Merge pull request #2509 from modflowpy/v3.9.3

Release 3.9.3

Author: wpbonelli

.docs/Notebooks/mf6_complex_model_example.py

@@ -267,7 +267,6 @@
             0.5,
             0.3,
             0.1,
-            None,
         )
 evt = flopy.mf6.ModflowGwfevt(
     gwf,

.docs/Notebooks/mf6_parallel_model_splitting_example.py

@@ -768,3 +768,69 @@ def string2geom(geostring, conversion=None):
             sa = np.array(seg)
             ax.plot(sa[:, 0], sa[:, 1], "b-")
 # -
+
+# ### Save node mapping data
+#
+# The `save_node_mapping()` method allows users to save a HDF5 representation of model splitter information that can be reloaded and used to reconstruct arrays at a later time
+
+# +
+filename = workspace / "node_mapping.hdf5"
+mfsplit.save_node_mapping(filename)
+# -
+
+# ### reloading node mapping data
+#
+# The `load_node_mapping()` method allows the user to instantiate a Mf6Splitter object from a hdf5 node mapping file for reconstructing output arrays
+
+# +
+mfs = Mf6Splitter.load_node_mapping(filename)
+# -
+
+# Reconstruct heads using the `Mf6Splitter` object we just created
+
+# +
+model_names = list(new_sim.model_names)
+head_dict = {}
+for modelname in model_names:
+    mnum = int(modelname.split("_")[-1])
+    head = new_sim.get_model(modelname).output.head().get_alldata()[-1]
+    head_dict[mnum] = head
+
+ra_heads = mfs.reconstruct_array(head_dict)
+ra_watertable = flopy.utils.postprocessing.get_water_table(ra_heads)
+# -
+
+# +
+with styles.USGSMap():
+    fig, axs = plt.subplots(nrows=3, figsize=(8, 12))
+    diff = ra_heads - heads
+    hv = [ra_heads, heads, diff]
+    titles = ["Multiple models", "Single model", "Multiple - single"]
+    for idx, ax in enumerate(axs):
+        ax.set_aspect("equal")
+        ax.set_title(titles[idx])
+
+        if idx < 2:
+            levels = contours
+            vmin = hmin
+            vmax = hmax
+        else:
+            levels = None
+            vmin = None
+            vmax = None
+
+        pmv = flopy.plot.PlotMapView(modelgrid=gwf.modelgrid, ax=ax, layer=0)
+        h = pmv.plot_array(hv[idx], vmin=vmin, vmax=vmax)
+        if levels is not None:
+            c = pmv.contour_array(
+                hv[idx], levels=levels, colors="white", linewidths=0.75, linestyles=":"
+            )
+            plt.clabel(c, fontsize=8)
+        pmv.plot_inactive()
+        plt.colorbar(h, ax=ax, shrink=0.5)
+
+        ax.plot(bp[:, 0], bp[:, 1], "r-")
+        for seg in segs:
+            sa = np.array(seg)
+            ax.plot(sa[:, 0], sa[:, 1], "b-")
+# -

.docs/Notebooks/plot_map_view_example.py

@@ -56,7 +56,7 @@
 sim_name = "freyberg"
 
 # Set the paths
-tempdir = TemporaryDirectory(delete=False)
+tempdir = TemporaryDirectory()
 modelpth = Path(tempdir.name)
 
 # Check if we are in the repository and define the data path.

.docs/md/generate_classes.md

@@ -10,7 +10,9 @@
 
 MODFLOW 6 input continues to evolve as new models, packages, and options are developed, updated, and supported. All MODFLOW 6 input is described by DFN (definition) files, which are simple text files that describe the blocks and keywords in each input file. These definition files are used to build the input and output guide for MODFLOW 6. These definition files are also used to automatically generate FloPy classes for creating, reading and writing MODFLOW 6 models, packages, and options.  FloPy and MODFLOW 6 are kept in sync by these DFN (definition) files, and therefore, it may be necessary for a user to update FloPy using a custom set of definition files, or a set of definition files from a previous release.
 
