diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 1e1944b6a..dd38e3eea 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -22,20 +22,18 @@ jobs: - name: Checkout repo uses: actions/checkout@v4 - - name: Setup Micromamba - uses: mamba-org/setup-micromamba@v2 + - name: Setup uv + uses: astral-sh/setup-uv@v5 with: - environment-file: etc/environment.yml - cache-environment: true - cache-downloads: true - create-args: >- - python=${{ matrix.python-version }} - init-shell: >- - bash - powershell + version: "0.5.18" + + - name: Setup Python + uses: actions/setup-python@v5 + with: + python-version-file: pyproject.toml - name: Install FloPy - run: pip install . + run: uv sync --all-extras - name: Install Modflow executables uses: modflowpy/install-modflow-action@v1 @@ -52,7 +50,7 @@ jobs: working-directory: autotest run: | mkdir -p .benchmarks - pytest -v --durations=0 --benchmark-only --benchmark-json .benchmarks/${{ matrix.os }}_python${{ matrix.python-version }}.json --keep-failed=.failed + uv run pytest -v --durations=0 --benchmark-only --benchmark-json .benchmarks/${{ matrix.os }}_python${{ matrix.python-version }}.json --keep-failed=.failed ls .benchmarks env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -85,17 +83,16 @@ jobs: - name: Checkout repo uses: actions/checkout@v4 + - name: Setup uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.5.18" + - name: Setup Python uses: actions/setup-python@v5 - with: - python-version: 3.12 - cache: 'pip' - cache-dependency-path: pyproject.toml - name: Install Python dependencies - run: | - pip install --upgrade pip - pip install numpy pandas matplotlib seaborn + run: uv pip install numpy pandas matplotlib seaborn - name: Download all artifacts uses: actions/download-artifact@v4 @@ -132,7 +129,7 @@ jobs: fi # process benchmarks - python scripts/process_benchmarks.py $path $path + uv run python scripts/process_benchmarks.py $path $path env: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/codegen.yml b/.github/workflows/codegen.yml index 69ec7e8ff..b319cd3c1 100644 --- a/.github/workflows/codegen.yml +++ b/.github/workflows/codegen.yml @@ -23,20 +23,18 @@ jobs: - name: Checkout repo uses: actions/checkout@v4 - - name: Setup Micromamba - uses: mamba-org/setup-micromamba@v1 + - name: Setup uv + uses: astral-sh/setup-uv@v5 with: - environment-file: etc/environment.yml - cache-environment: true - cache-downloads: true - create-args: >- - python=${{ matrix.python-version }} - init-shell: >- - bash - powershell + version: "0.5.18" + + - name: Setup Python + uses: actions/setup-python@v5 + with: + python-version-file: pyproject.toml - name: Install FloPy - run: pip install . + run: uv sync - name: Generate classes - run: python -m flopy.mf6.utils.generate_classes --ref ${{ matrix.ref }} --no-backup \ No newline at end of file + run: uv run python -m flopy.mf6.utils.generate_classes --ref ${{ matrix.ref }} --no-backup \ No newline at end of file diff --git a/.github/workflows/commit.yml b/.github/workflows/commit.yml index 68f310fa1..08d2212d4 100644 --- a/.github/workflows/commit.yml +++ b/.github/workflows/commit.yml @@ -20,25 +20,26 @@ jobs: - name: Checkout repo uses: actions/checkout@v4 + - name: Setup uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.5.18" + - name: Setup Python uses: actions/setup-python@v5 with: - python-version: 3.9 - cache: 'pip' - cache-dependency-path: pyproject.toml + python-version-file: pyproject.toml - name: Install Python dependencies run: | - pip install --upgrade pip - pip install build twine - pip install . - python -c "import flopy; print(f'{flopy.__version__}')" + uv sync --extra build + uv run python -c "import flopy; print(f'{flopy.__version__}')" - name: Build package - run: python -m build + run: uv build - name: Check package - run: twine check --strict dist/* + run: uv run twine check --strict dist/* lint: name: Lint @@ -52,32 +53,33 @@ jobs: - name: Checkout repo uses: actions/checkout@v4 + - name: Setup uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.5.18" + - name: Setup Python uses: actions/setup-python@v5 with: - python-version: 3.9 - cache: 'pip' - cache-dependency-path: pyproject.toml + python-version-file: pyproject.toml - name: Install Python dependencies - run: | - pip install . - pip install ".