diff --git a/examples/mf6/circle_partitioned.py b/examples/mf6/circle_partitioned.py index acf1cba94..4c89ac44b 100644 --- a/examples/mf6/circle_partitioned.py +++ b/examples/mf6/circle_partitioned.py @@ -7,6 +7,7 @@ case the 3 submodels are roughly equal sized partitions that have the shape of pie pieces. """ + import matplotlib.pyplot as plt from example_models import create_circle_simulation diff --git a/examples/mf6/different_ways_to_regrid_models.py b/examples/mf6/different_ways_to_regrid_models.py index ccc0ce927..240c37c67 100644 --- a/examples/mf6/different_ways_to_regrid_models.py +++ b/examples/mf6/different_ways_to_regrid_models.py @@ -15,6 +15,7 @@ regridding method for the horizontal conductivity field """ + # %% # We'll start with the usual imports. As this is an simple (synthetic) # structured model, we can make due with few packages. diff --git a/examples/mf6/ex01_twri.py b/examples/mf6/ex01_twri.py index 91aef92e0..5f47908c8 100644 --- a/examples/mf6/ex01_twri.py +++ b/examples/mf6/ex01_twri.py @@ -23,6 +23,7 @@ * Visualize the results. """ + # %% # We'll start with the usual imports. As this is an simple (synthetic) # structured model, we can make due with few packages. diff --git a/examples/mf6/example_1d_transport.py b/examples/mf6/example_1d_transport.py index 07f6158c2..760d6c327 100644 --- a/examples/mf6/example_1d_transport.py +++ b/examples/mf6/example_1d_transport.py @@ -23,6 +23,7 @@ shape of the front of the solute plume. """ + # %% import numpy as np diff --git a/examples/mf6/example_models.py b/examples/mf6/example_models.py index 9d126f1b7..1e0ea59f3 100644 --- a/examples/mf6/example_models.py +++ b/examples/mf6/example_models.py @@ -7,6 +7,7 @@ with it (such as regridding). """ + import numpy as np import scipy.ndimage import xarray as xr diff --git a/examples/mf6/lake.py b/examples/mf6/lake.py index a39ac3f59..d03926e77 100644 --- a/examples/mf6/lake.py +++ b/examples/mf6/lake.py @@ -17,6 +17,7 @@ * Visualize the results. """ + # %% # We'll start with the usual imports. As this is an simple (synthetic) # structured model, we can make due with few packages. diff --git a/examples/prepare/reproject.py b/examples/prepare/reproject.py index dac91212c..f6885d8db 100644 --- a/examples/prepare/reproject.py +++ b/examples/prepare/reproject.py @@ -5,6 +5,7 @@ In this example we will see how to reproject vector and raster datasets. """ + import matplotlib.pyplot as plt import pyproj diff --git a/examples/user-guide/01-raster-data.py b/examples/user-guide/01-raster-data.py index 1e56d7034..3a042c6dd 100644 --- a/examples/user-guide/01-raster-data.py +++ b/examples/user-guide/01-raster-data.py @@ -27,6 +27,7 @@ conveniences for such data, such as plotting or selecting. To demonstrate, we'll get some sample data provided with the imod package. """ + import xarray as xr # %% diff --git a/examples/user-guide/02-vector-data.py b/examples/user-guide/02-vector-data.py index 78b8aa077..74736ee61 100644 --- a/examples/user-guide/02-vector-data.py +++ b/examples/user-guide/02-vector-data.py @@ -35,6 +35,7 @@ DataFrame to store tabular data (the attribute table), and adds a geometry column to store the geospatial coordinates. """ + # %% import geopandas as gpd import numpy as np diff --git a/examples/user-guide/05-unstructured-grids.py b/examples/user-guide/05-unstructured-grids.py index