Flopy

This release includes various bugfixes as well as model splitter improvements. It also adds some capabilities for the soon forthcoming MF6 surface water model. Since the latter is still under development and not yet officially available, we do not consider these to be full-fledged features yet, and so this is a patch rather than a minor FloPy release.

New features

* [feat(cell1d)](https://github.com/modflowpy/flopy/commit/4ea71927f251c3675acf1b578bca623d023ccd2c): Add support for 1D vertex grids (#2296). Committed by langevin-usgs on 2024-08-23.

Bug fixes

* [fix(ParticleTrackFile.write_shapefile)](https://github.com/modflowpy/flopy/commit/f86881d6354071bf7c675384c2684ea184e281eb): Check for "k" even if "i", "j are not present (#2294). Committed by Joshua Larsen on 2024-08-17.
* [fix(modelgrid)](https://github.com/modflowpy/flopy/commit/c42d8787bbcd4131b2f493ebc5a5a384b2e8b861): Add more support for mf6 surface water models (#2295). Committed by langevin-usgs on 2024-08-22.

Refactoring

* [refactor(model_splitter.py)](https://github.com/modflowpy/flopy/commit/d02967db167b98e32cfaa26ef6636475ea2441a8): Update UnstructuredGrid support (#2292). Committed by Joshua Larsen on 2024-08-16.

This release includes a number of bugfixes, a few new features, and support for NumPy 2.

New features

* [feat(datafile)](https://github.com/modflowpy/flopy/commit/d36bb78c3b7a12ab6f77bbe31e3572915753c86b): Add .headers property with data frame (#2221). Committed by Mike Taves on 2024-06-11.
* [feat(lgr-disv)](https://github.com/modflowpy/flopy/commit/7dec7c52db7c7bf3f8bca61de4d4a953ac1317d2): Add to_disv_gridprops() method to lgr object (#2271). Committed by langevin-usgs on 2024-07-26.

Bug fixes

* [fix(docs)](https://github.com/modflowpy/flopy/commit/4a26cab4e0af4f49775fd0dc327c8f5ff51843f6): Section underline matches section title (#2208). Committed by Mike Taves on 2024-06-06.
* [fix(vtk)](https://github.com/modflowpy/flopy/commit/d81d7c089f0688173f25c1f6d1e860e08c3a17ba): Fix __transient_vector access (#2209). Committed by mickey-tsai on 2024-06-06.
* [fix(swt)](https://github.com/modflowpy/flopy/commit/667774231a3c3e40fb68067331ead4b8a576cbee): Pass load_only down to Mt3dms.load() (#2222). Committed by wpbonelli on 2024-06-11.
* [fix(ParticleTrackFile)](https://github.com/modflowpy/flopy/commit/f15caaa0554f306eb5839588e4c75f9e14ef9641): Fix particle filtering in get_alldata (#2223). Committed by martclanor on 2024-06-11.
* [fix(regression)](https://github.com/modflowpy/flopy/commit/c69990ac37ce5d6828472af1eadab4dc6687c1e8): Corrections to test_create_tests_transport (#2228). Committed by Mike Taves on 2024-06-13.
* [fix(binaryread)](https://github.com/modflowpy/flopy/commit/e2a85a38640656d5795f8859defb0de14cf668e6): Raise/handle EOFError, deprecate vartype=str (#2226). Committed by Mike Taves on 2024-06-13.
* [fix(pandas warnings)](https://github.com/modflowpy/flopy/commit/5cdd609748cc70d93859192519d87d34194aec40): Catch pandas warnings and display them in a more useful way (#2229). Committed by scottrp on 2024-06-14.
* [fix](https://github.com/modflowpy/flopy/commit/d9ebd81903bb6aa03864e156a0488128867286ef): Test_uzf_negative_iuzfopt (#2236). Committed by Mike Taves on 2024-06-17.
* [fix(PlotMapView)](https://github.com/modflowpy/flopy/commit/678bb61346bc226831ae5b66615bc9a00c355cc5): Default to all layers in plot_pathline() (#2242). Committed by wpbonelli on 2024-06-19.
* [fix(Raster)](https://github.com/modflowpy/flopy/commit/a2a159f1758781fc633710f68af5441eb1e4dafb): Reclassify np.float64 correctly (#2235). Committed by martclanor on 2024-06-24.
* [fix(HeadFile)](https://github.com/modflowpy/flopy/commit/9db562a3b1d18af3801036b1d79d74668c0f71c6): Fix dis reversal, expand tests (#2247). Committed by wpbonelli on 2024-06-25.
* [fix(mfmodel)](https://github.com/modflowpy/flopy/commit/576cefe5e9826a53a5085d7e3aee9ce7765be22f): Fix get_ims_package (#2272). Committed by martclanor on 2024-08-06.
* [fix(modelgrid)](https://github.com/modflowpy/flopy/commit/b64f2bdae803830936da89cf1c8e97ab4f660981): Fix missing coord info if disv (#2284). Committed by martclanor on 2024-08-07.
* [fix(examples)](https://github.com/modflowpy/flopy/commit/2eace7843409b78497bc941d49eab68394833bfb): Restore example notebooks skipped after #2264 (2286). Committed by wpbonelli on 2024-08-08.

