build(deps): bump actions/setup-python from 6 to 7

.github/workflows/build_docs.yaml

@@ -15,15 +15,15 @@ jobs:
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
       with:
         persist-credentials: false
 
     - name: Fetch all Git tags
       run: git fetch --prune --unshallow --tags
 
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v3
       with:
         environment-file: ci/test_environment.yaml
         cache-environment: false
@@ -80,7 +80,7 @@ jobs:
         make -C docs html
 
     - name: Deploy 🚀
-      uses: JamesIves/github-pages-deploy-action@v4.7.2
+      uses: JamesIves/github-pages-deploy-action@v4.8.0
       if: ${{ github.event_name == 'release' }}
       with:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -90,7 +90,7 @@ jobs:
         TARGET_FOLDER: ${{ github.ref }}
 
     - name: Deploy 🚀
-      uses: JamesIves/github-pages-deploy-action@v4.7.2
+      uses: JamesIves/github-pages-deploy-action@v4.8.0
       if: ${{ github.event_name == 'push' }}
       with:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/release.yml

@@ -22,7 +22,7 @@ jobs:
       pull-requests: write
     steps:
       - name: Checkout master branch
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           ref: master
       - name: Bump version and push tag
@@ -51,7 +51,7 @@ jobs:
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
       with:
         persist-credentials: false
         ref: master
@@ -67,7 +67,7 @@ jobs:
         echo ${{ steps.get_version.outputs.version }}
 
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v3
       with:
         environment-file: ci/test_environment.yml
         cache-environment: true
@@ -113,7 +113,7 @@ jobs:
         make -C docs html
 
     - name: Deploy 🚀
-      uses: JamesIves/github-pages-deploy-action@v4.7.2
+      uses: JamesIves/github-pages-deploy-action@v4.8.0
       with:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         BRANCH: gh-pages
@@ -137,13 +137,13 @@ jobs:
     steps:
 
       - name: Checkout master branch
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           ref: master
           fetch-tags: true
 
       - name: Setup Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: '3.x'
           cache: 'pip'
@@ -161,7 +161,7 @@ jobs:
         run: twine check --strict dist/*
 
       - name: Upload package
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: dist
           path: dist

.github/workflows/test.yaml

@@ -29,7 +29,7 @@ jobs:
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
       with:
         persist-credentials: false
 
@@ -41,7 +41,7 @@ jobs:
       run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"
 
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v3
       with:
         environment-file: ci/test_environment.yaml
         cache-environment: false
@@ -78,11 +78,27 @@ jobs:
         cp -r bin/$d/. "$HOME/.local/bin/"
         echo "$HOME/.local/bin" >> $GITHUB_PATH
         echo $GITHUB_PATH
-    # on Windows, test against last Flopy release
-    - name: Install latest PyPI flopy
+    - name: Test with latest PyPI flopy
       shell: bash -l {0}
-      if: contains(matrix.os, 'windows')
-      run: pip install flopy --force-reinstall
+      if: ${{ matrix.python-version == 3.12}}
+      run: |
+        pip install flopy
+        pip install git+https://github.com/aleaf/modflow-export@develop
+        pip install git+https://github.com/usgs/sfrmaker@develop
+    - name: Test with latest conda flopy
+      shell: bash -l {0}
+      if: ${{ matrix.python-version == 3.13}}
+      run: |
+        micromamba install flopy
+        pip install git+https://github.com/aleaf/modflow-export@develop
+        pip install git+https://github.com/usgs/sfrmaker@develop
+    - name: Test with latest develop flopy and pandas 3
+      shell: bash -l {0}
+      if: ${{ matrix.python-version == 3.14}}
+      run: |
+        pip install git+https://github.com/modflowpy/flopy@develop --no-deps
+        pip install git+https://github.com/aleaf/modflow-export@develop
+        pip install git+https://github.com/usgs/sfrmaker@develop
     - name: Install Modflow-setup and ipykernel
       shell: bash -l {0}
       run: |

