7 @@ def __str__(self):
         itemlist = sorted(list(self._d_index.items()), key=lambda x: x[1])
 
         # reference the value in list
-        itemlist = [self._elems[v] for (k, v) in itemlist]
+        itemlist = [self._elems[v] for (_, v) in itemlist]
 
         formatter = '    %s,'
         if len(itemlist) > 12:  # should we abbreviate the list at all?
@@ -306,26 +299,28 @@ def update(self, cstruct, refs=None):
             if isinstance(elem, dict):
                 id_ = elem.get('id', None)
                 if id_ is None:
-                    raise ValueError('id of element in OC update dict is missing')
+                    raise ValueError('id of element in OC update dict '
+                                     'is missing')
                 if id_ in self._d_index:
-                    #obj currently exists in this collection
+                    # obj currently exists in this collection
                     obj = self.get(id_)
                     obj.update(elem)
                 else:
-                    raise ValueError('{0} is not an object contained by this OC'.format(id))
+                    raise ValueError(f'{id} is not an object contained '
+                                     'by this OrderedCollection')
                 new_vals.append(obj)
             elif isinstance(elem, self.dtype):
                 new_vals.append(elem)
             else:
-                raise ValueError('update element is not dict or valid type for this OC')
+                raise ValueError('update element is not dict or valid type '
+                                 'for this OrderedCollection')
 
         self.clear()
         self.add(new_vals)
 
         return self
 
-
-    #JAH: This is why OCs can be serialized and lists cannot!
+    # JAH: This is why OCs can be serialized and lists cannot!
     def to_dict(self):
         '''
         Method takes the instance of ordered collection and outputs a list of
@@ -338,7 +333,7 @@ def to_dict(self):
 
         for obj in self:
             try:
-                obj_type = '{0.__module__}.{0.__class__.__name__}'.format(obj)
+                obj_type = f'{obj.__module__}.{obj.__class__.__name__}'
             except AttributeError:
                 obj_type = '{0.__class__.__name__}'.format(obj)
             item = {'obj_type': obj_type, 'id': self._s_id(obj)}
@@ -361,7 +356,7 @@ def register_callback(self, callback,
             if event not in ('add', 'remove', 'replace'):
                 raise ValueError("Events must be either "
                                  "('add', 'remove', 'replace'). "
-                                 "{0} is not supported".format(event))
+                                 f"{event} is not supported")
 
         self.callbacks.append((callback, events))
 
diff --git a/py_gnome/gnome/utilities/plume.py b/py_gnome/gnome/utilities/plume.py
index 47ff3af9b..a1f0ba9d6 100644
--- a/py_gnome/gnome/utilities/plume.py
+++ b/py_gnome/gnome/utilities/plume.py
@@ -3,7 +3,6 @@
 This module holds classes and supporting code for simulating the vertical
 plume that is generated by an underwater blowout.
 """
-
 from datetime import datetime, timedelta
 
 import numpy as np
@@ -164,7 +163,7 @@ def __iter__(self):
                 next_time = curr_time + timedelta(seconds=self.time_step_delta)
                 yield (curr_time,
                        list(zip(self.plume.coords,
-                           self.elems_in_range(curr_time, next_time))))
+                                self.elems_in_range(curr_time, next_time))))
         else:
             step = 0
             while True:
@@ -174,7 +173,7 @@ def __iter__(self):
                 step += 1
                 yield (curr_time,
                        list(zip(self.plume.coords,
-                           self.elems_in_range(curr_time, next_time))))
+                                self.elems_in_range(curr_time, next_time))))
 
 
 if __name__ == '__main__':
diff --git a/py_gnome/gnome/utilities/profiledeco.py b/py_gnome/gnome/utilities/profiledeco.py
index c919da3aa..f81829595 100644
--- a/py_gnome/gnome/utilities/profiledeco.py
+++ b/py_gnome/gnome/utilities/profiledeco.py
@@ -7,12 +7,12 @@
 def foo():
     sleep(1)
 
-this should profile foo whenever it is called and add it to the global profile stats.
+this should profile foo whenever it is called and add it to the
+global profile stats.
 
 '''
 import cProfile
 import pstats
-import io
 
 profiler = cProfile.Profile()
 
diff --git a/py_gnome/gnome/utilities/projections.py b/py_gnome/gnome/utilities/projections.py
index 9efc75c76..88fcf4be1 100644
--- a/py_gnome/gnome/utilities/projections.py
+++ b/py_gnome/gnome/utilities/projections.py
@@ -14,13 +14,6 @@
 NOTE: all coordinates are takes as (lon, lat, depth)
       even though depth is always ignored
 """
-
-
-
-
-
-
-
 import numpy as np
 from gnome.gnomeobject import GnomeId
 from gnome.persist.base_schema import ObjTypeSchema
@@ -378,9 +371,9 @@ def meters_to_lonlat(meters, ref_positions):
         :type ref_positions: NX3, numpy array (Only lat is used here)
 
         :returns delta_lon_lat: Differential (delta) positional values
-                                Nx3 numpy array of (delta-lon, delta-lat, delta-z)
+                                Nx3 numpy array of
+                                (delta-lon, delta-lat, delta-z)
         """
-
         # make a copy -- don't change meters
         delta_lon_lat = np.array(meters, dtype=np.float64)
         if len(delta_lon_lat.shape) == 1:

From 56ab860e92bca4b35ea99f54dd7e91ae1e44f6f9 Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Wed, 29 May 2024 18:04:20 -0700
Subject: [PATCH 88/99] cleaned up install docs a bit.

