ci: smoke test with/out optional dependencies, mark more tests

.github/workflows/commit.yml

@@ -106,6 +106,8 @@ jobs:
       run:
         shell: bash
     timeout-minutes: 10
+    env:
+      PYTHON_VERSION: 3.8
 
     steps:
       - name: Checkout repo
@@ -114,33 +116,37 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: ${{ env.PYTHON_VERSION }}
           cache: 'pip'
           cache-dependency-path: pyproject.toml
 
       - name: Install Python dependencies
         run: |
           pip install --upgrade pip
           pip install .
-          pip install ".[test, optional]"
-
+          pip install ".[test,optional]"
+      
       - name: Install Modflow executables
         uses: modflowpy/install-modflow-action@v1
-
-      - name: Run smoke tests
-        working-directory: ./autotest
-        run: |
-          pytest -v -n=auto --smoke --durations=0 --keep-failed=.failed
+
+      - name: Smoke test
+        working-directory: autotest
+        run: pytest -v -n=auto --smoke --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Upload failed test outputs
         uses: actions/upload-artifact@v3
         if: failure()
         with:
-          name: failed-smoke-${{ matrix.os }}-${{ matrix.python-version }}
-          path: |
-            ./autotest/.failed/**
+          name: failed-smoke-${{ runner.os }}-${{ env.PYTHON_VERSION }}
+          path: ./autotest/.failed/**
+
+      - name: Upload coverage
+        if: github.repository_owner == 'modflowpy' && (github.event_name == 'push' || github.event_name == 'pull_request')
+        uses: codecov/codecov-action@v3
+        with:
+          files: ./autotest/coverage.xml
 
   test:
     name: Test
@@ -220,7 +226,7 @@ jobs:
         if: runner.os != 'Windows'
         working-directory: ./autotest
         run: |
-          pytest -v -m="not example and not regression" -n=auto --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
+          pytest -v -m="not example and not regression" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
           coverage report
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -230,7 +236,7 @@ jobs:
         shell: bash -l {0}
         working-directory: ./autotest
         run: |
-          pytest -v -m="not example and not regression" -n=auto --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
+          pytest -v -m="not example and not regression" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
           coverage report
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -244,8 +250,7 @@ jobs:
             ./autotest/.failed/**
 
       - name: Upload coverage
-        if:
-          github.repository_owner == 'modflowpy' && (github.event_name == 'push' || github.event_name == 'pull_request')
+        if: github.repository_owner == 'modflowpy' && (github.event_name == 'push' || github.event_name == 'pull_request')
         uses: codecov/codecov-action@v3
         with:
           files: ./autotest/coverage.xml

.github/workflows/optional.yml

@@ -0,0 +1,75 @@
+name: FloPy optional dependency testing
+on:
+  schedule:
+    - cron: '0 8 * * *' # run at 8 AM UTC (12 am PST)
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+    timeout-minutes: 10
+    env:
+      PYTHON_VERSION: 3.8
+    strategy:
+      fail-fast: false
+      matrix:
+        optdeps:
+          # - "all optional dependencies"
+          - "no optional dependencies"
+          - "some optional dependencies"
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          cache: 'pip'
+          cache-dependency-path: pyproject.toml
+
+      - name: Install Python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install .
+          pip install ".[test]"
+
+          # Install optional dependencies according to matrix.optdeps.
+          # If matrix.optdeps is "some" remove 3 optional dependencies
+          # selected randomly using the current date as the seed.
+          if [[ ! "${{ matrix.optdeps }}" == *"no"* ]]; then
+            pip install ".[optional]"
+          fi
+          if [[ "${{ matrix.optdeps }}" == *"some"* ]]; then
+            deps=$(sed '/optional =/,/]/!d' pyproject.toml | sed -e '1d;$d' -e 's/\"//g' -e 's/,//g' | tr -d ' ' | cut -f 1 -d ';')
+            rmvd=$(echo $deps | tr ' ' '\n' | shuf --random-source <(yes date +%d.%m.%y) | head -n 3)
+            echo "Removing optional dependencies: $rmvd" >> removed_dependencies.txt
+            cat removed_dependencies.txt
+            pip uninstall --yes $rmvd
+          fi
+
+      - name: Upload removed dependencies log
+        uses: actions/upload-artifact@v3
+        with:
+          name: smoke-test-removed-dependencies
+          path: ./removed_dependencies.txt
+
+      - name: Install Modflow executables
+        uses: modflowpy/install-modflow-action@v1
+
+      - name: Smoke test (${{ matrix.optdeps }})
+        working-directory: autotest
+        run: pytest -v -n=auto --smoke --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Upload failed test outputs
+        uses: actions/upload-artifact@v3
+        if: failure()
+        with:
+          name: failed-smoke-${{ runner.os }}-${{ env.PYTHON_VERSION }}
+          path: ./autotest/.failed/**
+

autotest/test_export.py

@@ -52,6 +52,11 @@
 from flopy.utils.geometry import Polygon
 
 
+HAS_PYPROJ = has_pkg("pyproj", strict=True)
+if HAS_PYPROJ:
+    import pyproj
+
+
 def namfiles() -> List[Path]:
     mf2005_path = get_example_data_path() / "mf2005_test"
     return list(mf2005_path.rglob("*.nam"))
@@ -330,10 +335,7 @@ def test_write_gridlines_shapefile(function_tmpdir):
 
     for suffix in [".dbf", ".shp", ".shx"]:
         assert outshp.with_suffix(suffix).exists()
-    if has_pkg("pyproj"):
-        assert outshp.with_suffix(".prj").exists()
-    else:
-        assert not outshp.with_suffix(".prj").exists()
+    assert outshp.with_suffix(".prj").exists() == HAS_PYPROJ
 
     with shapefile.Reader(str(outshp)) as sf:
         assert sf.shapeType == shapefile.POLYLINE
@@ -1378,7 +1380,7 @@ def test_vtk_unstructured(function_tmpdir, example_data_path):
     assert np.allclose(np.ravel(top), top2), "Field data not properly written"
 
