feat(GeoDataFrame support): geopandas support for shapefile exporting #2671

jlarsen-usgs · 2025-12-16T00:51:08Z

This PR supersedes the draft PR #2573 and continues the cleanup of legacy shapefile exporting code and integration of geopandas GeoDataFrame support.

…across flopy

…port utilities

…upport

…frame()` routines

…code

codecov · 2025-12-23T01:38:48Z

Codecov Report

❌ Patch coverage is 56.47208% with 343 lines in your changes missing coverage. Please review.
✅ Project coverage is 72.3%. Comparing base (556c088) to head (f0e9211).
⚠️ Report is 99 commits behind head on develop.

Files with missing lines	Patch %	Lines
flopy/export/shapefile_utils.py	41.2%	47 Missing ⚠️
flopy/plot/plotutil.py	2.5%	38 Missing ⚠️
flopy/mf6/data/mfdatalist.py	40.9%	36 Missing ⚠️
flopy/mf6/data/mfdataplist.py	50.0%	30 Missing ⚠️
flopy/utils/binaryfile/__init__.py	7.4%	25 Missing ⚠️
flopy/modflow/mfsfr2.py	54.7%	24 Missing ⚠️
flopy/mf6/data/mfdataarray.py	65.1%	23 Missing ⚠️
flopy/utils/datafile.py	32.0%	17 Missing ⚠️
flopy/mf6/mfpackage.py	48.3%	16 Missing ⚠️
flopy/utils/util_array.py	68.0%	16 Missing ⚠️
... and 11 more

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #2671      +/-   ##
===========================================
+ Coverage     55.5%    72.3%   +16.7%     
===========================================
  Files          644      667      +23     
  Lines       124135   130272    +6137     
===========================================
+ Hits         68947    94231   +25284     
+ Misses       55188    36041   -19147

Files with missing lines	Coverage Δ
flopy/discretization/grid.py	`74.3% <100.0%> (-1.7%)`	⬇️
flopy/mf6/data/mfdatautil.py	`60.6% <100.0%> (-17.3%)`	⬇️
flopy/utils/geospatial_utils.py	`92.7% <100.0%> (-0.4%)`	⬇️
flopy/utils/gridgen.py	`75.8% <100.0%> (-11.3%)`	⬇️
flopy/mf6/mfmodel.py	`57.5% <88.2%> (-23.4%)`	⬇️
flopy/discretization/structuredgrid.py	`53.2% <72.7%> (+5.7%)`	⬆️
flopy/mbase.py	`70.2% <82.3%> (-2.6%)`	⬇️
flopy/utils/particletrackfile.py	`95.6% <94.8%> (-0.4%)`	⬇️
flopy/discretization/unstructuredgrid.py	`75.9% <66.6%> (-5.6%)`	⬇️
flopy/pakbase.py	`82.4% <73.6%> (-2.0%)`	⬇️
... and 15 more

... and 536 files with indirect coverage changes

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

jlarsen-usgs · 2025-12-23T17:49:47Z

@wpbonelli it looks like the smoke tests are failing on test_mf2005_copy and also failed on the prior commit to FloPy. I can't currently reproduce the error on Windows. Any insight into what might be causing this?

wpbonelli

Great to be able to lean on geopandas for shapefile export. I guess we should look at using xarray for netcdf export similarly

General comment re: deprecations, we usually put an expected removal version in the deprecation warning which I think is typically ~2 minor releases ahead?

wpbonelli · 2025-12-26T13:34:55Z

flopy/discretization/structuredgrid.py

+    @property
+    def geo_dataframe(self):
+        """
+        Returns a geopandas GeoDataFrame of the model grid


I think the running convention is to add deprecation notes to docstrings as well as the warning in the code itself

wpbonelli · 2025-12-26T13:36:58Z

flopy/export/shapefile_utils.py

    filename : str or PathLike
        path of the shapefile to write
-    mg : flopy.discretization.grid.Grid object
+    modelgrid : flopy.discretization.grid.Grid object


suggest keeping/deprecating mg just making it optional and introducing modelgrid alongside it to avoid breakage. or, since this function will go away soon, is it worth renaming this parameter at all?

wpbonelli · 2025-12-26T13:37:44Z

flopy/export/shapefile_utils.py


 def model_attributes_to_shapefile(
-    path: Union[str, PathLike],
+    filename: Union[str, PathLike],


same comment as mg/modelgrid above

wpbonelli · 2025-12-26T13:38:12Z

flopy/export/shapefile_utils.py

    Parameters
    ----------
-    shpname : str or PathLike
+    filename : str or PathLike


same comment as above

wpbonelli · 2025-12-26T13:38:19Z

flopy/export/shapefile_utils.py

    geoms,
-    shpname: Union[str, PathLike] = "recarray.shp",
-    mg=None,
+    filename: Union[str, PathLike] = "recarray.shp",


wpbonelli · 2025-12-26T13:47:07Z

flopy/mf6/mfmodel.py

+
+        return gdf
+
    def export(self, f, **kwargs):


