add IPRN value in example input files, refactor generate_classes test…

…s without pytest-virtualenv (fall back to virtualenv directly), remove scripts/pull_request_prepare.py (prep for ruff to replace other linting/formatting tools in subsequent PR)
modflowpy · Nov 13, 2023 · 7631f4b · 7631f4b
1 parent 77369b1
commit 7631f4b
Show file tree

Hide file tree

Showing 19 changed files with 224 additions and 817 deletions.
diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ 3.8, 3.9, "3.10", "3.11" ]
+        python-version: [ 3.8, 3.9, "3.10", "3.11", "3.12" ]
         exclude:
           # avoid shutil.copytree infinite recursion bug
           # https://github.com/python/cpython/pull/17098
@@ -27,56 +27,23 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Python
-        if: runner.os != 'Windows'
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
           cache-dependency-path: pyproject.toml
 
       - name: Install Python dependencies
-        if: runner.os != 'Windows'
         run: |
           pip install --upgrade pip
           pip install .
           pip install ".[test, optional]"
 
-      - name: Setup Micromamba
-        if: runner.os == 'Windows'
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: etc/environment.yml
-          cache-environment: true
-          cache-downloads: true
-          create-args: >-
-            python=${{ matrix.python-version }}
-          init-shell: >-
-            bash
-            powershell
-
-      - name: Install extra Python dependencies
-        if: runner.os == 'Windows'
-        shell: bash -l {0}
-        run: |
-          pip install xmipy
-          pip install .
-
       - name: Install Modflow executables
         uses: modflowpy/install-modflow-action@v1
 
       - name: Run benchmarks
-        if: runner.os != 'Windows'
-        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
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Run benchmarks
-        if: runner.os == 'Windows'
-        shell: bash -l {0}
-        working-directory: ./autotest
+        working-directory: autotest
         run: |
           mkdir -p .benchmarks
           pytest -v --durations=0 --benchmark-only --benchmark-json .benchmarks/${{ matrix.os }}_python${{ matrix.python-version }}.json --keep-failed=.failed
@@ -115,7 +82,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.12
           cache: 'pip'
           cache-dependency-path: pyproject.toml
 
@@ -151,7 +118,6 @@ jobs:
           fi
           python ./scripts/process_benchmarks.py ./autotest/.benchmarks ./autotest/.benchmarks
         env:
-          ARTIFACTS: ${{steps.run_tests.outputs.artifact_ids}}
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Upload benchmark results

diff --git a/.github/workflows/commit.yml b/.github/workflows/commit.yml
@@ -32,11 +32,10 @@ jobs:
           python -c "import flopy; print(f'{flopy.__version__}')"
 
       - name: Build package
-        run: |
-          python -m build
+        run: python -m build
+
       - name: Check package
-        run: |
-          twine check --strict dist/*
+        run: twine check --strict dist/*
 
   lint:
     name: Lint
@@ -135,13 +134,13 @@ jobs:
         if: failure()
         with:
           name: failed-smoke-${{ runner.os }}-${{ env.PYTHON_VERSION }}
-          path: ./autotest/.failed/**
+          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
+          files: autotest/coverage.xml
 
   test:
     name: Test
@@ -158,40 +157,25 @@ jobs:
           - python-version: '3.8.0'
     defaults:
       run:
-        shell: bash
+        shell: bash -l {0}
     timeout-minutes: 45
     steps:
 
       - name: Checkout repo
         uses: actions/checkout@v4
 
       - name: Setup Python
-        if: runner.os != 'Windows'
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
           cache-dependency-path: pyproject.toml
-
+      
       - name: Install Python dependencies
-        if: runner.os != 'Windows'
         run: |
           pip install --upgrade pip
           pip install .
-          pip install ".[test, optional]"
-
-      - name: Setup Micromamba
-        if: runner.os == 'Windows'
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: etc/environment.yml
-          cache-environment: true
-          cache-downloads: true
-          create-args: >-
-            python=${{ matrix.python-version }}
-          init-shell: >-
-            bash
-            powershell
+          pip install ".[test,optional]"
 
       - name: Install Modflow-related executables
         uses: modflowpy/install-modflow-action@v1
@@ -201,30 +185,17 @@ jobs:
         with:
           repo: modflow6-nightly-build
 
-      - name: Update FloPy packages
-        if: runner.os != 'Windows'
+      - name: Update package classes
         run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
 
