chore: switch to ruff, ignore known test warnings, numpy compat fixes (…

…modflowpy#2124)

* switch to ruff from black, isort, flake8, pylint, keep (mostly) the same settings
* apply some suggested linting/formatting rules, ignore others in pyproject.toml
* run ruff check --select NPY201 as suggested here, replace deprecated syntax
    * np.float_ -> np.float64
    * np.NaN -> np.nan
* ignore well-known python-dateutil and pandas warnings

.docs/Notebooks/modflow_postprocessing_example.py

@@ -100,7 +100,7 @@
     grid, os.path.join(workspace, "heads5_rot.tif"), hdslayer, nodata=nodata
 )
 
-results = np.loadtxt(os.path.join(workspace, f"heads5_rot.asc"), skiprows=6)
+results = np.loadtxt(os.path.join(workspace, "heads5_rot.asc"), skiprows=6)
 results[results == nodata] = np.nan
 plt.imshow(results)
 plt.colorbar()

.docs/Notebooks/modpath7_unstructured_lateral_example.py

@@ -436,7 +436,7 @@
 sim.set_sim_path(workspace)
 sim.write_simulation()
 success, buff = sim.run_simulation(silent=True, report=True)
-assert success, f"Failed to run MF6 simulation."
+assert success, "Failed to run MF6 simulation."
 for line in buff:
     print(line)
 

.docs/Notebooks/plot_cross_section_example.py

@@ -341,7 +341,10 @@
 # Plot a shapefile of
 shp = os.path.join(loadpth, "gis", "bedrock_outcrop_hole_rotate14")
 patch_collection = mapview.plot_shapefile(
-    shp, edgecolor="green", linewidths=2, alpha=0.5  # facecolor='none',
+    shp,
+    edgecolor="green",
+    linewidths=2,
+    alpha=0.5,  # facecolor='none',
 )
 # Plot a shapefile of a cross-section line
 shp = os.path.join(loadpth, "gis", "cross_section_rotate14")

.docs/Notebooks/plot_map_view_example.py

@@ -452,7 +452,10 @@
 # Plot a shapefile of
 shp = os.path.join(loadpth, "gis", "bedrock_outcrop_hole")
 patch_collection = mapview.plot_shapefile(
-    shp, edgecolor="green", linewidths=2, alpha=0.5  # facecolor='none',
+    shp,
+    edgecolor="green",
+    linewidths=2,
+    alpha=0.5,  # facecolor='none',
 )
 # Plot a shapefile of a cross-section line
 shp = os.path.join(loadpth, "gis", "cross_section")
@@ -488,7 +491,10 @@
 # Plot a shapefile of
 shp = os.path.join(loadpth, "gis", "bedrock_outcrop_hole_rotate14")
 patch_collection = mapview.plot_shapefile(
-    shp, edgecolor="green", linewidths=2, alpha=0.5  # facecolor='none',
+    shp,
+    edgecolor="green",
+    linewidths=2,
+    alpha=0.5,  # facecolor='none',
 )
 # Plot a shapefile of a cross-section line
 shp = os.path.join(loadpth, "gis", "cross_section_rotate14")
@@ -1024,7 +1030,7 @@ def load_iverts(fname):
     plt.colorbar(quadmesh, shrink=0.75)
 
     # change the font type to comic sans
-    styles.set_font_type(family="fantasy", fontname="Comic Sans MS"),
+    (styles.set_font_type(family="fantasy", fontname="Comic Sans MS"),)
 
     # use styles to add a heading, xlabel, ylabel, and remove tick marks
     styles.heading(

.docs/Notebooks/swi2package_example3.py

@@ -80,7 +80,7 @@ def MergeData(ndim, zdata, tb):
     found.fill(False)
     for idx, layer in enumerate(zdata):
         for jdx, z in enumerate(layer):
-            if found[jdx] == True:
+            if found[jdx] is True:
                 continue
             t0 = tb[idx][0] - sv
             t1 = tb[idx][1] + sv

.github/workflows/commit.yml

@@ -61,31 +61,11 @@ jobs:
           pip install .
           pip install ".[lint]"
 
-      - name: Run isort
-        run: |
-          echo "if isort check fails update isort using"
-          echo "  pip install isort --upgrade"
-          echo "and run"
-          echo "  isort ./flopy"
-          echo "and then commit the changes."
-          isort --check --diff ./flopy
-
-      - name: Run black
-        run: |
-          echo "if black check fails update black using"
-          echo "  pip install black --upgrade"
-          echo "and run"
-          echo "  black ./flopy"
-          echo "and then commit the changes."
-          black --check --diff ./flopy
-
-      - name: Run flake8
-        run: |
-          flake8 --count --show-source --exit-zero ./flopy
+      - name: Lint
+        run: ruff check .
 
