Modernize packaging (#122)

* Switch from setup.py to pyproject.toml

Replaced `setup.py` with `pyproject.toml` to modernize the build system and
align with PEP 517/518 standards. This update simplifies dependency management,
specifies build requirements, and provides project metadata in a standardized
format.

* Corrected project name in pyproject.toml

Updated the project name to "SalishSeaTools" for consistency with Python naming
conventions and to align with the repository's standard branding. This change
does not affect functionality but improves clarity and uniformity.

* Correct changelog URL in pyproject.toml

Corrected the GitHub URL for the changelog to point to the SalishSeaCast/tools
repository releases page. Ensures accurate navigation for users accessing
release information.

* Move coverage configuration to pyproject.toml

Relocated the coverage settings from .coveragerc to pyproject.toml for
centralized project configuration. This simplifies project management and
removes the need for a separate .coveragerc file.

* Remove >=1.0.0 version constraint from arrow dependency

The version constraint on the `arrow` dependency has been removed in both
`environment-dev.yaml` and `environment-test.yaml`. arrow=1.0.0 was released
>3 years ago. The version pin is no longer required because environments should
now be guaranteed to install a version that includes the v1.0.0 features we
need.

* Switch to Hatch for project build system

Add Hatch to environment-dev.yaml for package management and modify
pyproject.toml to use Hatchling for the build system. This change replaces
setuptools with hatchling, aligning the project build process with modern
package management practices.

* Move version identifier to __about__.py

Move the version identifier from `__pkg_metadata__.py` to a new `__about__.py`
file. The version is now dynamically read from that file to maintain the
consistency of version info. Removed obsolete `__pkg_metadata__.py` symlink.

* Update copyright year range

Change end of range to "present" to reflect ongoing, continuous development of
the package, and to avoid pointless annual updates.

* Remove unused future imports from Python modules

The `from __future__ import division` statement was removed across multiple
files, as it is no longer required in Python 3. This cleanup improves code
readability and aligns with modern Python standards.

* Update copyright references to "The SalishSeaCast contributors"

Updated copyright notices across multiple files to replace "The Salish Sea
MEOPAR contributors" with "The SalishSeaCast contributors". This change reflects
the current branding of the project.

* Remove redundant UTF-8 encoding declaration

The `# coding=utf-8` declaration was unnecessary as UTF-8 is the default
encoding in Python 3. This change simplifies the code without altering
functionality.

* Rename development doc to pkg_development for clarity

The development documentation file was renamed to better reflect its purpose as
related to package development. This improves clarity and consistency in naming
conventions within the documentation.

* Add release process documentation

Documented the steps for performing a release of SalishSeaTools, including
version bumping, tagging, creating milestones, and managing issues. This ensures
clarity and consistency in the release workflow.

* Update Sphinx configuration file to modern template

Refactored the Sphinx configuration file to use a cleaner and more concise
template. Removed unnecessary comments and adjusted the file to focus on
commonly used options. Added a reference link for full documentation.

I_ForcingFiles/Atmos/CheckAltitude.ipynb

@@ -22,7 +22,6 @@
      "collapsed": false,
      "input": [
       "%matplotlib inline\n",
-      "from __future__ import division\n",
       "import matplotlib.pyplot as plt\n",
       "import netCDF4 as nc\n",
       "import numpy as np\n",

I_ForcingFiles/Atmos/GetGrib.ipynb

@@ -20,7 +20,6 @@
      "collapsed": false,
      "input": [
       "# Standard Imports\n",
-      "from __future__ import division\n",
       "import arrow\n",
       "import os\n",
       "import urllib"

I_ForcingFiles/Atmos/InitialGEMCheck.ipynb

@@ -22,8 +22,6 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "from __future__ import division, print_function\n",
-      "\n",
       "import matplotlib.pyplot as plt\n",
       "import netCDF4 as nc\n",
       "import numpy as np\n",

