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Fix lgr sfr mover#107

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aleaf merged 66 commits intoDOI-USGS:developDOI-USGS/modflow-setup:developfrom aleaf:fix_lgr_sfr_moveraleaf/modflow-setup:fix_lgr_sfr_moverCopy head branch name to clipboardJan 16, 2025

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Commits on Jan 6, 2025

• fix(pyproject.toml): add tomli; python_version < 3.11 to requires; potential fix for pip install issue (missing setup.cfg) that seems to occur with python<3.11. Re-add python 3.10 to test.yaml matr…

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• minor fixes for mf6 model setup

  

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• fix(ci::test_mf6_shellmound.py::test_rch_setup): relative pct difference issue on osx

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• fix(sourcedata.py::setup_array): only make adjustments involving the original model top in a model creation context (not when working with a loaded model)

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• ci(test.yaml): turn off fail-fast

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• fix(fileio.py): uint overflow error that was occuring on macos CI with python 3.10 (recast unit arrays to int)

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• fix(mfsetup/tmr.py): geopandas.sjoin 'op' arg to 'predicate'

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• tests(test_lgr.py::test_lgr_model_setup): relax arbitrary head comparison criteria; differences probably due to discretization

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• fix(sourcedata.py; MFnwtModel): add _drop_thin_cells=False attribute to MFnwtModel for consistency with MF6model; only expand thin cells to the minimum thickness if drop_thin_cells=False; otherwise…

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• tests(test_mf6_shellmound.py::setup_sfr): add skipif for unknown macos CI failure (passes on other platforms, and locally on macos

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• feat: support for local grid refinement models that only occupy some layers of the enclosing parent model

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• refactor(bcs.py:setup_basic_stress_data): for models with LGR, drop non-well BCs within LGR areas. (assumes that CHD, DRN, GHB, and RIV cells all represent surface or near-surface features that sho…

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• fix(discretization.py:fill_empty_layers): get_next_above() was not actually returning the next layer above because of incorrect sorting. Include the model top when filling missing layers, in case t…

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• feat(wells.py::setup_wel_data): add layer assignment from screen top/botm to wells: dictionary input option to facilitate easier testing. LGR parent models, remove wells with >50% of their open int…

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• feat: partial LGR in the vertical direction (child model nested in a subset of parent layers).

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• refactor(mfmodel.py): add error trap for missing setup_grid input; fix error message in mf6model.py

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• docs(config-file): add note about whitespace-delimited dictionary input in YAML

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• refactor(grid.py): relax requirement that parent and inset model grids must exactly align when snap_to_parent=True. For example, we may want a model that is aligned, but only every n cells, because…

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• feat(grid.rasterize; shapefile source data): add exclude_features option to include all features in a shapefile except for those specified

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• fix(mf6model.write_input): handle cases of single model or multi-model LGR simulation by working with the simulation-level model dictionary to implement model write functionality that is not includ…

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• ci(test_environment.yaml): pin numpy<2.1 for now, to avoid this shapely error: shapely/shapely#2098

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• fix(MF6model.write_input): handle case of single obs package

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• fix(ic.py): handle cases where there is no strt source data configuration or default parent model source data. Add error trap for invalid strt source data and additional testing of strt input options.

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• refactor(mfmodel; fileio.load_cfg): non-conprehensive pathlib conversions; tests(conftest.py): convert path fixtures to pathlib objects

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• fix(sourcedata.py::setup_array): for LGR inset models with default_source_data=True, don't copy idomain from parent (which will result in all inactive cells in the inset model).

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• fix(fileio.py::set_cfg_paths_to_absolute): don't touch file paths within the 'lgr': 'cfg' sub-block (when LGR inset configuration is supplied in the same file; this is mostly done in a test context).