Refactoring

* [refactor(expired deprecation)](https://github.com/modflowpy/flopy/commit/31955a7536b1f53d2a572580e05ff282a933716e): Raise AttributeError with to_shapefile (#2200). Committed by Mike Taves on 2024-05-30.
* [refactor](https://github.com/modflowpy/flopy/commit/bbabf86c0292ed2b237f89371afba01140050592): Deprecate unused flopy.utils.binaryfile.binaryread_struct (#2201). Committed by Mike Taves on 2024-05-31.
* [refactor(exceptions)](https://github.com/modflowpy/flopy/commit/0d9947eb8301561569676d4e3bdbc28a869e5bad): Raise NotImplementedError where appropriate (#2213). Committed by Mike Taves on 2024-06-07.
* [refactor(datafile)](https://github.com/modflowpy/flopy/commit/e2d16df5cc1a27a43e274a5b16eee7d91d5decfa): Use len(obj) rather than obj.get_nrecords() (#2215). Committed by Mike Taves on 2024-06-11.
* [refactor(binarygrid_util)](https://github.com/modflowpy/flopy/commit/ae388ef5a2f40abc950c05ca5b156f7e42337983): Refactor get_iverts to be general and not dependent on grid type (#2230). Committed by langevin-usgs on 2024-06-14.
* [refactor(datafile)](https://github.com/modflowpy/flopy/commit/cfdedbcb35c2f812e2b7efd78706d4eaa8cdc8f5): Deprecate list_records() and other list_ methods (#2232). Committed by Mike Taves on 2024-06-14.
* [refactor](https://github.com/modflowpy/flopy/commit/1e44b3fd57bfad1602a06247e44878a7237e0e3a): Fixes for numpy-2.0 deprecation warnings, require numpy>=1.20.3 (#2237). Committed by Mike Taves on 2024-06-17.
* [refactor](https://github.com/modflowpy/flopy/commit/59040d0948337245d6527671960b56446d39d4d3): Np.where(cond) -> np.asarray(cond).nonzero() (#2238). Committed by wpbonelli on 2024-06-17.
* [refactor(dependencies)](https://github.com/modflowpy/flopy/commit/e48198c661d8b10d1c1120a88a6cd0c7987d7b22): Support numpy 2 (#2241). Committed by wpbonelli on 2024-06-19.
* [refactor(get-modflow)](https://github.com/modflowpy/flopy/commit/baf8dff95ae3cc55adee54ec3e141437ae153b9c): Support ARM macs by default (previously opt-in) (#2225). Committed by wpbonelli on 2024-06-21.
* [refactor(Raster)](https://github.com/modflowpy/flopy/commit/bad483b3910218dc828c993863d540793111090d): Add new methods and checks (#2267). Committed by Joshua Larsen on 2024-07-17.
* [refactor(resample_to_grid)](https://github.com/modflowpy/flopy/commit/bd7f0a578b9093697948255eb9ecc164d5574f6e): Filter raster nan values from scipy resampling routines (#2285). Committed by Joshua Larsen on 2024-08-08.

Support for [MODFLOW 6.5.0](https://github.com/MODFLOW-USGS/modflow6/releases/tag/6.5.0) as well as fixes and enhancements.

---

New features

* [feat(get-modflow)](https://github.com/modflowpy/flopy/commit/53a94a9c6d57f8311318836b4291ac73b4b7f728): Support ARM mac nightly build (#2115). Committed by wpbonelli on 2024-02-23.
* [feat(binaryfile)](https://github.com/modflowpy/flopy/commit/5ec612a1a5b21c094bd910c9ed39f3ea5fef5084): Get budget by second package name `paknam2` (#2050). Committed by Michael OuSSPA on 2024-03-14.
* [feat(get-modflow)](https://github.com/modflowpy/flopy/commit/43e5178db2b52f136cab3d53cb290c2576af21ee): Support windows parallel nightly build (#2128). Committed by wpbonelli on 2024-03-22.
* [feat](https://github.com/modflowpy/flopy/commit/f75853f9fe9921c5ed1aa4e6ab4cec594338905f): Add optional custom print callable (#2121). Committed by Mike Müller on 2024-03-25.
* [feat(dis2d)](https://github.com/modflowpy/flopy/commit/18014af25dff00d659ebe30f9b5dc82da0143be3): Introduce limited support for a 2D structured grid (for overland flow) (#2131). Committed by langevin-usgs on 2024-04-01.
* [feat(vtk)](https://github.com/modflowpy/flopy/commit/3028863dc48b6eb8622b0dcd1a4918cd31547429): Improve vtk particle track export (#2132). Committed by wpbonelli on 2024-04-02.
* [feat(disv2d)](https://github.com/modflowpy/flopy/commit/e023235ad40cd373d428ce5c1533bd0047109a96): Introduce support for a 2D vertex grid (for overland flow) (#2151). Committed by langevin-usgs on 2024-04-15.
* [feat(vtk)](https://github.com/modflowpy/flopy/commit/43cbe4762f6f339a554052a1d0d5836d863da13f): Include all arrays on pathline input (#2161). Committed by wpbonelli on 2024-04-19.
* [feat(mp7particledata)](https://github.com/modflowpy/flopy/commit/e50ab9ae4fce67db947a022da994b26150df13aa): Add localz option for PRT PRP conversions (#2166). Committed by wpbonelli on 2024-04-24.
* [feat(sim options block packages)](https://github.com/modflowpy/flopy/commit/4e1d53ac3685d9027b1ced45749c9e20d8b701d5): Support for packages declared in simulation name file's options block (#2164, 2174). Committed by spaulins-usgs on 2024-05-01.
* [feat(MfList)](https://github.com/modflowpy/flopy/commit/712221918b1f32b881244a19781d01f92d150196): Support kper field in stress period data (#2179). Committed by wpbonelli on 2024-05-04.