---
 Install_without_conda.rst                     | 24 +++++--------------
 Installing.rst                                | 15 ++++--------
 .../current_uncertainty_example.py            |  2 +-
 .../script_plume_HI.py                        |  5 ++++
 4 files changed, 17 insertions(+), 29 deletions(-)

diff --git a/Install_without_conda.rst b/Install_without_conda.rst
index 9c18e3df1..c633fb75e 100644
--- a/Install_without_conda.rst
+++ b/Install_without_conda.rst
@@ -28,7 +28,7 @@ Building everything by hand / with pip
 
 It is always good practice to create and run a complex system like this in a virtual environment of some sort: virtualenv, pipenv, etc.
 
-A virtual environment is **not required** to run PyGNOME.
+A virtual environment is *not required* to run PyGNOME.
 But you may be working in an environment (on a corporate network, for example) that restricts your access to the system files on your computer.
 In such a case, you may require a virtualenv in order to freely install python packages in python's site-packages dir. (site-packages is the standard place where python installers will put packages after building them)
 
@@ -121,7 +121,7 @@ Download and install the newest Windows executable distribution of
 
 `Python 3.10 <http://www.python.org/download/>`_
 
-(3.9 -- 3.11 shoule work)
+(3.9 -- 3.12 should work)
 
 A number of the packages that GNOME depends on have very complex and
 brittle build processes, and depend on third-party libraries that can be
@@ -129,10 +129,6 @@ a challenge to build.
 
 Fortunately, many of them are available as binary wheels on PyPi
 
-Another option is to use a Python scientific distribution, such as
-`Anaconda <https://www.anaconda.com/products/distribution>`_ -- in which case, stop and read the ``Installing.rst`` file.
-
-
 Dependencies can be installed using the command::
 
     > pip install -r requirements.txt
@@ -152,25 +148,17 @@ Build PyGNOME
     > cd PyGNOME/py_gnome
     > pip install -r requirements.txt
 
-3. Install the adios_db pacakge -- it is under active development along  with py_gnome, so it's best to install that from source as well:
+3. Install the adios_db package -- it is under active development along  with py_gnome, so it's best to install that from source as well:
 
    https://github.com/NOAA-ORR-ERD/adios_oil_database/tree/production/adios_db
 
-4. build the ``py_gnome`` module in develop or install mode:
+4. build the ``py_gnome`` module in editable or install mode.
 
-   ``> python setup.py build``
+   ``> python -m pip install ./``
 
    or
 
-   ``> python setup.py install``
-
-   or
-
-   ``> python setup.py develop``
-
-The other option you may need is ``cleanall``, which should clean the development environment -- good to do after puling new code from git::
-
-   > python setup.py cleanall
+   ``> python -m pip install --editable ./``
 
 
 5. If this successfully completes, then run the unit tests::
diff --git a/Installing.rst b/Installing.rst
index 2ce8b02df..9c44e6bd6 100644
--- a/Installing.rst
+++ b/Installing.rst
@@ -87,9 +87,9 @@ independent environment for it.
 **NOTES:**
 
 PyGNOME requires Python version 3.9 or greater (version 3.10 is currently used
-operationally -- 3.11 should work, but it not well tested)
+operationally -- 3.11 and 3.12 should work, but it not well tested)
 
-Anaconda (and miniconda) can be installed in either single-user or multi-user mode:
+Anaconda (and miniconda and miniforge) can be installed in either single-user or multi-user mode:
 
 https://docs.continuum.io/anaconda/install
 
@@ -172,9 +172,6 @@ conda packages for download.  The way this is done is through anaconda
 "channels", which can be thought of simply as places on ``anaconda.org``
 where collections of packages are bundled together by the people hosting them.
 
-Many of the dependencies that PyGNOME requires come out of the box
-with Anaconda (or the conda "defaults" channel), but a few important
-ones don't.
 
 **The "conda-forge" project:**
 
@@ -191,7 +188,7 @@ conda channel configuration::
 
     > conda config --add channels conda-forge
 
-.. note:: MiniForge comes pre-configured to work with conda-forge, this step is not neccesary of you are using the miniforge distribution.
+.. note:: MiniForge comes pre-configured to work with conda-forge, this step is not necessary if you are using the miniforge distribution.
 
 When you add a channel to conda, it puts it at the top of the list.
 So now when you install a package, conda will first look in conda-forge,
@@ -246,7 +243,6 @@ To use that environment, you activate it with::
 
     > conda activate gnome
 
-
 and when you are done, you can deactivate it with::
 
     > conda deactivate
@@ -526,9 +522,8 @@ Running pip as a module ensures we are referencing the correct environment
 for installation*
 
 If you are planning to develop or debug the PyGNOME source code itself,
-then you may want to perform a "develop" install.  A "develop" install allows
-changes in the python code to be immediately available in your python
-environment without re-installing.
+then you may want to perform a "editable" install.  A "editable" install
+puts a links intot he source code, rather than copying it into the Python install, so that changes in the python code are immediately available in your python environment without re-installing.
 
