From f502ba42de780475b1e43abfda9829951c65d262 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 5 Jan 2026 11:13:21 +0000
Subject: [PATCH 01/14] build(deps): bump actions/checkout from 5 to 6

Bumps [actions/checkout](https://github.com/actions/checkout) from 5 to 6.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v5...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/build_docs.yaml   | 2 +-
 .github/workflows/release.yml       | 6 +++---
 .github/workflows/test.yaml         | 2 +-
 .github/workflows/test_releases.yml | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build_docs.yaml b/.github/workflows/build_docs.yaml
index 8322999a..1094300d 100644
--- a/.github/workflows/build_docs.yaml
+++ b/.github/workflows/build_docs.yaml
@@ -15,7 +15,7 @@ jobs:
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
       with:
         persist-credentials: false
 
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 3d3571a0..e44bd977 100644
--- a/.github/workflows/release.yml
+++ b/.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
@@ -137,7 +137,7 @@ jobs:
     steps:
 
       - name: Checkout master branch
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           ref: master
           fetch-tags: true
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 0b7f37ee..a589c4ff 100644
--- a/.github/workflows/test.yaml
+++ b/.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
 
diff --git a/.github/workflows/test_releases.yml b/.github/workflows/test_releases.yml
index e1b577e9..9ed60d44 100644
--- a/.github/workflows/test_releases.yml
+++ b/.github/workflows/test_releases.yml
@@ -16,7 +16,7 @@ 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

From f021ee3662c6a24fce044c48b904ecb293d1200e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 5 Jan 2026 11:13:14 +0000
Subject: [PATCH 02/14] build(deps): bump actions/upload-artifact from 4 to 6

Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4 to 6.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](https://github.com/actions/upload-artifact/compare/v4...v6)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index e44bd977..a4fe6fb2 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -161,7 +161,7 @@ jobs:
         run: twine check --strict dist/*
 
       - name: Upload package
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: dist
           path: dist

From 8a2f4a24e55d43c0b4428baf8e62c914321da34a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 5 Jan 2026 11:13:09 +0000
Subject: [PATCH 03/14] build(deps): bump JamesIves/github-pages-deploy-action

Bumps [JamesIves/github-pages-deploy-action](https://github.com/jamesives/github-pages-deploy-action) from 4.7.2 to 4.7.6.
- [Release notes](https://github.com/jamesives/github-pages-deploy-action/releases)
- [Commits](https://github.com/jamesives/github-pages-deploy-action/compare/v4.7.2...v4.7.6)

---
updated-dependencies:
- dependency-name: JamesIves/github-pages-deploy-action
  dependency-version: 4.7.6
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/build_docs.yaml | 4 ++--
 .github/workflows/release.yml     | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build_docs.yaml b/.github/workflows/build_docs.yaml
index 1094300d..15c93ac3 100644
--- a/.github/workflows/build_docs.yaml
+++ b/.github/workflows/build_docs.yaml
@@ -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@v4.7.6
       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@v4.7.6
       if: ${{ github.event_name == 'push' }}
       with:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index a4fe6fb2..65032c5f 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -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@v4.7.6
       with:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         BRANCH: gh-pages

From 486992005da51be212ce1093759f6dcfea30ef3e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 12 Jan 2026 13:24:06 +0000
Subject: [PATCH 04/14] build(deps): bump JamesIves/github-pages-deploy-action

Bumps [JamesIves/github-pages-deploy-action](https://github.com/jamesives/github-pages-deploy-action) from 4.7.6 to 4.8.0.
- [Release notes](https://github.com/jamesives/github-pages-deploy-action/releases)
- [Commits](https://github.com/jamesives/github-pages-deploy-action/compare/v4.7.6...v4.8.0)

---
updated-dependencies:
- dependency-name: JamesIves/github-pages-deploy-action
  dependency-version: 4.8.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/build_docs.yaml | 4 ++--
 .github/workflows/release.yml     | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build_docs.yaml b/.github/workflows/build_docs.yaml
index 15c93ac3..a8482fd5 100644
--- a/.github/workflows/build_docs.yaml
+++ b/.github/workflows/build_docs.yaml
@@ -80,7 +80,7 @@ jobs:
         make -C docs html
 
     - name: Deploy 🚀
-      uses: JamesIves/github-pages-deploy-action@v4.7.6
+      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@v4.7.6
+      uses: JamesIves/github-pages-deploy-action@v4.8.0
       if: ${{ github.event_name == 'push' }}
       with:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 65032c5f..24b3d3d4 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -113,7 +113,7 @@ jobs:
         make -C docs html
 
     - name: Deploy 🚀
-      uses: JamesIves/github-pages-deploy-action@v4.7.6
+      uses: JamesIves/github-pages-deploy-action@v4.8.0
       with:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         BRANCH: gh-pages

From 34ca9110c12e271e48771379288b00984c6e1942 Mon Sep 17 00:00:00 2001
From: "Leaf, Andrew T" <aleaf@usgs.gov>
Date: Fri, 23 Jan 2026 07:51:11 -0600
Subject: [PATCH 05/14] fix(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  * fix some lingering pandas delim_whitespace=True args