Bug fixes

* [fix(PRT)](https://github.com/modflowpy/flopy/commit/dda482b18a6e857ca66a44bbbd69bc3145a68060): Allow empty recarray or dataframe for output conversion fns (#2103). Committed by wpbonelli on 2024-02-19.
* [fix(gridintersect)](https://github.com/modflowpy/flopy/commit/40c03913bdf4329e8540d365ccfffe1c2bf4fccf): Gridintersect does not work for rotated vertex grids (#2107). Committed by Davíd Brakenhoff on 2024-02-20.
* [fix(str and repr)](https://github.com/modflowpy/flopy/commit/1fe51578309a693fae45d843e50aa6f9c86ad70c): Better repr and str output for transient data with multiple blocks (#2058) (2102). Committed by scottrp on 2024-03-13.
* [fix(get_package and model_time)](https://github.com/modflowpy/flopy/commit/11f573b0341b461a584faae4fd82ea4b2bbffc69): #2117, 2118 (2123). Committed by spaulins-usgs on 2024-03-20.
* [fix(modflow)](https://github.com/modflowpy/flopy/commit/aa9f410a4cfd2eecb9f5fa824fbf20103bf45bc0): Dataframe support was patchy in a few packages (#2136). Committed by wpbonelli on 2024-04-04.
* [fix(dependencies)](https://github.com/modflowpy/flopy/commit/0fe415058118ca67a1e02cd5e583ce589a65c9f1): Pin pyzmq >= 25.1.2 for arm macs (#2138). Committed by wpbonelli on 2024-04-05.
* [fix(empty transient data)](https://github.com/modflowpy/flopy/commit/0f14f1fdc02a34338795396549f15758e3ab2ba0): Empty first stress period block (#1091) (2139). Committed by spaulins-usgs on 2024-04-05.
* [fix(comma delimited, scientific notation)](https://github.com/modflowpy/flopy/commit/5aaa5fff0fd9004d16f1699261ed8ef72577a67c): #2053 (2144). Committed by spaulins-usgs on 2024-04-11.
* [fix(empty transient arrays)](https://github.com/modflowpy/flopy/commit/f4a4274ce676713614f47fc4968315ed30297b35): #2145 (2146). Committed by spaulins-usgs on 2024-04-12.
* [fix(2152)](https://github.com/modflowpy/flopy/commit/57cf82ebfcfabfaaf65bde88619070a20a7744ac): Improve gridintersect geometry creation for vertex grids (#2154). Committed by Davíd Brakenhoff on 2024-04-15.
* [fix(grb)](https://github.com/modflowpy/flopy/commit/30e03490e4afadda6ed155cff1c319ebd3c6d5b0): Update binary grid file reader for new grid types (#2157). Committed by langevin-usgs on 2024-04-17.
* [fix(OptionBlock)](https://github.com/modflowpy/flopy/commit/187885b4a3b9f54dbe27d568639931b8094b488e): Deprecate attribute typo 'auxillary' -> 'auxiliary' (#2159). Committed by Mike Taves on 2024-04-19.
* [fix(typos)](https://github.com/modflowpy/flopy/commit/ff82488c0105db52931730fac801fa49a504d1cf): Fixed a variety of typos throughout project (#2160). Committed by Mike Taves on 2024-04-19.
* [fix(cvfdutil)](https://github.com/modflowpy/flopy/commit/bb5461ba32a2047d7451ca53d96ab1643f47309b): Polygon area and centroid calculations now use shapely (#2165). Committed by langevin-usgs on 2024-04-23.
* [fix(gridgen)](https://github.com/modflowpy/flopy/commit/50bbd01a5bae8e80d8345c3f314cabd03df5bb22): Remove duplicate disv grid vertices #1492 (2119). Committed by wpbonelli on 2024-05-02.
* [fix(mfmodel)](https://github.com/modflowpy/flopy/commit/8e16aab76b6e4f892fcf7031488324c3d490b75b): Fix budgetkey for transport models (#2176). Committed by wpbonelli on 2024-05-03.
* [fix(gridintersect)](https://github.com/modflowpy/flopy/commit/15d1d7f5eaf5f50455ff99a876e05c93a947aa5b): Relax cell boundary checks with np.isclose (#2173). Committed by wpbonelli on 2024-05-06.
* [fix(MFFileAccessArray)](https://github.com/modflowpy/flopy/commit/344579b9e23484cd7947948a9ca24a01e161b20e): Read_text_data_from_file modified for non-layered (#2183). Committed by langevin-usgs on 2024-05-06.
* [fix(styles)](https://github.com/modflowpy/flopy/commit/acfd0d37ec0dcb186635af8e70f8a5afbd1eadb6): Remove need for platform evaluation (#2188). Committed by jdhughes-usgs on 2024-05-09.
* [fix(get_structured_faceflows)](https://github.com/modflowpy/flopy/commit/29e247dbe464a861be8ccb4a7ad84f3c4020dd59): Fix lower face flows when idomain is -1 (#2192). Committed by vincentpost on 2024-05-17.
* [fix(tutorial, verbosity setter)](https://github.com/modflowpy/flopy/commit/7879c2f0e41299f70ec0b3b03d756feaf4f20f37): Fixed tutorial model name and verbosity setter (#2182) (2193). Committed by scottrp on 2024-05-21.