 For this, run the following::
 
diff --git a/py_gnome/scripts/example_scripts/current_uncertainty/current_uncertainty_example.py b/py_gnome/scripts/example_scripts/current_uncertainty/current_uncertainty_example.py
index 61961a503..6da3d55f0 100644
--- a/py_gnome/scripts/example_scripts/current_uncertainty/current_uncertainty_example.py
+++ b/py_gnome/scripts/example_scripts/current_uncertainty/current_uncertainty_example.py
@@ -49,7 +49,7 @@
 #                                 )
 model.movers += current_mover
 
-# Turn Diffusion off to see the effects of the uncertainty
+# Turn Diffusion down to see the effects of the uncertainty
 model.movers += gs.RandomMover(diffusion_coef=1e1)
 
 renderer = gs.Renderer(mymap,
diff --git a/py_gnome/scripts/testing_scripts/script_3dcurrents_hawaii/script_plume_HI.py b/py_gnome/scripts/testing_scripts/script_3dcurrents_hawaii/script_plume_HI.py
index 383527f43..d51f81369 100644
--- a/py_gnome/scripts/testing_scripts/script_3dcurrents_hawaii/script_plume_HI.py
+++ b/py_gnome/scripts/testing_scripts/script_3dcurrents_hawaii/script_plume_HI.py
@@ -84,6 +84,11 @@ def make_model():
                                      horizontal_diffusion_coef_below_ml = 100000,
                                      mixed_layer_depth=20)
 
+    ncout = gs.NetCDFOutput(filename="HI_output.nc",
+                        output_timestep=gs.hours(1),
+                        )
+
+    model.outputters += ncout
     return model
 
 

From 1b446beaabb85d3ca4f6b1e4189b735e3a337c07 Mon Sep 17 00:00:00 2001
From: Chris Barker <Chris.Barker@noaa.gov>
Date: Wed, 29 May 2024 19:19:21 -0700
Subject: [PATCH 89/99] renamed the erma_data_package dir so that scikit builds
 editable mode doesn't get confused.

---
 .../gnome/outputters/erma_data_package.py     |  54 ++++++------------
 .../SHAPES.TTF                                | Bin
 .../default_beached_template.json             |   0
 .../default_contour_template.json             |   0
 .../default_floating_template.json            |   0
 .../default_polygon_cartoline_template.json   |   0
 .../default_polygon_template.json             |   0
 .../default_spill_location_template.json      |   0
 .../layer_template.json                       |   0
 9 files changed, 18 insertions(+), 36 deletions(-)
 rename py_gnome/gnome/outputters/{erma_data_package => erma_data_package_data}/SHAPES.TTF (100%)
 rename py_gnome/gnome/outputters/{erma_data_package => erma_data_package_data}/default_beached_template.json (100%)
 rename py_gnome/gnome/outputters/{erma_data_package => erma_data_package_data}/default_contour_template.json (100%)
 rename py_gnome/gnome/outputters/{erma_data_package => erma_data_package_data}/default_floating_template.json (100%)
 rename py_gnome/gnome/outputters/{erma_data_package => erma_data_package_data}/default_polygon_cartoline_template.json (100%)
 rename py_gnome/gnome/outputters/{erma_data_package => erma_data_package_data}/default_polygon_template.json (100%)
 rename py_gnome/gnome/outputters/{erma_data_package => erma_data_package_data}/default_spill_location_template.json (100%)
 rename py_gnome/gnome/outputters/{erma_data_package => erma_data_package_data}/layer_template.json (100%)

diff --git a/py_gnome/gnome/outputters/erma_data_package.py b/py_gnome/gnome/outputters/erma_data_package.py
index dc48f339f..f61a7b050 100644
--- a/py_gnome/gnome/outputters/erma_data_package.py
+++ b/py_gnome/gnome/outputters/erma_data_package.py
@@ -23,6 +23,9 @@
 from gnome.utilities import convert_mass_to_mass_or_volume
 from .outputter import Outputter, BaseOutputterSchema
 