---
 mfsetup/fileio.py                    |  4 +-
 mfsetup/mf6model.py                  | 13 +++-
 mfsetup/mfmodel.py                   | 93 ++++++++++++++--------------
 mfsetup/mfnwtmodel.py                | 10 ++-
 mfsetup/tests/test_mf6_shellmound.py |  4 +-
 5 files changed, 70 insertions(+), 54 deletions(-)

diff --git a/mfsetup/fileio.py b/mfsetup/fileio.py
index c0884299..45ee28dd 100644
--- a/mfsetup/fileio.py
+++ b/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 = []
diff --git a/mfsetup/mf6model.py b/mfsetup/mf6model.py
index a552c458..e6621d09 100644
--- a/mfsetup/mf6model.py
+++ b/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]
diff --git a/mfsetup/mfmodel.py b/mfsetup/mfmodel.py
index ab92dbf8..48f64358 100644
--- a/mfsetup/mfmodel.py
+++ b/mfsetup/mfmodel.py
@@ -1382,6 +1382,36 @@ def _setup_basic_stress_package(self, package, flopy_package_class,
         print("finished in {:.2f}s\n".format(time.time() - t0))
         return pckg
 
+
+    def adjust_sfr_layers_model_bottom(self):
+        # assign layers to the sfr reaches
+        botm = self.dis.botm.array.copy()
+        if self.version == 'mf6':
+            idomain = self.dis.idomain.array
+        else:
+            idomain = self.bas6.ibound.array
+        layers, new_botm = assign_layers(self.sfrdata.reach_data,
+                                         botm_array=botm,
+                                         idomain=idomain)
+        self.sfrdata.reach_data['k'] = layers
+        if new_botm is not None:
+            # run thru setup_array so that DIS input remains open/close
+            self._setup_array('dis', 'botm',
+                              data={i: arr for i, arr in enumerate(new_botm)},
+                              datatype='array3d', write_fmt='%.2f', dtype=int)
+            # reset the bottom array in flopy (and in memory)
+            # is this necessary? =
+            self.dis.botm = new_botm
+            # set bottom array to external files
+            if self.version == 'mf6':
+                self.dis.botm = self.cfg['dis']['griddata']['botm']
+            else:
+                self.dis.botm = self.cfg['dis']['botm']
+            print('\nModel cell bottom elevations adjusted after assigning '
+                  'SFR reaches to layers\n(to accommodate SFR reach bottoms '
+                  'below the previous model bottom)\n')
+
+
     def setup_grid(self):
         """Set up the attached modelgrid instance from configuration input
         """
@@ -1584,32 +1614,10 @@ def setup_sfr(self, **kwargs):
         else:
             sfr.reach_data['strtop'] = sfr.interpolate_to_reaches('elevup', 'elevdn')
 
-        # assign layers to the sfr reaches
-        botm = self.dis.botm.array.copy()
-        if self.version == 'mf6':
-            idomain = self.dis.idomain.array
-        else:
-            idomain = self.bas6.ibound.array
-        layers, new_botm = assign_layers(sfr.reach_data,
-                                         botm_array=botm,
-                                         idomain=idomain)
-        sfr.reach_data['k'] = layers
-        if new_botm is not None:
-            # run thru setup_array so that DIS input remains open/close
-            self._setup_array('dis', 'botm',
-                              data={i: arr for i, arr in enumerate(new_botm)},
-                              datatype='array3d', write_fmt='%.2f', dtype=int)
-            # reset the bottom array in flopy (and in memory)
-            # is this necessary? =
-            self.dis.botm = new_botm
-            # set bottom array to external files
-            if self.version == 'mf6':
-                self.dis.botm = self.cfg['dis']['griddata']['botm']
-            else:
-                self.dis.botm = self.cfg['dis']['botm']
-            print('\nModel cell bottom elevations adjusted after assigning '
-                  'SFR reaches to layers\n(to accommodate SFR reach bottoms '
-                  'below the previous model bottom)\n')
+        # attach the sfrmaker.sfrdata instance as an attribute
+        self.sfrdata = sfr
+
+        self.adjust_sfr_layers_model_bottom()
 
         # option to convert reaches to the River Package
         if self.cfg['sfr'].get('to_riv'):
@@ -1617,7 +1625,7 @@ def setup_sfr(self, **kwargs):
                           DeprecationWarning)
             self.cfg['sfr']['sfrmaker_options']['to_riv'] = self.cfg['sfr'].get('to_riv')
         if self.cfg['sfr'].get('sfrmaker_options', {}).get('to_riv'):
-            rivdata = sfr.to_riv(line_ids=self.cfg['sfr']['sfrmaker_options']['to_riv'],
+            rivdata = self.sfrdata.to_riv(line_ids=self.cfg['sfr']['sfrmaker_options']['to_riv'],
                                  drop_in_sfr=True)
             # setup of RIV package from SFRmaker-derived RIVdata
             # and any user input
@@ -1679,10 +1687,10 @@ def setup_sfr(self, **kwargs):
             inflows_input['flowline_routing'] = routing
             if self.version == 'mf6':
                 inflows_input['variable'] = 'inflow'
-                method = sfr.add_to_perioddata
+                method = self.sfrdata.add_to_perioddata
             else:
                 inflows_input['variable'] = 'flow'
-                method = sfr.add_to_segment_data
+                method = self.sfrdata.add_to_segment_data
             kwargs = get_input_arguments(inflows_input.copy(), method)
             method(**kwargs)
 
@@ -1710,45 +1718,36 @@ def setup_sfr(self, **kwargs):
             runoff_input['variable'] = 'runoff'
             runoff_input['distribute_flows_to_reaches'] = True
             if self.version == 'mf6':
-                method = sfr.add_to_perioddata
+                method = self.sfrdata.add_to_perioddata
             else:
-                method = sfr.add_to_segment_data
+                method = self.sfrdata.add_to_segment_data
             kwargs = get_input_arguments(runoff_input.copy(), method)
             method(**kwargs)
 
