release: version 3.3.5 #1367
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release: version 3.3.5 #1367
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modflowpy#1174) * grid fix iverts and verts; expose laycbd for use in utilities * plotting add RuntimeError exception to matplotlib imports to fix Condor containerization issues with flopy
@aleaf @jtwhite79 has addressed this issue. See modified test (`t004_test_utilarray.py`) for an example of using external files for list data. Reopen if this does not solve your issue. Closes modflowpy#1073
…odflowpy#1173) * update(MF6Output): updates to access the list file using <model>.output.list() * revert unintended changes due to version conflict in mfmodel.py
…flowpy#1184) flopy fails on checking mfusg unstructured RIV packages * add unstructured clause / disu reference to modflow/mfriv * modify autotest/t016.py test_usg_rch_evt_models01 to include a riv file and check() call
Also modified gridintersect.plot_linestring to accept a matplotlib colormap string.
) * fix(plot/plot_bc) plot_bc fails with unstructured models In plot/map.py, with unstructred models, numpy throws "too many indices for array" error when indexing plotarray with a tuple of boundary condition node numbers. * Revert plotarray BC indices to stress_period_data list[kper]["node"] as-is for unstructured models. * add plot_bc tests to t506_test.py for unstructured mf6 and mfusg models
…y#1190) Also set minimum NumPy version to >= 1.15. Add python 3.9 to GitHub action workflows and remove python 3.6. Closes modflowpy#1176 Closes modflowpy#1177
* update MF6Output gwt list() method to use MfListBudget * Added test to t504_test.py for adding new observations
Remove deprecated plot_discharge and plot_specific_discharge
) in pakbase/_check_storage.py, np.asarray() still throws an error when using a jagged list for unstructured models modflowpy#1187 (comment) * change to np.concatenate jagged list to a flat array * skip storage check if no convertible layers Closes modflowpy#1187
modflowpy#1195) deprecated mfdis and mfdisu thickness property
… bed layers (modflowpy#1197) * added Grid.remove_confining_beds() * added test_ncb_thick() to t076_modelgrid_thick.py
…owpy#1202) Update t007 so that it does not fail if there is no internet connection on GitHub Actions VMs.
…es (modflowpy#1209) * autotest updates for deprecations and updates * updates(zonbud, output_util, mfwel, OptionBlock): updates * remove deprecated code from zonbud.py * remove deprecated code form mfwel.py * fix MF6Output.list(), update to use Mf6ListBudget * fix Package.load() for mfnwt_options, well options not passed to well file when option block detected * Remove references to deprecated code from notebooks
update remaining tests to use new testing functionality to avoid possible race conditions with parallel pytest
… and smoothing_level_horizontal (modflowpy#1322) Close modflowpy#1317
…y#1323) * Close modflowpy#1299 * Voronoi issues in example were caused by closed polygons being passed to triangle * Revised examples to meet requirements * Add check for duplicate vertices in triangular mesh * Updated t075 to check for invalid cells * Changed several filtering loops in grid methods to use standard list comprehension
…s of the same package stored in dfn files (modflowpy#1239) (modflowpy#1321)
…ith specified model cells (modflowpy#1140) (modflowpy#1325) * feat(inspect cells): new feature that returns model data associated with specified model cells (modflowpy#1140) * feat(inspect cells): added tests for new feature (modflowpy#1140) * feat(inspect cells) * feat(inspect cells): dependent variable and budget inspection * feat(inspect cells): tests * feat(inspect cells): doc update * feat(inspect_cells) * feat(inspect_cells)
…thod (modflowpy#1326) * update(Grid.intersect): added optional z-coordinate to intersect() method * implemented intersect method for UnstructuredGrid * update(Grid): Added interface change warnings to intersect method
* Convert line endings to UNIX; remove BOM * Use relative imports
…t dtype (modflowpy#1328) * update(test_raster_sampling_methods): update for mean resampling
modflowpy#1333) * function was fixed to support multi-layer models * test added to ensure face flow calculations work
Update flopy using latest version of black. Add autotest\pull_request_prepare.py to help contributors to run isort and black prior to a pull request. Clean-up unused examples/Testing directory. Modified t064_test_performance.py to guard against failures on macOS.
…files when many blocks exist in OBS file. (modflowpy#1351) update header_exists: when None is provided for key, do not check against block header names (significantly speeds OBS loading).
…h multiple layers (modflowpy#1352) Previously code read the entire file without stripping headers after first layer. Enforce read_multi_layer=True if data_size != ncpl * update to support both "layered" binary files and flat binary files * update(read_binary_data_from_file): check for ncpl as numpy array * added test_binary_read to t505_test.py
…y#1347) * update(t074_test_geospatial_util.py): update tests for pyshp 2.2.0 * fix typo in AG package * update Raster for slightly faster grid resampling * update(geometry.py): added __reversed__ to geometery object as patch for pyshp 2.2.0 vs 2.1.0 differences * updated t074_test_geospatial_util.py * linted repository * isort mfag.py * update black and perform linting * update(requirements): merge upstream pyshp requirements with fork * update(requirements): update pyshp requirements to pyshp >= 2.0.0 * update(requirements.txt): resolve conflict
…tourf routines (modflowpy#1353) * added filled kwarg to contour_array for filled contours * update PlotCrossSection.contour_array() to mask out edge triangles outside of cross-section boundaries * update export_contourf, provide support for multipolygon contours and update support for holes * update export_contourf, remove shapely dependency. Replaced with flopy geometry objects * update t007_test.py, test_export_contourf()
modflowpy#1344) Added lake tab file back in to t504 tests (modflowpy#1337). Modified lak test to test tab files in different folders. Changed lakeex1b.lak test file path to contain mac-style forward slash path Co-authored-by: Scott Paulinski <spaulinski@usgs.gov> closes modflowpy#1337
…y#1357) * feat(mvt): add simulation-level support for mover transport * run black
…s (through MFSimulation) (modflowpy#1363) * fix(exchange obs): fixed building of obs package through MFSimulation class * fix(exchange obs): updated comments * fix(exchange obs): test coverage for exchange obs
Codecov Report
@@ Coverage Diff @@
## master #1367 +/- ##
==============================================
- Coverage 73.889% 30.068% -43.822%
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Files 231 249 +18
Lines 51692 52148 +456
==============================================
- Hits 38195 15680 -22515
- Misses 13497 36468 +22971
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