+
+erma_data_package_data_dir = pathlib.Path(__file__).parent / "erma_data_package_data"
+
 class ERMADataPackageSchema(BaseOutputterSchema):
     filename = FilenameSchema(
         missing=drop, save=True, update=True, test_equal=False
@@ -414,9 +417,7 @@ def build_package(self):
         # Write out some empty dirs for now for attachments etc.
         zipf.writestr(zipfile.ZipInfo('attachment/'), '')
         # Needed font file
-        font_path = os.path.join(os.path.split(__file__)[0],
-                                 'erma_data_package',
-                                 'SHAPES.TTF')
+        font_path = erma_data_package_data_dir / 'SHAPES.TTF'
         zipf.write(font_path,
                    arcname='support_files/fonts/SHAPES.TTF')
         zipf.close()
@@ -429,13 +430,11 @@ def make_contour_polygon_package_layer(self, id, shapefile_filename,
         generic_name = 'contour_certain'
         generic_description = 'Contour Certain'
         layer_template = None
-        layer_template_path = os.path.join(os.path.split(__file__)[0],
-                                           'erma_data_package',
-                                           'layer_template.json')
+
+        layer_template_path = erma_data_package_data_dir / 'layer_template.json'
         contour_template = None
-        contour_template_path = os.path.join(os.path.split(__file__)[0],
-                                             'erma_data_package',
-                                             'default_contour_template.json')
+        contour_template_path = erma_data_package_data_dir / 'default_contour_template.json'
+
         with open(layer_template_path) as f:
             layer_template = json.load(f)
         with open(contour_template_path) as f:
@@ -523,13 +522,9 @@ def make_boundary_polygon_package_layer(self, id, uncertain, shapefile_filename,
         generic_name = f'boundary_{"uncertain" if uncertain else "certain"}'
         generic_description = f'Boundary {"Uncertain" if uncertain else "Certain"}'
         layer_template = None
-        layer_template_path = os.path.join(os.path.split(__file__)[0],
-                                           'erma_data_package',
-                                           'layer_template.json')
+        layer_template_path = erma_data_package_data_dir / 'layer_template.json'
         polygon_template = None
-        polygon_template_path = os.path.join(os.path.split(__file__)[0],
-                                             'erma_data_package',
-                                             'default_polygon_cartoline_template.json')
+        polygon_template_path = erma_data_package_data_dir / 'default_polygon_cartoline_template.json'
         with open(layer_template_path) as f:
             layer_template = json.load(f)
         with open(polygon_template_path) as f:
@@ -613,13 +608,10 @@ def make_map_polygon_package_layer(self, id, map_polygon_name, shapefile_name,
         shz_name = os.path.join(self.tempdir.name, shapefile_name+'.shz')
         shapefile_pathlib_path = pathlib.Path(shz_name)
         layer_template = None
-        layer_template_path = os.path.join(os.path.split(__file__)[0],
-                                           'erma_data_package',
-                                           'layer_template.json')
+        layer_template_path = erma_data_package_data_dir / 'layer_template.json'
         polygon_template = None
-        polygon_template_path = os.path.join(os.path.split(__file__)[0],
-                                             'erma_data_package',
-                                             'default_polygon_template.json')
+        polygon_template_path = erma_data_package_data_dir / 'default_polygon_template.json'
+
         with open(layer_template_path) as f:
             layer_template = json.load(f)
         with open(polygon_template_path) as f:
@@ -675,13 +667,9 @@ def make_spill_location_package_layer(self, id):
         shz_name = os.path.join(self.tempdir.name, shapefile_name+'.shz')
         shapefile_pathlib_path = pathlib.Path(shz_name)
         layer_template = None
-        layer_template_path = os.path.join(os.path.split(__file__)[0],
-                                           'erma_data_package',
-                                           'layer_template.json')
+        layer_template_path = erma_data_package_data_dir / 'layer_template.json'
         default_spill_location_template = None
-        default_spill_location_template_path = os.path.join(os.path.split(__file__)[0],
-                                                            'erma_data_package',
-                                                            'default_spill_location_template.json')
+        default_spill_location_template_path = erma_data_package_data_dir / 'default_spill_location_template.json'
         with open(layer_template_path) as f:
             layer_template = json.load(f)
         with open(default_spill_location_template_path) as f:
@@ -816,15 +804,9 @@ def generate_cutoff_struct(self):
     def make_particle_package_layer(self, id, layer_name, uncertain, shapefile_filename):
         dir, basefile = os.path.split(shapefile_filename)
         output_path = dir+"/"+str(id)+".json"
-        layer_template_path = os.path.join(os.path.split(__file__)[0],
-                                           'erma_data_package',
-                                           'layer_template.json')
-        default_floating_template_path = os.path.join(os.path.split(__file__)[0],
-                                                      'erma_data_package',
-                                                      'default_floating_template.json')
-        default_beached_template_path = os.path.join(os.path.split(__file__)[0],
-                                                     'erma_data_package',
-                                                     'default_beached_template.json')
+        layer_template_path = erma_data_package_data_dir / 'layer_template.json'
+        default_floating_template_path = erma_data_package_data_dir / 'default_floating_template.json'
+        default_beached_template_path = erma_data_package_data_dir / 'default_beached_template.json'
         layer_template = None
         default_floating_template = default_beached_template = None
         with open(layer_template_path) as f:
diff --git a/py_gnome/gnome/outputters/erma_data_package/SHAPES.TTF b/py_gnome/gnome/outputters/erma_data_package_data/SHAPES.TTF
similarity index 100%
rename from py_gnome/gnome/outputters/erma_data_package/SHAPES.TTF
rename to py_gnome/gnome/outputters/erma_data_package_data/SHAPES.TTF
diff --git a/py_gnome/gnome/outputters/erma_data_package/default_beached_template.json b/py_gnome/gnome/outputters/erma_data_package_data/default_beached_template.json
similarity index 100%
rename from py_gnome/gnome/outputters/erma_data_package/default_beached_template.json
rename to py_gnome/gnome/outputters/erma_data_package_data/default_beached_template.json
diff --git a/py_gnome/gnome/outputters/erma_data_package/default_contour_template.json b/py_gnome/gnome/outputters/erma_data_package_data/default_contour_template.json
similarity index 100%
rename from py_gnome/gnome/outputters/erma_data_package/default_contour_template.json
rename to py_gnome/gnome/outputters/erma_data_package_data/default_contour_template.json
diff --git a/py_gnome/gnome/outputters/erma_data_package/default_floating_template.json b/py_gnome/gnome/outputters/erma_data_package_data/default_floating_template.json
similarity index 100%
rename from py_gnome/gnome/outputters/erma_data_package/default_floating_template.json
rename to py_gnome/gnome/outputters/erma_data_package_data/default_floating_template.json
diff --git a/py_gnome/gnome/outputters/erma_data_package/default_polygon_cartoline_template.json b/py_gnome/gnome/outputters/erma_data_package_data/default_polygon_cartoline_template.json
similarity index 100%
rename from py_gnome/gnome/outputters/erma_data_package/default_polygon_cartoline_template.json
rename to py_gnome/gnome/outputters/erma_data_package_data/default_polygon_cartoline_template.json
diff --git a/py_gnome/gnome/outputters/erma_data_package/default_polygon_template.json b/py_gnome/gnome/outputters/erma_data_package_data/default_polygon_template.json
similarity index 100%
rename from py_gnome/gnome/outputters/erma_data_package/default_polygon_template.json
rename to py_gnome/gnome/outputters/erma_data_package_data/default_polygon_template.json
diff --git a/py_gnome/gnome/outputters/erma_data_package/default_spill_location_template.json b/py_gnome/gnome/outputters/erma_data_package_data/default_spill_location_template.json
similarity index 100%
rename from py_gnome/gnome/outputters/erma_data_package/default_spill_location_template.json
rename to py_gnome/gnome/outputters/erma_data_package_data/default_spill_location_template.json
diff --git a/py_gnome/gnome/outputters/erma_data_package/layer_template.json b/py_gnome/gnome/outputters/erma_data_package_data/layer_template.json
similarity index 100%
rename from py_gnome/gnome/outputters/erma_data_package/layer_template.json
rename to py_gnome/gnome/outputters/erma_data_package_data/layer_template.json