.github/workflows/test_releases.yml

@@ -16,14 +16,14 @@ jobs:
         shell: bash -l {0}
     steps:
     - name: Checkout source
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
     - name: Fetch all Git tags
       run: git fetch --prune --unshallow --tags
     - name: Get current date
       id: date
       run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"
     - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v3
       with:
         environment-file: ci/test_environment.yaml
         cache-environment: false

ci/test_environment.yaml

@@ -27,7 +27,7 @@ dependencies:
 - coverage
 - flake8
 - pytest
-- sphinx=8.1.3
+- sphinx
 - numpydoc
 - nbsphinx  # for rendering notebooks in sphinx-generated docs
 - sphinx-copybutton
@@ -36,6 +36,3 @@ dependencies:
 - pip:
   - gis-utils
   - pytest-timeout
-  - git+https://github.com/modflowpy/flopy@develop
-  - git+https://github.com/aleaf/modflow-export@develop
-  - git+https://github.com/usgs/sfrmaker@develop

docs/source/conf.py

@@ -75,6 +75,11 @@
 autosummary_generate = True
 numpydoc_show_class_members = False
 
+# Only generate for top n sections
+# (and then only use sections headers need to be unique;
+#  duplicate headers are allowed below this level)
+#autosectionlabel_maxdepth=2
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

docs/source/release-history.rst

@@ -2,22 +2,31 @@
 Release History
 ===============
 
+Version 0.8.0 (2026-02-xx)
+----------------------------------------
+**New Features:**
+ * Add support for Pandas 3
+ * Add support for geopackage input with layernames (specified in format: filename>.gpkg|layername=<layer name> or filename>.gpkg|layer=<layer name>), for example as a way to specify the active model extent (e.g. in the source_data: idomain: block for Modflow 6 models)
+
+**Bug Fixes:**
+ * fixes to SFR Package setup:
+     * re-adjust SFR package layering each time idomain is adjusted, to prevent SFR in inactive cells (SFR reaches with no groundwater connections)
+     * write SFR Package shapefiles when MODFLOW input is written, so that the shapefiles reflect the final state of the SFR package
+
 Version 0.7.0 (2025-12-31)
 ----------------------------------------
-New Features:
-**************
+**New Features:**
  * Added partial support for GeoPackages (.gpkg) input
  * Added support for SFRmaker streambed top field elevations input.
  * Add auto_flow_reduce = 0.1 by default in MF6 model Well Packages
 
-Bug Fixes:
-*************
+**Bug Fixes:**
  * Refactor np.in1d to np.isin to resolve numpy error
  * Refactoring to support various Flopy interface changes
  * Allow shapefile input with no 'id_column' for basic stress packages
  * Fix issue with Well Package layer assignment in cases where there is no open interval information (only well bottom). When there is only screen_top or screen_botm, or screen_top == screen_botm, set the screen_top and screen_botm to the top/bottom of layer intersecting the well bottom (i.e. so that the well is placed in this layer). Previously, a zero open interval thickness in these situations was resulting in the well getting re-assigned to the highest transmissivity layer at that i, j location.
-* Fix issue with MODFLOW 6 configuration file defaults: Well Package auto_flow_reduce needs to be a float (not True, which will result in an auto flow reduce value of 1.0 being assigned (almost full suppression of pumping); set auto_flow_reduce default of 0.1
-* Fix issue with Well Package Setup: Pass non-default screen_top_col and screen_botm_col to assign_layers_from_screen_top_botm; otherwise an error results when non-default names for these are used.
+ * Fix issue with MODFLOW 6 configuration file defaults: Well Package auto_flow_reduce needs to be a float (not True, which will result in an auto flow reduce value of 1.0 being assigned (almost full suppression of pumping); set auto_flow_reduce default of 0.1.
+ * Fix issue with Well Package Setup: Pass non-default screen_top_col and screen_botm_col to assign_layers_from_screen_top_botm; otherwise an error results when non-default names for these are used.
 
 Version 0.6.1 (2025-03-17)
 ----------------------------------------

mfsetup/bcs.py

@@ -92,7 +92,7 @@ def setup_basic_stress_data(model, shapefile=None, csvfile=None,
         return
 