b2ba06a5d..fb801828a 100644 --- a/examples/user-guide/05-unstructured-grids.py +++ b/examples/user-guide/05-unstructured-grids.py @@ -8,6 +8,7 @@ 2D), or 6 neighbors (in 3D). """ + # %% diff --git a/examples/user-guide/06-lazy-evaluation.py b/examples/user-guide/06-lazy-evaluation.py index de1b71501..87d4f5519 100644 --- a/examples/user-guide/06-lazy-evaluation.py +++ b/examples/user-guide/06-lazy-evaluation.py @@ -20,6 +20,7 @@ We will explain these concepts with a number of examples. """ + # %% import dask.array import numpy as np diff --git a/imod/data/sample_data.py b/imod/data/sample_data.py index ef74b933e..1eb7150dc 100644 --- a/imod/data/sample_data.py +++ b/imod/data/sample_data.py @@ -1,6 +1,7 @@ """ Functions to load sample data. """ + import importlib from pathlib import Path from typing import Union diff --git a/imod/formats/prj/disv_conversion.py b/imod/formats/prj/disv_conversion.py index a00874ff2..02fde3ea3 100644 --- a/imod/formats/prj/disv_conversion.py +++ b/imod/formats/prj/disv_conversion.py @@ -2,6 +2,7 @@ Most of the functionality here attempts to replicate what iMOD does with project files. """ + import itertools import pickle from collections import Counter diff --git a/imod/formats/prj/prj.py b/imod/formats/prj/prj.py index 52b8d117a..bf13ca979 100644 --- a/imod/formats/prj/prj.py +++ b/imod/formats/prj/prj.py @@ -1,6 +1,7 @@ """ Utilities for parsing a project file. """ + import shlex from collections import defaultdict from datetime import datetime diff --git a/imod/mf6/adv.py b/imod/mf6/adv.py index 62b49c73b..e693330eb 100644 --- a/imod/mf6/adv.py +++ b/imod/mf6/adv.py @@ -8,6 +8,7 @@ Upstream weighting is a fast alternative, and TVD is a more expensive and more robust alternative. """ + from copy import deepcopy from imod.mf6.package import Package diff --git a/imod/mf6/interfaces/ipackage.py b/imod/mf6/interfaces/ipackage.py index c2004557b..b0277f689 100644 --- a/imod/mf6/interfaces/ipackage.py +++ b/imod/mf6/interfaces/ipackage.py @@ -5,7 +5,6 @@ class IPackage(IPackageBase, metaclass=abc.ABCMeta): - """ The base methods and attributes available in all packages """ diff --git a/imod/mf6/mf6_wel_adapter.py b/imod/mf6/mf6_wel_adapter.py index 46b2c46e5..de8391dea 100644 --- a/imod/mf6/mf6_wel_adapter.py +++ b/imod/mf6/mf6_wel_adapter.py @@ -11,6 +11,7 @@ GIS systems. The low-level classes contain a dataset based on cellid, consisting of layer, row, and column, closely resembling input for Modflow6. """ + from typing import Optional import numpy as np diff --git a/imod/mf6/out/__init__.py b/imod/mf6/out/__init__.py index dac578b78..d65653805 100644 --- a/imod/mf6/out/__init__.py +++ b/imod/mf6/out/__init__.py @@ -37,6 +37,7 @@ def open_cbc( (These could be implemented via Reader classes, but why bother with mutable state or a class with exclusively staticmethods?) """ + from typing import Any, Callable, Dict, Optional, Union import numpy as np diff --git a/imod/mf6/out/cbc.py b/imod/mf6/out/cbc.py index a8114bc6e..db00f2826 100644 --- a/imod/mf6/out/cbc.py +++ b/imod/mf6/out/cbc.py @@ -1,6 +1,7 @@ """ Cell-by-cell flows """ + import os import struct from collections import defaultdict diff --git a/imod/mf6/package.py b/imod/mf6/package.py index 4ed89edbc..6bd44789c 100644 --- a/imod/mf6/package.py +++ b/imod/mf6/package.py @@ -547,9 +547,9 @@ def mask(self, domain: GridDataArray) -> Any: if is_scalar(da.values[()]): masked[var] = da.values[()] # For scalars, such as options else: - masked[ - var - ] = da # For example for arrays with only a layer dimension + masked[var] = ( + da # For example for arrays with only a layer dimension + ) else: masked[var] = None diff --git a/imod/mf6/validation.py b/imod/mf6/validation.py index 563996733..7e2e46c03 100644 --- a/imod/mf6/validation.py +++ b/imod/mf6/validation.py @@ -1,6 +1,7 @@ """ This module contains specific validation utilities for Modflow 6. """ + import numpy as np import xarray as xr diff --git a/imod/msw/landuse.py b/imod/msw/landuse.py index 04320a6bf..cc9d31a05 100644 --- a/imod/msw/landuse.py +++ b/imod/msw/landuse.py @@ -160,12 +160,12 @@ def __init__( self.dataset["start_sprinkling_season"] = start_sprinkling_season self.dataset["end_sprinkling_season"] = end_sprinkling_season self.dataset["interception_option"] = interception_option - self.dataset[ - "interception_capacity_per_LAI_Rutter" - ] = interception_capacity_per_LAI - self.dataset[ - "interception_capacity_per_LAI_VonHoyningen" - ] = interception_capacity_per_LAI + self.dataset["interception_capacity_per_LAI_Rutter"] = ( + interception_capacity_per_LAI + ) + self.dataset["interception_capacity_per_LAI_VonHoyningen"] = ( + interception_capacity_per_LAI + ) self.dataset["interception_intercept"] = interception_intercept self._pkgcheck() diff --git a/imod/msw/model.py b/imod/msw/model.py index 23e53ed80..dfc22e65c 100644 --- a/imod/msw/model.py +++ b/imod/msw/model.py @@ -100,9 +100,9 @@ def __init__(self, unsaturated_database): super().__init__() self.simulation_settings = copy(DEFAULT_SETTINGS) - self.simulation_settings[ - "unsa_svat_path" - ] = self._render_unsaturated_database_path(unsaturated_database) + self.simulation_settings["unsa_svat_path"] = ( + self._render_unsaturated_database_path(unsaturated_database) + ) def _render_unsaturated_database_path(self, unsaturated_database): # Force to Path object diff --git a/imod/prepare/common.py b/imod/prepare/common.py index 426bc86e2..6b3e3a913 100644 --- a/imod/prepare/common.py +++ b/imod/prepare/common.py @@ -5,6 +5,7 @@ xarray.DataArrays, as well as aggregation methods operating on weights and values. """ + import cftime import numba import numpy as np diff --git a/imod/prepare/interpolate.py b/imod/prepare/interpolate.py index bf2f5effc..361c1c04c 100644 --- a/imod/prepare/interpolate.py +++ b/imod/prepare/interpolate.py @@ -94,6 +94,7 @@ * nd_interp: collects the weights, reshapes the array so iter_interp will take it. """ + import numba import numpy as np diff --git a/imod/prepare/pcg.py b/imod/prepare/pcg.py index 6ffee9298..5037e3fda 100644 --- a/imod/prepare/pcg.py +++ b/imod/prepare/pcg.py @@ -2,6 +2,7 @@ This is a translation of the fortran77 modflow2000 pcg2.f module. """ + import numba diff --git a/imod/prepare/regrid.py b/imod/prepare/regrid.py index c313c0fb7..feb8b2cf4 100644 --- a/imod/prepare/regrid.py +++ b/imod/prepare/regrid.py @@ -24,6 +24,7 @@ values from the source array (src), and pass it on to the aggregation method. The single aggregated value is then filled into the destination array (dst). """ + from collections import namedtuple import dask diff --git a/imod/prepare/wells.py b/imod/prepare/wells.py index a98780978..4f09edf85 100644 --- a/imod/prepare/wells.py +++ b/imod/prepare/wells.py @@ -1,6 +1,7 @@ """ Assign wells to layers. """ + from typing import Optional, Union import numpy as np diff --git a/imod/tests/fixtures/mf6_small_models_fixture.py b/imod/tests/fixtures/mf6_small_models_fixture.py index c339ed759..c54e0e259 100644 --- a/imod/tests/fixtures/mf6_small_models_fixture.py +++ b/imod/tests/fixtures/mf6_small_models_fixture.py @@ -73,8 +73,10 @@ def grid_data_unstructured_layered( def _make_model( - grid_data_function: Callable[[type, Union[int, float], float], xr.DataArray] - | Callable[[type, Union[int, float], float], xu.UgridDataArray], + grid_data_function: ( + Callable[[type, Union[int, float], float], xr.DataArray] + | Callable[[type, Union[int, float], float], xu.UgridDataArray] + ), cellsize: float, ) -> imod.mf6.GroundwaterFlowModel: gwf_model = imod.mf6.GroundwaterFlowModel() diff --git a/imod/tests/test_mf6/test_mf6_hfb.py b/imod/tests/test_mf6/test_mf6_hfb.py index 8b0e72453..10bfb9d07 100644 --- a/imod/tests/test_mf6/test_mf6_hfb.py +++ b/imod/tests/test_mf6/test_mf6_hfb.py @@ -302,9 +302,9 @@ def test_to_mf6_remove_invalid_edges( ): # Arrange. idomain, top, bottom = parameterizable_basic_dis - idomain.loc[ - {"x": idomain.coords["x"][-1]} - ] = inactivity_marker # make cells inactive + idomain.loc[{"x": idomain.coords["x"][-1]}] = ( + inactivity_marker # make cells inactive + ) k = ones_like(top) barrier_y = [0.0, 2.0] diff --git a/imod/tests/test_mf6/test_mf6_uzf_model.py b/imod/tests/test_mf6/test_mf6_uzf_model.py index e329468c5..557761383 100644 --- a/imod/tests/test_mf6/test_mf6_uzf_model.py +++ b/imod/tests/test_mf6/test_mf6_uzf_model.py @@ -111,9 +111,9 @@ def uzf_model(): ) uds["extinction_depth"] = ones_shape_time * -10.0 - uds[ - "simulate_groundwater_seepage" - ] = False # Model doesn't converge if set to True.... + uds["simulate_groundwater_seepage"] = ( + False # Model doesn't converge if set to True.... + ) gwf_model["uzf"] = imod.mf6.UnsaturatedZoneFlow(**uds) diff --git a/imod/tests/test_mf6/test_package_sanity.py b/imod/tests/test_mf6/test_package_sanity.py index d7feb6a2e..08af029bf 100644 --- a/imod/tests/test_mf6/test_package_sanity.py +++ b/imod/tests/test_mf6/test_package_sanity.py @@ -11,6 +11,7 @@ * Tests whether writing and saving results in the same object state (as Python None is turned into numpy NaN). 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pysocks >=1.5.6,<2.0,!=1.5.7 - python >=3.7 - url: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.1.0-pyhd8ed1ab_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.0-pyhd8ed1ab_0.conda hash: - md5: f8ced8ee63830dec7ecc1be048d1470a - sha256: eff5029820b4eaeab3a291a39854a6cd8fc8c4216264087f68c2d8d59822c869 + md5: 6a7e0694921f668a030d52f0c47baebd + sha256: 61a8a3bd36d235c349aedaf1aa6a79cce15d6fe89dca4bb593b596d0211513c6 build: pyhd8ed1ab_0 arch: x86_64 subdir: linux-64 @@ -31723,23 +33839,23 @@ package: license: MIT license_family: MIT noarch: python - size: 85324 - timestamp: 1699933655057 + size: 94513 + timestamp: 1706638243438 purls: - pkg:pypi/urllib3 - platform: osx-64 name: urllib3 - version: 2.1.0 + version: 2.2.0 category: main manager: conda dependencies: - brotli-python >=1.0.9 - pysocks >=1.5.6,<2.0,!