From fbb782d289ad528fc74c77518a84ad7c235bed7b Mon Sep 17 00:00:00 2001
From: Jay Hennen <jay.hennen@noaa.gov>
Date: Thu, 30 May 2024 09:30:44 -0700
Subject: [PATCH 90/99] removed kludge Grid_U init

---
 py_gnome/gnome/environment/gridded_objects_base.py | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/py_gnome/gnome/environment/gridded_objects_base.py b/py_gnome/gnome/environment/gridded_objects_base.py
index 6106b1f7f..68269f8e0 100644
--- a/py_gnome/gnome/environment/gridded_objects_base.py
+++ b/py_gnome/gnome/environment/gridded_objects_base.py
@@ -127,15 +127,6 @@ class Grid_U(gridded.grids.Grid_U, GnomeId):
 
     _schema = GridSchema
 
-    def __init__(self, **kwargs):
-        super(Grid_U, self).__init__(**kwargs)
-
-        #This is for the COOPS case, where their coordinates go from 0-360 starting at prime meridian
-        for lon in [self.node_lon,]:
-            if lon is not None and lon.max() > 180:
-                self.logger.warning('Detected longitudes > 180 in {0}. Rotating -360 degrees'.format(self.name))
-                lon -= 360
-
     def draw_to_plot(self, ax, features=None, style=None):
         import matplotlib
         def_style = {'color': 'blue',

From f428d27f52578b93e70ee45c76c72904fb54ec41 Mon Sep 17 00:00:00 2001
From: Caitlin O'Connor <caitlin.oconnor@noaa.gov>
Date: Thu, 30 May 2024 15:00:16 -0700
Subject: [PATCH 91/99] added parens to include return in error check

---
 py_gnome/lib_gnome/CATSMover_c.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/py_gnome/lib_gnome/CATSMover_c.cpp b/py_gnome/lib_gnome/CATSMover_c.cpp
index 44bc63a93..66bdaba0d 100644
--- a/py_gnome/lib_gnome/CATSMover_c.cpp
+++ b/py_gnome/lib_gnome/CATSMover_c.cpp
@@ -302,9 +302,10 @@ OSErr CATSMover_c::PrepareForModelStep(const Seconds &model_time,
 
 	err = this->ComputeVelocityScale(model_time);
 	if (err)
+	{
 		printError("An error occurred in TCATSMover::PrepareForModelStep");
 		return err;
-
+	}
 	// in m/s
 	//note: DIVIDED by timestep because this is later multiplied by the timestep
 	this->fOptimize.isOptimizedForStep = true;

From 1cbb42ac736108482a117a2731de762b7bb23bb2 Mon Sep 17 00:00:00 2001
From: Caitlin O'Connor <caitlin.oconnor@noaa.gov>
Date: Fri, 31 May 2024 09:41:39 -0700
Subject: [PATCH 92/99] added test to make sure tide is working with cats mover

---
 .../unit_tests/test_movers/test_cats_mover.py | 28 ++++++++++++++++++-
 1 file changed, 27 insertions(+), 1 deletion(-)

diff --git a/py_gnome/tests/unit_tests/test_movers/test_cats_mover.py b/py_gnome/tests/unit_tests/test_movers/test_cats_mover.py
index 29e63abfe..a602a3ce2 100644
--- a/py_gnome/tests/unit_tests/test_movers/test_cats_mover.py
+++ b/py_gnome/tests/unit_tests/test_movers/test_cats_mover.py
@@ -94,6 +94,19 @@ def run_loop():
 
     return delta
 
+def run_no_tide_loop():
+    """
+    test one time step with no tide attached to the mover
+    will check move is different from mover with tide.
+    also checks the motion is same for all LEs
+    """
+
+    pSpill = sample_sc_release(num_le, start_pos, rel_time)
+    cats = CatsMover(curr_file)
+    delta = _certain_loop(pSpill, cats)
+
+    return delta
+
 def test_uncertain_loop():
     """
     test one time step with uncertainty on the spill
@@ -133,10 +146,23 @@ def test_certain_uncertain():
     assert np.all(delta[:, :2] != u_delta[:, :2])
     assert np.all(delta[:, 2] == u_delta[:, 2])
 