I_ForcingFiles/Atmos/ProcessPramodArchive.ipynb

@@ -19,7 +19,6 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "from __future__ import division\n",
       "import arrow\n",
       "import glob\n",
       "import matplotlib.pyplot as plt\n",
@@ -475,7 +474,7 @@
         "    History: created by wgrib2\n",
         "    GRIB2_grid_template: 20\n",
         "    dimensions(sizes): y(266), x(256), time(62)\n",
-        "    variables(dimensions): float64 \u001b[4my\u001b[0m(y), float64 \u001b[4mx\u001b[0m(x), float64 \u001b[4mlatitude\u001b[0m(y,x), float64 \u001b[4mlongitude\u001b[0m(y,x), float64 \u001b[4mtime\u001b[0m(time), float32 \u001b[4mDSWRF_surface\u001b[0m(time,y,x)\n",
+        "    variables(dimensions): float64 \u001B[4my\u001B[0m(y), float64 \u001B[4mx\u001B[0m(x), float64 \u001B[4mlatitude\u001B[0m(y,x), float64 \u001B[4mlongitude\u001B[0m(y,x), float64 \u001B[4mtime\u001B[0m(time), float32 \u001B[4mDSWRF_surface\u001B[0m(time,y,x)\n",
         "    groups: \n",
         "\n",
         "<type 'netCDF4.Dataset'>\n",
@@ -484,7 +483,7 @@
         "    History: created by wgrib2\n",
         "    GRIB2_grid_template: 20\n",
         "    dimensions(sizes): y(266), x(256), time(62)\n",
-        "    variables(dimensions): float64 \u001b[4my\u001b[0m(y), float64 \u001b[4mx\u001b[0m(x), float64 \u001b[4mlatitude\u001b[0m(y,x), float64 \u001b[4mlongitude\u001b[0m(y,x), float64 \u001b[4mtime\u001b[0m(time), float32 \u001b[4mDSWRF_surface\u001b[0m(time,y,x)\n",
+        "    variables(dimensions): float64 \u001B[4my\u001B[0m(y), float64 \u001B[4mx\u001B[0m(x), float64 \u001B[4mlatitude\u001B[0m(y,x), float64 \u001B[4mlongitude\u001B[0m(y,x), float64 \u001B[4mtime\u001B[0m(time), float32 \u001B[4mDSWRF_surface\u001B[0m(time,y,x)\n",
         "    groups: \n"
        ]
       },
@@ -703,9 +702,9 @@
       "\n",
       "    # dataset attributes\n",
       "    nc_tools.init_dataset_attrs(\n",
-      "        ncfile, \n",
-      "        title='Atmos 2.5km Ops Forecast', \n",
-      "        notebook_name='ProcessPramodArchive', \n",
+      "        ncfile,\n",
+      "        title='Atmos 2.5km Ops Forecast',\n",
+      "        notebook_name='ProcessPramodArchive',\n",
       "        nc_filepath='/ocean/sallen/allen/research/MEOPAR/Operational/'+ncfilename,\n",
       "        comment='Dec processing',\n",
       "        )\n",

I_ForcingFiles/Atmos/README.md

@@ -37,7 +37,7 @@ Descriptions below the links are from the first cell of the notebooks
     combined into a file with the name pattern required by NEMO.
     Since new files need to be created the opportunity is taken to reduce storage requirements
     by creating them as netCDF4 files with variable-level compression enabled.
-    Metadata that conforms to [CF-1.6 and Salish Sea MEOPAR project conventions][netCDF4 conventions] is included
+    Metadata that conforms to [CF-1.6 and SalishSeaCast project conventions][netCDF4 conventions] is included
     in the new files.
 
