chore: format tests, colorize pytest CI output (#1961)

.github/workflows/benchmark.yml

@@ -69,7 +69,7 @@ jobs:
         working-directory: ./autotest
         run: |
           mkdir -p .benchmarks
-          pytest -v --durations=0 --benchmark-only --benchmark-json .benchmarks/${{ matrix.os }}_python${{ matrix.python-version }}.json --keep-failed=.failed
+          pytest -v --color=yes --durations=0 --benchmark-only --benchmark-json .benchmarks/${{ matrix.os }}_python${{ matrix.python-version }}.json --keep-failed=.failed
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
@@ -79,7 +79,7 @@ jobs:
         working-directory: ./autotest
         run: |
           mkdir -p .benchmarks
-          pytest -v --durations=0 --benchmark-only --benchmark-json .benchmarks/${{ matrix.os }}_python${{ matrix.python-version }}.json --keep-failed=.failed
+          pytest -v --color=yes --durations=0 --benchmark-only --benchmark-json .benchmarks/${{ matrix.os }}_python${{ matrix.python-version }}.json --keep-failed=.failed
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 

.github/workflows/commit.yml

@@ -131,7 +131,7 @@ jobs:
 
       - name: Smoke test
         working-directory: autotest
-        run: pytest -v -n=auto --smoke --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed
+        run: pytest -v -n=auto --smoke --color=yes --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
@@ -226,7 +226,7 @@ jobs:
         if: runner.os != 'Windows'
         working-directory: ./autotest
         run: |
-          pytest -v -m="not example and not regression" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
+          pytest -v -m="not example and not regression" -n=auto --color=yes --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
           coverage report
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -236,7 +236,7 @@ jobs:
         shell: bash -l {0}
         working-directory: ./autotest
         run: |
-          pytest -v -m="not example and not regression" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
+          pytest -v -m="not example and not regression" -n=auto --color=yes --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
           coverage report
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/examples.yml

@@ -97,7 +97,7 @@ jobs:
         if: runner.os != 'Windows'
         working-directory: ./autotest
         run: |
-          pytest -v -m="example" -n=auto -s --durations=0 --keep-failed=.failed
+          pytest -v -m="example" -n=auto -s --color=yes --durations=0 --keep-failed=.failed
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
@@ -106,7 +106,7 @@ jobs:
         shell: bash -l {0}
         working-directory: ./autotest
         run: |
-          pytest -v -m="example" -n=auto -s --durations=0 --keep-failed=.failed
+          pytest -v -m="example" -n=auto -s --color=yes --durations=0 --keep-failed=.failed
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 

.github/workflows/mf6.yml

@@ -82,12 +82,12 @@ jobs:
       env:
         GITHUB_TOKEN: ${{ github.token }}
       run: |
-        pytest -v --durations=0 get_exes.py
+        pytest -v --color=yes --durations=0 get_exes.py
 
     - name: Run tests
       working-directory: modflow6/autotest
       run: |
-        pytest -v -n auto -k "test_gw" --durations=0 --cov=flopy --cov-report=xml
+        pytest -v --color=yes --cov=flopy --cov-report=xml --durations=0 -k "test_gw" -n auto
 
     - name: Print coverage report before upload
       working-directory: ./modflow6/autotest

.github/workflows/optional.yml

@@ -62,7 +62,7 @@ jobs:
 
       - name: Smoke test (${{ matrix.optdeps }})
         working-directory: autotest
-        run: pytest -v -n=auto --smoke --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed
+        run: pytest -v -n=auto --smoke --color=yes --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 

.github/workflows/regression.yml

@@ -80,15 +80,15 @@ jobs:
       - name: Run regression tests
         if: runner.os != 'Windows'
         working-directory: ./autotest
-        run: pytest -v -m="regression" -n=auto --durations=0 --keep-failed=.failed
+        run: pytest -v -m="regression" -n=auto --color=yes --durations=0 --keep-failed=.failed
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Run regression tests
         if: runner.os == 'Windows'
         shell: bash -l {0}
         working-directory: ./autotest
-        run: pytest -v -m="regression" -n=auto --durations=0 --keep-failed=.failed
+        run: pytest -v -m="regression" -n=auto --color=yes --durations=0 --keep-failed=.failed
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 

.github/workflows/release.yml

@@ -71,7 +71,7 @@ jobs:
 
       - name: Run tests
         working-directory: autotest
-        run: pytest -v -m="not example and not regression" -n=auto --durations=0 --keep-failed=.failed --dist loadfile
+        run: pytest -v -m="not example and not regression" -n=auto --color=yes --durations=0 --keep-failed=.failed --dist loadfile
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 

.github/workflows/rtd.yml

@@ -79,7 +79,7 @@ jobs:
 
       - name: Run tutorial and example notebooks
         working-directory: autotest
-        run: pytest -v -n auto test_notebooks.py
+        run: pytest -v -n auto --color=yes test_notebooks.py
 