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• fix(mover.py::get_sfr_package_connections): refactor to use GWFGWF exchanges and a threshold distance to determine SFR Package connections between a parent and inset/child LGR model. This fixes pre…

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• fix(SFR Package water mover setup for LGR models): apparently the mover package file reference was not getting written to the GWFGWF Exchange file in at least some cases. Integrate GWFGWF and Mover…

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• fix(tdis.py::aggregate_xarray_to_stress_period): copy period_stat input so that it doesn't get modified by multiple function calls; this affected instances where list input to a period_stats sub-bl…

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• fix(MF6model.write_input): don't check for mover package if mover is in the SFR options block (not clear that this check is needed). Previously was not passing mover option if simulation-level move…

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• fix(lakes.py::get_flux_variable_from_config): support direct flux input (precip, evap., etc) by lake; for MODFLOW 6 models, more direct flux input to perioddata: sub-block

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• feat(Lake Package): direct flux input by lake and by period

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• Specifying raster file to zonal_stats in setup_basic_stress_data() lead to proj issues. Bypassed when source raster is loaded with rasterio and affine transform specified

  

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• added simulate_high_k_lakes condition to setup_array in sourcedata

  

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• fix(sourcedata.py): when setting up the bottom array(s), only make edits to the model top if the lake package is being built, and a lake bathymetry raster was supplied (to be subtracted from the in…

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• refactor(discretization.fill_cells_vertically): only return bottom array, since top shouldn't be modified; refactor(sourcedata.setup_array): move resetting of model top to branch where the top modi…

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• fix(MF6model._set_idomain): Don't inactivate Lake BCs for MF6 models

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• fix(grid.py::setup_structured_grid): when snapping to parent grid, snap lower left corner to nearest vertex, since lower left is what is typically specified (previously was snapping upper left corn…

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• ci: switch to setup-micromamba@v2; try removing init-shell arg; not clear that this was ever needed

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• fix(grid.py): more fixes to logic for snapping grid to parent model, esp. for grids based on buffers around features

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• fix(mfsetup/fileio.py): refactor flopy_mfsimulation_load() and flopy_mf6model_load() for compatibility with flopy f378f84a5677b99191ce178bb1c5b67ac1d1bd66

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• fix(equality.py): add support for Flopy mf6.mfbase.PackageContainer class

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• ci: revert to mamba-org/setup-micromamba@v1

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• fix(equality.py::package_eq): skip packages within packages to avoid RecursionError in Flopy < 3.9

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• refactor(Pleasant_lake_lgr_example.ipynb): center example parent model around inset model after changes to grid-snapping; include lake connections in layer 0 (default for MF6 is now to keep layer 1…

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• fix(fileio.py::flopy_mfsimulation_load): _package_container AttributeError for Flopy<3.9

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• tests(test_lgr.py::test_mover_get_sfr_package_connections): fix the test

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• docs: remove html_theme_path; deprecated in Sphinx>=8

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• tests(test_mf6_shellmound.py): fixes to support string identifiers in sfrmaker; switch test outlet location to hopefully make setup_sfr test more robust

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• tests(test_lgr.py): fix test_meandering_sfr_connections

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• ci(release.yml): setup automated releases from PRs

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• ci: add GitHub dependabot for ci dependency management

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• refactor(discretization.make_lgr_domain): add error trap for LGR grid corners outside of the parent model grid

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• fix(initial conditions/strt array setup): add option to explicitly specify strt: from_model_top in source_data: block; needed in the case where there is a parent model and default_source_data is se…

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• fix(partial vertical LGR): remove hard-coding in sourcedata.py::setup_array that was causing vertical gaps between LGR inset and parent models with horizontal refinments other than 5.

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• feat(initial conditions/strt array setup): add option to explicitly set starting heads from parent starting heads

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• tests(initial conditions/strt array setup): add and consolidate tests

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• docs: Add page on initial conditions setup; with example script for updating starting heads from a previous run

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• build(deps): bump JamesIves/github-pages-deploy-action

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• build(deps): bump actions/checkout from 3 to 4

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• build(deps): bump JamesIves/github-pages-deploy-action

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• build(deps): bump JamesIves/github-pages-deploy-action

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• fix(mover.py::get_sfr_package_connections): when two outlets are connected across a LGR model interface and the connection threshold distance is large, a circular or double connection going both wa…

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• docs: update release notes and readme

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• Merge branch 'master' into develop

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Commits on Jan 16, 2025

• fix(Mover Package SFR connections across LGR model interfaces (mover.py::get_sfr_package_connections)): Follow-up fix to fbe1bb1; handle cases where parent model SFR reach along the LGR interface h…

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