-The FloPy classes for MODFLOW 6 are largely generated by a utility which converts DFN files in a modflow6 repository on GitHub or on the local machine into Python source files in your local FloPy install. For instance (output much abbreviated):
+The FloPy classes for MODFLOW 6 are largely generated by a utility which converts DFN files in a modflow6 repository on GitHub or on the local machine into Python source files in your local FloPy install.
+
+**Note**: to use this functionality, the `codegen` optional dependency group must be installed.
 
 ```bash
 $ python -m flopy.mf6.utils.generate_classes
@@ -19,9 +21,9 @@ $ python -m flopy.mf6.utils.generate_classes
 
 ************************************************************************
 Updating the flopy MODFLOW 6 classes
-  Updating the MODFLOW 6 classes using MODFLOW-USGS/modflow6/master
-  Downloading MODFLOW 6 repository from https://github.com/MODFLOW-USGS/modflow6/archive/master.zip
-Downloading https://github.com/MODFLOW-USGS/modflow6/archive/master.zip
+  Updating the MODFLOW 6 classes using MODFLOW-ORG/modflow6/master
+  Downloading MODFLOW 6 repository from https://github.com/MODFLOW-ORG/modflow6/archive/master.zip
+Downloading https://github.com/MODFLOW-ORG/modflow6/archive/master.zip
    file size: 15,821,180 bytes
 
 total download time: 0.88 seconds
@@ -65,7 +67,7 @@ user.
 
 options:
   -h, --help         show this help message and exit
-  --owner OWNER      GitHub repository owner; default is 'MODFLOW-USGS'.
+  --owner OWNER      GitHub repository owner; default is 'MODFLOW-ORG'.
   --repo REPO        Name of GitHub repository; default is 'modflow6'.
   --ref REF          Branch name, tag, or commit hash to use to update the
                      definition; default is 'master'.

.docs/md/get_modflow.md

@@ -75,7 +75,7 @@ Other auto-select options are only available if the current user can write files
 
 ## Selecting a distribution
 
-By default the distribution from the [`MODFLOW-USGS/executables` repository](https://github.com/MODFLOW-USGS/executables) is installed. This includes the MODFLOW 6 binary `mf6` and over 20 other related programs. The utility can also install from the main [MODFLOW 6 repo](https://github.com/MODFLOW-USGS/modflow6) or the [nightly build](https://github.com/MODFLOW-USGS/modflow6-nightly-build) distributions, which contain only:
+By default the distribution from the [`MODFLOW-ORG/executables` repository](https://github.com/MODFLOW-ORG/executables) is installed. This includes the MODFLOW 6 binary `mf6` and over 20 other related programs. The utility can also install from the main [MODFLOW 6 repo](https://github.com/MODFLOW-ORG/modflow6) or the [nightly build](https://github.com/MODFLOW-ORG/modflow6-nightly-build) distributions, which contain only:
 
 - `mf6`
 - `mf5to6`

.docs/md/optional_dependencies.md

@@ -13,7 +13,7 @@ Dependencies for optional features are listed below. These may be installed with
 | `.resample_to_grid()` in `flopy.utils.rasters`                                       | **scipy.interpolate**                                                    |
 | `.interpolate()` in `flopy.mf6.utils.reference` `StructuredSpatialReference` class   | **scipy.interpolate**                                                    |
 | `.get_authority_crs()` in `flopy.utils.crs`                                          | **pyproj** >= 2.2.0                                                      |
-| `.generate_classes()` in `flopy.mf6.utils`                                           | [**modflow-devtools**](https://github.com/MODFLOW-USGS/modflow-devtools) |
+| `.generate_classes()` in `flopy.mf6.utils`                                           | [**modflow-devtools**](https://github.com/MODFLOW-ORG/modflow-devtools) |
 | `GridIntersect()` in `flopy.utils.gridintersect`                                     | **shapely**                                                              |
 | `GridIntersect().plot_polygon()` in `flopy.utils.gridintersect`                      | **shapely** and **descartes**                                            |
 | `Raster()` in `flopy.utils.Raster`                                                   | **rasterio**, **rasterstats**, **affine**, and **scipy**                 |

.docs/md/version_changes.md

@@ -1,4 +1,33 @@
 # Changelog
+### Version 3.9.3
+
+#### New features
+
+* [feat(modeltime)](https://github.com/modflowpy/flopy/commit/932bdcc8c07a10148cf733c02ba9190167239066): Add from_headers and reverse methods (#2481). Committed by wpbonelli on 2025-03-29.
+* [feat](https://github.com/modflowpy/flopy/commit/d8048a868b51d75039f0c3c097429144c6d44714): Add the angldegx to the kw dictionary produced by the get_disu_kwargs method (#2484). Committed by Sunny Titus on 2025-04-14.
+
+#### Bug fixes
+
+* [fix(resolve_exe)](https://github.com/modflowpy/flopy/commit/ca3adb34031285bc795b58fa42c4965d67278adc): Typecast exe name to string before passing to _resolve (#2457). Committed by martclanor on 2025-02-20.
+* [fix(HeadFile,CellBudgetFile)](https://github.com/modflowpy/flopy/commit/39d8d32625151979d78b82e709fa46ca4f5f7d9f): Fix tdis reversal (#2460). Committed by wpbonelli on 2025-02-25.
+* [fix(output_util.py)](https://github.com/modflowpy/flopy/commit/61e52f03ff69ec50b03a17c863738ad4a3c1dc4b): Trap grb in MF6Output (#2468). Committed by wpbonelli on 2025-03-07.