 
-@requires_pkg("pyvista")
+@requires_pkg("vtk", "pyvista")
 def test_vtk_to_pyvista(function_tmpdir, example_data_path):
     from autotest.test_mp7_cases import Mp7Cases
 

autotest/test_grid.py

@@ -1,6 +1,7 @@
 import os
 import re
 import warnings
+from contextlib import nullcontext
 from warnings import warn
 
 import matplotlib
@@ -22,7 +23,7 @@
 from flopy.utils.triangle import Triangle
 from flopy.utils.voronoi import VoronoiGrid
 
-HAS_PYPROJ = has_pkg("pyproj")
+HAS_PYPROJ = has_pkg("pyproj", strict=True)
 if HAS_PYPROJ:
     import pyproj
 
@@ -594,9 +595,14 @@ def do_checks(g):
     do_checks(UnstructuredGrid(**d, crs=crs))
     do_checks(VertexGrid(vertices=d["vertices"], crs=crs))
 
+    # only check deprecations if pyproj is available
+    pyproj_avail_context = (
+        pytest.deprecated_call() if HAS_PYPROJ else nullcontext()
+    )
+
     # test deprecated 'epsg' parameter
     if isinstance(crs, int):
-        with pytest.deprecated_call():
+        with pyproj_avail_context:
             do_checks(StructuredGrid(delr=delr, delc=delc, epsg=crs))
 
     if HAS_PYPROJ and crs == 26916:
@@ -612,14 +618,14 @@ def do_checks(g):
         do_checks(StructuredGrid(delr=delr, delc=delc, prjfile=prjfile))
 
         # test deprecated 'prj' parameter
-        with pytest.deprecated_call():
+        with pyproj_avail_context:
             do_checks(StructuredGrid(delr=delr, delc=delc, prj=prjfile))
 
         # test deprecated 'proj4' parameter
         with warnings.catch_warnings():
             warnings.simplefilter("ignore")  # pyproj warning about conversion
             proj4 = crs_obj.to_proj4()
-        with pytest.deprecated_call():
+        with pyproj_avail_context:
             do_checks(StructuredGrid(delr=delr, delc=delc, proj4=proj4))
 
 
@@ -675,9 +681,14 @@ def do_checks(g, *, exp_srs=expected_srs, exp_epsg=expected_epsg):
     sg.set_coord_info(crs=26915, merge_coord_info=False)
     do_checks(sg, exp_srs="EPSG:26915", exp_epsg=26915)
 
+    # only check deprecations if pyproj is available
+    pyproj_avail_context = (
+        pytest.deprecated_call() if HAS_PYPROJ else nullcontext()
+    )
+
     # test deprecated 'epsg' parameter
     if isinstance(crs, int):
-        with pytest.deprecated_call():
+        with pyproj_avail_context:
             sg.set_coord_info(epsg=crs)
         do_checks(sg)
 
@@ -827,8 +838,9 @@ def test_grid_crs_exceptions():
 
     # test non-existing file
     not_a_file = "not-a-file"
-    with pytest.raises(FileNotFoundError):
-        StructuredGrid(delr=delr, delc=delc, prjfile=not_a_file)
+    if HAS_PYPROJ:
+        with pytest.raises(FileNotFoundError):
+            StructuredGrid(delr=delr, delc=delc, prjfile=not_a_file)
     # note "sg.prjfile = not_a_file" intentionally does not raise anything
 
     # test unhandled keyword

autotest/test_gridgen.py

@@ -14,6 +14,7 @@
 from flopy.utils.gridgen import Gridgen
 
 
+@requires_exe("gridgen")
 def test_ctor_accepts_path_or_string(function_tmpdir):
     grid = GridCases().structured_small()
 

autotest/test_gridintersect.py

@@ -14,7 +14,7 @@
 from flopy.utils.gridintersect import GridIntersect
 from flopy.utils.triangle import Triangle
 
-if has_pkg("shapely"):
+if has_pkg("shapely", strict=True):
     from shapely.geometry import (
         LineString,
         MultiLineString,
@@ -1221,7 +1221,7 @@ def test_polygon_offset_rot_structured_grid_shapely(rtree):
 # %% test rasters
 
 
-@requires_pkg("rasterstats", "scipy")
+@requires_pkg("rasterstats", "scipy", "shapely")
 def test_rasters(example_data_path):
     ws = example_data_path / "options"
     raster_name = "dem.img"

autotest/test_mf6.py

@@ -5,7 +5,7 @@
 
 import numpy as np
 import pytest
-from modflow_devtools.markers import requires_exe
+from modflow_devtools.markers import requires_exe, requires_pkg
 from modflow_devtools.misc import set_dir
 
 import flopy
@@ -637,6 +637,7 @@ def test_binary_write(function_tmpdir, layered):
 
 
 @requires_exe("mf6")
+@requires_pkg("shapely", "scipy")
 @pytest.mark.parametrize("layered", [True, False])
 def test_vor_binary_write(function_tmpdir, layered):
     # build voronoi grid

autotest/test_model_splitter.py

@@ -200,6 +200,7 @@ def test_metis_splitting_with_lak_sfr(function_tmpdir):
 
 
 @requires_exe("mf6")
+@requires_pkg("pymetis")
 def test_save_load_node_mapping(function_tmpdir):
     sim_path = get_example_data_path() / "mf6-freyberg"
     new_sim_path = function_tmpdir / "mf6-freyberg/split_model"