     # create polygons of model grid cells
-    if bc_cells.dtype == object:
+    if pd.api.types.is_string_dtype(bc_cells.dtype):
         cells_with_bc = bc_cells.flat != ''
     else:
         cells_with_bc = bc_cells.flat > 0
@@ -108,7 +108,7 @@ def setup_basic_stress_data(model, shapefile=None, csvfile=None,
                        'i': i.flat,
                        'j': j.flat})
     # add the boundnames
-    if bc_cells.dtype == object:
+    if pd.api.types.is_string_dtype(bc_cells.dtype):
         df_0['boundname'] = bc_cells.flat
         nan_boundnames = df_0.boundname.isna() | df_0.boundname.isin({'', 'nan'})
         df_0.loc[nan_boundnames, 'boundname'] = 'unnamed'

mfsetup/fileio.py

@@ -124,7 +124,7 @@ def load_array(filename, shape=None, nodata=-9999):
         print(txt, end=', ')
         # arr = np.loadtxt
         # pd.read_csv is >3x faster than np.load_txt
-        arr = pd.read_csv(f, delim_whitespace=True, header=None).values
+        arr = pd.read_csv(f, sep=r'\s+', header=None).values
         if shape2d is not None:
             if arr.shape != shape2d:
                 if arr.size == np.prod(shape2d):
@@ -1146,7 +1146,7 @@ def read_ggofile(gagefile, model,
         names = [n.lower() for n in names]
         df = pd.read_csv(src, skiprows=0,
                             header=None,
-                            delim_whitespace=True,
+                            sep=r'\s+',
                             names=names
                             )
     kstp = []

mfsetup/grid.py

@@ -633,7 +633,7 @@ def write_bbox_shapefile(modelgrid, outshp):
     gdf.to_file(outshp, index=False)
 
 
-def rasterize(feature, grid, id_column=None,
+def rasterize(feature, grid, layer=None, id_column=None,
               include_ids=None, exclude_ids=None, names_column=None,
               crs=None, **kwargs):
     """Rasterize a feature onto the model grid, using
@@ -642,8 +642,10 @@ def rasterize(feature, grid, id_column=None,
 
     Parameters
     ----------
-    feature : str (shapefile path), list of shapely objects,
+    feature : str (shapefile or geopackage path), list of shapely objects,
               or dataframe with geometry column
+    layer : str
+        Layer name containing the feature (for example, in a geopackage)
     id_column : str
         Column with unique integer identifying each feature; values
         from this column will be assigned to the output raster.
@@ -695,7 +697,7 @@ def rasterize(feature, grid, id_column=None,
     trans = get_transform(grid)
 
     if isinstance(feature, str) or isinstance(feature, Path):
-        df = gpd.read_file(feature)
+        df = gpd.read_file(feature, layer=layer)
     elif isinstance(feature, pd.DataFrame):
         df = feature.copy()
         df = gpd.GeoDataFrame(df, crs=crs)
@@ -747,7 +749,7 @@ def rasterize(feature, grid, id_column=None,
         numbers = list(range(1, len(df)+1))
     # if IDs are strings, get a number for each one
     # pd.DataFrame.unique() generally preserves order
-    elif df[id_column].dtype == object:
+    elif pd.api.types.is_string_dtype(df[id_column].dtype):
         unique_values = df[id_column].unique()
         values = dict(zip(unique_values, range(1, len(unique_values) + 1)))
         numbers = [values[n] for n in df[id_column]]

mfsetup/mf6model.py

@@ -220,7 +220,7 @@ def _set_idomain(self):
 
         # remove cells that are above stream cells
         if self.get_package('sfr') is not None:
-            idomain = deactivate_idomain_above(idomain, self.sfr.packagedata)
+            idomain = deactivate_idomain_above(idomain, self.sfrdata.reach_data)
 
         # inactivate any isolated cells that could cause problems with the solution
         idomain = find_remove_isolated_cells(idomain, minimum_cluster_size=20)
@@ -262,7 +262,10 @@ def _set_idomain(self):
                                 data={0: irch},
                                 datatype='array2d',
                                 write_fmt='%d', dtype=int)
-        #self.dis.irch = self.cfg['dis']['irch']
+
+        if hasattr(self, 'sfrdata'):
+            self.adjust_sfr_layers_model_bottom()
+
 
     def _update_grid_configuration_with_dis(self):
         """Update grid configuration with any information supplied to dis package
@@ -1045,6 +1048,12 @@ def skip_write(**kwargs):
                                         options=options,
                                         external_files_path=model.external_path
                                         )
+                # write reach and segment data tables
+                model.sfrdata.write_tables('{}/{}'.format(self._tables_path, self.name))
+
+                # export shapefiles of lines, routing, cell polygons, inlets and outlets
+                model.sfrdata.write_shapefiles('{}/{}'.format(self._shapefiles_path, self.name))
+
             # add version info to package file headers
             files = [model.namefile]
             files += [p.filename for p in model.packagelist]