Refactoring

* [refactor(datautil)](https://github.com/modflowpy/flopy/commit/b58a70379030d55735858201b16b2599b266ec50): In is_int/float use .item() for np arrays (#2068). Committed by wpbonelli on 2024-02-19.
* [refactor(plotting)](https://github.com/modflowpy/flopy/commit/4e6f4c1b788ec5e64559975afffbcea539def8ac): Check for user set axes limits (#2108). Committed by Joshua Larsen on 2024-02-21.
* [refactor(get_cell_vertices)](https://github.com/modflowpy/flopy/commit/00b3d1c75bcb98bd0ab99c4a9fb45cd8f829e8d3): Raise helpful messages, improve docs, add tests (#2125). Committed by Mike Taves on 2024-03-18.
* [refactor(modpathfile)](https://github.com/modflowpy/flopy/commit/77e5e1dfbadad3fac3be9bf9cf6f0de64f826f66): Toward unified particle tracking api (#2127). Committed by wpbonelli on 2024-03-28.
* [refactor(MFSimulationBase)](https://github.com/modflowpy/flopy/commit/9e87acddcf0740aac491826ef86fd45ae2304dac): Allow simulations to have no attached models (#2140). Committed by Joshua Larsen on 2024-04-06.
* [refactor(lgrutil)](https://github.com/modflowpy/flopy/commit/029a4e165caed6af760517ed7bc1f2e62e218858): Convert numpy types to builtins for np2 compat (#2158). Committed by wpbonelli on 2024-04-19.
* [refactor(mp7particledata)](https://github.com/modflowpy/flopy/commit/c7af787110eb1d984fa660c49014c999d87b0774): Match mp7 order in to_coords()/to_prp() (#2172). Committed by wpbonelli on 2024-05-01.

Support for [MODFLOW 6.4.3](https://github.com/MODFLOW-USGS/modflow6/releases/tag/6.4.3) as well as fixes and enhancements. A highlight is [geopandas](https://geopandas.org/en/stable/getting_started/introduction.html) integration for some APIs.

---

New features

* [feat(set all data external options)](https://github.com/modflowpy/flopy/commit/02a2f91e802185fd6b31929f99e31fecbb41c499): Additional parameters added (#2041). Committed by scottrp on 2023-12-18.
* [feat(PRT)](https://github.com/modflowpy/flopy/commit/a53cda7ff8f724dfc362b432ac9be8c98cc04165): Add conversion/plotting utils for MF6 particle tracking models (#1753). Committed by wpbonelli on 2023-12-22.
* [feat](https://github.com/modflowpy/flopy/commit/6899553828725a302e23b5ec787cea481ce85d59): Add static methods to read gridgen quadtreegrid files (#2061). Committed by Martin Vonk on 2024-01-17.
* [feat(GeoSpatialCollection)](https://github.com/modflowpy/flopy/commit/f8eac0feafd981d84367128a0fdf8e7e1789fa9b): Add support for GeoDataFrame objects (#2063). Committed by Joshua Larsen on 2024-01-26.
* [feat(GeoSpatialCollection)](https://github.com/modflowpy/flopy/commit/86eb092bf5f4d44cc449a458b77114dcefcbdda7): Add support for geopandas GeoSeries and GeoArray (#2085). Committed by Joshua Larsen on 2024-02-02.