+def test_tide_notide():
+    """
+    make sure cats with tide and cats with no tide results in different deltas
+    """
+
+    tide_delta = run_loop()
+    no_tide_delta = run_no_tide_loop()
+    print()
+    print(tide_delta)
+    print(no_tide_delta)
+    assert np.all(tide_delta[:, :2] != no_tide_delta[:, :2])
+    assert np.all(tide_delta[:, 2] == no_tide_delta[:, 2])
+
 
 c_cats = CatsMover(curr_file)
 
-0
+
 def test_default_props():
     """
     test default properties

From 29940bd5136abd1515c321f09ec3206b5eabf1a0 Mon Sep 17 00:00:00 2001
From: Caitlin O'Connor <caitlin.oconnor@noaa.gov>
Date: Fri, 31 May 2024 13:52:21 -0700
Subject: [PATCH 93/99] added test for wind not in model range for evaporation

---
 .../test_weatherers/test_evaporation.py       | 49 ++++++++++++++++++-
 1 file changed, 48 insertions(+), 1 deletion(-)

diff --git a/py_gnome/tests/unit_tests/test_weatherers/test_evaporation.py b/py_gnome/tests/unit_tests/test_weatherers/test_evaporation.py
index 7bf89be89..66712460e 100644
--- a/py_gnome/tests/unit_tests/test_weatherers/test_evaporation.py
+++ b/py_gnome/tests/unit_tests/test_weatherers/test_evaporation.py
@@ -16,13 +16,60 @@
 from gnome.environment import constant_wind, Water, Wind
 from gnome.weatherers import Evaporation
 from gnome.outputters import WeatheringOutput
-from gnome.basic_types import oil_status
+from gnome.basic_types import oil_status, datetime_value_2d
 
 from .conftest import weathering_data_arrays, test_oil
 from ..conftest import (# sample_model,
                         sample_model_weathering)
 
 
+def test_evaporation_bad_wind():
+    series = np.zeros((2, ), dtype=datetime_value_2d)
+    start_time = datetime(2000, 1, 1, 1) # same as conftest time
+
+    series[0] = (start_time + timedelta(hours=24), (10, 45))	# starts after model start
+    series[1] = (start_time + timedelta(hours=48), (10, 90))
+    wind = Wind(timeseries=series, units='m/s')
+    wind.extrapolate=True # add separate
+
+    evap = Evaporation(Water(), wind=wind)
+    (sc, time_step) = weathering_data_arrays(evap.array_types, evap.water)[:2]
+
+    model_time = (sc.spills[0].release_time +
+                  timedelta(seconds=time_step))
+
+    evap.prepare_for_model_run(sc)
+    evap.prepare_for_model_step(sc, time_step, model_time)
+    with pytest.raises(ValueError)as excinfo:
+        evap.weather_elements(sc, time_step, model_time)
+    assert "not within the bounds" in str(excinfo.value)
+
+@pytest.mark.xfail
+def test_evaporation_extrapolate_bad_wind():
+    """
+    NOTE: This test should work once we allow extrapolation for weatherers
+    """
+    series = np.zeros((2, ), dtype=datetime_value_2d)
+    start_time = datetime(2000, 1, 1, 1) # same as conftest time
+
+    series[0] = (start_time + timedelta(hours=24), (10, 45))	# starts after model start
+    series[1] = (start_time + timedelta(hours=48), (10, 90))
+    wind = Wind(timeseries=series, units='m/s', extrapolation_is_allowed=True)
+
+    evap = Evaporation(Water(), wind=wind)
+    (sc, time_step) = weathering_data_arrays(evap.array_types, evap.water)[:2]
+
+    model_time = (sc.spills[0].release_time +
+                  timedelta(seconds=time_step))
+
+    evap.prepare_for_model_run(sc)
+    evap.prepare_for_model_step(sc, time_step, model_time)
+    evap.weather_elements(sc, time_step, model_time)
+    for spill in sc.spills:
+        mask = sc.get_spill_mask(spill)
+        assert np.all(sc['evap_decay_constant'][mask, :] < 0.0)
+
+
 def test_evaporation_no_wind():
     evap = Evaporation(Water(), wind=constant_wind(0., 0))
     (sc, time_step) = weathering_data_arrays(evap.array_types, evap.water)[:2]

From 5f9d95ea8761df325767c01ff1d2a441882dc6ae Mon Sep 17 00:00:00 2001
From: Caitlin O'Connor <caitlin.oconnor@noaa.gov>
Date: Sun, 2 Jun 2024 13:56:00 -0700
Subject: [PATCH 94/99] fix for line spill that starts after model start so
 particles release correctly