+* [fix(binaryfile)](https://github.com/modflowpy/flopy/commit/02ab7f1ff18a5c03f06d98fe1b35d6d6f7ad12df): Tdis in head/budget reversal methods (#2475). Committed by wpbonelli on 2025-03-18.
+* [fix(binaryfile)](https://github.com/modflowpy/flopy/commit/0eba4babad994a7cd73a3853714b9ff3bb326c90): Fix head/budget file reversal (#2483). Committed by wpbonelli on 2025-04-01.
+* [fix(flopy/utils/sfroutputfile.py::SfrFile.get_results)](https://github.com/modflowpy/flopy/commit/bf02be00ded034d2765948c7d7b075bf9d6ed4f1): Refactor deprecated DataFrame.append() call to pandas.concat() (#2491). Committed by aleaf on 2025-04-21.
+* [fix(model_splitter.py)](https://github.com/modflowpy/flopy/commit/838b37cc999c713aa7e71c4215f7535c5c9df27b): Add trap for obs packages in bc packages (#2493). Committed by Joshua Larsen on 2025-04-22.
+* [fix(evt)](https://github.com/modflowpy/flopy/commit/dcba9cf5ca1d8b946b568748f713a6dcf21e2bc3): Optional field mishandling (#2490). Committed by mjreno on 2025-04-23.
+* [fix](https://github.com/modflowpy/flopy/commit/0d9c91489a6a9df2c2c51c962e59cb5e9dd4ff2b): Update numpy array comparisons to use isin (#2504). Committed by Emmanuel Ferdman on 2025-05-06.
+* [fix(column lengths)](https://github.com/modflowpy/flopy/commit/351c5b72401b5de52d230ef9f0897f58e4edf475): Autoscale array write to ncol for structured multi-model simulations (#2507). Committed by Joshua Larsen on 2025-05-12.
+
+#### Refactoring
+
+* [refactor(resolve_exe)](https://github.com/modflowpy/flopy/commit/c61643fd8d61e6e4866527104324a6c468eb0e41): Also fix tests (#2464). Committed by Mike Taves on 2025-03-03.
+* [refactor(createpackages)](https://github.com/modflowpy/flopy/commit/c5b5a41f626ad24d8f0e564a83ab8dc673cc9b7b): Use jinja for mf6 module code generation (#2333). Committed by wpbonelli on 2025-03-07.
+* [refactor(Mf6Splitter)](https://github.com/modflowpy/flopy/commit/20829b704b20be5175119fcd685fe808c55d51b6): Change how node mapping is stored and loaded (#2465). Committed by Joshua Larsen on 2025-03-14.
+* [refactor(gridutil)](https://github.com/modflowpy/flopy/commit/48f46fb87a1a23bc13a41be881f3852fdab7d682): Improve arg handling in get_disu_kwargs (#2480). Committed by wpbonelli on 2025-04-01.
+* [refactor(model_splitter.py)](https://github.com/modflowpy/flopy/commit/14640530dd46598d8d76417b6b640db0850cbf80): Support for SSM and ATS (#2505). Committed by Joshua Larsen on 2025-05-08.
+* [refactor(codegen)](https://github.com/modflowpy/flopy/commit/69f6e09a8bea004454e9a83b76e5b37f8c0a7810): Move dfn utils from devtools (#2508). Committed by wpbonelli on 2025-05-13.
+
 ### Version 3.9.2
 
 #### New features

.github/workflows/benchmark.yml

@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ 3.9, "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.11", "3.12" ]
     defaults:
       run:
         shell: bash -l {0}
@@ -23,7 +23,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Python ${{ matrix.python-version }}
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           cache-dependency-glob: "**/pyproject.toml"
           python-version: ${{ matrix.python-version }}
@@ -80,13 +80,16 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           cache-dependency-glob: "**/pyproject.toml"
 
       - name: Install FloPy
         run: uv sync
 
+      - name: Install seaborn
+        run: uv pip install seaborn
+
       - name: Download all artifacts
         uses: actions/download-artifact@v4
         with:

.github/workflows/codegen.yml

@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ 3.9, "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.11", "3.12" ]
         ref: ["develop", "master", "6.4.1", "4458f9f", "4458f9f7a6244182e6acc2430a6996f9ca2df367"]
     defaults:
       run:
@@ -24,7 +24,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Python ${{ matrix.python-version }}
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           cache-dependency-glob: "**/pyproject.toml"
           python-version: ${{ matrix.python-version }}

.github/workflows/commit.yml

@@ -21,7 +21,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           enable-cache: false
 
@@ -44,7 +44,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           enable-cache: false
 
@@ -71,14 +71,14 @@ jobs:
         shell: bash
     timeout-minutes: 10
     env:
-      PYTHON_VERSION: 3.9
+      PYTHON_VERSION: '3.10'
 
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           cache-dependency-glob: "**/pyproject.toml"
 
@@ -116,7 +116,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ 3.9, "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.11", "3.12" ]
     defaults:
       run:
         shell: bash -l {0}
@@ -127,7 +127,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Python ${{ matrix.python-version }}
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
           cache-dependency-glob: "**/pyproject.toml"
           python-version: ${{ matrix.python-version }}

.github/workflows/examples.yml

@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ 3.9, "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.11", "3.12" ]
     defaults:
       run:
         shell: bash -l {0}
@@ -34,7 +34,9 @@ jobs:
             powershell
 
       - name: Install FloPy
-        run: pip install .
+        run: |
+          pip install .
+          pip install ".[codegen]"
 
       - name: OpenGL workaround on Linux
         if: runner.os == 'Linux'