     [netCDF4 conventions]: https://salishsea-meopar-docs.readthedocs.org/en/latest/code-notes/salishsea-nemo/nemo-forcing/netcdf4.html#netcdf4-file-conventions

I_ForcingFiles/Atmos/RadiationCheck.ipynb

@@ -30,7 +30,6 @@
      "collapsed": false,
      "input": [
       "%matplotlib inline\n",
-      "from __future__ import division\n",
       "import matplotlib.pyplot as plt\n",
       "import netCDF4 as nc\n",
       "import numpy as np\n",
@@ -704,9 +703,7 @@
     {
      "cell_type": "markdown",
      "metadata": {},
-     "source": [
-      "So Pramod's files do not begin at Dec 1, 2012 00:00. Check that ind matches with Kao Shen's time. "
-     ]
+     "source": "So Pramod's files do not begin at Dec 1, 2012 00:00. Check that ind matches with Kao Shen's time."
     },
     {
      "cell_type": "code",

I_ForcingFiles/Atmos/RebaseCGRF.ipynb

@@ -27,7 +27,7 @@
       "combined into a file with the name pattern required by NEMO.\n",
       "Since new files need to be created the opportunity is taken to reduce storage requirements\n",
       "by creating them as netCDF4 files with variable-level compression enabled.\n",
-      "Metadata that conforms to [CF-1.6 and Salish Sea MEOPAR project conventions][netCDF4 conventions] is included\n",
+      "Metadata that conforms to [CF-1.6 and SalishSeaCast project conventions][netCDF4 conventions] is included\n",
       "in the new files.\n",
       "\n",
       "[netCDF4 conventions]: https://salishsea-meopar-docs.readthedocs.org/en/latest/code-notes/salishsea-nemo/nemo-forcing/netcdf4.html#netcdf4-file-conventions\n",
@@ -142,7 +142,7 @@
       "and the `time_counter` variable `units` and `time_origin` metadata\n",
       "values need to be corrected.\n",
       "The global attributes need to be augmented to bring them into conformance\n",
-      "with [CF-1.6 and Salish Sea MEOPAR project conventions][netCDF4 conventions],\n",
+      "with [CF-1.6 and SalishSeaCast project conventions][netCDF4 conventions],\n",
       "and the `history` attribute needs to reflect the file's provenance.\n",
       "Use the `python-netCDF4` library to do those tasks.\n",
       "\n",
@@ -650,7 +650,6 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "from __future__ import division\n",
       "import cStringIO\n",
       "import matplotlib.pyplot as plt\n",
       "import requests\n",

I_ForcingFiles/Atmos/VerifyAtmosphericForcing.ipynb

@@ -19,7 +19,6 @@
      "collapsed": false,
      "input": [
       "%matplotlib inline\n",
-      "from __future__ import division\n",
       "import pprint\n",
       "import matplotlib.pyplot as plt\n",
       "import netCDF4 as nc\n",
@@ -442,7 +441,7 @@
      "collapsed": false,
      "input": [
       "for p in cgrf_pts:\n",
-      "    print (bathy.variables['nav_lat'][p['nearest_ji']], \n",
+      "    print (bathy.variables['nav_lat'][p['nearest_ji']],\n",
       "           bathy.variables['nav_lon'][p['nearest_ji']])"
      ],
      "language": "python",
@@ -667,7 +666,7 @@
       "at the 1st time step implies that a non-uniform field of values\n",
       "have been applied by NEMO.\n",
       "\n",
-      "**Notes:** \n",
+      "**Notes:**\n",
       "\n",
       "* The run that produced these result was done before\n",
       "  removal of the degenerate bathymetry at the east end of Jervis Inlet\n",
@@ -841,9 +840,9 @@
       "The values are close,\n",
       "but nowhere near as close as expected.\n",
       "Susan dug into the NEMO code and concluded that\n",
-      "the calculated wind components are subject to \n",
-      "atmospheric stability criteria manipulations \n",
-      "and are rescaled to be in a neutral atmosphere, \n",
+      "the calculated wind components are subject to\n",
+      "atmospheric stability criteria manipulations\n",
+      "and are rescaled to be in a neutral atmosphere,\n",
       "so they do not directly reflect the applied forcing values."
      ]
     },
@@ -944,7 +943,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "It is evident that the expected wind component values \n",
+      "It is evident that the expected wind component values\n",
       "from the CGRF files are being read by NEMO and interpolated\n",
       "to the NEMO grid points."
      ]
@@ -1223,7 +1222,7 @@
      "collapsed": false,
      "input": [
       "u_wind_1 = np.array((\n",
-      "    -2.4427305818641006E-002, -2.3924413357676255E-002, -2.3421520896711501E-002, -2.2918628435746748E-002, \n",
+      "    -2.4427305818641006E-002, -2.3924413357676255E-002, -2.3421520896711501E-002, -2.2918628435746748E-002,\n",
       "    -2.2415735974781997E-002, -2.1912843513817250E-002, -2.1409951052852497E-002, -2.0907058591887746E-002,\n",
       "    -2.0404166130922993E-002, -1.9901273669958246E-002))"
      ],