         # add observations
         observations_input = self.cfg['sfr'].get('source_data', {}).get('observations')
         if self.version != 'mf6':
-            sfr.gage_starting_unit_number = self.cfg['gag']['starting_unit_number']
+            self.sfrdata.gage_starting_unit_number = self.cfg['gag']['starting_unit_number']
         if observations_input is not None:
             key = 'filename' if 'filename' in observations_input else 'filenames'
             observations_input['data'] = observations_input[key]
-            kwargs = get_input_arguments(observations_input.copy(), sfr.add_observations)
-            obsdata = sfr.add_observations(**kwargs)
+            kwargs = get_input_arguments(observations_input.copy(), self.sfrdata.add_observations)
+            obsdata = self.sfrdata.add_observations(**kwargs)
             # resample observations to model stress periods; write to table
 
-        # write reach and segment data tables
-        sfr.write_tables('{}/{}'.format(self._tables_path, self.name))
-
-        # export shapefiles of lines, routing, cell polygons, inlets and outlets
-        sfr.write_shapefiles('{}/{}'.format(self._shapefiles_path, self.name))
-
         # create the flopy SFR package instance
-        sfr.create_modflow_sfr2(model=self, istcb2=223)
+        self.sfrdata.create_modflow_sfr2(model=self, istcb2=223)
         if self.version != 'mf6':
-            sfr_package = sfr.modflow_sfr2
+            sfr_package = self.sfrdata.modflow_sfr2
         else:
             # pass options kwargs through to mf6 constructor
             kwargs = flatten({k:v for k, v in self.cfg[package].items() if k not in
                               {'source_data', 'flowlines', 'inflows', 'observations',
                                'inflows_routing', 'dem', 'sfrmaker_options'}})
             kwargs = get_input_arguments(kwargs, mf6.ModflowGwfsfr)
-            sfr_package = sfr.create_mf6sfr(model=self, **kwargs)
+            sfr_package = self.sfrdata.create_mf6sfr(model=self, **kwargs)
             # monkey patch ModflowGwfsfr instance to behave like ModflowSfr2
-            sfr_package.reach_data = sfr.modflow_sfr2.reach_data
-
-        # attach the sfrmaker.sfrdata instance as an attribute
-        self.sfrdata = sfr
+            sfr_package.reach_data = self.sfrdata.modflow_sfr2.reach_data
 
         # reset dependent arrays
         self._reset_bc_arrays()
diff --git a/mfsetup/mfnwtmodel.py b/mfsetup/mfnwtmodel.py
index f659ee49..9dbe0226 100644
--- a/mfsetup/mfnwtmodel.py
+++ b/mfsetup/mfnwtmodel.py
@@ -200,7 +200,7 @@ def _set_ibound(self):
 
         # remove cells that are above stream cells
         if self.get_package('sfr') is not None:
-            ibound = deactivate_idomain_above(ibound, self.sfr.reach_data)
+            ibound = deactivate_idomain_above(ibound, self.sfrdata.reach_data)
         # remove cells that are above ghb cells
         if self.get_package('ghb') is not None:
             ibound = deactivate_idomain_above(ibound, self.ghb.stress_period_data[0])
@@ -215,6 +215,10 @@ def _set_ibound(self):
                           datatype='array3d', write_fmt='%d', dtype=int)
         self.bas6.ibound = self.cfg['bas6']['ibound']
 
+        if hasattr(self, 'sfrdata'):
+            self.adjust_sfr_layers_model_bottom()
+
+
     def _set_parent(self):
         """Set attributes related to a parent or source model
         if one is specified."""
@@ -851,6 +855,10 @@ def write_input(self):
         # gage package was already set-up and then written by Flopy
         if 'SFR' in self.get_package_list():
             self.sfrdata.write_package(write_observations_input=False)
+            # write reach and segment data tables
+            self.sfrdata.write_tables('{}/{}'.format(self._tables_path, self.name))
+            # export shapefiles of lines, routing, cell polygons, inlets and outlets
+            self.sfrdata.write_shapefiles('{}/{}'.format(self._shapefiles_path, self.name))
 
         # add version info to file headers
         files = [self.namefile]
diff --git a/mfsetup/tests/test_mf6_shellmound.py b/mfsetup/tests/test_mf6_shellmound.py
index 8c060948..4cfd8889 100644
--- a/mfsetup/tests/test_mf6_shellmound.py
+++ b/mfsetup/tests/test_mf6_shellmound.py
@@ -749,7 +749,7 @@ def test_wel_setup(shellmound_model_with_dis):
 #                    reason='This test fails on macos CI for an unknown reason; passes locally on macos')
 def test_sfr_setup(model_with_sfr, project_root_path):
     m = model_with_sfr
-    m.sfr.write()
+    m.write_input()
     assert os.path.exists(os.path.join(m.model_ws, m.sfr.filename))
     assert isinstance(m.sfr, mf6.ModflowGwfsfr)
     output_path = m._shapefiles_path
@@ -971,7 +971,7 @@ def test_model_setup_no_nans(model_setup):
         assert pckg in package_list
     assert 'RIV_1' not in package_list
     m.write_input()
-    df = pd.read_csv(m.model_ws / 'external/riv_000.dat', delim_whitespace=True)
+    df = pd.read_csv(m.model_ws / 'external/riv_000.dat', sep=r'\s+')
     # single RIV external file should have Lake Henry (from riv: block)
     # and Tallahatchie/Yazoo (via SFRmaker to_riv:)
     # does flopy force boundnames to lower case as of v3.3.7?

