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FloPy 3.3.6

15 Dec 16:31
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3.3.6
793d8dc
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FloPy 3.3.6

New features

  • feat(time step length): Added feature that returns time step lengths from listing file (#1435) (#1437). Committed by scottrp on 2022-06-30.
  • feat: Get modflow utility (#1465). Committed by Mike Taves on 2022-07-27.
  • feat(Gridintersect): New grid intersection options (#1468). Committed by Davíd Brakenhoff on 2022-07-27.
  • feat: Unstructured grid from specification file (#1524). Committed by w-bonelli on 2022-09-08.
  • feat(aux variable checking): Check now performs aux variable checking (#1399) (#1536). Committed by spaulins-usgs on 2022-09-12.
  • feat(get/set data record): Updated get_data/set_data functionality and new get_record/set_record methods (#1568). Committed by spaulins-usgs on 2022-10-06.
  • feat(get_modflow): Support modflow6 repo releases (#1573). Committed by w-bonelli on 2022-10-11.
  • feat(contours): Use standard matplotlib contours for StructuredGrid map view plots (#1615). Committed by w-bonelli on 2022-11-10.

Bug fixes

  • fix(geometry): Is_clockwise() now works as expected for a disv problem (#1374). Committed by Eric Morway on 2022-03-16.
  • fix(packaging): Include pyproject.toml to sdist, check package for PyPI (#1373). Committed by Mike Taves on 2022-03-21.
  • fix(url): Use modern DOI and USGS prefixes; upgrade other HTTP->HTTPS (#1381). Committed by Mike Taves on 2022-03-23.
  • fix(packaging): Add docs/*.md to MANIFEST.in for sdist (#1391). Committed by Mike Taves on 2022-04-01.
  • fix(_plot_transient2d_helper): Fix filename construction for saving plots (#1388). Committed by Joshua Larsen on 2022-04-01.
  • fix(simulation packages): *** Breaks interface *** (#1394). Committed by spaulins-usgs on 2022-04-19.
  • fix(plot_pathline): Split recarray into particle list when it contains multiple particle ids (#1400). Committed by Joshua Larsen on 2022-04-30.
  • fix(lgrutil): Child delr/delc not correct if parent has variable row/col spacings (#1403). Committed by langevin-usgs on 2022-05-03.
  • fix(ModflowUzf1): Fix for loading negative iuzfopt (#1408). Committed by Joshua Larsen on 2022-05-06.
  • fix(features_to_shapefile): Fix missing bracket around linestring for shapefile (#1410). Committed by Joshua Larsen on 2022-05-06.
  • fix(mp7): Ensure shape in variables 'zones' and 'retardation' is 3d (#1415). Committed by Ruben Caljé on 2022-05-11.
  • fix(ModflowUzf1): Update load for iuzfopt = -1 (#1416). Committed by Joshua Larsen on 2022-05-17.
  • fix(recursion): Infinite recursion fix for getattr. Spelling error fix in notebook. (#1414). Committed by scottrp on 2022-05-19.
  • fix(get_structured_faceflows): Fix index issue in lower right cell (#1417). Committed by jdhughes-usgs on 2022-05-19.
  • fix(package paths): Fixed auto-generated package paths to make them unique (#1401) (#1425). Committed by spaulins-usgs on 2022-05-31.
  • fix(get-modflow/ci): Use GITHUB_TOKEN to side-step ratelimit (#1473). Committed by Mike Taves on 2022-07-29.
  • fix(get-modflow/ci): Handle 404 error to retry request from GitHub (#1480). Committed by Mike Taves on 2022-08-04.
  • fix(intersect): Update to raise error only when interface is called improperly (#1489). Committed by Joshua Larsen on 2022-08-11.
  • fix(GridIntersect): Fix DeprecationWarnings for Shapely2.0 (#1504). Committed by Davíd Brakenhoff on 2022-08-19.
  • fix: CI, tests & modpathfile (#1495). Committed by w-bonelli on 2022-08-22.
  • fix(HeadUFile): Fix #1503 (#1510). Committed by w-bonelli on 2022-08-26.
  • fix(setuptools): Only include flopy and flopy.* packages (not autotest) (#1529). Committed by Mike Taves on 2022-09-01.
  • fix(mfpackage): Modify maxbound evaluation (#1530). Committed by jdhughes-usgs on 2022-09-02.
  • fix(PlotCrossSection): Update number of points check (#1533). Committed by Joshua Larsen on 2022-09-08.
  • fix(parsenamefile): Only do lowercase comparison when parent dir exists (#1554). Committed by Mike Taves on 2022-09-22.
  • fix(obs): Modify observations to load single time step files (#1559). Committed by jdhughes-usgs on 2022-09-29.
  • fix(PlotMapView notebook): Remove exact contour count assertion (#1564). Committed by w-bonelli on 2022-10-03.
  • fix(test markers): Add missing markers for exes required (#1577). Committed by w-bonelli on 2022-10-07.
  • fix(csvfile): Default csvfile to retain all characters in column names (#1587). Committed by langevin-usgs on 2022-10-14.
  • fix(csvfile): Correction to read_csv args, close file handle (#1590). Committed by Mike Taves on 2022-10-16.
  • fix(data shape): Fixed incorrect data shape for sfacrecord (#1584). Fixed a case where time array series data did not load correctly from a file when the data shape could not be determined (#1594). (#1598). Committed by spaulins-usgs on 2022-10-21.
  • fix(write_shapefile): Fix transform call for exporting (#1608). Committed by Joshua Larsen on 2022-10-27.
  • fix(multiple): Miscellanous fixes/enhancements (#1614). Committed by w-bonelli on 2022-11-03.
  • fix: Not reading comma separated data correctly (#1634). Committed by Michael Ou on 2022-11-23.
  • fix(get-modflow): Fix code.json handling (#1641). Committed by w-bonelli on 2022-12-08.
  • fix(quotes+exe_path+nam_file): Fixes for quoted strings, exe path, and nam file (#1645). Committed by spaulins-usgs on 2022-12-08.

