Release 3.3.2 #1011
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Release 3.3.2 #1011
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* Fix(plotting): Bug fixes for issues #587 and #588 * updates to PlotMapView.contour_array() and _VertexCrossSection.contour_array() to allow nan to be passed in the array * added test_tricountour_NaN() to t007_test.py * updates to PlotMapView.contour_array() and plot_array() to drop extra dimension from head array with using vertex model grid #588 * updates to UnstructuredPlotUtilities, added irregular_shape_patch() as patch for cross section drawing of vertex and unstructured modelgrids that include multiple geometries (found during fix #588) * update to geometry.transform() to set x and y dtypes to float (found during fix #588) * Added updated t007_test.py * Update test_tricontour_NaN() * Codacy updates for PR * Updated drop axis routine to squeeze axis 1 for vertex grids
* suppressing error when proj4_str is None * fixed long line to molify Codacy
* docs(ModflowHob): Explicitly state that variables irefsp, layer, row, and column are zero-based integers. Minor formatting changes-->uniform capitalization and alignment with parallel variables in the ModflowFlwob docstring. * refactor(ModflowFlowb): Treat variables irefsp, layer, row, and column as zero-based integers to align behavior with ModflowHob. Updated write_file method and docstring accordingly. * refactor(codacy): Refactor docstrings to break up long lines. * refactor(t041_test): Update test041 to specify irefsp, layer, row, and column as zero-based indices.
* Required changes to flopy.utils.geometry so that the Polygon.pyshp_prts handled holes correctly for multiple shapefile versions * codacy fixes
* feat(ModflowFlwob): Add various flow-obs types to model.mfnam_packages dictionary. * feat(ModflowFlwob): Add method to load package from file. * feat(ModflowFlwob): Use supplied unit number when loading package to avoid unit collisions. * feat(ModflowFlwob): Add additional width and precision for toffset to avoid string-conversions that result in numbers greater than total simulation time. * feat(ModflowFlwob): Account for case where nqclfb is negative. * feat(ModflowFlwob): Append filename using relative path with respect to the model working directory to ensure the correct filename is written to the namefile. * feat(ModflowFlwob): Add new autotest to check loading functionality. * revert: "feat(ModflowFlwob): Append filename using relative path with respect to the model working directory to ensure the correct filename is written to the namefile." This reverts commit 6f52006. * feat(ModflowFlwob): Add 1 to zero-based "irefsp" when writing file. * feat(ModflowFlwob): Try to make Codacy happy. * feat(ModflowFlwob): Add "ftype" attribute and retrieval method. * feat(ModflowFlwob): Use ext_unit_dict to get proper flowtype and ftype from filename. * feat(ModflowFlwob): Remove unused variable and extra whitespace. * feat(ModflowFlwob): Catch dict items explicitly even if they are unused. * Revert "feat(ModflowFlwob): Try to make Codacy happy." This reverts commit eca305a.
Instantiation of UZT class was generating IUZBND as a 3D array, should be 2D
…ntour with matplotlib 3.1.1 (#613)
…a.keys(); fails for pers where itmp < 0 (#612)
…dows (#623) * fix(autotest): move some output files to their own folder * fix(run_model): improve normal_msg and fix Python 2.7 memory issue
* fix(reference): fix UnboundLocalError error, deprecate crs class * fix(shapefile_utils.CRS): fix typo and UnboundLocalError error
* fix(ja array): CellID now increments and decrements correctly. * feat(jagged arrays): format disu arrays (ja, cl12) as jagged arrays in output files * fix(disu arrays): Added more testing for disu arrays * Fix(flopy write): Copy external files before writing out package files. Package file writing can require access to external files. * fix(np types): Changed code from using np.int to explicitly defining integer type np.int32. * fix(#616): Shapefile export code fix * fix(#614): Wel package added to multi-package list. Fix to always get multiple packages when searching by package type. * fix(different int types): Different systems appear to use different types of ints. Int type check changed to be more generic. * refact(CR/LF): Removed CR line endings
* add gridintersect to flopy utils * add gridintersect tests * make codacy happy * attempt 2 making codacy happy * add keepzerolengths option to strtree method * add gridintersection demo notebook * update travis to install shapely minor edit in gridintersect * fix py27 error * make codacy happy again * last codacy fix
* fix(travis 2.7): Memory is not getting released from the plotting tests when run on python 2.7. Two of the more memory intensive plotting tests have been disabled as a work around for the out of memory errors intermittently appearing on Travis.