---
 py_gnome/gnome/spills/release.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/py_gnome/gnome/spills/release.py b/py_gnome/gnome/spills/release.py
index a9bf23982..56f429787 100644
--- a/py_gnome/gnome/spills/release.py
+++ b/py_gnome/gnome/spills/release.py
@@ -586,6 +586,9 @@ def initialize_LEs(self, to_rel, sc, start_time, end_time):
         '''
         # if time_step == 0:
         #     time_step = 1  # to deal with initializing position in instantaneous release case
+        if self.release_duration == 0 and start_time != end_time: # special case for instantaneous spill with release after model start
+            if self.release_time <= end_time and self.release_time>=start_time:
+                 start_time = end_time = self.release_time
         if start_time == end_time:
             end_time += timedelta(seconds=1)
         sl = slice(-to_rel, None, 1)

From dca267f25c7863b12cc4c968b2e1d656e879f713 Mon Sep 17 00:00:00 2001
From: Caitlin O'Connor <caitlin.oconnor@noaa.gov>
Date: Mon, 3 Jun 2024 15:42:36 -0700
Subject: [PATCH 95/99] test for instantaneous line release

---
 .../unit_tests/test_spills/test_release.py    | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/py_gnome/tests/unit_tests/test_spills/test_release.py b/py_gnome/tests/unit_tests/test_spills/test_release.py
index 13b124bfc..7914ac7ce 100644
--- a/py_gnome/tests/unit_tests/test_spills/test_release.py
+++ b/py_gnome/tests/unit_tests/test_spills/test_release.py
@@ -198,6 +198,46 @@ def test_serialization(self, r1):
         deser = PointLineRelease.deserialize(ser)
         assert deser == r1
 
+    def test_LE_initialization_instantaneous(self, r2):
+        #initialize_LEs(self, to_rel, data, current_time, time_step)
+        data = LEData()
+        ts = 900
+        r = r2
+        num_le = 0
+        r.prepare_for_model_run(ts)
+
+        data.prepare_for_model_run(r.array_types, None)
+        data.extend_data_arrays(10)
+        #initialize over the time interval 0-10%
+        r.initialize_LEs(10, data, r.release_time, r.release_time+timedelta(seconds=ts))
+
+        #particles should have positions spread over the
+        #line from start_position to end_position
+        assert len(data['positions']) == 10
+        for pos in data['positions']:
+            for d in [0,1,2]:
+                #instantaneous so particles should be spread across whole line
+                assert pos[d] >= r.start_position[d] + num_le
+            num_le += 1
+
+        assert np.all(data['mass'] == r._mass_per_le)
+
+        #reset and try overlap beginning
+        data.rewind()
+        num_le = 0
+        data.prepare_for_model_run(r.array_types, None)
+        data.extend_data_arrays(100)
+        #initialize 100 LEs overlapping the start of the release
+        r.initialize_LEs(100, data, r.release_time - timedelta(seconds=ts/2), r.release_time)
+        for pos in data['positions']:
+            for d in [0,1,2]:
+                #instantaneous so particles should be spread across whole line
+                assert pos[d] >= r.start_position[d] + num_le*.1
+            num_le += 1
+
+        assert np.all(data['mass'] == r._mass_per_le)
+
+
     #This isn't supported yet in pytest????
     #@pytest.mark.parametrize('r', [r1, r3])
     def test_LE_initialization(self, r1, r3):

From 309e853823caa2a9acc6b731233bb3f6cedf7bd9 Mon Sep 17 00:00:00 2001
From: Caitlin O'Connor <caitlin.oconnor@noaa.gov>
Date: Tue, 4 Jun 2024 13:26:08 -0700
Subject: [PATCH 96/99] added deprecation warning for parammap

---
 py_gnome/gnome/maps/map.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/py_gnome/gnome/maps/map.py b/py_gnome/gnome/maps/map.py
index 1af2a1a12..d82e4dbb9 100644
--- a/py_gnome/gnome/maps/map.py
+++ b/py_gnome/gnome/maps/map.py
@@ -468,6 +468,7 @@ def __init__(self, center=(0.0, 0.0), distance=30000, bearing=90,
         :param bearing: The bearing the closest point on the shoreline is
                         from the center.
         """
+        warnings.warn("ParamMap is deprecated. Code is no longer being updated", DeprecationWarning)
         refloat_halflife = kwargs.pop('refloat_halflife', 1)
         self._refloat_halflife = refloat_halflife * 3600
         self.build(center, distance, bearing, units)

From 6a56160ab220b91b965a3b6c1e404322280ece80 Mon Sep 17 00:00:00 2001
From: Rachael Mueller <rachael.mueller@noaa.gov>
Date: Wed, 5 Jun 2024 01:19:35 +0000
Subject: [PATCH 97/99] Add error messages and fixes to tech_notes.rst

---
 py_gnome/documentation/source/tech_notes.rst | 25 ++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/py_gnome/documentation/source/tech_notes.rst b/py_gnome/documentation/source/tech_notes.rst
index 50f336525..d8ec96366 100644
--- a/py_gnome/documentation/source/tech_notes.rst
+++ b/py_gnome/documentation/source/tech_notes.rst
@@ -6,6 +6,31 @@ Assorted technical notes about GNOME and its algorithms and use.
 
 These are often responses to questions from users.
 