-      - name: Run pylint
-        run: |
-          pylint --jobs=2 --errors-only --exit-zero ./flopy
+      - name: Check format
+        run: ruff format . --check
 
       - name: Check CITATION.cff
         run: |

autotest/pytest.ini

@@ -15,4 +15,9 @@ markers =
     meta: tests run by other tests
     mf6: tests for MODFLOW 6 support
     regression: tests comparing multiple versions
-    slow: tests not completing in a few seconds
+    slow: tests not completing in a few seconds
+filterwarnings =
+    # from python-dateutil, used by arrow, jupyter_client, matplotlib, pandas
+    ignore:datetime.datetime.utcfromtimestamp  
+    # from pandas, see https://github.com/pandas-dev/pandas/issues/54466
+    ignore:\n.*Pyarrow  

autotest/regression/conftest.py

@@ -18,10 +18,10 @@ def get_mf6_examples_path() -> Path:
     __mf6_examples_lock.acquire()
     try:
         if __mf6_examples_path.is_dir() and any(__mf6_examples_path.glob("*")):
-            print(f"Example models already exist")
+            print("Example models already exist")
         else:
             __mf6_examples_path.mkdir(exist_ok=True)
-            print(f"Downloading example models")
+            print("Downloading example models")
             download_and_unzip(
                 url="https://github.com/MODFLOW-USGS/modflow6-examples/releases/download/current/modflow6-examples.zip",
                 path=str(__mf6_examples_path),

autotest/regression/test_mf6.py

@@ -299,7 +299,7 @@ def test_np001(function_tmpdir, example_data_path):
         )
     except FlopyException:
         ex = True
-    assert ex == True
+    assert ex is True
 
     kwargs = {}
     kwargs["xul"] = 20.5
@@ -855,9 +855,9 @@ def test_np002(function_tmpdir, example_data_path):
     sim.simulation_data.max_columns_of_data = 22
 
     name = sim.name_file
-    assert name.continue_.get_data() == None
-    assert name.nocheck.get_data() == True
-    assert name.memory_print_option.get_data() == None
+    assert name.continue_.get_data() is None
+    assert name.nocheck.get_data() is True
+    assert name.memory_print_option.get_data() is None
 
     tdis_rc = [(6.0, 2, 1.0), (6.0, 3, 1.0)]
     tdis_package = ModflowTdis(
@@ -1885,7 +1885,7 @@ def test005_create_tests_advgw_tidal(function_tmpdir, example_data_path):
     assert model.name_file.filename == "new_name.nam"
     package_type_dict = {}
     for package in model.packagelist:
-        if not package.package_type in package_type_dict:
+        if package.package_type not in package_type_dict:
             filename = os.path.split(package.filename)[1]
             assert filename == f"new_name.{package.package_type}"
             package_type_dict[package.package_type] = 1
@@ -1901,7 +1901,7 @@ def test005_create_tests_advgw_tidal(function_tmpdir, example_data_path):
     sim.rename_all_packages("all_files_same_name")
     package_type_dict = {}
     for package in model.packagelist:
-        if not package.package_type in package_type_dict:
+        if package.package_type not in package_type_dict:
             filename = os.path.split(package.filename)[1]
             assert filename == f"all_files_same_name.{package.package_type}"
             package_type_dict[package.package_type] = 1
@@ -2220,9 +2220,9 @@ def test035_create_tests_fhb(function_tmpdir, example_data_path):
     )
     time = model.modeltime
     assert (
-        time.steady_state[0] == False
-        and time.steady_state[1] == False
-        and time.steady_state[2] == False
+        time.steady_state[0] is False
+        and time.steady_state[1] is False
+        and time.steady_state[2] is False
     )
     wel_period = {0: [((0, 1, 0), "flow")]}
     wel_package = ModflowGwfwel(
@@ -3771,10 +3771,10 @@ def test005_advgw_tidal(function_tmpdir, example_data_path):
     model = sim.get_model(model_name)
     time = model.modeltime
     assert (
-        time.steady_state[0] == True
-        and time.steady_state[1] == False
-        and time.steady_state[2] == False
-        and time.steady_state[3] == False
+        time.steady_state[0] is True
+        and time.steady_state[1] is False
+        and time.steady_state[2] is False
+        and time.steady_state[3] is False
     )
     ghb = model.get_package("ghb")
     obs = ghb.obs

autotest/test_copy.py

@@ -1,5 +1,4 @@
-"""Test copying of flopy objects.
-"""
+"""Test copying of flopy objects."""
 