From 8a341ad93060fb463d748e2d7b51ccdf77a13cab Mon Sep 17 00:00:00 2001
From: "Leaf, Andrew T" <aleaf@usgs.gov>
Date: Fri, 23 Jan 2026 09:10:38 -0600
Subject: [PATCH 06/14] ci: still working on pandas 3.0 support  * add
 --no-deps to pip reinstall of flopy from latest release; apparently this was
 clobbering the conda installs of pandas and other packages on the Windows CI
 runs

---
 .github/workflows/test.yaml | 2 +-
 ci/test_environment.yaml    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index a589c4ff..bf3190c5 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -82,7 +82,7 @@ jobs:
     - name: Install latest PyPI flopy
       shell: bash -l {0}
       if: contains(matrix.os, 'windows')
-      run: pip install flopy --force-reinstall
+      run: pip install flopy --force-reinstall --no-deps
     - name: Install Modflow-setup and ipykernel
       shell: bash -l {0}
       run: |
diff --git a/ci/test_environment.yaml b/ci/test_environment.yaml
index c92d62e4..b1d7ab58 100644
--- a/ci/test_environment.yaml
+++ b/ci/test_environment.yaml
@@ -13,7 +13,7 @@ dependencies:
 - scipy
 - xarray
 - netcdf4
-- pandas
+- pandas<3
 - geopandas
 - gdal
 - fiona
@@ -27,7 +27,7 @@ dependencies:
 - coverage
 - flake8
 - pytest
-- sphinx=8.1.3
+- sphinx
 - numpydoc
 - nbsphinx  # for rendering notebooks in sphinx-generated docs
 - sphinx-copybutton

From 5425beb717c2cd1d03030ba272d38c898ab88232 Mon Sep 17 00:00:00 2001
From: "Leaf, Andrew T" <aleaf@usgs.gov>
Date: Fri, 6 Feb 2026 12:37:49 -0600
Subject: [PATCH 07/14] tests(test_sourcedata.py::test_parse_source_data): add
 TransientArraySourceData.from_config with individual raster input for
 recharge.

---
 mfsetup/tests/test_sourcedata.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/mfsetup/tests/test_sourcedata.py b/mfsetup/tests/test_sourcedata.py
index ddfd33f4..8a80aa80 100644
--- a/mfsetup/tests/test_sourcedata.py
+++ b/mfsetup/tests/test_sourcedata.py
@@ -148,8 +148,10 @@ def test_parse_source_data(source_data_cases,
     # test conversion to model units
     for i, f in cases[4]['infiltration_arrays']['filenames'].items():
         cases[4]['infiltration_arrays']['filenames'][i] = os.path.join(project_root_path, f)
-    sd = ArraySourceData.from_config(cases[4]['infiltration_arrays'],
-                                     variable=var,
+    sd = TransientArraySourceData.from_config(cases[4]['infiltration_arrays'],
+                                     variable='recharge',
+                                     data_type='transient2d',
+                                     resample_method='nearest',
                                      dest_model=model)
     assert isinstance(sd.filenames, dict)
     assert sd.unit_conversion == convert_length_units('inches', 'meters') /\

From bc64fdbc2c035395c168391513502e8bb23e39d1 Mon Sep 17 00:00:00 2001
From: "Leaf, Andrew T" <aleaf@usgs.gov>
Date: Fri, 6 Feb 2026 14:31:38 -0600
Subject: [PATCH 08/14] feat: 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)

---
 docs/source/conf.py                           |   5 +++
 docs/source/release-history.rst               |  21 ++++++---
 mfsetup/grid.py                               |   8 ++--
 mfsetup/sourcedata.py                         |  41 +++++++++++++-----
 mfsetup/tdis.py                               |   2 +
 mfsetup/tests/data/shellmound.yml             |   2 +-
 .../data/shellmound/shps/active_area.gpkg     | Bin 0 -> 98304 bytes
 mfsetup/tests/test_mf6_shellmound.py          |  11 +++--
 mfsetup/tests/test_pleasant_mfnwt_inset.py    |   2 +-
 9 files changed, 66 insertions(+), 26 deletions(-)
 create mode 100644 mfsetup/tests/data/shellmound/shps/active_area.gpkg

diff --git a/docs/source/conf.py b/docs/source/conf.py
index cadd2a5f..b80ebb32 100644
--- a/docs/source/conf.py
+++ b/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']
 
diff --git a/docs/source/release-history.rst b/docs/source/release-history.rst
index 8888257a..af94cb54 100644
--- a/docs/source/release-history.rst
+++ b/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)
 ----------------------------------------
diff --git a/mfsetup/grid.py b/mfsetup/grid.py
index 1a08000b..34701395 100644
--- a/mfsetup/grid.py
+++ b/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)
diff --git a/mfsetup/sourcedata.py b/mfsetup/sourcedata.py
index 25849b36..f72c9f88 100644
--- a/mfsetup/sourcedata.py
+++ b/mfsetup/sourcedata.py
@@ -68,6 +68,8 @@ def __init__(self, filenames=None, values=None, variable=None, length_units='unk
 
         """
         self.filenames = filenames
+        # optional layer names for geopackages parsed from filenames
+        self.file_layers = None
         self.values = values
         self.variable = variable
         self.length_units = length_units
@@ -113,21 +115,35 @@ def time_unit_conversion(self):
 
     def set_filenames(self, filenames):
 
-        def normpath(f):
-            if self.dest_model is not None and isinstance(f, str):
-                path = os.path.join(self.dest_model._config_path, f)
+        def normpath(file_path):
+            if self.dest_model is not None and isinstance(file_path, str):
+                file_path = file_path.split('|')[0]
+                path = os.path.join(self.dest_model._config_path, file_path)
                 normpath = os.path.normpath(path)
                 return normpath
-            return f
+            return file_path
+
+        def get_layer_name(file_path):
+            if isinstance(file_path, str) and len(file_path.split('|')) > 1:
+                layer_name = file_path.split('|')[1]
+                layer_name = layer_name.replace('layer=', '')\
+                    .replace('layername=', '')
+                return layer_name
 
         if isinstance(filenames, str):
             self.filenames = {0: normpath(filenames)}
+            # optional layernames for geopackages, denoted with syntax:
+            # <filename>.gpkg|layername=<layer name>
+            self.file_layers = {0: get_layer_name(filenames)}
         elif isinstance(filenames, list):
             self.filenames = {i: normpath(f) for i, f in enumerate(filenames)}
+            self.file_layers = {i: get_layer_name(f) for i, f in enumerate(filenames)}
         elif isinstance(filenames, dict):
             self.filenames = {i: normpath(f) for i, f in filenames.items()}
+            self.file_layers = {i: get_layer_name(f) for i, f in filenames.items()}
         else:
-            self.filenames = None
+            self.filenames = dict()
+            self.file_layers = dict()
 