=1.5.7 - python >=3.7 - url: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.1.0-pyhd8ed1ab_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.0-pyhd8ed1ab_0.conda hash: - md5: f8ced8ee63830dec7ecc1be048d1470a - sha256: eff5029820b4eaeab3a291a39854a6cd8fc8c4216264087f68c2d8d59822c869 + md5: 6a7e0694921f668a030d52f0c47baebd + sha256: 61a8a3bd36d235c349aedaf1aa6a79cce15d6fe89dca4bb593b596d0211513c6 build: pyhd8ed1ab_0 arch: x86_64 subdir: osx-64 @@ -31747,23 +33863,23 @@ package: license: MIT license_family: MIT noarch: python - size: 85324 - timestamp: 1699933655057 + size: 94513 + timestamp: 1706638243438 purls: - pkg:pypi/urllib3 - platform: osx-arm64 name: urllib3 - version: 2.1.0 + version: 2.2.0 category: main manager: conda dependencies: - brotli-python >=1.0.9 - pysocks >=1.5.6,<2.0,!=1.5.7 - python >=3.7 - url: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.1.0-pyhd8ed1ab_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.0-pyhd8ed1ab_0.conda hash: - md5: f8ced8ee63830dec7ecc1be048d1470a - sha256: eff5029820b4eaeab3a291a39854a6cd8fc8c4216264087f68c2d8d59822c869 + md5: 6a7e0694921f668a030d52f0c47baebd + sha256: 61a8a3bd36d235c349aedaf1aa6a79cce15d6fe89dca4bb593b596d0211513c6 build: pyhd8ed1ab_0 arch: aarch64 subdir: osx-arm64 @@ -31771,23 +33887,23 @@ package: license: MIT license_family: MIT noarch: python - size: 85324 - timestamp: 1699933655057 + size: 94513 + timestamp: 1706638243438 purls: - pkg:pypi/urllib3 - platform: win-64 name: urllib3 - version: 2.1.0 + version: 2.2.0 category: main manager: conda dependencies: - brotli-python >=1.0.9 - pysocks >=1.5.6,<2.0,!=1.5.7 - python >=3.7 - url: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.1.0-pyhd8ed1ab_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.0-pyhd8ed1ab_0.conda hash: - md5: f8ced8ee63830dec7ecc1be048d1470a - sha256: eff5029820b4eaeab3a291a39854a6cd8fc8c4216264087f68c2d8d59822c869 + md5: 6a7e0694921f668a030d52f0c47baebd + sha256: 61a8a3bd36d235c349aedaf1aa6a79cce15d6fe89dca4bb593b596d0211513c6 build: pyhd8ed1ab_0 arch: x86_64 subdir: win-64 @@ -31795,8 +33911,8 @@ package: license: MIT license_family: MIT noarch: python - size: 85324 - timestamp: 1699933655057 + size: 94513 + timestamp: 1706638243438 purls: - pkg:pypi/urllib3 - platform: linux-64 @@ -32715,6 +34831,7 @@ package: - matplotlib-base >=3.5 - h5netcdf >=1.0 license: Apache-2.0 + license_family: APACHE noarch: python size: 730686 timestamp: 1706057006199 @@ -32760,6 +34877,7 @@ package: - matplotlib-base >=3.5 - h5netcdf >=1.0 license: Apache-2.0 + license_family: APACHE noarch: python size: 730686 timestamp: 1706057006199 @@ -32805,6 +34923,7 @@ package: - matplotlib-base >=3.5 - h5netcdf >=1.0 license: Apache-2.0 + license_family: APACHE noarch: python size: 730686 timestamp: 1706057006199 @@ -32850,6 +34969,7 @@ package: - matplotlib-base >=3.5 - h5netcdf >=1.0 license: Apache-2.0 + license_family: APACHE noarch: python size: 730686 timestamp: 1706057006199 diff --git a/pixi.toml b/pixi.toml index f8778cd2c..105fdb608 100644 --- a/pixi.toml +++ b/pixi.toml @@ -56,7 +56,7 @@ bottleneck = "*" cftime = ">=1" contextily = ">=1" cytoolz = "*" -dask = "*" +dask = "<2024.1.0" # Newer version incompatible with rasterio fastcore = "*" flopy = "*" geopandas = "*" @@ -75,7 +75,7 @@ pooch = "*" pydata-sphinx-theme = "*" pymetis = "*" pyproj = "*" -pytest = "*" +pytest = "<8" # Newer version incompatible with pytest-cases pytest-benchmark = "*" pytest-cases = "*" pytest-cov = "*"