Bug fixes

* [fix(gridgen)](https://github.com/modflowpy/flopy/commit/b3510e99b062ba9e950c68db4df95e87375a1ab8): Fix add_refinement_feature() shapefile support (#2022). Committed by wpbonelli on 2023-11-30.
* [fix(gridgen)](https://github.com/modflowpy/flopy/commit/51109751cf0f6c4ebfbc70ccf0ba0ced7fabd4b8): Support arbitrary path-like for shapefiles (#2026). Committed by wpbonelli on 2023-12-04.
* [fix(subpackages)](https://github.com/modflowpy/flopy/commit/788a8df62b1519a621c2721bec12f75cfb11a8d7): Fixed detection issue of subpackages in some filein records (#2025). Committed by scottrp on 2023-12-04.
* [fix(recarrays with cellid)](https://github.com/modflowpy/flopy/commit/a8800396b987e676bf0710a9d52a8cdce7b4d13f): Fixes bug when setting data as recarrays with cellids (#2029). Committed by scottrp on 2023-12-05.
* [fix(Mf6Splitter)](https://github.com/modflowpy/flopy/commit/44abb51b4fb2034d94d82cf686f44c3ddf238a1f): Preserve MFSimulation version & exe_name (#2033). Committed by wpbonelli on 2023-12-07.
* [fix(data storage)](https://github.com/modflowpy/flopy/commit/97da3961f531b26001e8cf55db0de45fc41befad): Added numpy type check for consistent integer and float sizes (32-bit vs 64-bit) (#2062). Committed by scottrp on 2024-01-17.
* [fix(obs package loading)](https://github.com/modflowpy/flopy/commit/a017b77493482124c2f9a635bad19a0c0dfed8c9): Fixed problem with loading multiple continuous blocks (#2058) (2064). Committed by scottrp on 2024-01-22.
* [fix(particledata)](https://github.com/modflowpy/flopy/commit/ea73e0d2f52cf22511c211ea4f5dd5b0a96be69b): Support 1D numpy array for partlocs (#2074). Committed by wpbonelli on 2024-01-25.
* [fix(tri2vor)](https://github.com/modflowpy/flopy/commit/1ab25fe1cd9b55a5128eaade60bd09122f82d096): Remove invalid geometries from voronoi nodes (#2076). Committed by Joshua Larsen on 2024-01-26.
* [fix(MFSimulationList)](https://github.com/modflowpy/flopy/commit/f37610d1f775dbfcc935b129d76c13c407b30e3b): Fix comma spacing in error message (#2090). Committed by wpbonelli on 2024-02-04.
* [fix(numpy 2.0 deprecation)](https://github.com/modflowpy/flopy/commit/ad35b8dda86959f8cdf4560934ab5f309dc28d56): Replace np.alltrue with np.all (#2088). Committed by mnfienen on 2024-02-04.
* [fix(usgcln)](https://github.com/modflowpy/flopy/commit/4ffa04e0757aabf000e6d87a33901c7265b1fa9d): add explicit second dimension to util2d.load calls (#2097). Committed by cnicol-gwlogic on 2024-02-07.

Refactoring

* [refactor(.gitattributes)](https://github.com/modflowpy/flopy/commit/0f33a22f1a01a46949cbb56b61bf41a0c73d78f2): Configure github-linguist exclusions (#2023). Committed by Mike Taves on 2023-12-01.
* [refactor(remap_array)](https://github.com/modflowpy/flopy/commit/5a4533bf115dc4876a811b11d87d353ae01da8ea): Trap for None type idomain (#2034). Committed by Joshua Larsen on 2023-12-07.
* [refactor(mbase)](https://github.com/modflowpy/flopy/commit/66b18624f78f36acd587c5a5bdcd90503397c3d1): Append not prepend flopy bindir to PATH (#2037). Committed by wpbonelli on 2023-12-08.
* [refactor(pyproject.toml)](https://github.com/modflowpy/flopy/commit/b94745dc4f72a4568ab084a762f4d6a1502afbfd): Add dev dependency group (#2075). Committed by wpbonelli on 2024-01-25.
* [refactor(contour_array)](https://github.com/modflowpy/flopy/commit/92853a95f6d38b73e561e3e155d92b75b93afb5d): Add tri_mask kwarg to parameters (#2078). Committed by Joshua Larsen on 2024-02-01.
* [refactor(dependencies)](https://github.com/modflowpy/flopy/commit/da8a3bdd6ecdbced4a22054b57c45dca470ec709): Remove python-dateutil (#2080). Committed by wpbonelli on 2024-02-01.
* [refactor(_plot_package_helper)](https://github.com/modflowpy/flopy/commit/cff4f2351d92ef8f894633481248b645c07f5c83): Pass kwargs to datatype helpers (#2081). Committed by Joshua Larsen on 2024-02-02.
* [refactor(convert_grid)](https://github.com/modflowpy/flopy/commit/b9ca77160cab2bf0e1af1d1d17ac82f3fa6e9d84): Added offset and angrot info to conversion (#2083). Committed by Joshua Larsen on 2024-02-02.
* [refactor(dependencies)](https://github.com/modflowpy/flopy/commit/391a3690c57ccf2951f7d618c1afd4168dfa0f9b): Pin numpy<2 until other reqs support it (#2092). Committed by wpbonelli on 2024-02-07.
* [refactor(mf6)](https://github.com/modflowpy/flopy/commit/d3e8a2a4342766288166e2251e96721007f5217f): Update DFNS for mf6.4.3, regen/reformat .py files (#2095). Committed by wpbonelli on 2024-02-07.

---

⚠️ Breaking changes

* `rno`, `iuzno`, `lakeno`, `wellno` attributes were standardized to `ifno` (for "feature number") &mdash; a 3.5.x patch may provide backwards-compatibility as this was released somewhat prematurely

Highlights

Python 3.12 support

While previous releases may be compatible with Python 3.12, this release adds official support. **Note:** the wheel for `pyzmq`, a core dependency of `IPython`/`jupyter`, may fail to build when installing optional dependencies via e.g. `pip install "flopy[test]"` or `pip install "flopy[optional]"`. To work with notebooks in the meantime Conda is recommended.