     @classmethod
     def from_config(cls, data, **kwargs):
@@ -365,7 +381,7 @@ def dest_source_layer_mapping(self):
                                 "but {} are specified: {}"
                                 .format(nlay, nspecified, self.from_source_model_layers))
             return self.from_source_model_layers
-        elif self.filenames is not None:
+        elif self.filenames:
             nspecified = len(self.filenames)
             if self.datatype == 'array3d' and nspecified != nlay:
                 raise Exception("Variable should have {} layers "
@@ -441,7 +457,7 @@ def regrid_from_source_model(self, source_array,
                                            self.dest_modelgrid.ncol))
         return regridded
 
-    def _read_array_from_file(self, filename):
+    def _read_array_from_file(self, filename, layername=None):
         f = filename
         if isinstance(f, numbers.Number):
             data = f
@@ -456,8 +472,9 @@ def _read_array_from_file(self, filename):
                                            method=self.resample_method)
                 arr = np.reshape(arr, (self.dest_modelgrid.nrow,
                                        self.dest_modelgrid.ncol))
-            elif f.endswith('.shp'):
-                arr = rasterize(f, self.dest_modelgrid, id_column=self.id_column)
+            elif any([f.lower().endswith(i) for i in ['shp', 'gpkg']]):
+                arr = rasterize(f, self.dest_modelgrid, layer=layername,
+                                id_column=self.id_column)
             # TODO: add code to interpret hds and cbb files
             # interpolate from source model using source model grid
             # otherwise assume the grids are the same
@@ -483,9 +500,9 @@ def get_data(self):
             data = populate_values(self.values, array_shape=(self.dest_modelgrid.nrow,
                                                              self.dest_modelgrid.ncol))
 
-        if self.filenames is not None:
+        if self.filenames:
             for i, f in self.filenames.items():
-                data[i] = self._read_array_from_file(f)
+                data[i] = self._read_array_from_file(f, layername=self.file_layers.get(i))
 
             # interpolate any missing arrays from consecutive files based on weights
             for i, arr in data.items():
@@ -600,7 +617,7 @@ def get_data(self):
 
         # get data from list of files; one per stress period
         # (files are assumed to be sorted)
-        if self.filenames is not None:
+        if self.filenames:
             source_data = []
             for i, f in self.filenames.items():
                 source_data.append(self._read_array_from_file(f))
diff --git a/mfsetup/tdis.py b/mfsetup/tdis.py
index cfd0dba2..9fb753ec 100644
--- a/mfsetup/tdis.py
+++ b/mfsetup/tdis.py
@@ -680,8 +680,10 @@ def aggregate_dataframe_to_stress_period(data, id_column, data_column, datetime_
                 data[end_datetime_column] = pd.to_datetime(data[end_datetime_column])
             if start_datetime is None:
                 start_datetime = data[datetime_column].iloc[0]
+            start_datetime = pd.Timestamp(start_datetime)
             if end_datetime is None:
                 end_datetime = data[datetime_column].iloc[-1]
+            end_datetime = pd.Timestamp(end_datetime)
             # >= includes the start datetime
             # if there is no end_datetime column, select values that have start_datetimes within the period
             # this excludes values that start before the period but don't have an end date
diff --git a/mfsetup/tests/data/shellmound.yml b/mfsetup/tests/data/shellmound.yml
index d7cd8544..67a51e2a 100644
--- a/mfsetup/tests/data/shellmound.yml
+++ b/mfsetup/tests/data/shellmound.yml
@@ -106,7 +106,7 @@ dis:
         12: 'shellmound/rasters/mdwy_surf.tif' # Midway confining unit (top)
       elevation_units: 'feet'
     idomain:
-      filename: 'shellmound/shps/active_area.shp'
+      filename: 'shellmound/shps/active_area.gpkg|layername=active_area_poly'
   minimum_layer_thickness: 1 # layers less than this thickness are converted to vertical pass-through cells
   drop_thin_cells: True
 
