fix(mem): address memory leaks #3029
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: MODFLOW 6 continuous integration | |
| on: | |
| push: | |
| paths-ignore: | |
| - '**.md' | |
| - '**.pdf' | |
| - '**.tex' | |
| - '**.jpg' | |
| - '**.jpeg' | |
| - '**.png' | |
| - '**.bbl' | |
| - '**.bib' | |
| - 'doc/**.dat' | |
| - 'doc/**.ipynb' | |
| - 'doc/**.py' | |
| - 'doc/**.sh' | |
| - 'doc/**.xlsx' | |
| - '.hpc/**' | |
| pull_request: | |
| branches: | |
| - master | |
| - develop | |
| paths-ignore: | |
| - '**.md' | |
| - '**.pdf' | |
| - '**.tex' | |
| - '**.jpg' | |
| - '**.jpeg' | |
| - '**.png' | |
| - '**.bbl' | |
| - '**.bib' | |
| - 'doc/**.dat' | |
| - 'doc/**.ipynb' | |
| - 'doc/**.py' | |
| - 'doc/**.sh' | |
| - 'doc/**.xlsx' | |
| - '.hpc/**' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| PIXI_BETA_WARNING_OFF: true | |
| jobs: | |
| lint: | |
| name: Check format | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| - uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| - name: Check Fortran source formatting | |
| run: pixi run check-format | |
| - name: Check MSVS project files | |
| run: pixi run check-vfproj | |
| - name: Check python lint | |
| run: pixi run check-python-lint | |
| - name: Check python format | |
| run: pixi run check-python-format | |
| - name: Check CITATION.cff | |
| uses: dieghernan/cff-validator@v3 | |
| build: | |
| name: Build | |
| runs-on: ubuntu-22.04 | |
| env: | |
| FC: gfortran | |
| FC_V: 13 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| - name: Setup ${{ env.FC }} ${{ env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.FC_V }} | |
| - uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| - name: Meson setup | |
| run: pixi run setup -Dwerror=true builddir | |
| - name: Meson compile | |
| run: pixi run build builddir | |
| - name: Show build log | |
| if: failure() | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Meson test | |
| run: pixi run test builddir | |
| smoke_test: | |
| name: Smoke test | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| env: | |
| FC: gfortran | |
| FC_V: 13 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Checkout test-drive | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: fortran-lang/test-drive | |
| path: test-drive | |
| - name: Setup ${{ env.FC }} ${{ env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.FC_V }} | |
| - name: Setup pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| manifest-path: "modflow6/pixi.toml" | |
| - name: Custom pixi install | |
| working-directory: modflow6 | |
| run: pixi run install | |
| - name: Build test-drive | |
| working-directory: test-drive | |
| run: | | |
| pixi run --manifest-path=../modflow6/pixi.toml meson setup builddir --prefix=$(pwd) --libdir=lib | |
| pixi run --manifest-path=../modflow6/pixi.toml meson install -C builddir | |
| echo "PKG_CONFIG_PATH=$(pwd)/lib/pkgconfig:$PKG_CONFIG_PATH" >> $GITHUB_ENV | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| pixi run setup builddir | |
| pixi run build builddir | |
| - name: Show build log | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Unit test programs | |
| working-directory: modflow6 | |
| run: pixi run test builddir | |
| - name: Update flopy | |
| working-directory: modflow6 | |
| run: pixi run update-flopy | |
| - name: Get executables | |
| working-directory: modflow6 | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pixi run get-exes | |
| - name: Test programs | |
| working-directory: modflow6 | |
| run: | | |
| if [ "${{ github.ref_name }}" == "master" ]; then | |
| pixi run autotest -m "not slow and not regression and not developmode" | |
| else | |
| pixi run autotest --smoke | |
| fi | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-smoke-${{ runner.os }}-${{ env.FC }}-${{ env.FC_V }} | |
| path: modflow6/autotest/.failed | |
| test_gfortran: | |
| name: Test gnu fortran | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-22.04, macos-12, macos-14, windows-2022 ] | |
| defaults: | |
| run: | |
| shell: bash | |
| env: | |
| FC: gfortran | |
| FC_V: 13 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Checkout modflow6-testmodels | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-testmodels | |
| path: modflow6-testmodels | |
| - name: Checkout modflow6-examples | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-examples | |
| path: modflow6-examples | |
| - name: Setup ${{ env.FC }} ${{ contains(fromJSON('["macos-14"]'), matrix.os) && 12 || env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ contains(fromJSON('["macos-14"]'), matrix.os) && 12 || env.FC_V }} | |
| - name: Setup pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| manifest-path: "modflow6/pixi.toml" | |
| - name: Custom pixi install | |
| working-directory: modflow6 | |
| run: pixi run install | |
| - name: Set LDFLAGS (macOS) | |
| if: matrix.os == 'macos-14' | |
| run: | | |
| os_ver=$(sw_vers -productVersion | cut -d'.' -f1) | |
| if (( "$os_ver" > 12 )); then | |
| ldflags="$LDFLAGS -Wl,-ld_classic" | |
| echo "LDFLAGS=$ldflags" >> $GITHUB_ENV | |
| fi | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| setupargs="" | |
| if [[ "${{ matrix.os }}" == "macos-14" ]]; then | |
| setupargs="-Doptimization=1" | |
| fi | |
| pixi run setup builddir $setupargs | |
| pixi run build builddir | |
| - name: Show build log | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Unit test programs | |
| working-directory: modflow6 | |
| run: pixi run test builddir | |
| - name: Update flopy | |
| working-directory: modflow6 | |
| run: pixi run update-flopy | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pixi run get-exes | |