 import copy
 import inspect
@@ -64,10 +63,10 @@ def model_is_copy(m1, m2):
             continue
         elif k not in m2.__dict__:
             return False
-        elif type(v) == bool:
+        elif isinstance(v, bool):
             if not v == v2:
                 return False
-        elif type(v) in [str, int, float, dict, list]:
+        elif isinstance(v, (str, int, float, dict, list)):
             if v != v2:
                 return False
             continue
@@ -118,13 +117,13 @@ def package_is_copy(pk1, pk2):
                 return False
         elif k not in pk2.__dict__:
             return False
-        elif type(v) == bool:
+        elif isinstance(v, bool):
             if not v == v2:
                 return False
-        elif type(v) in [str, int, float, dict]:
+        elif isinstance(v, (str, int, float, dict)):
             if v != v2:
                 return False
-        elif type(v) == list:
+        elif isinstance(v, list):
             for item, item2 in zip(v, v2):
                 if not isinstance(item, MFPackage):
                     if item != item2:

autotest/test_export.py

@@ -520,7 +520,7 @@ def test_shapefile_ibound(function_tmpdir, example_data_path):
     field_names = [item[0] for item in shape.fields][1:]
     ib_idx = field_names.index("ibound_1")
     txt = f"should be int instead of {type(shape.record(0)[ib_idx])}"
-    assert type(shape.record(0)[ib_idx]) == int, txt
+    assert isinstance(shape.record(0)[ib_idx], int), txt
     shape.close()
 
 

autotest/test_get_modflow.py

@@ -1,4 +1,5 @@
 """Test get-modflow utility."""
+
 import os
 import platform
 import sys

autotest/test_grid.py

@@ -1119,7 +1119,7 @@ def test_voronoi_grid(request, function_tmpdir, grid_info):
     # ensure proper number of cells
     almost_right = ncpl == 538 and gridprops["ncpl"] == 535
     if almost_right:
-        warn(f"off-by-3")
+        warn("off-by-3")
 
     # ensure that all cells have 3 or more points
     invalid_cells = [i for i, ivts in enumerate(vor.iverts) if len(ivts) < 3]

autotest/test_gridintersect.py

@@ -135,7 +135,9 @@ def test_rect_grid_3d_point_outside():
 
 @requires_pkg("shapely")
 def test_rect_grid_3d_point_inside():
-    botm = np.concatenate([np.ones(4), 0.5 * np.ones(4), np.zeros(4)]).reshape(3, 2, 2)
+    botm = np.concatenate([np.ones(4), 0.5 * np.ones(4), np.zeros(4)]).reshape(
+        3, 2, 2
+    )
     gr = get_rect_grid(top=np.ones(4), botm=botm)
     ix = GridIntersect(gr, method="structured")
     result = ix.intersect(Point(2.0, 2.0, 0.2))
@@ -454,7 +456,9 @@ def test_rect_grid_linestring_in_and_out_of_cell():
 def test_rect_grid_linestring_in_and_out_of_cell2():
     gr = get_rect_grid()
     ix = GridIntersect(gr, method="structured")
-    result = ix.intersect(LineString([(5, 15), (5.0, 9), (15.0, 5.0), (5.0, 1.0)]))
+    result = ix.intersect(
+        LineString([(5, 15), (5.0, 9), (15.0, 5.0), (5.0, 1.0)])
+    )
     assert len(result) == 3
     # assert result.cellids[0] == (1, 0)
     # assert result.cellids[1] == (1, 1)
@@ -751,7 +755,9 @@ def test_rect_grid_polygon_outside():
 def test_rect_grid_polygon_in_2cells():
     gr = get_rect_grid()
     ix = GridIntersect(gr, method="structured")
-    result = ix.intersect(Polygon([(2.5, 5.0), (7.5, 5.0), (7.5, 15.0), (2.5, 15.0)]))
+    result = ix.intersect(
+        Polygon([(2.5, 5.0), (7.5, 5.0), (7.5, 15.0), (2.5, 15.0)])
+    )
     assert len(result) == 2
     assert result.areas.sum() == 50.0
 