Pandas integration

* Promote [Pandas](https://github.com/pandas-dev/pandas) from optional to core dependency (note `pandas >= 2` is required)
* Reimplement MF6 internal data storage with Pandas &mdash; may provide significant speedups reading/writing MF6 input files. To fall back to the old implementation, set `use_pandas=False` on `MFSimulation.load()` or at init time.
* Support `DataFrame` for `flopy.modflow.*` package input data, e.g. `node_data` and `stress_period_data`

Deprecations

Several deprecated features are removed or turned into errors:

* `sr` property from `Mt3dms`
* `flopy.export.vtk` functions `export_model()`, `export_package()`, `export_transient()`, `export_heads()`, `export_array()`, `export_cbc()`
* `flopy.plot.plotutil` functions `centered_specific_discharge()`, `cvfd_to_patch_collection()`, `plot_cvfd()`
* `layer` kwarg in `MFTransientArray`'s `get_data()` method
* `MFSimulation` functions `get_mvr_file()`, `get_mvt_file()`, `get_gnc_file()`, `get_ims_package()`
* `nwt_11_fmt` parameter from `ModflowUzf1` initializer
* `Grid.thick` and `.saturated_thick` properties

Other changes

* `rno`, `iuzno`, `lakeno`, `wellno` standardized to `ifno` (for "feature number")

Several features are newly deprecated:

* `ra_slice()` from `flopy.utils.recarray_utils`, suggest `numpy.lib.recfunctions.repack_fields()`
* `recarray()` from `flopy.utils.recarray_utils`, suggest `numpy.core.records.fromrecords()`
* `epsg`, `proj4`, and `proj4_str` are replaced with a single `crs` parameter on MF6 `Grid` and `ModflowDis` classes and various utilities
* `branch` option for `flopy.mf6.utils.generate_classes` utility replaced with `ref`

See specific commits below for more info on suggested replacements.

---

New features

* [feat(simulation+model options)](https://github.com/modflowpy/flopy/commit/a16a379ef61cc16594ac6ac9eadb5ce4c6a4cee1): Dynamically generate simulation options from simulation namefile dfn (#1842). Committed by spaulins-usgs on 2023-07-10.
* [feat(binaryfile)](https://github.com/modflowpy/flopy/commit/79311120d0daeb3ba1281c70faf97fcd92a1fde5): Add reverse() method to HeadFile, CellBudgetFile (#1829). Committed by w-bonelli on 2023-07-29.
* [feat(get-modflow)](https://github.com/modflowpy/flopy/commit/1cb7594d12a2aa385a567613e9f840de63ba7157): Allow specifying repo owner (#1910). Committed by w-bonelli on 2023-08-08.
* [feat(generate_classes)](https://github.com/modflowpy/flopy/commit/e02030876c20d6bf588134bc0ab0cc1c75c0c46e): Create a command-line interface (#1912). Committed by Mike Taves on 2023-08-16.
* [feat(gridutil)](https://github.com/modflowpy/flopy/commit/e20a29814afd97650d6ee2b10f0939893be64551): Add function to help create DISV grid (#1952). Committed by langevin-usgs on 2023-09-18.
* [feat(pandas list)](https://github.com/modflowpy/flopy/commit/6a46a9b75286d7e268d4addc77946246ccb5db56): Fix for handling special case where boundname set but not used (#1982). Committed by scottrp on 2023-10-06.
* [feat(MfSimulationList)](https://github.com/modflowpy/flopy/commit/b34f154362320059d92050b54014ec1fc9c9f09f): Add functionality to parse the mfsim.lst file (#2005). Committed by jdhughes-usgs on 2023-11-14.
* [feat(modflow)](https://github.com/modflowpy/flopy/commit/be104c4a38d2b1f4acfbdd5a49a5b3ddb325f852): Support dataframe for pkg data (#2010). Committed by wpbonelli on 2023-11-22.
* [feat(mfsimlist)](https://github.com/modflowpy/flopy/commit/121ca78f6073813cec082cfd01f483dad6838781): Add functionality to parse memory_print_options (#2009). Committed by jdhughes-usgs on 2023-11-22.

