Merge pull request #313 from jmccreight/feat_tidy4release

tidy for release

.github/workflows/ci_examples.yaml

@@ -46,7 +46,7 @@ jobs:
         uses: mamba-org/[email protected]
         with:
           micromamba-version: '1.5.10-0'
-          environment-file: environment.yml
+          environment-file: environment_w_jupyter.yml
           cache-environment: true
           cache-downloads: true
 

doc/api/flow_graph.rst

@@ -13,9 +13,9 @@ FlowGraph base classes and subclasses. See :class:`FlowGraph` for an overview of
    FlowGraph
    FlowNode
    FlowNodeMaker
-   PassThroughNode
+   PassThroughFlowNode
    PassThroughNodeMaker
-   ObsInNode
+   ObsInFlowNode
    ObsInNodeMaker
    StarfitFlowNode
    StarfitFlowNodeMaker

doc/api/hydrology.rst

@@ -1,6 +1,6 @@
 .. currentmodule:: pywatershed
 
-		   
+
 ----------
 Hydrology
 ----------
@@ -13,7 +13,10 @@ Hydrologic model components.
    PRMSCanopy
    PRMSSnow
    PRMSRunoff
+   PRMSRunoffNoDprst
    PRMSSoilzone
+   PRMSSoilzoneNoDprst
    PRMSGroundwater
+   PRMSGroundwaterNoDprst
    PRMSChannel
    Starfit

doc/index.rst

@@ -66,24 +66,26 @@ and the `extended release notes <https://ec-usgs.github.io/pywatershed/2023/12/1
 for version 1.0.0.
 
 ===================================
-Current version: 2.0.0 (unreleased)
+Version: 2.0.0 (2024-11-14)
 ===================================
 With pywatershed version 2.0.0, we introduce the :class:`FlowGraph` capabilities that allow
 users to combine different kinds flow solutions in arbitrary order on a "flow graph". 
 
-Version 2.0.0 also introduces several important PRMS capabilities beyond those included in
+Version 2.0.0 introduces several important PRMS capabilities beyond those included in
 the `National Hydrolgical Model <https://pubs.usgs.gov/publication/tm6B9>`__ (NHM, Regan et al.,
-2018).
+2018): Dunnian flow in Soilzone is 2-way coupled to PRMSRunoff, preferential flows is implemented
+in PRMSSoilzone, and depression storage can be optionally selected (across PRMSRunoff, PRMSSoilzone,
+and PRMSGroundwater).
 
 Version 2.0.0 also includes capabilties to translate :class:`PRMSChannel` simulations
-into 1-D diffusive wave simulations in MODFLOW 6's development branch.
+into 1-D diffusive wave simulations in MODFLOW 6's development branch using :class:`MmrToMf6Dfw`.
 
 For more information on version 2.0.0 see the
 `release notes <https://github.com/EC-USGS/pywatershed/releases/tag/2.0.0>`_
-and the `extended release notes <https://ec-usgs.github.io/pywatershed/2024/12/18/v2-0-0-overview>`_.
+and the `extended release notes <https://ec-usgs.github.io/pywatershed/2024/11/14/v2-0-0-overview>`_.
 
 ============================================
-Upcoming development in 2024
+Upcoming development
 ============================================
 The broad goal is to reproduce GSFLOW coupling using the MODFLOW 6 API. This will include
 gridded configurations and cascading flows.

doc/whats-new.rst

@@ -12,9 +12,9 @@ What's New
     np.random.seed(123456)
 
 
-.. _whats-new.1.2.0:
+.. _whats-new.2.0.0:
 