Refactoring

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FloPy version 3.3.5

09 Mar 02:36
@jdhughes-usgs jdhughes-usgs
3.3.5
05b538c
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FloPy version 3.3.5

  • New features:

    • feat(mvt): Add simulation-level support for mover transport (#1357). Committed by langevin-usgs on 2022-02-18.
    • feat(gwtgwt-mvt): Add support for gwt-gwt with mover transport (#1356). Committed by langevin-usgs on 2022-02-18.
    • feat(inspect cells): New feature that returns model data associated with specified model cells (#1140) (#1325). Committed by spaulins-usgs on 2022-01-11.
    • feat(multiple package instances): Flopy support for multiple instances of the same package stored in dfn files (#1239) (#1321). Committed by spaulins-usgs on 2022-01-07.
    • feat(Gridintersect): Add shapetype kwarg (#1301). Committed by Davíd Brakenhoff on 2021-12-03.
    • feat(get_ts): Added support to get_ts for headufile (#1260). Committed by Ross Kushnereit on 2021-10-09.
    • feat(CellBudget): Add support for full3d keyword (#1254). Committed by jdhughes-usgs on 2021-10-05.
    • feat(mf6): Allow multi-package for stress package concentrations (spc) (#1242). Committed by langevin-usgs on 2021-09-16.
    • feat(lak6): Support none lake bedleak values (#1189). Committed by jdhughes-usgs on 2021-08-16.

  • Bug fixes:

    • fix(exchange obs): Fixed building of obs package for exchange packages (through mfsimulation) (#1363). Committed by spaulins-usgs on 2022-02-28.
    • fix(tab files): Fixed searching for tab file packages (#1337) (#1344). Committed by scottrp on 2022-02-16.
    • fix(ModflowUtllaktab): Utl-lak-tab.dfn is redundant to utl-laktab.dfn (#1339). Committed by Mike Taves on 2022-01-27.
    • fix(cellid): Fixes some issues with flopy properly identifying cell ids (#1335) (#1336). Committed by spaulins-usgs on 2022-01-25.
    • fix(postprocessing): Get_structured_faceflows fix to support 3d models (#1333). Committed by langevin-usgs on 2022-01-21.
    • fix(Raster): Resample_to_grid failure no data masking failure with int dtype (#1328). Committed by Joshua Larsen on 2022-01-21.
    • fix(voronoi): Clean up voronoi examples and add error check (#1323). Committed by langevin-usgs on 2022-01-03.
    • fix(filenames): Fixed how spaces in filenames are handled (#1236) (#1318). Committed by spaulins-usgs on 2021-12-16.
    • fix(paths): Path code made more robust so that non-standard model folder structures are supported (#1311) (#1316). Committed by scottrp on 2021-12-09.
    • fix(UnstructuredGrid): Load vertices for unstructured grids (#1312). Committed by Chris Nicol on 2021-12-09.
    • fix(array): Getting array data (#1028) (#1290). Committed by spaulins-usgs on 2021-12-03.
    • fix(plot_pathline): Sort projected pathline points by travel time instead of cell order (#1304). Committed by Joshua Larsen on 2021-12-03.
    • fix(autotests): Added pytest.ini to declare test naming convention (#1307). Committed by Joshua Larsen on 2021-12-03.
    • fix(geospatial_utils.py): Added pyshp and shapely imports check to geospatial_utils.py (#1305). Committed by Joshua Larsen on 2021-12-03.
    • fix(path): Fix subdirectory path issues (#1298). Committed by Brioch Hemmings on 2021-11-18.
    • fix(): fix(mfusg/str) (#1296). Committed by Chris Nicol on 2021-11-11.
    • fix(io): Read comma separated list (#1285). Committed by Michael Ou on 2021-11-02.
    • fixes(1247): Make flopy buildable with pyinstaller (#1248). Committed by Tim Mitchell on 2021-10-20.
    • fix(keystring records): Fixed problem with keystring records containing multiple keywords (#1266). Committed by spaulins-usgs on 2021-10-15.
    • fix(ModflowFhb): Update datasets 4, 5, 6, 7, 8 loading routine for multiline records (#1264). Committed by Joshua Larsen on 2021-10-15.
    • fix(MFFileMgmt.string_to_file_path): Updated to support unc paths (#1256). Committed by Joshua Larsen on 2021-10-06.
    • fix(_mg_resync): Added checks to reset the modelgrid resync (#1258). Committed by Joshua Larsen on 2021-10-06.
    • fix(MFPackage): Fix mfsim.nam relative paths (#1252). Committed by Joshua Larsen on 2021-10-01.
    • fix(voronoi): Voronoigrid class upgraded to better support irregular domains (#1253). Committed by langevin-usgs on 2021-10-01.
    • fix(writing tas): Fixed writing non-constant tas (#1244) (#1245). Committed by spaulins-usgs on 2021-09-22.
    • fix(numpy elementwise comparison): Fixed numpy futurewarning. no elementwise compare is needed if user passes in a numpy recarray, this is only necessary for dictionaries. (#1235). Committed by spaulins-usgs on 2021-09-13.
    • fix(): fix(shapefile_utils) unstructured shapefile export (#1220) (#1222). Committed by Chris Nicol on 2021-09-03.
    • fix(rename and comments): Package rename code and comment propagation (#1226). Committed by spaulins-usgs on 2021-09-03.
    • fix(numpy): Handle deprecation warnings from numpy 1.21 (#1211). Committed by Mike Taves on 2021-08-23.
    • fix(Grid.saturated_thick): Update saturated_thick to filter confining bed layers (#1197). Committed by Joshua Larsen on 2021-08-18.
    • fix(): fix(pakbase) unstructured storage check (#1187) (#1194). Committed by Chris Nicol on 2021-08-17.
    • fix(MF6Output): Fix add new obs package issue (#1193). Committed by Joshua Larsen on 2021-08-17.
    • fix(): fix(plot/plot_bc) plot_bc fails with unstructured models (#1185). Committed by Chris Nicol on 2021-08-16.
    • fix(): fix(modflow/mfriv) unstructured mfusg RIV package load check fix (#1184). Committed by Chris Nicol on 2021-08-16.
    • fix(pakbase): Specify dtype=bool for 0-d active array used for usg (#1188). Committed by Mike Taves on 2021-08-16.
    • fix(raster): Rework raster threads to work on osx (#1180). Committed by jdhughes-usgs on 2021-08-10.
    • fix(): fix(loading mflist from file) (#1179). Committed by J Dub on 2021-08-09.
    • fix(grid, plotting): Bugfixes for all grid instances and plotting code (#1174). Committed by Joshua Larsen on 2021-08-09.
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FloPy version 3.3.4

06 Aug 23:20
@jdhughes-usgs jdhughes-usgs
3.3.4
1f21a86
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FloPy version 3.3.4

  • New features:

    • feat(mf6-lake): Add helper function to create lake connections (#1163). Committed by jdhughes-usgs on 2021-08-04.
    • feat(data storage): Data automatically stored internally when simulation or model relative path changed (#1126) (#1157). Committed by spaulins-usgs on 2021-07-29.
    • feat(get_reduced_pumping): Update to read external pumping reduction files (#1162). Committed by Joshua Larsen on 2021-07-29.
    • feat(raster): Add option to extrapolate using nearest method (#1159). Committed by jdhughes-usgs on 2021-07-26.
    • Feat(ZoneBudget6): Added zonebudget6 class to zonbud.py (#1149). Committed by Joshua Larsen on 2021-07-12.
    • feat(grid): Add thickness method for all grid types (#1138). Committed by jdhughes-usgs on 2021-06-25.
    • feat(flopy for mf6 docs): Documentation added and improved for flopy (#1121). Committed by spaulins-usgs on 2021-06-01.
    • Feat(.output): Added output property method to mf6 packages and models (#1100). Committed by Joshua Larsen on 2021-04-23.

  • Bug fixes:

    • fix(flopy_io): Limit fixed point format string to fixed column widths (#1172). Committed by jdhughes-usgs on 2021-08-06.
    • fix(modpath7): Address #993 and #1053 (#1170). Committed by jdhughes-usgs on 2021-08-05.
    • fix(lakpak_utils): Fix telev and belev for horizontal connections (#1168). Committed by jdhughes-usgs on 2021-08-05.
    • fix(mfsfr2.check): Make reach_connection_gaps.chk.csv a normal csv file (#1151). Committed by Mike Taves on 2021-07-27.
    • fix(modflow/mfrch,mfevt): Mfusg rch,evt load and write fixes (#1148). Committed by Chris Nicol on 2021-07-13.
    • fix(Raster): Update default dtypes to include unsigned integers (#1147). Committed by Joshua Larsen on 2021-07-12.
    • fix(utils/check): File check for mfusg unstructured models (#1145). Committed by Chris Nicol on 2021-07-09.
    • fix(list parsing): Fixed errors caused by parsing certain lists with keywords in the middle (#1135). Committed by spaulins-usgs on 2021-06-25.
    • fix(plotutil.py, grid.py): Fix .plot() method using mflay parameter (#1134). Committed by Joshua Larsen on 2021-06-16.
    • fix(map.py): Fix slow plotting routines (#1118). Committed by Joshua Larsen on 2021-06-11.
    • fix(plot_pathline): Update modpath intersection routines (#1112). Committed by Joshua Larsen on 2021-06-11.
    • fix(gridgen): Mfusg helper function not indexing correctly (#1124). Committed by langevin-usgs on 2021-05-28.
    • fix(numpy): Aliases of builtin types is deprecated (#1105). Committed by Mike Taves on 2021-05-07.
    • fix(mfsfr2.py): Dataset 6b and 6c write routine, remove blank lines (#1101). Committed by Joshua Larsen on 2021-04-26.
    • fix(performance): Implemented performance improvements including improvements suggested by @briochh (#1092) (#1097). Committed by spaulins-usgs on 2021-04-12.
    • fix(package write): Allow user to define and write empty stress period blocks to package files (#1091) (#1093). Committed by scottrp on 2021-04-08.
    • fix(imports): Fix shapely and geojson imports (#1083). Committed by jdhughes-usgs on 2021-03-20.
    • fix(shapely): Handle deprecation warnings from shapely 1.8 (#1069). Committed by Mike Taves on 2021-03-19.
    • fix(mp7particledata): Update dtype comparison for unstructured partlocs (#1071). Committed by rodrperezi on 2021-03-19.
    • fix(get_file_entry): None text removed from empty stress period data with aux variable (#1080) (#1081). Committed by scottrp on 2021-03-19.
    • fix(data check): Minimum number of data columns check fixed (#1062) (#1067). Committed by spaulins-usgs on 2021-03-17.
    • fix(plotutil): Number of plottable layers should be from util3d.shape[0] (#1077). Committed by Mike Taves on 2021-03-15.
    • fix(data check): Minimum number of data columns check fixed (#1062) (#1065). Committed by spaulins-usgs on 2021-02-19.

Contributors

briochh
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FloPy version 3.3.3

18 Feb 21:27
@jdhughes-usgs jdhughes-usgs
3.3.3
446008d
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FloPy version 3.3.3

  • New features:

    • feat(voronoi): Add voronoigrid class (#1034). Committed by langevin-usgs on 2021-01-05.
    • feat(unstructured): Improve unstructured grid support for modflow 6 and modflow-usg (#1021). Committed by langevin-usgs on 2020-11-27.

  • Bug fixes:

    • fix(createpackages): Avoid creating invalid escape characters (#1055). Committed by Mike Taves on 2021-02-17.
    • fix(DeprecationWarning): Use collections.abc module instead of collections (#1057). Committed by Mike Taves on 2021-02-15.
    • fix(DeprecationWarning): Related to numpy (#1058). Committed by Mike Taves on 2021-02-15.
    • fix(numpy): Aliases of builtin types is deprecated as of numpy 1.20 (#1052). Committed by Mike Taves on 2021-02-11.
    • fix(): fix(get_active) include the cbd layers when checking layer thickness before BAS is loaded (#1051). Committed by Michael Ou on 2021-02-08.
    • fix(dis): Fix for dis.get_lrc() and dis.get_node() (#1049). Committed by langevin-usgs on 2021-02-04.
    • fix(): fix(modflow/mflpf) mfusg unstructured lpf ikcflag addition (#1044). Committed by Chris Nicol on 2021-02-01.
    • fix(print MFArray): Fixed printing of layered arrays - issue #1043 (#1045). Committed by spaulins-usgs on 2021-01-29.
    • fix(GridIntersect): Fix vertices for offset grids (#1037). Committed by Davíd Brakenhoff on 2021-01-13.
    • fix(PlotMapView.plot_array()): Fix value masking code for masked_values parameter (#1026). Committed by Joshua Larsen on 2020-12-03.
    • fix(sfr ic option): Made ic optional and updated description (#1020). Committed by spaulins-usgs on 2020-11-27.
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FloPy version 3.3.2

27 Oct 13:09
@jdhughes-usgs jdhughes-usgs
3.3.2
09afe60
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FloPy version 3.3.2

  • New features:

  • Bug fixes:

    • fix(gridintersect): Use linestrings and structured grid (#996). Committed by Tom van Steijn on 2020-09-25.
    • fix(): fix(extraneous blocks and zero length data in a list) (#990). Committed by spaulins-usgs on 2020-09-03.
    • fix(internal): Flopy fixed to correctly reads in internal keyword when no multiplier supplied. also, header line added to package files. (#962). Committed by spaulins-usgs on 2020-08-13.
    • fix(mfsfr2.py: Find_path): wrap find_path() so that the routing dictionary (graph) can still be copied, but won't be copied with every call of find_path() as it recursively finds the routing connections along a path in the sfr network. this was severely impacting performance for large sfr networks. (#955). Committed by aleaf on 2020-08-11.
    • fix(#958): Fix gridintersect._vtx_grid_to_shape_generator rtree for cells with more than 3 vertices (#959). Committed by mkennard-aquaveo on 2020-08-07.
    • fix(GridIntersect): Fix crash intersecting 3d points that are outside… (#957). Committed by mkennard-aquaveo on 2020-08-05.
    • fix(mvr): Added documentation explaining the difference between the two flopy mvr classes (#950). Committed by spaulins-usgs on 2020-07-31.
    • fix(check): Get_active() error for confining bed layers (#937). Committed by Michael Ou on 2020-07-29.
    • fix(rcha and evta): Irch and ievt arrays now zero based. fix for issue #941. also changed createpackages.py to always produce python scripts with unix-style line endings. (#949). Committed by spaulins-usgs on 2020-07-29.
    • fix(lgrutil): Corrected bug in child to parent vertical exchanges (#948). Committed by langevin-usgs on 2020-07-27.
    • fix(time series slowness): Speeds up performance when a large number of time series are used by a single stress package (#943). Committed by spaulins-usgs on 2020-07-17.
    • fix: Restore python 3.5 compatibility (modulenotfounderror -> importerror) (#933). Committed by Mike Taves on 2020-07-09.
    • fix(read binary file): Fix for reading binary files with array data (#931). Committed by spaulins-usgs on 2020-06-30.
    • fix(idomain): Data checks now treat all positive idomain values as active (#929). Committed by spaulins-usgs on 2020-06-29.
    • fix(Modpath7Sim): Fix timepointinterval calculation for timepointoption 3 (#927). Committed by jdhughes-usgs on 2020-06-26.
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FloPy version 3.3.1

26 Jun 18:57
@jdhughes-usgs jdhughes-usgs
3.3.1
efb8d0a
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FloPy version 3.3.1

  • New features:

    • feat(ModflowAg): Add the modflowag package for nwt (pull request #922). Committed by Joshua Larsen on 2020-06-25.
    • feat(GridIntersect): #902 (#903). Committed by Davíd Brakenhoff on 2020-06-10.
    • feat(mbase): Suppress duplicate package warning if verbose is false (#908). Committed by Hughes, J.D on 2020-06-09.
    • feat(ModflowSms): Add support for simple, moderate, complex (#906). Committed by langevin-usgs on 2020-06-09.
    • feat(str): Add irdflg and iptflg control to str (#905). Committed by Hughes, J.D on 2020-06-09.
    • feat(Mf6ListBudget): Add support for mf6 budgets with multiple packages with same name (#900). Committed by langevin-usgs on 2020-06-02.
    • feat(mfchd.py): Prevent write chk-file always (#869). Committed by Ralf Junghanns on 2020-05-08.
    • feat(set all data external): Set all data external for simulation (#846). Committed by spaulins-usgs on 2020-04-08.
    • feat(vtk): Improve export at vertices (#844). Committed by Etienne Bresciani on 2020-04-06.
    • feat(netcdf): Use modern features from pyproj>=2.2.0 (#840). Committed by Mike Taves on 2020-03-31.
    • feat(vtk): Export vectors to vtk. Committed by Etienne Bresciani on 2020-03-31.
    • feat(vtk): Export in .vti and .vtr when possible. Committed by Etienne Bresciani on 2020-03-28.
    • feat(vectors): Vector plots when stresses applied along boundaries (#817). Committed by langevin-usgs on 2020-03-05.
    • feat(plot_bc): Updated plot_bc for maw, uzf, sfr, and multiple bc packages (#808). Committed by Joshua Larsen on 2020-02-11.
    • feat(disl grids): Support for 1d vertex grids. fix for writing gridlines to shapefile (#799). Committed by spaulins-usgs on 2020-02-04.
    • feat(zb netcdf): Zonebudget netcdf export support added (#781). Committed by Joshua Larsen on 2020-01-17.
    • feat(mf6 checker): Input data check for mf6 (#779). Committed by spaulins-usgs on 2020-01-16.

  • Bug fixes:

    • fix(#280, #835): Set_all_data_external now includes constants, cellids in list data are checked (#920). Committed by spaulins-usgs on 2020-06-23.
    • fix(mfsfr2.check): Negative segments for lakes no longer included in segment numbering order check (#915). Committed by aleaf on 2020-06-23.
    • fix(GridIntersect): Fixes #916 and #917 (#918). Committed by Davíd Brakenhoff on 2020-06-22.
    • fix(ZoneBudget): Fix faulty logic in ZoneBudget (#911). Committed by Jason Bellino on 2020-06-22.
    • fix(SwtListBudget): Totim was not being read correctly for seawat list file (#910). Committed by langevin-usgs on 2020-06-10.
    • fix(Seawat.modelgrid): Pass lenuni from dis file into modelgrid instance (#901). Committed by Joshua Larsen on 2020-06-02.
    • fix(mfsimulation): Repair change for case insensitive model names (#897). Committed by langevin-usgs on 2020-06-01.
    • fix(_plot_util3d_helper, export_array): (#895). Committed by Joshua Larsen on 2020-06-01.
    • fix(): fix building in clean env (#894). Committed by Ritchie Vink on 2020-05-28.
    • fix(setup.py): Read package name, version, etc. from version.py (#893). Committed by Hughes, J.D on 2020-05-26.
    • fix(MFSimulation): Remove case sensitivity from register_ims_package() (#890). Committed by Joshua Larsen on 2020-05-25.
    • fix(modelgrid): Fix offset for xul and yul in read_usgs_model_reference_file and attribs_from_namfile_header (#889). Committed by Joshua Larsen on 2020-05-19.
    • fix(#886): Mfarray aux variable now always returned as an numpy.ndarray. fixed problem with pylistutil not fully supporting numpy.ndarray type. (#887). Committed by spaulins-usgs on 2020-05-19.
    • fix(CellBudgetFile): Update for auto precision with imeth = 5 or 6 (#876). Committed by Joshua Larsen on 2020-05-14.
    • fix(#870): Update ims name file record after removing ims package (#880). Committed by Joshua Larsen on 2020-05-14.
    • fix: #868, #874, #879 (#881). Committed by spaulins-usgs on 2020-05-14.
    • fix(#867): Fixed minimum record entry count for lists to never include keywords in the count (#875). Committed by spaulins-usgs on 2020-05-11.
    • fix(SfrFile): Update sfrfile for streambed elevation when present (#866). Committed by Joshua Larsen on 2020-05-04.
    • fix(#831,#858): Data length check and case-insensitive lookup (#864). Committed by spaulins-usgs on 2020-05-01.
    • fix(#856): Specifying period data with value none now only removes data from that period. also, fixed an unrelated problem by updating the multi-package list. (#857). Committed by spaulins-usgs on 2020-04-22.
    • fix(plot_array): Update plot_array method to mask using np.ma.masked_values (#851). Committed by Joshua Larsen on 2020-04-15.
    • fix(ModflowDis): Zero based get_node() and get_lrc()… (#847). Committed by Joshua Larsen on 2020-04-10.
    • fix(binaryfile_utils, CellbudgetFile): Update for imeth == 6 (#823). Committed by Joshua Larsen on 2020-04-10.
    • fix(utils.gridintersect): Bug in gridintersect for vertex grids (#845). Committed by Davíd Brakenhoff on 2020-04-06.
    • fix(mflmt.py): Clean up docstring for package_flows argument in lmt. Committed by emorway-usgs on 2020-03-31.
    • fix(str): Add consistent fixed and free format approach (#838). Committed by Hughes, J.D on 2020-03-31.
    • fix(vtk): Issues related to nan and type cast. Committed by Etienne Bresciani on 2020-03-31.
    • fix(pyproj): Pyproj.proj's errcheck keyword option not reliable (#837). Committed by Mike Taves on 2020-03-29.
    • fix: (#830): handling 'none' cellids in sfr package (#834). Committed by spaulins-usgs on 2020-03-25.
    • fix(): Fix quasi3d plotting (#819). Committed by Ruben Caljé on 2020-03-02.
    • fix(ModflowSfr2.export): Update modflowsfr2.export() to use grid instead of spatialreference (#820). Committed by Joshua Larsen on 2020-02-28.
      ...
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FloPy version 3.3.0

14 Dec 16:28
@jdhughes-usgs jdhughes-usgs
3.3.0
184e716
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FloPy version 3.3.0

  • Dropped support for python 2.7

  • Switched from pangeo binder binder to mybinder.org binder

  • Added support for MODFLOW 6 Skeletal Compaction and Subsidence (CSUB) package

  • Bug fixes:

    • Fix issue in MNW2 when the input file had spaced between lines in Dataset 2. #736
    • Fix issue in MNW2 when the input file uses wellids with inconsistent cases in Dataset 2 and 4. Internally the MNW2 will convert all wellids to lower case strings. #736
    • Fix issue with VertexGrid plotting errors, squeeze proper dimension for head output, in PlotMapView and PlotCrossSection
    • Fix issue in PlotUtilities._plot_array_helper mask MODFLOW-6 no flow and dry cells before plotting
    • Removed assumption that transient SSM data appears in the first stress period #754 #756. Fix includes a new autotest (t068_test_ssm.py) that adds transient concentration data after the first stress period.
    • Fix issues with add_record method for MfList #758
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FloPy version 3.2.13

18 Nov 12:36
@jdhughes-usgs jdhughes-usgs
3.2.13
2a92634
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FloPy version 3.2.13

Support for Python versions < 3.5 will be dropped in the next version of FloPy (version 3.3.0)

  • ModflowFlwob: Variable irefsp is now a zero-based integer (#596)

  • ModflowFlwob: Added a load method and increased precision of toffset when writing to file (#598)

  • New feature GridIntersect (#610): The GridIntersect object allows the user to intersect shapes (Points, LineStrings and Polygons) with a MODFLOW grid. These intersections return a numpy.recarray containing the intersection information, i.e. cell IDs, lengths or areas, and a shapely representation of the intersection results. Grids can be structured or vertex grids. Two intersections methods are implemented: "structured" and "strtree": the former accelerates intersections with structured grids. The latter is more flexible and also works for vertex grids. The GridIntersect class is available through flopy.utils.gridintersect. The functionality requires the Shapely module. See the example notebook for an overview of this new feature.