       - name: Upload notebooks artifact for ReadtheDocs
         if: github.repository_owner == 'modflowpy' && github.event_name == 'push' && runner.os == 'Linux'

autotest/test_model_splitter.py

@@ -1,9 +1,9 @@
 import numpy as np
-import flopy
 import pytest
 from autotest.conftest import get_example_data_path
 from modflow_devtools.markers import requires_exe, requires_pkg
 
+import flopy
 from flopy.mf6 import MFSimulation
 from flopy.mf6.utils import Mf6Splitter
 
@@ -260,11 +260,7 @@ def test_control_records(function_tmpdir):
     tdis = flopy.mf6.ModflowTdis(
         sim,
         nper=nper,
-        perioddata=(
-            (1., 1, 1.),
-            (1., 1, 1.),
-            (1., 1, 1.)
-        )
+        perioddata=((1.0, 1, 1.0), (1.0, 1, 1.0), (1.0, 1, 1.0)),
     )
 
     gwf = flopy.mf6.ModflowGwf(sim, save_flows=True)
@@ -279,20 +275,20 @@ def test_control_records(function_tmpdir):
         delc=1,
         top=35,
         botm=[30, botm2],
-        idomain=1
+        idomain=1,
     )
 
     ic = flopy.mf6.ModflowGwfic(gwf, strt=32)
     npf = flopy.mf6.ModflowGwfnpf(
         gwf,
         k=[
-            1.,
+            1.0,
             {
                 "data": np.ones((10, 10)) * 0.75,
                 "filename": "k.l2.txt",
                 "iprn": 1,
-                "factor": 1
-            }
+                "factor": 1,
+            },
         ],
         k33=[
             np.ones((nrow, ncol)),
@@ -301,41 +297,29 @@ def test_control_records(function_tmpdir):
                 "filename": "k33.l2.bin",
                 "iprn": 1,
                 "factor": 1,
-                "binary": True
-            }
-        ]
-
+                "binary": True,
+            },
+        ],
     )
 
-    wel_rec = [((0, 4, 5), -10), ]
+    wel_rec = [
+        ((0, 4, 5), -10),
+    ]
 
     spd = {
         0: wel_rec,
-        1: {
-            "data": wel_rec,
-            "filename": "wel.1.txt"
-        },
-        2: {
-            "data": wel_rec,
-            "filename": "wel.2.bin",
-            "binary": True
-        }
+        1: {"data": wel_rec, "filename": "wel.1.txt"},
+        2: {"data": wel_rec, "filename": "wel.2.bin", "binary": True},
     }
 
-    wel = flopy.mf6.ModflowGwfwel(
-        gwf,
-        stress_period_data=spd
-    )
+    wel = flopy.mf6.ModflowGwfwel(gwf, stress_period_data=spd)
 
     chd_rec = []
     for cond, j in ((30, 0), (22, 9)):
         for i in range(10):
             chd_rec.append(((0, i, j), cond))
 
-    chd = flopy.mf6.ModflowGwfchd(
-        gwf,
-        stress_period_data={0: chd_rec}
-    )
+    chd = flopy.mf6.ModflowGwfchd(gwf, stress_period_data={0: chd_rec})
 
     arr = np.zeros((10, 10), dtype=int)
     arr[0:5, :] = 1
@@ -354,14 +338,18 @@ def test_control_records(function_tmpdir):
             "External ascii files not being preserved for MFArray"
         )
 
-    k33ls =  ml1.npf.k33._data_storage.layer_storage.multi_dim_list
+    k33ls = ml1.npf.k33._data_storage.layer_storage.multi_dim_list
     if k33ls[1].data_storage_type.value != 3 or not k33ls[1].binary:
         raise AssertionError(
             "Binary file input not being preserved for MFArray"
         )
 
-    spd_ls1 = ml1.wel.stress_period_data._data_storage[1].layer_storage.multi_dim_list[0]
-    spd_ls2 = ml1.wel.stress_period_data._data_storage[2].layer_storage.multi_dim_list[0]
+    spd_ls1 = ml1.wel.stress_period_data._data_storage[
+        1
+    ].layer_storage.multi_dim_list[0]
+    spd_ls2 = ml1.wel.stress_period_data._data_storage[
+        2
+    ].layer_storage.multi_dim_list[0]
 
     if spd_ls1.data_storage_type.value != 3 or spd_ls1.binary:
         raise AssertionError(
@@ -372,5 +360,3 @@ def test_control_records(function_tmpdir):
         raise AssertionError(
             "External binary file input not being preseved for MFList"
         )
-
-

autotest/test_modflow.py

@@ -7,8 +7,8 @@
 import numpy as np
 import pytest
 from autotest.conftest import get_example_data_path
-from modflow_devtools.misc import has_pkg
 from modflow_devtools.markers import excludes_platform, requires_exe
+from modflow_devtools.misc import has_pkg
 
 from flopy.discretization import StructuredGrid
 from flopy.mf6 import MFSimulation