+Error messages and fixes
+=========================
+
+Here are some known errors and tips for fixing them.
+
+Datetime errors from using `xarray`:
+------------------------------------
+
+
+
+ TypeError: '<' not supported between instances of 'int' and 'datetime.datetime'
+
+`xarray` converts time to a numpy.datetime64 format that isn't compatible with the `datetime.datetime` format that is used throughout PyGNOME.  The fix is to convert the time array from `numpy.datetime64` format to a `datetime` format.  This can be accomplished with appending `.values.astype('datetime64[s]').tolist()` to the `numpy.datetime64` array, e.g.:
+
+ compatible_time = u_xr.time_counter.values.astype('datetime64[s]').tolist()
+
+
+
+Dimension errors from using `xarray`:
+------------------------------------
+ ValueError: dimensions ('y', 'x') must have the same length as the number of data dimensions, ndim=1
+
+This error reflects PyGNOME's dislike of `xarray.DataArray` and is fixed by slapping `.values` at the end of all  `xarray.DataArray`, e.g.:
+
+ node_lon = lon_psi.values
 
 The role of mass in GNOME
 =========================

From 99ddf9bafdcc8f92c9d566b9a74c2e52e37bfe45 Mon Sep 17 00:00:00 2001
From: "Rachael D. Mueller" <rachael.mueller@noaa.gov>
Date: Tue, 4 Jun 2024 18:46:33 -0700
Subject: [PATCH 98/99] fixed header formatting problem

---
 py_gnome/documentation/source/tech_notes.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/py_gnome/documentation/source/tech_notes.rst b/py_gnome/documentation/source/tech_notes.rst
index d8ec96366..9570bdabe 100644
--- a/py_gnome/documentation/source/tech_notes.rst
+++ b/py_gnome/documentation/source/tech_notes.rst
@@ -25,7 +25,7 @@ Datetime errors from using `xarray`:
 
 
 Dimension errors from using `xarray`:
-------------------------------------
+-------------------------------------
  ValueError: dimensions ('y', 'x') must have the same length as the number of data dimensions, ndim=1
 
 This error reflects PyGNOME's dislike of `xarray.DataArray` and is fixed by slapping `.values` at the end of all  `xarray.DataArray`, e.g.:

From 5a104cf5dc1b098fb6fb3d6a08612dbd52626891 Mon Sep 17 00:00:00 2001
From: "James.Makela" <james.makela@noaa.gov>
Date: Wed, 5 Jun 2024 13:09:37 -0700
Subject: [PATCH 99/99] Cleanup code on the map_canvas module, consistent
 package build in the dockerfile.

---
 dockerfile                             |  2 +-
 py_gnome/gnome/utilities/map_canvas.py | 17 +++++++++++------
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/dockerfile b/dockerfile
index 851d58cba..18d4ecac3 100644
--- a/dockerfile
+++ b/dockerfile
@@ -18,7 +18,7 @@ RUN conda install python=$PYTHON_VER \
 
 RUN cd oil_database/adios_db && python -m pip install ./
 
-RUN cd py_gnome && pip install ./
+RUN cd py_gnome && python -m pip install ./
 
 # to check if they got installed properly
 #RUN python -c "import adios_db"
diff --git a/py_gnome/gnome/utilities/map_canvas.py b/py_gnome/gnome/utilities/map_canvas.py
index 954d74ac9..73092346c 100644
--- a/py_gnome/gnome/utilities/map_canvas.py
+++ b/py_gnome/gnome/utilities/map_canvas.py
@@ -11,7 +11,6 @@
 This should have the basic drawing stuff. Ideally nothing in here is
 GNOME-specific.
 """
-
 import bisect
 
 import numpy as np
@@ -197,8 +196,8 @@ def add_colors(self, color_list):
         """
         Add a list of colors to the pallette
 
-        :param color_list: list of colors. Each element of the list is a 2-tuple:
-                           ('color_name', (r,g,b))
+        :param color_list: list of colors. Each element of the list
+                           is a 2-tuple: ('color_name', (r,g,b))
         """
         self.fore_image.add_colors(color_list)
         self.back_image.add_colors(color_list)
@@ -207,7 +206,8 @@ def add_color_ramp(self, color_scheme, min_val, max_val):
         """
         generate depth colors to the gd images
         :param color_scheme: color scheme to render images
-        type: 'magma', 'inferno', 'plasma', 'viridis', 'cividis', 'twilight', 'twilight_shifted', 'turbo'
+        type: 'magma', 'inferno', 'plasma', 'viridis', 'cividis',
+              'twilight', 'twilight_shifted', 'turbo'
         :param min_val: value to map to the first color in the scheme
         :param max_val: value to map to the last color in the scheme
         """
@@ -215,12 +215,14 @@ def add_color_ramp(self, color_scheme, min_val, max_val):
 
         # print(existing_colors)
 
-        cr = py_gd.color_ramp.ColorRamp(color_scheme, min_val, max_val, base_colorscheme=len(existing_colors))
+        cr = py_gd.color_ramp.ColorRamp(color_scheme,
+                                        min_val, max_val,
+                                        base_colorscheme=len(existing_colors))
 
         self.fore_image.add_colors(cr.colorlist)
         self.back_image.add_colors(cr.colorlist)
 
-        self._color_ramp=cr
+        self._color_ramp = cr
 
     def get_color_names(self):
         """
@@ -441,6 +443,9 @@ def save(self, filename, file_type='png'):
         This copies the foreground image on top of the
         background image and saves the whole thing.
 
+        Fixme: filename & file_type appear to not be used at all here.
+               Are we passing them in to satisfy some api specification?
+
         :param filename: full path of file to be saved to
         :type filename: string