Unsuccessfully tried to get the memory released by calling matplotlib's plt.close('all') and then gc.collect() at the end of each plotting test. Since support for python 2.7 is going to be discontinued soon, it may be sufficient just to use this work around.
* feat(deepcopy support): Flopy for MF6 MFSimulation object can now be copied with deepcopy. * feat(rename all packages): rename_all_packages method added to the mf6 model and simulation classes to allow the user to rename all of the packages at once. * refact(dfn sync): sync dfn with MODFLOW6 repository
… and allow ncpl to be specified as a list (#631) * Fix(UnstructuredGrid): fix for ncpl provided as a list or numpy array * Fix(plot_array): fix for CVFD masked_values when plotting arrays
* Read WEL Reductions from List File Adds a method to the ListBudget class to read in data from the list file on automatic reductions to WEL extractions. This method supports both NWT and USG list files. Adds auto tests for both success and failure. I couldn't find any included data sets with reductions written to the LST, so I updated a USG data set to allow for the auto test. * Removed Trailing Whitespace Removed trailing whitespace id'd by codacy. * Updated to work with python 2.7 Updated code to run with python 2.7. Used autopep8 to formalize some formatting.
…flopy.utils (#634) * Feat(rasters.py): Added raster intersection capability and an example notebook (Notebooks/flopy3_raster_intersection.ipynb) * Update requirements for travis to include SciPy for raster unit tests * Removed Scipy from python27 requirements * Update flopy3_raster_intersection.ipynb for running on travis * Update flopy3_raster_intersection.ipynb for travis * revert flopy3_lake_example.ipynb * update(rasters.py): codacy updates * update(rasters.py): codacy fixes * update(rasters.py): _point_in_polygon changed to static method
…arate integers (#976) * feat(cellid not as tuple): list data input may now have cellids as separate integers rather than as integers in a tuple. flopy still internally stores the integers as a tuple.
Refactor to improve use of glob for creating documentation. Also reorganized tutorials so directory structure can be used to develop tutorial rst file.
* fix(extraneous package data): extraneous package data is stored as comments * fix(loading list data): fix handles case where jagged data in a list has size zero * fix(reading repeating data): variable initialization fix * fix(test update): update test to properly function with the way flopy now treats extra stress periods as comment text
…on in IRRDIVERSION block. (#994)
The modflow6 disv constructor in flopy needs a list of vertices and cell2d information. The flopy.util.cvfdutil package was updated to include a new method that takes a list of flopy.discretization.structuredgrid.StructuredGrid objects and stitches them together to create a dictionary of arguments that can be passed info flopy.modflow6.ModflowGwfdisv. For nested grids, idomain must be set to zero in any parent grids in order for the child grid to be patched in properly. This new tool can be used to construct vertices and cell2d information needed to make disv nested grids.
… ids (#1003) * For test_dis_sr, remove use of deprecated SpatialReference object which cannot parse "us-ft" units from older pyproj versions. This test works fine with supported StructuredGrid module. * And for deprecated reference module, tidy up one "to_meter" error
* *Added GeoSpatialUtil for geospatial conversions *Added GeoSpatialCollection for batch conversion of "Collection" objects *Updated geometry.py and added additional geometry types to geometry.py *updates to gridgen, shapefile_utils, triangle, rasters, and gridintersect modules that allow the user to supply any supported shape object to these geospatial methods. Supported shape objects are, geojson, shapely, shapefile, flopy.utils.geometry, and lists of vertices. *Added t074_test_geospatial_util.py issue #772 * remove intersect_linestring, intersect_point, and intersect_polygon from GridIntersect. *Refactored t065_test_gridintersect.py for intersect() method *Updated flopy3_grid_intersection_demo.ipynb for intersect() method
Convert notebook autotest script to use jupytext instead of nbconvert. Update dfns with revised dfns. Fix issue with groundwater paper notebooks on Travis.
Codecov Report
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