I_ForcingFiles/Atmos/altitude.py

@@ -1,4 +1,4 @@
-# Copyright 2013-2021 The Salish Sea MEOPAR contributors
+# Copyright 2013 – present by the SalishSeaCast contributors
 # and The University of British Columbia
 
 # Licensed under the Apache License, Version 2.0 (the "License");

I_ForcingFiles/Atmos/correct_pressure.py

@@ -1,4 +1,4 @@
-# Copyright 2013-2021 The Salish Sea MEOPAR contributors
+# Copyright 2013 – present by the SalishSeaCast contributors
 # and The University of British Columbia
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -20,7 +20,6 @@
 
 # Call like this: python correct_pressure.py pressure_file temperature_file save_directory
 
-from __future__ import division
 import matplotlib.pyplot as plt
 import netCDF4 as nc
 import numpy as np

I_ForcingFiles/Atmos/weather.py

@@ -1,4 +1,4 @@
-# Copyright 2013-2021 The Salish Sea MEOPAR contributors
+# Copyright 2013 – present by the SalishSeaCast contributors
 # and The University of British Columbia
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,7 +16,7 @@
 """A collection of tools for comparing atmospheric forcing with
 observations from the Salish Sea Model.
 """
-from __future__ import division
+
 
 import datetime
 import netCDF4 as NC

I_ForcingFiles/Initial/Create New TS file-bathymetry6&9.ipynb

@@ -17,7 +17,6 @@
    },
    "outputs": [],
    "source": [
-    "from __future__ import division, print_function\n",
     "from salishsea_tools import tidetools  # for nearest point function\n",
     "from salishsea_tools import nc_tools\n",
     "import matplotlib.pyplot as plt\n",
@@ -301,7 +300,7 @@
    "source": [
     "## modify temperature for some grid cells\n",
     "tempwanted = 5\n",
-    "k = 0 \n",
+    "k = 0\n",
     "i = 413\n",
     "j = 351\n",
     "T[:, i, j:j+5] = tempwanted ## for(413, 351:355) from 0 to 4m\n",
@@ -409,9 +408,9 @@
     "filename = '../../../NEMO-forcing/initial_strat/TS_01dec2002b.nc'\n",
     "new_TS = nc.Dataset(filename, 'w')\n",
     "nc_tools.init_dataset_attrs(\n",
-    "    new_TS, \n",
-    "    title='Salinity Temperature Initial Conditions based on spinup Dec 1 2002 for bathymetry6', \n",
-    "    notebook_name='Create New TS file bathymetry6&9', \n",
+    "    new_TS,\n",
+    "    title='Salinity Temperature Initial Conditions based on spinup Dec 1 2002 for bathymetry6',\n",
+    "    notebook_name='Create New TS file bathymetry6&9',\n",
     "    nc_filepath=filename,\n",
     "    comment='Salinity Temperature Initial Conditions based on spinup Dec 1 2002 for bathymetry6')\n",
     "new_TS.createDimension('y', 898)\n",
@@ -436,17 +435,17 @@
     "deptht = depths\n",
     "time_counter = new_TS.createVariable('time_counter', 'float32', ('time_counter'))\n",
     "time_counter.long_name = 'Time axis'\n",
-    "vosaline = new_TS.createVariable('vosaline', 'float32', \n",
+    "vosaline = new_TS.createVariable('vosaline', 'float32',\n",
     "                               ('time_counter','deptht','y','x'))\n",
     "vosaline.units = 'none'\n",
-    "vosaline.long_name = 'Practical Salinity'  \n",
+    "vosaline.long_name = 'Practical Salinity'\n",
     "vosaline.coordinates = 'nav_lon nav_lat deptht time_counter'\n",
     "vosaline.grid = 'SalishSea6, north extended Fraser'\n",
     "vosaline[0] = S\n",
-    "votemper = new_TS.createVariable('votemper', 'float32', \n",
+    "votemper = new_TS.createVariable('votemper', 'float32',\n",
     "                               ('time_counter','deptht','y','x'))\n",
     "votemper.units = 'degC'\n",
-    "votemper.long_name = 'Temperature' \n",
+    "votemper.long_name = 'Temperature'\n",
     "votemper.coordinates = 'nav_lon nav_lat deptht time_counter'\n",
     "votemper[0] = T\n",
     "new_TS.history = \"\"\"[2015-12-05] Created\"\"\""