| - name: Test modflow6 | |
| working-directory: modflow6 | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| markers="" | |
| if [[ "${{ github.ref_name }}" == "master" ]]; then | |
| markers="not large and not developmode" | |
| else | |
| markers="not large" | |
| fi | |
| filters="" | |
| if [[ "${{ matrix.os }}" == "macos-14" ]]; then | |
| # comparison fails on macos-14 with optimization=1 | |
| filters="not test028_sfr_rewet" | |
| fi | |
| pixi run autotest -m "$markers" -k "$filters" | |
| - name: Install executables | |
| if: runner.os == 'Linux' | |
| uses: modflowpy/install-modflow-action@v1 | |
| - name: Test mf6 examples | |
| if: runner.os == 'Linux' | |
| working-directory: modflow6 | |
| shell: pixi run bash -e {0} | |
| run: | | |
| cp bin/mf6 $(which mf6) | |
| cd ../modflow6-examples/autotest | |
| pytest -v -n auto test_scripts.py | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-${{ matrix.os }}-${{ env.FC }}-${{ env.FC_V }} | |
| path: modflow6/autotest/.failed | |
| - name: Checkout usgslatex | |
| if: runner.os == 'Linux' | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/usgslatex | |
| path: usgslatex | |
| - name: Install TeX Live | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt install texlive-science \ | |
| texlive-latex-extra \ | |
| texlive-font-utils \ | |
| texlive-fonts-recommended \ | |
| texlive-fonts-extra | |
| - name: Install USGS LaTeX style files and Univers font | |
| if: runner.os == 'Linux' | |
| working-directory: usgslatex/usgsLaTeX | |
| run: sudo ./install.sh --all-users | |
| - name: Test distribution scripts | |
| working-directory: modflow6 | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pixi run test-dist-scripts | |
| test_intel_fortran: | |
| name: Test intel fortran | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| FC: intel-classic | |
| FC_V: "2021.7" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-22.04, macos-12, windows-2022] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Checkout modflow6-testmodels | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-testmodels | |
| path: modflow6-testmodels | |
| - name: Checkout modflow6-examples | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-examples | |
| path: modflow6-examples | |
| - name: Setup pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| manifest-path: "modflow6/pixi.toml" | |
| - name: Custom pixi install | |
| working-directory: modflow6 | |
| run: pixi run install | |
| - name: Setup ${{ env.FC }} ${{ env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: ${{ env.FC }} | |
| version: ${{ env.FC_V }} | |
| - name: Update version files | |
| working-directory: modflow6 | |
| run: pixi run update-version | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| pixi run setup builddir | |
| pixi run build builddir | |
| - name: Show build log | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Unit test programs | |
| working-directory: modflow6 | |
| run: pixi run test builddir | |
| - name: Update flopy | |
| working-directory: modflow6 | |
| run: pixi run update-flopy | |
| - name: Get executables | |
| working-directory: modflow6 | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pixi run get-exes | |
| - name: Test programs | |
| working-directory: modflow6 | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| if [ "${{ github.ref_name }}" == "master" ]; then | |
| pixi run autotest -m "not large and not developmode" | |
| else | |
| pixi run autotest -m "not large" | |
| fi | |
| - name: Install executables | |
| if: runner.os == 'Linux' | |
| uses: modflowpy/install-modflow-action@v1 | |
| - name: Test mf6 examples | |
| if: runner.os == 'Linux' | |
| working-directory: modflow6 | |
| shell: pixi run bash -e {0} | |
| run: | | |
| cp bin/mf6 $(which mf6) | |
| cd ../modflow6-examples/autotest | |
| pytest -v -n auto test_scripts.py | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-${{ matrix.os }}-${{ env.FC }}-${{ env.FC_V }} | |
| path: modflow6/autotest/.failed | |
| - name: Test scripts | |
| working-directory: modflow6 | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pixi run test-dist-scripts | |
| parallel_test: | |
| name: Parallel testing | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-22.04, macos-12, windows-2022 ] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Setup pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| manifest-path: "modflow6/pixi.toml" | |
| - name: Custom pixi install | |
| working-directory: modflow6 | |
| run: pixi run install | |
| - name: Test parallel MF6 | |
| if: runner.os != 'Windows' | |
| uses: ./modflow6/.github/actions/test-par | |
| - name: Test parallel MF6 (Windows) | |
| if: runner.os == 'Windows' | |
| uses: ./modflow6/.github/actions/test-par-win | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-${{ matrix.os }} | |
| path: modflow6/autotest/.failed | |
| extended_test: | |
| name: Extended executable testing | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-22.04, macos-12 ] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Setup pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| manifest-path: "modflow6/pixi.toml" | |
| - name: Custom pixi install | |
| working-directory: modflow6 | |
| run: pixi run install | |
| - name: Install additional netcdf testing packages | |
| working-directory: modflow6 | |
| run: pixi run pip install xugrid xarray netcdf4 | |
| - name: Test Extended MF6 | |
| uses: ./modflow6/.github/actions/test-extended | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-${{ matrix.os }} | |
| path: modflow6/autotest/.failed |