-v2.0.0 (Unreleased)
+v2.0.0 (14 November 2024)
 ---------------------
 
 New Features
@@ -23,7 +23,7 @@ New Features
   combine different kinds flow solutions in arbitrary order on a "flow graph".
   The accompanying base classes :class:`FlowNode` and :class:`FlowNodeMaker`
   are introduced along with their subclasses for modeling
-  :class:`PassThroughNode`\ s, :class:`ObsInNode`\ s (flow replacement by
+  :class:`PassThroughFlowNode`\ s, :class:`ObsInFlowNode`\ s (flow replacement by
   observations with sink and source tracking in mass balance),
   :class:`PRMSChannelFlowNode`\ s, and :class:`StarfitFlowNode`\ s. A new
   example notebook,
@@ -37,26 +37,21 @@ New Features
   conditions. A new notebook runs the Delaware River Basin using MF6 DFW:
   `examples/07_mmr_to_mf6_chf_dfw.ipynb <https://github.com/EC-USGS/pywatershed/blob/develop/examples/07_mmr_to_mf6_chf_dfw.ipynb>`__.
   (:pull:`290`) By `James McCreight <https://github.com/jmccreight>`_.
-- The depression storage option for PRMSRunoff is implemented and tested.
-  (:pull:`279`) By `James McCreight <https://github.com/jmccreight>`_.
 - No depression storage subclasses are available for PRMSRunoff, PRMSSoilzone,
   and PRMSGroundwater by adding "NoDprst" to the end of the names. Depression
   storage is switched off in sagehen_5yr and in new nhm_no_dprst
   configurations.
   (:pull:`288`) By `James McCreight <https://github.com/jmccreight>`_.
-- Dunnian flow is implemented (in PRMSSoilzone) and tested for sagehen_5yr
-  whereas it was effectively off in all NHM configurations and its effect
-  on the sroff variable (in PRMSRunoff) incorrect.
+- Dunnian flow is implemented (in PRMSSoilzone) and tested for sagehen_5yr.
   (:pull:`288`) By `James McCreight <https://github.com/jmccreight>`_.
-- Preferential flow is implemented (in PRMSSoilzone) and tested for sagehen_5yr
-  whereas it was effectively off in all NHM configurations.
+- Preferential flow is implemented (in PRMSSoilzone) and tested for sagehen_5yr.
   (:pull:`288`) By `James McCreight <https://github.com/jmccreight>`_.
 - Control instances have a diff method to compare with other instances.
   (:pull:`288`) By `James McCreight <https://github.com/jmccreight>`_.
 - Feature to standardize subsetting input data (parameters and forcings) in
   space and time either from file (:func:`utils.netcdf_utils.subset_netcdf_file`) or
   in memory (:func:`utils.netcdf_utils.subset_xr`).
-  (:pull:`304`) By `James McCreight <https://github.com/jmccreight>`_.  
+  (:pull:`304`) By `James McCreight <https://github.com/jmccreight>`_.
 
 Breaking Changes
 ~~~~~~~~~~~~~~~~

environment.yml

@@ -5,7 +5,6 @@ channels:
   - pyviz
   - bioconda
 dependencies:
-  - bash_kernel
   - cartopy
   - dataretrieval
   - contextily
@@ -18,8 +17,6 @@ dependencies:
   - holoviews
   - hvplot
   - ipython
-  - ipywidgets
-  - nb_conda_kernels
   - nbconvert
   - netCDF4
   - networkx

environment_w_jupyter.yml

@@ -5,7 +5,6 @@ channels:
   - pyviz
   - bioconda
 dependencies:
-  - bash_kernel
   - cartopy
   - dataretrieval
   - contextily
@@ -21,7 +20,6 @@ dependencies:
   - ipywidgets
   - jupyter
   - jupyterlab
-  - nb_conda_kernels
   - nbconvert
   - netCDF4
   - networkx

pywatershed/base/flow_graph.py

@@ -182,7 +182,7 @@ class FlowGraph(ConservativeProcess):
     :func:`prms_channel_flow_graph_to_model_dict`
     and :func:`prms_channel_flow_graph_postprocess`.
 
-    For developers looking to add new :class:`FlowNode`s, please read the
+    For developers looking to add new :class:`FlowNode`\s, please read the
     :class:`FlowNode` base class code and also the code for
     :class:`FlowNodeMaker`.
 

pywatershed/hydrology/prms_soilzone.py

@@ -35,6 +35,10 @@ class PRMSSoilzone(ConservativeProcess):
     Techniques and Methods, 6, B7.
     <https://pubs.usgs.gov/tm/6b7/pdf/tm6-b7.pdf>`__
 
+    Note that as of pywatershed version 2.0.0, pref_flow_infil_frac is a
+    required parameters which is optional in PRMS. Specifying zeros for all
+    HRUs gives the same behavior as not supplying the parameter to PRMS.
+
     Args:
         control: a Control object
         discretization: a discretization of class Parameters

pywatershed/hydrology/prms_soilzone_no_dprst.py

@@ -22,6 +22,10 @@ class PRMSSoilzoneNoDprst(PRMSSoilzone):
     Techniques and Methods, 6, B7.
     <https://pubs.usgs.gov/tm/6b7/pdf/tm6-b7.pdf>`__
 
+    Note that as of pywatershed version 2.0.0, pref_flow_infil_frac is a
+    required parameters which is optional in PRMS. Specifying zeros for all
+    HRUs gives the same behavior as not supplying the parameter to PRMS.
+
     Args:
         control: a Control object
         discretization: a discretization of class Parameters