I_ForcingFiles/Initial/README.md

@@ -14,7 +14,7 @@ Descriptions below the links are from the first cell of the notebooks
 
 ##License
 
-These notebooks and files are copyright 2013-2021
+These notebooks and files are copyright 2013 – present
 by the [Salish Sea MEOPAR Project Contributors](https://github.com/SalishSeaCast/docs/blob/master/CONTRIBUTORS.rst)
 and The University of British Columbia.
 

I_ForcingFiles/Initial/make_readme.py

@@ -1,7 +1,7 @@
 """Salish Sea NEMO Jupyter Notebook collection README generator
 
 
-Copyright 2013-2021 The Salish Sea MEOPAR Contributors
+Copyright 2013 – present The Salish Sea MEOPAR Contributors
 and The University of British Columbia
 
 Licensed under the Apache License, Version 2.0 (the "License");

I_ForcingFiles/LookAtOthersFiles/README.md

@@ -15,7 +15,7 @@ Descriptions below the links are from the first cell of the notebooks
 
 ##License
 
-These notebooks and files are copyright 2013-2021
+These notebooks and files are copyright 2013 – present
 by the [Salish Sea MEOPAR Project Contributors](https://github.com/SalishSeaCast/docs/blob/master/CONTRIBUTORS.rst)
 and The University of British Columbia.
 

I_ForcingFiles/LookAtOthersFiles/make_readme.py

@@ -1,7 +1,7 @@
 """Salish Sea NEMO Jupyter Notebook collection README generator
 
 
-Copyright 2013-2021 The Salish Sea MEOPAR Contributors
+Copyright 2013 – present The Salish Sea MEOPAR Contributors
 and The University of British Columbia
 
 Licensed under the Apache License, Version 2.0 (the "License");

I_ForcingFiles/OBC/README.md

@@ -74,8 +74,8 @@ Descriptions below the links are from the first cell of the notebooks
 
 ##License
 
-These notebooks and files are copyright 2013-2021
-by the [Salish Sea MEOPAR Project Contributors](https://github.com/SalishSeaCast/docs/blob/master/CONTRIBUTORS.rst)
+These notebooks and files are copyright 2013 – present
+by the [SalishSeaCast Project Contributors](https://github.com/SalishSeaCast/docs/blob/master/CONTRIBUTORS.rst)
 and The University of British Columbia.
 
 They are licensed under the Apache License, Version 2.0.

I_ForcingFiles/OBC/Reading Neah Bay Surge website.ipynb

@@ -48,8 +48,6 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "from __future__ import division\n",
-      "\n",
       "import netCDF4 as nc\n",
       "import numpy as np\n",
       "\n",

I_ForcingFiles/OBC/make_readme.py

@@ -1,7 +1,7 @@
 """Salish Sea NEMO Jupyter Notebook collection README generator
 
 
-Copyright 2013-2021 The Salish Sea MEOPAR Contributors
+Copyright 2013– present by the SalishSeaCast Contributors
 and The University of British Columbia
 
 Licensed under the Apache License, Version 2.0 (the "License");
@@ -63,7 +63,7 @@
 ##License
 
 These notebooks and files are copyright 2013-{this_year}
-by the [Salish Sea MEOPAR Project Contributors](https://github.com/SalishSeaCast/docs/blob/master/CONTRIBUTORS.rst)
+by the [SalishSeaCast Project Contributors](https://github.com/SalishSeaCast/docs/blob/master/CONTRIBUTORS.rst)
 and The University of British Columbia.
 