  • New feature Raster (#634): The Raster object allows the user to load raster files (Geotiff, arc ascii, .img) and sample points, sample polygons, create cross sections, crop, and resample raster data to a Grid. Cropping has been implemented using a modified version of the ray casting algorithm for speed purposes. Resampling a raster can be performed with structured, vertex, and unstructured Grids. Rasters will return a numpy array of resampled data in the same shape as the Grid. The Raster class is available by calling flopy.utils.Raster. The functionality requires rasterio, affine, and scipy. See the (example notebook) for an overview of this feature.

  • Modify NAM and MFList output files to remove excessive whitespace (#622, #722)

  • Deprecate crs class from flopy.utils.reference in favor of CRS class from flopy.export.shapefile_utils (#608)

  • New feature in PlotCrossSection (#660). Added a geographic_coords parameter flag to PlotCrossSection which allows the user to plot cross sections with geographic coordinates on the x-axis. The default behavior is to plot distance along cross sectional line on the x-axis. See the (example notebook) for an overview of this feature.

  • New feature with binaryfile readers, including HeadFile and CellBudgetFile (#669): with statement is supported to open files for reading in a context manager, which automatically close when done or if an exception is raised.

  • Improved the flopy list reader for MODFLOW stress packages (for mf2005, mfnwt, etc.), which may use SFAC to scale certain columns depending on the package. The list reading now supports reading from external files, in addition to open/close. The (binary) option is also supported for both open/close and external. This new list reader is used for reading standard stress package lists and also lists used to create parameters. The new list reader should be consistent with MODFLOW behavior.

  • SfrFile detects additional columns (#708)

  • Add a default_float_format property to mfsfr2, which is string formatted by NumPy versions > 1.14.0, or {:.8g} for older NumPy versions (#710)

  • Support for pyshp 1.2.1 dropped, pyshp 2.1.0 support maintained

  • Improved VTK export capabilities. Added export for VTK at array level, package level, and model level. Added binary head file export and cell by cell file export. Added the ability to export point scalars in addition to cell scalars, and added smooth surface generation. VTK export now supports writing transient data as well as exporting to binary .vtu files.

  • Support for copying model and package instances with copy.deepcopy()

  • Added link to Binder on README and notebooks_examples markdown documents. Binder provides an environment that runs and interactively serves the FloPy Jupyter notebooks.

  • Bug fixes:

    • When using the default iuzfbnd=None in the __init__ routine of mtuzt.py, instantiation of IUZBND was generating a 3D array instead of a 2D array. Now generates a 2D array
    • ModflowSfr2 __init__ was being slowed considerably by the ModflowSfr2.all_segments property method. Modified the ModflowSfr2.graph property method that describes routing connections between segments to handle cases where segments aren't listed in stress period 0.
    • Ensure disordered fields in reach_data (Dataset 2) can be supported in ModflowSfr2 and written to MODFLOW SFR input files.
    • When loading a MF model with UZF active, item 8 ("[IUZROW] [IUZCOL] IFTUNIT [IUZOPT]") wasn't processed correctly when a user comment appeared at the end of the line
    • MODFLOW-6 DISU JA arrays are now treated as zero-based cell IDs. JA, IHC, CL12 are outputted as jagged arrays.
    • Models with multiple MODFLOW-6 WEL packages now load and save correctly.
    • Exporting individual array and list data to a shapefile was producing an invalid attribute error. Attribute reference has been fixed.
    • Fix UnboundLocalError and typo with flopy.export.shapefile_utils.CRS class (#608)
    • Fix Python 2.7 issue with flopy.export.utils.export_contourf (#625)
    • When loading a MT3D-USGS model, keyword options (if used) were ignored (#649)
    • When loading a modflow model, spatial reference information was not being passed to the SpatialReference class (#659)
    • Fix specifysurfk option in UZF, ModflowUZF1 read and write surfk variable
    • Fix minor errors in flopy gridgen wrapper
    • Close opened files after loading, to reduce ResourceWarning messages (#673)
    • Fix bugs related to flake8's F821 "undefined name 'name'", which includes issues related to Mt3dPhc, ModflowSfr2, ModflowDe4, ListBudget, and ModflowSms (#686)
    • Fix bugs related to flake8's F811 "redefinition of unused 'name'" (#688)
    • Fix bugs related to flake8's W605 "invalid escape sequence '\s'" (or similar) (#700)
    • Fix EpsgReference class behavior with JSON user files (#702)
    • Fix ModflowSfr2 read write logic for all combinations of isfropt and icalc
    • IRCH array of the Recharge Package is now a zero-based variable, which means an IRCH value of 0 corresponds to the top model layer (#715)
    • MODFLOW lists were not always read correctly if they used the SFAC or binary options or were used to define parameters (#683)
    • Changed VDF Package density limiter defaults to zero (#646)
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FloPy version 3.2.12

01 Jun 03:25
@jdhughes-usgs jdhughes-usgs
3.2.12
0dac08e
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FloPy version 3.2.12

  • Added a check method for OC package (#558)

  • Change default map projection from EPSG:4326 to None (#535)

  • Refactor warning message visibility and categories (#554, #575)

  • Support for MODFLOW 6 external binary files added. Flopy can read/write binary files containing list and array data (#470, #553).