@@ -788,7 +794,9 @@ def test_rect_grid_polygon_running_along_boundary():
 def test_rect_grid_polygon_on_inner_boundary():
     gr = get_rect_grid()
     ix = GridIntersect(gr, method="structured")
-    result = ix.intersect(Polygon([(5.0, 10.0), (15.0, 10.0), (15.0, 5.0), (5.0, 5.0)]))
+    result = ix.intersect(
+        Polygon([(5.0, 10.0), (15.0, 10.0), (15.0, 5.0), (5.0, 5.0)])
+    )
     assert len(result) == 2
     assert result.areas.sum() == 50.0
 
@@ -969,7 +977,9 @@ def test_rect_grid_polygon_outside_shapely(rtree):
 def test_rect_grid_polygon_in_2cells_shapely(rtree):
     gr = get_rect_grid()
     ix = GridIntersect(gr, method="vertex", rtree=rtree)
-    result = ix.intersect(Polygon([(2.5, 5.0), (7.5, 5.0), (7.5, 15.0), (2.5, 15.0)]))
+    result = ix.intersect(
+        Polygon([(2.5, 5.0), (7.5, 5.0), (7.5, 15.0), (2.5, 15.0)])
+    )
     assert len(result) == 2
     assert result.areas.sum() == 50.0
 
@@ -990,7 +1000,9 @@ def test_rect_grid_polygon_on_outer_boundary_shapely(rtree):
 def test_rect_grid_polygon_on_inner_boundary_shapely(rtree):
     gr = get_rect_grid()
     ix = GridIntersect(gr, method="vertex", rtree=rtree)
-    result = ix.intersect(Polygon([(5.0, 10.0), (15.0, 10.0), (15.0, 5.0), (5.0, 5.0)]))
+    result = ix.intersect(
+        Polygon([(5.0, 10.0), (15.0, 10.0), (15.0, 5.0), (5.0, 5.0)])
+    )
     assert len(result) == 2
     assert result.areas.sum() == 50.0
 
@@ -1073,7 +1085,9 @@ def test_tri_grid_polygon_in_2cells(rtree):
     if gr == -1:
         return
     ix = GridIntersect(gr, rtree=rtree)
-    result = ix.intersect(Polygon([(2.5, 5.0), (5.0, 5.0), (5.0, 15.0), (2.5, 15.0)]))
+    result = ix.intersect(
+        Polygon([(2.5, 5.0), (5.0, 5.0), (5.0, 15.0), (2.5, 15.0)])
+    )
     assert len(result) == 2
     assert result.areas.sum() == 25.0
 
@@ -1098,7 +1112,9 @@ def test_tri_grid_polygon_on_inner_boundary(rtree):
     if gr == -1:
         return
     ix = GridIntersect(gr, rtree=rtree)
-    result = ix.intersect(Polygon([(5.0, 10.0), (15.0, 10.0), (15.0, 5.0), (5.0, 5.0)]))
+    result = ix.intersect(
+        Polygon([(5.0, 10.0), (15.0, 10.0), (15.0, 5.0), (5.0, 5.0)])
+    )
     assert len(result) == 4
     assert result.areas.sum() == 50.0
 
@@ -1374,7 +1390,9 @@ def test_rasters(example_data_path):
     if (np.max(data) - 2608.557) > 1e-4:
         raise AssertionError
 
-    data = rio.resample_to_grid(ml.modelgrid, band=rio.bands[0], method="nearest")
+    data = rio.resample_to_grid(
+        ml.modelgrid, band=rio.bands[0], method="nearest"
+    )
     if data.size != 5913:
         raise AssertionError
     if abs(np.min(data) - 1942.1735) > 1e-4:
@@ -1423,11 +1441,15 @@ def test_raster_sampling_methods(example_data_path):
     }
 
     for method, value in methods.items():
-        data = rio.resample_to_grid(ml.modelgrid, band=rio.bands[0], method=method)
+        data = rio.resample_to_grid(
+            ml.modelgrid, band=rio.bands[0], method=method
+        )
 
         print(data[30, 37])
         if np.abs(data[30, 37] - value) > 1e-05:
-            raise AssertionError(f"{method} resampling returning incorrect values")
+            raise AssertionError(
+                f"{method} resampling returning incorrect values"
+            )
 
 
 if __name__ == "__main__":