 They are licensed under the Apache License, Version 2.0.

I_ForcingFiles/Rivers/README.md

@@ -25,7 +25,7 @@ Descriptions below the links are from the first cell of the notebooks
 
 ##License
 
-These notebooks and files are copyright 2013-2021
+These notebooks and files are copyright 2013 – present
 by the [Salish Sea MEOPAR Project Contributors](https://github.com/SalishSeaCast/docs/blob/master/CONTRIBUTORS.rst)
 and The University of British Columbia.
 

I_ForcingFiles/Rivers/Rivers_2m.ipynb

@@ -11,9 +11,7 @@
     {
      "cell_type": "markdown",
      "metadata": {},
-     "source": [
-      "Notebook to create new river files at 2 m depth. "
-     ]
+     "source": "Notebook to create new river files at 2 m depth."
     },
     {
      "cell_type": "code",
@@ -23,7 +21,6 @@
       "import netCDF4 as NC\n",
       "import numpy as np\n",
       "from salishsea_tools import nc_tools\n",
-      "from __future__ import division\n",
       "import matplotlib.pylab as plt\n",
       "\n",
       "%matplotlib inline"
@@ -161,7 +158,7 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "#rivers_2m.variables['rodepth'][:] = \n",
+      "#rivers_2m.variables['rodepth'][:] =\n",
       "rivers2m=NC.Dataset('rivers_2m_month.nc','r+')\n",
       "rivers2m.description = 'Monthly Averages, All Rivers, depth 2m'\n",
       "rivers2m.history = 'River files to 2 m depth'\n",
@@ -190,7 +187,7 @@
         "    description: Monthly Averages, All Rivers, depth 2m\n",
         "    history: River files to 2 m depth\n",
         "    dimensions(sizes): x(398), y(898), time_counter(12)\n",
-        "    variables(dimensions): float32 \u001b[4mnav_lat\u001b[0m(y,x), float32 \u001b[4mnav_lon\u001b[0m(y,x), float32 \u001b[4mtime_counter\u001b[0m(time_counter), float32 \u001b[4mrorunoff\u001b[0m(time_counter,y,x), float32 \u001b[4mrodepth\u001b[0m(y,x)\n",
+        "    variables(dimensions): float32 \u001B[4mnav_lat\u001B[0m(y,x), float32 \u001B[4mnav_lon\u001B[0m(y,x), float32 \u001B[4mtime_counter\u001B[0m(time_counter), float32 \u001B[4mrorunoff\u001B[0m(time_counter,y,x), float32 \u001B[4mrodepth\u001B[0m(y,x)\n",
         "    groups: \n",
         "\n"
        ]

I_ForcingFiles/Rivers/make_readme.py

@@ -1,7 +1,7 @@
 """Salish Sea NEMO Jupyter Notebook collection README generator
 
 
-Copyright 2013-2021 The Salish Sea MEOPAR Contributors
+Copyright 2013 – present by the SalishSeaCast Contributors
 and The University of British Columbia
 
 Licensed under the Apache License, Version 2.0 (the "License");
@@ -59,7 +59,7 @@
 ##License
 
 These notebooks and files are copyright 2013-{this_year}
-by the [Salish Sea MEOPAR Project Contributors](https://github.com/SalishSeaCast/docs/blob/master/CONTRIBUTORS.rst)
+by the [SalishSeaCast Project Contributors](https://github.com/SalishSeaCast/docs/blob/master/CONTRIBUTORS.rst)
 and The University of British Columbia.
 
 They are licensed under the Apache License, Version 2.0.