Bug fixes

* [fix(exchange and gnc package cellids)](https://github.com/modflowpy/flopy/commit/a84d88596f8b8e8f9f8fa074ad8fce626a84ebd0): #1866 (1871). Committed by spaulins-usgs on 2023-07-11.
* [fix(modelgrid)](https://github.com/modflowpy/flopy/commit/99f680feb39cb9450e1ce052024bb3da45e264d8): Retain crs data from classic nam files (#1904). Committed by Mike Taves on 2023-08-10.
* [fix(generate_classes)](https://github.com/modflowpy/flopy/commit/4f6cd47411b96460495b1f7d6582860a4d655060): Use branch arg if provided (#1938). Committed by w-bonelli on 2023-08-31.
* [fix(remove_model)](https://github.com/modflowpy/flopy/commit/71855bdfcd37e95194b6e5928ae909a6f7ef15fa): Remove_model method fix and tests (#1945). Committed by scottrp on 2023-09-14.
* [fix(model_splitter.py)](https://github.com/modflowpy/flopy/commit/5b5eb4ec20c833df4117415d433513bf3a1b4aa5): Standardizing naming of iuzno, rno, lakeno, & wellno to ifno (#1963). Committed by Eric Morway on 2023-09-25.
* [fix(pandas list)](https://github.com/modflowpy/flopy/commit/f77989d33955baa76032d9341226385215e45821): Deal with cellids with inconsistent types (#1980). Committed by scottrp on 2023-10-06.
* [fix(model_splitter)](https://github.com/modflowpy/flopy/commit/5ebc216822a86f32c7a2ab9a3735f021475dc0f4): Check keys in mftransient array (#1998). Committed by jdhughes-usgs on 2023-11-13.
* [fix(benchmarks)](https://github.com/modflowpy/flopy/commit/16183c3059f4a9bb10d74423500b566eb41d3d6e): Fix benchmark post-processing (#2004). Committed by wpbonelli on 2023-11-14.
* [fix(MfSimulationList)](https://github.com/modflowpy/flopy/commit/7cc5e6f0b4861e2f9d85eb1e25592721d0427227): Add missing seek to get_runtime method (#2006). Committed by mjr-deltares on 2023-11-15.
* [fix(get_disu_kwargs)](https://github.com/modflowpy/flopy/commit/419ae0e0c15b4f95f6ea334fe49f79e29917130b): Incorrect indexing of delr and delc (#2011). Committed by langevin-usgs on 2023-11-21.
* [fix(PlotCrossSection)](https://github.com/modflowpy/flopy/commit/6e3c7911c1e94a9f8c36563662471c68a7aeeefc): Boundary conditions not plotting for DISU (#2012). Committed by langevin-usgs on 2023-11-21.
* [fix(release.yml)](https://github.com/modflowpy/flopy/commit/11f518cd68be596c3f07b052f9d3320880c38170): Don't regenerate pkgs from mf6 main on release (#2014). Committed by wpbonelli on 2023-11-24.
* [fix(release.yml)](https://github.com/modflowpy/flopy/commit/0da6b8ecc9087cc9c68a7d90999f61eb78f0f9ac): Fix update changelog step (#2015). Committed by wpbonelli on 2023-11-25.

Refactoring

* [refactor(_set_neighbors)](https://github.com/modflowpy/flopy/commit/9168b3a538a5f604010ad5df17ea7e868b8f913f): Check for closed iverts and remove closing ivert (#1876). Committed by Joshua Larsen on 2023-07-14.
* [refactor(crs)](https://github.com/modflowpy/flopy/commit/02fae7d8084f52e852722338038b6ef7a2691e61): Provide support without pyproj, other deprecations (#1850). Committed by Mike Taves on 2023-07-19.
* [refactor(Notebooks)](https://github.com/modflowpy/flopy/commit/c261ee8145e2791be2c2cc944e5a55cf19ef1560): Apply pyformat and black QA tools (#1879). Committed by Mike Taves on 2023-07-24.
* [refactor](https://github.com/modflowpy/flopy/commit/8c3d7dbbaa753893d746965f9ecc48dc68b274cd): Require pandas>=2.0.0 as core dependency (#1887). Committed by w-bonelli on 2023-08-01.
* [refactor(expired deprecation)](https://github.com/modflowpy/flopy/commit/47e5e359037518f29d14469531db68999d308a0f): Raise AttributeError with Grid.thick and Grid.saturated_thick (#1884). Committed by Mike Taves on 2023-08-01.
* [refactor(pathline/endpoint plots)](https://github.com/modflowpy/flopy/commit/54d6099eb71a7789121bcfde8816b23fa06c258e): Support recarray or dataframe (#1888). Committed by w-bonelli on 2023-08-01.
* [refactor(expired deprecation)](https://github.com/modflowpy/flopy/commit/70b9a37153bf51be7cc06db513b24950ce122fd2): Remove warning for third parameter of Grid.intersect (#1883). Committed by Mike Taves on 2023-08-01.
* [refactor(dependencies)](https://github.com/modflowpy/flopy/commit/dd77e72b9676be8834dcf0a08e6f55fd35e2bc29): Constrain sphinx >=4 (#1898). Committed by w-bonelli on 2023-08-02.
* [refactor(dependencies)](https://github.com/modflowpy/flopy/commit/03fa01fe09db45e30fe2faf4c5160622b78f1b24): Constrain sphinx-rtd-theme >=1 (#1900). Committed by w-bonelli on 2023-08-03.
* [refactor(mf6)](https://github.com/modflowpy/flopy/commit/809e624fe77c4d112e482698434e2199345e68c2): Remove deprecated features (#1894). Committed by w-bonelli on 2023-08-03.
* [refactor(plotutil)](https://github.com/modflowpy/flopy/commit/cf675c6b892a0d484f91465a4ad6600ffe4d518e): Remove deprecated utilities (#1891). Committed by w-bonelli on 2023-08-03.
* [refactor(shapefile_utils)](https://github.com/modflowpy/flopy/commit/6f2da88f9b2d53f94f9c003ddfde3daf6952e3ba): Remove deprecated SpatialReference usages (#1892). Committed by w-bonelli on 2023-08-03.
* [refactor(vtk)](https://github.com/modflowpy/flopy/commit/ca838b17e89114be8952d07e85d88b128d2ec2c3): Remove deprecated export_* functions (#1890). Committed by w-bonelli on 2023-08-03.
* [refactor(generate_classes)](https://github.com/modflowpy/flopy/commit/72370269e2d6933245c65b3c93beb532016593f3): Deprecate branch for ref, introduce repo, test commit hashes (#1907). Committed by w-bonelli on 2023-08-09.
* [refactor(expired deprecation)](https://github.com/modflowpy/flopy/commit/ed3a0cd68ad1acb68fba750f415fa095a19b741a): Remaining references to SpatialReference (#1914). Committed by Mike Taves on 2023-08-11.
* [refactor(Mf6Splitter)](https://github.com/modflowpy/flopy/commit/3a1ae0bba3171561f0b4b78a2bb892fdd0c55e90): Control record and additional splitting checks (#1919). Committed by Joshua Larsen on 2023-08-21.
* [refactor(triangle)](https://github.com/modflowpy/flopy/commit/9ca601259604b1805d8ec1a30b0a883a7b5f019a): Raise if output files not found (#1954). Committed by wpbonelli on 2023-09-22.
* [refactor(recarray_utils)](https://github.com/modflowpy/flopy/commit/941a5f105b10f50fc71b14ea05abf499c4f65fa5): Deprecate functions, use numpy builtins (#1960). Committed by wpbonelli on 2023-09-27.
* [refactor(contour_array)](https://github.com/modflowpy/flopy/commit/4ed68a2be1e6b4f607e27c38ce5eab9f66492e3f): Add layer param, update docstrings, expand tests (#1975). Committed by wpbonelli on 2023-10-18.
* [refactor(model_splitter.py)](https://github.com/modflowpy/flopy/commit/4ef699e10b1fbd80055b85ca00a17b96d1c627ce): (#1994). Committed by Joshua Larsen on 2023-11-01.
* [refactor(modflow)](https://github.com/modflowpy/flopy/commit/696a209416f91bc4a9e61b4392f4218e9bd83408): Remove deprecated features (#1893). Committed by wpbonelli on 2023-11-03.
* [refactor](https://github.com/modflowpy/flopy/commit/af8954b45903680a2931573453228b03ea7beb6b): Support python3.12, simplify tests and dependencies (#1999). Committed by wpbonelli on 2023-11-13.
* [refactor(msfsr2)](https://github.com/modflowpy/flopy/commit/4eea1870cb27aa2976cbf5366a6c2cb942a2f0c4): Write sfr_botm_conflicts.chk to model workspace (#2002). Committed by wpbonelli on 2023-11-14.
* [refactor(shapefile_utils)](https://github.com/modflowpy/flopy/commit/0f8b521407694442c3bb2e50ce3d4f6207f86e48): Warn if fieldname truncated per 10 char limit (#2003). Committed by wpbonelli on 2023-11-14.
* [refactor(pakbase)](https://github.com/modflowpy/flopy/commit/09b59ce8c0e33b32727e0f07e44efadf166ffba2): Standardize ipakcb docstrings/defaults (#2001). Committed by wpbonelli on 2023-11-22.
* [refactor(.gitattributes)](https://github.com/modflowpy/flopy/commit/338f6d073d6ba7edecc12405f3da83ea51e6cc26): Exclude examples/data from linguist (#2017). Committed by wpbonelli on 2023-11-25.