-      - name: Update FloPy packages
-        if: runner.os == 'Windows'
-        shell: bash -l {0}
-        run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
-
-      - name: Run tests
-        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
-          coverage report
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
       - name: Run tests
-        if: runner.os == 'Windows'
-        shell: bash -l {0}
-        working-directory: ./autotest
+        working-directory: autotest
         run: |
-          pytest -v -m="not example and not regression" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
+          m="not example and not regression"
+          if [[ "${{ matrix.python-version}}" == "3.12" ]]; then
+            m="$m and not generation"
+          fi
+          pytest -v -m="$m" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
           coverage report
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -234,11 +205,10 @@ jobs:
         if: failure()
         with:
           name: failed-${{ matrix.os }}-${{ matrix.python-version }}
-          path: |
-            ./autotest/.failed/**
+          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
+          files: autotest/coverage.xml
diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ 3.8, 3.9, "3.10", "3.11" ]
+        python-version: [ 3.8, 3.9, "3.10", "3.11", "3.12" ]
         exclude:
           # avoid shutil.copytree infinite recursion bug
           # https://github.com/python/cpython/pull/17098
@@ -25,23 +25,7 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v4
 
-      - name: Setup Python
-        if: runner.os != 'Windows'
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: pyproject.toml
-
-      - name: Install Python dependencies
-        if: runner.os != 'Windows'
-        run: |
-          pip install --upgrade pip
-          pip install .
-          pip install ".[test, optional]"
-
       - name: Setup Micromamba
-        if: runner.os == 'Windows'
         uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: etc/environment.yml
@@ -53,14 +37,10 @@ jobs:
             bash
             powershell
 
-      - name: Install extra Python dependencies
-        if: runner.os == 'Windows'
-        shell: bash -l {0}
-        run: |
-          pip install xmipy
-          pip install .
+      - name: Install FloPy
+        run: pip install .
 
-      - name: Workaround OpenGL issue on Linux
+      - name: OpenGL workaround on Linux
         if: runner.os == 'Linux'
         run: |
           # referenced from https://github.com/pyvista/pyvista/blob/main/.github/workflows/vtk-pre-test.yml#L53
@@ -85,28 +65,11 @@ jobs:
           repo: modflow6-nightly-build
 
       - name: Update FloPy packages
-        if: runner.os != 'Windows'
-        run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
-
-      - name: Update FloPy packages
-        if: runner.os == 'Windows'
-        shell: bash -l {0}
         run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
 
       - name: Run example tests
-        if: runner.os != 'Windows'
-        working-directory: ./autotest
-        run: |
-          pytest -v -m="example" -n=auto -s --durations=0 --keep-failed=.failed
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Run example tests
-        if: runner.os == 'Windows'
-        shell: bash -l {0}
-        working-directory: ./autotest
-        run: |
-          pytest -v -m="example" -n=auto -s --durations=0 --keep-failed=.failed
+        working-directory: autotest
+        run: pytest -v -m="example" -n=auto -s --durations=0 --keep-failed=.failed
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
@@ -115,5 +78,4 @@ jobs:
         if: failure()
         with:
           name: failed-example-${{ matrix.os }}-${{ matrix.python-version }}
-          path: |
-            ./autotest/.failed/**
+          path: autotest/.failed/**
diff --git a/.github/workflows/regression.yml b/.github/workflows/regression.yml
@@ -12,34 +12,19 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ 3.8, 3.9, "3.10", "3.11" ]
+        python-version: [ 3.8, 3.9, "3.10", "3.11", "3.12" ]
         exclude:
           # avoid shutil.copytree infinite recursion bug
           # https://github.com/python/cpython/pull/17098
           - python-version: '3.8.0'
     defaults:
       run:
-        shell: bash
+        shell: bash -l {0}
     timeout-minutes: 90
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
 
-      - name: Setup Python
-        if: runner.os != 'Windows'
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: pyproject.toml
-
-      - name: Install Python dependencies
-        if: runner.os != 'Windows'
-        run: |
-          pip install --upgrade pip
-          pip install .
-          pip install ".[test, optional]"
-
       - name: Setup Micromamba
         if: runner.os == 'Windows'
         uses: mamba-org/setup-micromamba@v1
@@ -53,12 +38,8 @@ jobs:
             bash
             powershell
 
-      - name: Install extra Python dependencies
-        if: runner.os == 'Windows'
-        shell: bash -l {0}
-        run: |
-          pip install xmipy
-          pip install .
+      - name: Install FloPy
+        run: pip install .
 
       - name: Install Modflow-related executables
         uses: modflowpy/install-modflow-action@v1
@@ -69,25 +50,10 @@ jobs:
           repo: modflow6-nightly-build
 
       - name: Update FloPy packages
-        if: runner.os != 'Windows'
-        run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
-
-      - name: Update FloPy packages
-        if: runner.os == 'Windows'
-        shell: bash -l {0}
         run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
 
       - name: Run regression tests
-        if: runner.os != 'Windows'
-        working-directory: ./autotest
-        run: pytest -v -m="regression" -n=auto --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
+        working-directory: autotest
         run: pytest -v -m="regression" -n=auto --durations=0 --keep-failed=.failed
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -97,5 +63,4 @@ jobs:
         if: failure()
         with:
           name: failed-regression-${{ matrix.os }}-${{ matrix.python-version }}
-          path: |
-            ./autotest/.failed/**
+          path: autotest/.failed/**