diff --git a/mfsetup/tests/data/shellmound/shps/active_area.gpkg b/mfsetup/tests/data/shellmound/shps/active_area.gpkg
new file mode 100644
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zD&64jB%qOCw0jAS^uB=c)|R7Q1-TmBdiiCKcYc0wE4G)69i+3wx|hi0^06ez?b*;i
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zc&}VxcP<;XGpzJRwCnUt6J1wi%jQnYhH0o?aJxNHhoRkk+e9r?TegB6TcRbA*9szO
z-O6m*2Mv+tiwA>CUmegZzHHRnx^1M2@2rV(L3EvdrK#So$bh~(5u!PR`tSeQ5rLsE
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z2!H?xfB*=900@8p2!H?xfB*=9z!4&FhV2a>bAO%6wEut1jQscrNeWRw00ck)1V8`;
zKmY_l00ck)1VG^b34s-MAUqm==aSoA*MIVE{D{H);fC?Ns8vm?UB7yDeSLk5M%RSG
zL!l&&(Z>Z`Rcm4)5*@$#wZ;z#jC|_~ec)8MDwj9)=l`=KzhvkO2MB-w2!H?xfB*=9
z00@8p2!H?xfWQkyAlOeg4_fZ^x7#}~@Be?njC}DzRS?3000@8p2!H?xfB*=900@8p
z2!H?xbVs0<K5F2YVgH{9GxUW61V8`;KmY_l00ck)1VF$^;7^v=KIR9n(jff-UHZX(
z^x;<vAARsU|9)#=^!;0&SBMdce;@z?An*bZ(CvSQK9&#%2!H?xfB*=900@8p2!H?x
zfB*=9z?YZ6&~cd=WL{?mzdi7a{%`kw(4(^J%<IGd`0O>_{<`0Dz7!tZdBgJUYQ0&W
zhWQohYJN=-`2zJmptZPsbwB68_Fibad3~nBy7KsXi;E{x#PTU^JW`=rQmAw?bv&u5
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zaPrh=gQ$t_lH7#$F2TmKz$LjHN2uHE-5lXo%f%KyxF#<v@9j)_aS!LVCK{<oS)`K-
zV?N!#?G3`E7Ph}}*>gS{9(?TSqV8)o>U34Sc96<jMcB2sy@>B#`?|Q~(oK@$?whh3
zj({Ehc1a?e$|sW~ozWfic5n^64`fs^19d4v4H-=3*}40w0q|Slt^rOS9N^@k1EemN
z4T9ZySl$Q5Ce1tA9-6mjzh<=Q&hK~KrqP49Y1G}Ow~6Kcy2Id5S4`TopG)s(YF0X+
z?8JO#e;DeT-SolPP5<w)>$YR)9mgCe^q=<m+K)&^a~bh&XXQu9L-|hOlG%oLyKcj&
zgSX+-(QCsFZQrIPt;wvD`*okOl%d|YH)wxt>tDViY}j#bH}ksF?s~Q+$MU8tZ!1pN
zXo|CzMaJA;A0ckgp2{$N;<K+Tkpl!k00g=uu>JKwdqdQ;qYlXs?W!<)dg*9!9oP^J
IAHWd(A5?}h9{>OV

literal 0
HcmV?d00001

diff --git a/mfsetup/tests/test_mf6_shellmound.py b/mfsetup/tests/test_mf6_shellmound.py
index 4cfd8889..44992ce9 100644
--- a/mfsetup/tests/test_mf6_shellmound.py
+++ b/mfsetup/tests/test_mf6_shellmound.py
@@ -327,9 +327,14 @@ def test_dis_setup(shellmound_model_with_grid):
             model_array = model_array[k]
         assert np.array_equal(model_array, data)
 
-   # test that written idomain array reflects supplied shapefile of active area
-    active_area = rasterize(m.cfg['dis']['source_data']['idomain']['filename'],
-                            m.modelgrid)
+    # test that written idomain array reflects supplied shapefile of active area
+    fpath = m.cfg['dis']['source_data']['idomain']['filename']
+    fname = fpath.split("|")[0]
+    if len(fpath.split('|')) > 1:
+        layer_name = fpath.split('|')[1]
+        layer_name = layer_name.replace('layer=', '')\
+            .replace('layername=', '')
+    active_area = rasterize(fname, m.modelgrid, layer=layer_name)
     isactive = active_area >= 1
     written_idomain = load_array(m.cfg['dis']['griddata']['idomain'])
     assert np.all(written_idomain[:, ~isactive] <= 0)
diff --git a/mfsetup/tests/test_pleasant_mfnwt_inset.py b/mfsetup/tests/test_pleasant_mfnwt_inset.py
index 44ae4a48..84d61c03 100644
--- a/mfsetup/tests/test_pleasant_mfnwt_inset.py
+++ b/mfsetup/tests/test_pleasant_mfnwt_inset.py
@@ -133,7 +133,7 @@ def test_model_setup(full_pleasant_nwt):
 
     # check that streambed elevation data were incorporated correctly
     reach_data = m.sfrdata.reach_data
-    assert reach_data.loc[reach_data['name'] == 'Chaffee Creek', 'strtop'].max() == 296.9
+    assert np.allclose(reach_data.loc[reach_data['name'] == 'Chaffee Creek', 'strtop'].max(), 296.9)
 
 
 def test_model_setup_and_run(pleasant_nwt_model_run):

From e556f9eda16775d857b086f5dc670fdbd6313a1c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 2 Mar 2026 12:04:14 +0000
Subject: [PATCH 09/14] build(deps): bump actions/upload-artifact from 6 to 7

Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 6 to 7.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](https://github.com/actions/upload-artifact/compare/v6...v7)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 24b3d3d4..689edd99 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -161,7 +161,7 @@ jobs:
         run: twine check --strict dist/*
 
       - name: Upload package
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7
         with:
           name: dist
           path: dist

From 26319eb0778bac4e02a18a1de02baddc2cb51356 Mon Sep 17 00:00:00 2001
From: "Leaf, Andrew T" <aleaf@usgs.gov>
Date: Wed, 4 Mar 2026 10:49:08 -0600
Subject: [PATCH 10/14] fix(pandas 3 support): Refactor Series.dtype == object
 checks to pd.api.types.is_string_dtype()