Provide interim support for Matplotlib 3.8+, which [changed the way contours are represented](https://github.com/matplotlib/matplotlib/pull/25247/files#diff-918125f8b0a3d8085b15096d948f8e005d5dc938ea54501ba3c1f7a36ad74f7f) and broke `export_contours()` and `export_contourf()`.

**Note**: with MPL 3.8+, FloPy can no longer export interior polygons (i.e. holes) for filled contours. This is a backwards-incompatible change, and could be considered worthy of a major release &mdash; with some compunction, FloPy follows MPL's example here, and this remains a patch release. A future version may [reimplement contour export and restore support for interior polygons](https://github.com/modflowpy/flopy/issues/1973). In the meantime, users requiring interior polygons should pin MPL below 3.8.

Bug fixes

* [fix(export_contours/f)](https://github.com/modflowpy/flopy/commit/30209f2ca2e69289227203e4afd2f33bfceed097): Support matplotlib 3.8+ (#1951). Committed by wpbonelli on 2023-09-19.
* [fix(usg bcf)](https://github.com/modflowpy/flopy/commit/d2dbacb65d2579e42bbd7965c1321a89ccce7d56): ksat util3d call --> util2d call (#1959). Committed by cnicol-gwlogic on 2023-09-22.
* [fix(resolve_exe)](https://github.com/modflowpy/flopy/commit/3522dced8a49dc93fb0140d9ac360a88f31b11bb): Support extensionless abs/rel paths on windows (#1957). Committed by wpbonelli on 2023-09-24.
* [fix(mbase)](https://github.com/modflowpy/flopy/commit/b848f968af4179d8618b811cd4fe6f8de66d09cb): Warn if duplicate pkgs or units (#1964). Committed by wpbonelli on 2023-09-26.
* [fix(get_structured_faceflows)](https://github.com/modflowpy/flopy/commit/92632d26be2ecb21b6d9d56717faadaa13e08369): Cover edge cases, expand tests (#1968). Committed by wpbonelli on 2023-09-29.
* [fix(CellBudgetFile)](https://github.com/modflowpy/flopy/commit/015d6399baa48819f9f0f78bf2f34f60bdd8ef18): Detect compact fmt by negative nlay (#1966). Committed by wpbonelli on 2023-09-30.