  • Added silent option for MODFLOW 6 write_simulation (#552)

  • Refactored MODFLOW-6 data classes. File writing operations moved from mfdata*.py to new classes created in mffileaccess.py. Data storage classes moved from mfdata.py to mfdatastorage.py. MFArray, MFList, and MFScalar interface classes simplified with most of the data processing code moved to mfdatastorage.py and mffileaccess.py.

  • Added MODFLOW 6 quickstart example to front page.

  • Added lgrutil test as autotest/t063_test_lgrutil.py and implemented a get_replicated_parent_array() method to the Lgr class so that the user can pass in a parent array and get back an array that is the size of the child model.

  • Refactored much of the flopy code style to conform with Python conventions and those checked by Codacy. Added an automated Codacy check as part of the pull request and commit checks.

  • Bug fixes:

    • Fixed bug in Mt3dms.load to show correct error message when loading non-existent NAM file (#545)
    • Removed errant SFT parameter contained in Mt3dUzt.init routine (#572)
    • Fixed DISV shapefile export bug that applied layer 1 parameter values to all model layers during export (#508)
    • Updated ModflowSfr2.load to store channel_geometry and channel_flow_data (6d, 6e) by nseg instead of itmp position (#546)
    • Fixed bug in ModflowMnw2.make_node_data to be able to set multiple wells with different numbers of nodes (#556)
    • Fixed bug reading MODFLOW 6 comma separated files (#509)
    • Fixed bug constructing a grid class with MODFLOW-USG (#513)
    • Optimized performance of grid class by minimizing redundant operations through use of data result caching (#520)
    • Fixed bug passing multiple auxiliary variables for MODFLOW 6 array data (#533)
    • Fixed bug in Mt3dUzt.init; the variable ioutobs doesn't exist in the UZT package and was removed.
    • Fixed MODFLOW-LGR bug in which ascii files were not able to be created for some output. Added better testing of the MODFLOW-LGR capabilities to t035_test.py.
    • Fixed multiple issues in mfdis that resulted in incorrect row column determination when using the method get_rc_from_node_coordinates (#560). Added better testing of this to t007_test.py.
    • Fixed the export_array_contours function as contours would not export in some cases (#577). Added tests of export_array_contours and export_array to t007_test.py as these methods were not tested at all.
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FloPy version 3.2.11

23 Mar 00:43
@jdhughes-usgs jdhughes-usgs
3.2.11
018ad10
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FloPy version 3.2.11

  • Added support for the drain return package.

  • Added support for pyshp version 2.x, which contains a different call signature for the writer than earlier versions.

  • Added a new flopy3_MT3DMS_examples notebook, which uses Flopy to reproduce the example problems described in the MT3DMS documentation report by Zheng and Wang (1999).

  • Pylint is now used on Travis for the Python 3.5 distribution to check for coding errors.

  • Added testing with Python 3.7 on Travis, dropped testing Python 3.4.

  • Added a new htop argument to the vtk writer, which allows cell tops to be defined by the simulated head.

  • Generalized exporting and plotting to also work with MODFLOW 6. Added a new grid class and deprecated SpatialReference class. Added new plotting interfaces, PlotMapView and PlotCrossSection. Began deprecation of ModelMap and ModelCrossSection classes.

  • Spatial reference system cache moved to epsgref.json in the user's data directory.

  • Attempts to read empty files from flopy.utils raise a IOError exception.

  • Changed interface for creating and accessing MODFLOW 6 observation, time series, and time array series packages. These packages can now be created and accessed directly from the package that references them. These changes are not backward compatible, and will require existing scripts to be modified. See the flopy3_mf6_obs_ts_tas.ipynb notebook for instructions.

  • Changed the MODFLOW 6 fname argument to be filename. This change is not backward compatible, and will require existing scripts to be modified if the fname argument was used in the package constructor.

  • Added modflow-nwt options support for ModflowWel, ModflowSfr2, and ModflowUzf1 via the OptionBlock class.

  • Bug fixes:

    • Removed variable MXUZCON from mtuzt.py that was present during the development of MT3D-USGS, but was not included in the release version of MT3D-USGS.
    • Now account for UZT -> UZT2 changes with the release of MT3D-USGS 1.0.1. Use of UZT is no longer supported.
    • Fixed bug in mfuzf1.py when reading and writing surfk when specifysurfk = True.
    • Fixed bug in ModflowStr.load(), utility would fail to load when comments were present.
    • Fixed bug in MNW2 in which nodes were not sorted correctly.
    • Ensure that external 1-D free arrays are written on one line.
    • Typos corrected for various functions, keyword arguments, property names, input file options, and documentation.
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