---
 mfsetup/bcs.py            | 4 ++--
 mfsetup/grid.py           | 2 +-
 mfsetup/obs.py            | 2 +-
 mfsetup/sourcedata.py     | 2 +-
 mfsetup/tdis.py           | 8 ++++----
 mfsetup/tests/test_obs.py | 4 +++-
 6 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/mfsetup/bcs.py b/mfsetup/bcs.py
index cf03813e..f8258b34 100644
--- a/mfsetup/bcs.py
+++ b/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'
diff --git a/mfsetup/grid.py b/mfsetup/grid.py
index 34701395..48ae3d70 100644
--- a/mfsetup/grid.py
+++ b/mfsetup/grid.py
@@ -749,7 +749,7 @@ def rasterize(feature, grid, layer=None, 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]]
diff --git a/mfsetup/obs.py b/mfsetup/obs.py
index 605298e9..95b37d39 100644
--- a/mfsetup/obs.py
+++ b/mfsetup/obs.py
@@ -156,7 +156,7 @@ def setup_head_observations(model, filenames=None,
     df = pd.concat([heads_all_layers, non_heads], axis=0)
 
     # dtypes
-    assert df[obsname_column].dtype == object
+    assert pd.api.types.is_string_dtype(df[obsname_column].dtype)
     df['klay'] = df.klay.astype(int)
 
     print('Culling observations to cells allowed by iobs_domain...')
diff --git a/mfsetup/sourcedata.py b/mfsetup/sourcedata.py
index f72c9f88..ad787f0d 100644
--- a/mfsetup/sourcedata.py
+++ b/mfsetup/sourcedata.py
@@ -1116,7 +1116,7 @@ def get_data(self):
         df.index = pd.to_datetime(df[self.datetime_column])
 
         # convert IDs to strings if any were read in (resulting in object dtype)
-        if df[self.id_column].dtype == object:
+        if pd.api.types.is_string_dtype(df[self.id_column].dtype):
             df[self.id_column] = df[self.id_column].astype(str)
 
         # rename any columns specified in config file to required names
diff --git a/mfsetup/tdis.py b/mfsetup/tdis.py
index 9fb753ec..7871c928 100644
--- a/mfsetup/tdis.py
+++ b/mfsetup/tdis.py
@@ -673,10 +673,10 @@ def aggregate_dataframe_to_stress_period(data, id_column, data_column, datetime_
             assert datetime_column in data.columns, \
                 "datetime_column needed for " \
                 "resampling irregular data to model stress periods"
-            if data[datetime_column].dtype == object:
+            if pd.api.types.is_string_dtype(data[datetime_column].dtype):
                 data[datetime_column] = pd.to_datetime(data[datetime_column])
             if end_datetime_column in data.columns and \
-                    data[end_datetime_column].dtype == object:
+                    pd.api.types.is_string_dtype(data[end_datetime_column].dtype):
                 data[end_datetime_column] = pd.to_datetime(data[end_datetime_column])
             if start_datetime is None:
                 start_datetime = data[datetime_column].iloc[0]
@@ -700,7 +700,7 @@ def aggregate_dataframe_to_stress_period(data, id_column, data_column, datetime_
             # and end datetimes that are after the period start
             # in other words, include all values that overlap in time with the period
             else:
-                if data[end_datetime_column].dtype == object:
+                if pd.api.types.is_string_dtype(data[end_datetime_column].dtype):
                     data[end_datetime_column] = pd.to_datetime(data[end_datetime_column])
                 data_overlaps_period = (data[datetime_column] < end_datetime) & \
                                        (data[end_datetime_column] > start_datetime)
@@ -808,7 +808,7 @@ def aggregate_xarray_to_stress_period(data, datetime_coords_name='time',
                 "datetime_column needed for " \
                 "resampling irregular data to model stress periods"
             # not sure if this is needed for xarray
-            if data[datetime_coords_name].dtype == object:
+            if pd.api.types.is_string_dtype(data[datetime_coords_name].dtype):
                 data[datetime_coords_name] = pd.to_datetime(data[datetime_coords_name])
             # default to aggregating whole dataset
             # if start_ and end_datetime not provided
diff --git a/mfsetup/tests/test_obs.py b/mfsetup/tests/test_obs.py
index a0d6c5f6..3d25ce2b 100644
--- a/mfsetup/tests/test_obs.py
+++ b/mfsetup/tests/test_obs.py
@@ -1,3 +1,5 @@
+import pandas as pd
+
 from mfsetup.obs import make_obsname, read_observation_data
 
 
@@ -30,5 +32,5 @@ def test_read_observation_data(test_data_path):
     results = read_observation_data(csvfile, column_info={},#'x_location_col', 'x',
                                                           #'y_location_col', 'y'},
                           column_mappings={'obsname': 'comid'})
-    assert results['obsname'].dtype == object
+    assert pd.api.types.is_string_dtype(results['obsname'].dtype)
     assert isinstance(results['obsname'].values[0], str)

From 450b6c36501ab462c9238264e2a96faf0886a2d7 Mon Sep 17 00:00:00 2001
From: "Leaf, Andrew T" <aleaf@usgs.gov>
Date: Wed, 4 Mar 2026 10:49:08 -0600
Subject: [PATCH 11/14] fix(pandas 3 support): Refactor Series.dtype == object
 checks to pd.api.types.is_string_dtype() and other misc fixes

---
 mfsetup/obs.py                       | 2 +-
 mfsetup/tests/test_mf6_shellmound.py | 5 +++--
 mfsetup/wateruse.py                  | 9 ++++-----
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/mfsetup/obs.py b/mfsetup/obs.py
index 95b37d39..b9567fe6 100644
--- a/mfsetup/obs.py
+++ b/mfsetup/obs.py
@@ -186,7 +186,7 @@ def setup_head_observations(model, filenames=None,
     elif obs_package == 'obs':  # mf6 observation utility
         obstype = {'BAS': 'HEAD'}
         renames = {'pckg': 'obstype'}
-        df.pckg.replace(obstype, inplace=True)
+        df['pckg'] = df['pckg'].replace(obstype)
         df.rename(columns=renames, inplace=True)
         df['id'] = list(zip(df.klay, df.i, df.j))
         # drop observations located in inactive cels
diff --git a/mfsetup/tests/test_mf6_shellmound.py b/mfsetup/tests/test_mf6_shellmound.py
index 44992ce9..85c4d71b 100644
--- a/mfsetup/tests/test_mf6_shellmound.py
+++ b/mfsetup/tests/test_mf6_shellmound.py
@@ -778,7 +778,8 @@ def test_sfr_setup(model_with_sfr, project_root_path):
     # verify that reaches were consolidated to one per cell
     assert len(m.sfrdata.reach_data.node.unique()) == len(m.sfrdata.reach_data)
 