I guess we would ideally deprecate export() now that the geodataframe approach is the recommended way to export to shapefile, but since export() also handles netcdf we have to wait til there is a similar netcdf export capability via e.g. xarray? working in the same way as the geopandas approach in this PR like to_xarray().to_netcdf()?

wpbonelli · 2025-12-26T14:02:36Z

flopy/mf6/data/mfdataplist.py

        self.repeating = True
        self.empty_keys = {}

+    def to_geodataframe(self, gdf=None, kper=0, sparse=False, truncate_attrs=False, **kwargs):


What's the use case you have in mind for sparse=False? Since stress period data is sparse by default (at least in 3.x) it seems reasonable to return a sparse geodataframe too, either exclusively or at least by default?

Kind of like what you're doing in shapefile_export_example.py for WEL.

I guess I'm wondering when someone calling to_geodataframe() on stress period data would want one containing the whole grid, rather than just the relevant boundary conditions. In that case couldn't they get the grid geodataframe and .merge() it manually with the SPD frame or pass the grid frame into the gdf parameter here.

Performance wise, it seems expensive to always do the full grid then dropna().

wpbonelli · 2025-12-26T14:06:43Z

flopy/utils/geospatial_utils.py


    @property
-    def geo_dataframe(self):
+    def geodataframe(self):


why to_geodataframe... elsewhere and not here, other than the fact the old property didn't have to_...?

suggest also deprecating the old one to avoid breakage?

wpbonelli · 2025-12-26T14:13:25Z

flopy/mf6/data/mfdataarray.py

+            optional attribute name, default uses util2d name
+        forgive : bool
+            optional flag to continue if data shape not compatible with GeoDataFrame
+        truncate_attrs : bool


I think GeoDataFrame.to_file() already truncates for you when writing to shapefile, is this parameter necessary? It seems like having our own API for this would be useful if we let the user customize the truncation but otherwise redundant?

wpbonelli · 2025-12-26T14:15:18Z

.docs/Notebooks/shapefile_export_example.py

+geoms = GeoSpatialCollection(geoms, "Point")
+gdf = gpd.GeoDataFrame.from_features(geoms)
+
+for col in list(welldata):


instead of looping to add columns, could this just be

gdf = gpd.GeoDataFrame(welldata, geometry=geoms)

jlarsen-usgs added 22 commits December 8, 2025 14:00

merge work and refactor "geo_dataframe" methods to "to_geodataframe" …

1074446

…across flopy

Begin scattering geopandas support and removing pyshp support from ex…

8e4f5ae

…port utilities

Work on deprecating old shapefile exporting code and removing pyshp s…

021602a

…upport

Scatter shapefile attribute truncation options throughout `to_geodata…

9b5e3f0

…frame()` routines

More shapefile and export utilities work to cleanup legacy shapefile …

5338125

…code

update "Grid" import for shapefile_utils.py

86e28b5

woof

58a20f7

fix typo

4b2395f

Remove circular import

a301620

Updates for tests

9412c47

move grid_line_geodataframe call to individual Grid objects

beeeb6a

updates for test_export.py

51fb7a0

woof

60b2cb3

cleanup errors in legacy code

3906504

update shapefile_utils for to_geodataframe

e3301da

update modelgrid_examples.py notebook example

49d8353

update shapefile_export_example.py for to_geodataframe() functionality

805afee

update legacy sfr exporting

d5bd349

update shapefile_feature_examples.py

0cd534c

woof

965340a

Merge branch 'modflowpy:develop' into develop

ded7eaa

refactor .mg to .modelgrid for consistency

957269d

jlarsen-usgs added 3 commits December 23, 2025 07:43

Update test_get_destination_data for geopandas exporting

d115145

woof

c260033

update test_gridgen.py fix unbound error in MFList export

c2b6ec5

jlarsen-usgs marked this pull request as ready for review December 23, 2025 17:35

jlarsen-usgs requested a review from wpbonelli December 23, 2025 17:50

update test_copy.py for numpy immutable deepcopy reference

7d79f96

woof

f0e9211

wpbonelli reviewed Dec 26, 2025

View reviewed changes

feat(GeoDataFrame support): geopandas support for shapefile exporting #2671

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