-    # check that add_outlets works
+    # check that add_outlets works;
+    # these lines were specified as outlets in the configuration file
     expected_outlets = {'17957815', '17956199'}
     for outlet_id in expected_outlets:
         # handle either int-based or str-based line_ids
@@ -862,7 +863,7 @@ def test_sfr_inflows_from_csv(model_with_sfr):
     rno = lookup.get(str(line_id), lookup.get(line_id))
     right = sfr_pd.loc[sfr_pd.rno == rno].loc['2007-04-01':, 'inflow']
     left = left.loc[:right.index[-1]]
-    pd.testing.assert_series_equal(left, right, check_names=False, check_freq=False)
+    pd.testing.assert_series_equal(left, right, check_names=False, check_freq=False, check_index_type=False)
 
 
 @pytest.mark.xfail(reason='flopy remove_package() issue')
diff --git a/mfsetup/wateruse.py b/mfsetup/wateruse.py
index b036ba74..15a58df1 100644
--- a/mfsetup/wateruse.py
+++ b/mfsetup/wateruse.py
@@ -338,7 +338,8 @@ def resample_pumping_rates(wu_file, wu_points, model,
     for site, sitedata in monthly_data.groupby('site_no'):
         if site not in well_info.index:
             continue
-        sitedata.index = sitedata.datetime
+        sitedata = sitedata.copy()
+        sitedata.set_index('datetime', inplace=True)
         assert not sitedata.index.duplicated().any()
 
         if dropna:
@@ -351,10 +352,8 @@ def resample_pumping_rates(wu_file, wu_points, model,
                 if verbose:
                     years = set(site_period_data.loc[isna, 'year'])
                     years = ', '.join(list(years))
-                    print('Site {} has {} times with nans (in years {})- filling with {}s'.format(site,
-                                                                                    np.sum(isna),
-                                                                                    years,
-                                                                                    na_fill_value))
+                    print(f'Site {site} has {np.sum(isna)} times with nans (in years {years})\n- '
+                          f'filling with {na_fill_value}s')
             site_period_data['site_no'] = site
             site_period_data['year'] = site_period_data.index.year
             site_period_data['month'] = site_period_data.index.month

From 9a182cff5f82d2ad20e5f57117cfbffb61b6c41d Mon Sep 17 00:00:00 2001
From: "Leaf, Andrew T" <aleaf@usgs.gov>
Date: Wed, 4 Mar 2026 15:10:06 -0600
Subject: [PATCH 12/14] ci: test against pip conda and GitHub (develop) Flopys;
 install also with --no-deps to prevent reinstall of pandas < 3

---
 .github/workflows/test.yaml | 24 ++++++++++++++++++++----
 ci/test_environment.yaml    |  5 +----
 2 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index bf3190c5..93ceb85a 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -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 --no-deps
+      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: |
diff --git a/ci/test_environment.yaml b/ci/test_environment.yaml
index b1d7ab58..c04fca3f 100644
--- a/ci/test_environment.yaml
+++ b/ci/test_environment.yaml
@@ -13,7 +13,7 @@ dependencies:
 - scipy
 - xarray
 - netcdf4
-- pandas<3
+- pandas
 - geopandas
 - gdal
 - fiona
@@ -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

From 0c4c5663dc6a3fa7d01dd6acb62e3bff5666faa6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 30 Mar 2026 11:54:43 +0000
Subject: [PATCH 13/14] build(deps): bump mamba-org/setup-micromamba from 1 to
 3

Bumps [mamba-org/setup-micromamba](https://github.com/mamba-org/setup-micromamba) from 1 to 3.
- [Release notes](https://github.com/mamba-org/setup-micromamba/releases)
- [Commits](https://github.com/mamba-org/setup-micromamba/compare/v1...v3)

---
updated-dependencies:
- dependency-name: mamba-org/setup-micromamba
  dependency-version: '3'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/build_docs.yaml   | 2 +-
 .github/workflows/release.yml       | 2 +-
 .github/workflows/test.yaml         | 2 +-
 .github/workflows/test_releases.yml | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build_docs.yaml b/.github/workflows/build_docs.yaml
index a8482fd5..1a6bac46 100644
--- a/.github/workflows/build_docs.yaml
+++ b/.github/workflows/build_docs.yaml
@@ -23,7 +23,7 @@ jobs:
       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
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 689edd99..99f9697a 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -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
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 93ceb85a..9d5358db 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -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
diff --git a/.github/workflows/test_releases.yml b/.github/workflows/test_releases.yml
index 9ed60d44..30b63873 100644
--- a/.github/workflows/test_releases.yml
+++ b/.github/workflows/test_releases.yml
@@ -23,7 +23,7 @@ jobs:
       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

From 3e4e79f1825e641fa22f63162155d74a003151f8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 20 Jul 2026 11:12:14 +0000
Subject: [PATCH 14/14] build(deps): bump actions/setup-python from 6 to 7

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 6 to 7.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v6...v7)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 99f9697a..bb8775c8 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -143,7 +143,7 @@ jobs:
           fetch-tags: true
 
       - name: Setup Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@v7
         with:
           python-version: '3.x'
           cache: 'pip'