[lint]" + run: uv sync --extra lint - name: Lint - run: ruff check . + run: uv run ruff check . - name: Check format - run: ruff format . --check + run: uv run ruff format . --check - name: Check spelling - run: codespell + run: uv run codespell - name: Check CITATION.cff run: | - cffconvert --validate - cffconvert -f apalike - cffconvert -f bibtex + uv run cffconvert --validate + uv run cffconvert -f apalike + uv run cffconvert -f bibtex smoke: name: Smoke test @@ -93,25 +95,26 @@ jobs: - name: Checkout repo uses: actions/checkout@v4 + - name: Setup uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.5.18" + - name: Setup Python uses: actions/setup-python@v5 with: - python-version: ${{ env.PYTHON_VERSION }} - cache: 'pip' - cache-dependency-path: pyproject.toml + python-version-file: pyproject.toml - name: Install Python dependencies - run: | - pip install --upgrade pip - pip install . - pip install ".[test, optional]" + # temp. allow prereleases for vtk on aarch64 + run: uv sync --all-extras --prerelease=allow - name: Install Modflow executables uses: modflowpy/install-modflow-action@v1 - name: Smoke test working-directory: autotest - run: pytest -v -n=auto --smoke --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed + run: uv run pytest -v -n=auto --smoke --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -146,20 +149,18 @@ jobs: - name: Checkout repo uses: actions/checkout@v4 - - name: Setup Micromamba - uses: mamba-org/setup-micromamba@v1 + - name: Setup uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.5.18" + + - name: Setup Python + uses: actions/setup-python@v5 with: - environment-file: etc/environment.yml - cache-environment: true - cache-downloads: true - create-args: >- - python=${{ matrix.python-version }} - init-shell: >- - bash - powershell + python-version-file: pyproject.toml - name: Install FloPy - run: pip install . + run: uv sync --all-extras - name: Install Modflow-related executables uses: modflowpy/install-modflow-action@v1 @@ -178,18 +179,18 @@ jobs: subset: triangle - name: Update package classes - run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup + run: uv run python -m flopy.mf6.utils.generate_classes --ref develop --no-backup - name: Run tests working-directory: autotest run: | - pytest -v -m="not example" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile + uv run pytest -v -m="not example" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - name: Report coverage working-directory: autotest - run: coverage report + run: uv run coverage report - name: Upload failed test outputs uses: actions/upload-artifact@v4 diff --git a/.github/workflows/mf6.yml b/.github/workflows/mf6.yml index 50a3ccce1..e6f774b0c 100644 --- a/.github/workflows/mf6.yml +++ b/.github/workflows/mf6.yml @@ -24,21 +24,23 @@ jobs: - name: Checkout flopy repo uses: actions/checkout@v4 + - name: Setup uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.5.18" + - name: Setup Python uses: actions/setup-python@v5 with: - python-version: 3.9 - cache: 'pip' - cache-dependency-path: pyproject.toml + python-version-file: pyproject.toml - name: Install Python dependencies run: | - pip install --upgrade pip - pip install https://github.com/modflowpy/pymake/zipball/master - pip install https://github.com/Deltares/xmipy/zipball/develop - pip install https://github.com/MODFLOW-USGS/modflowapi/zipball/develop - pip install .[test,optional] - pip install meson ninja + uv sync --all-extras + uv pip install https://github.com/modflowpy/pymake/archive/master.zip + uv pip install https://github.com/Deltares/xmipy/archive/develop.zip + uv pip install https://github.com/MODFLOW-USGS/modflowapi/archive/develop.zip + uv pip install meson ninja - name: Setup GNU Fortran uses: fortran-lang/setup-fortran@v1 @@ -55,27 +57,27 @@ jobs: - name: Build and install MF6 working-directory: modflow6 run: | - meson setup builddir --buildtype=debugoptimized --prefix=$(pwd) --libdir=bin - meson install -C builddir - meson test --verbose --no-rebuild -C builddir + uv run meson setup builddir --buildtype=debugoptimized --prefix=$(pwd) --libdir=bin + uv run meson install -C builddir + uv run meson test --verbose --no-rebuild -C builddir - name: Update package classes working-directory: modflow6/autotest - run: python update_flopy.py + run: uv run python update_flopy.py - name: Install executables working-directory: modflow6/autotest env: GITHUB_TOKEN: ${{ github.token }} - run: pytest -v --durations=0 get_exes.py + run: uv run pytest -v --durations=0 get_exes.py - name: Run tests working-directory: modflow6/autotest - run: pytest -v --cov=flopy --cov-report=xml --cov-append --durations=0 -n auto -m "not repo and not regression" + run: uv run pytest -v --cov=flopy --cov-report=xml --cov-append --durations=0 -n auto -m "not repo and not regression" - name: Print coverage report before upload working-directory: ./modflow6/autotest - run: coverage report + run: uv run coverage report - name: Upload coverage to Codecov if: @@ -107,22 +109,24 @@ jobs: repository: MODFLOW-USGS/modflow6-examples path: modflow6-examples + - name: Setup uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.5.18" + - name: Setup Python uses: actions/setup-python@v5 with: - python-version: 3.9 - cache: 'pip' - cache-dependency-path: pyproject.toml + python-version-file: pyproject.toml - name: Install Python dependencies run: | - pip install --upgrade pip - pip install https://github.com/modflowpy/pymake/zipball/master - pip install https://github.com/Deltares/xmipy/zipball/develop - pip install https://github.com/MODFLOW-USGS/modflowapi/zipball/develop - pip install .[test,optional] - pip install meson ninja - pip install -r modflow6-examples/etc/requirements.pip.txt + uv sync --all-extras + uv pip install https://github.com/modflowpy/pymake/archive/master.zip + uv pip install https://github.com/Deltares/xmipy/archive/develop.zip + uv pip install https://github.com/MODFLOW-USGS/modflowapi/archive/develop.zip + uv pip install meson ninja + uv pip install -r modflow6-examples/etc/requirements.pip.txt - name: Setup GNU Fortran uses: fortran-lang/setup-fortran@v1 @@ -136,15 +140,15 @@ jobs: - name: Build and install MF6 working-directory: modflow6 run: | - meson setup builddir --buildtype=debugoptimized --prefix=$(pwd) --libdir=bin - meson install -C builddir - meson test --verbose --no-rebuild -C builddir + uv run meson setup builddir --buildtype=debugoptimized --prefix=$(pwd) --libdir=bin + uv run meson install -C builddir + uv run meson test --verbose --no-rebuild -C builddir cp bin/* ~/.local/bin/modflow/ - name: Update package classes working-directory: modflow6/autotest - run: python update_flopy.py + run: uv run python update_flopy.py - name: Test MF6 examples working-directory: modflow6-examples/autotest - run: pytest -v -n=auto --durations=0 test_scripts.py + run: uv run pytest -v -n=auto --durations=0 test_scripts.py diff --git a/.github/workflows/optional.yml b/.github/workflows/optional.yml index c1962380a..967b2bdf2 100644 --- a/.github/workflows/optional.yml +++ b/.github/workflows/optional.yml @@ -27,31 +27,32 @@ jobs: - name: Checkout repo uses: actions/checkout@v4 + - name: Setup uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.5.18" + - name: Setup Python uses: actions/setup-python@v5 with: - python-version: ${{ env.PYTHON_VERSION }} - cache: 'pip' - cache-dependency-path: pyproject.toml + python-version-file: pyproject.toml - name: Install Python dependencies run: | - pip install --upgrade pip - pip install . - pip install ".[test]" + uv sync --extra test # Install optional dependencies according to matrix.optdeps. # If matrix.optdeps is "some" remove 3 optional dependencies # selected randomly using the current date as the seed. if [[ ! "${{ matrix.optdeps }}" == *"no"* ]]; then - pip install ".[optional]" + uv 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 + uv pip uninstall --yes $rmvd fi - name: Upload removed dependencies log @@ -65,7 +66,7 @@ jobs: - name: Smoke test (${{ matrix.optdeps }}) working-directory: autotest - run: pytest -v -n=auto -m "not regression and not example" --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed + run: uv run pytest -v -n=auto -m "not regression and not example" --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 4b482bb4e..0ecfd3383 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -24,24 +24,23 @@ jobs: with: fetch-depth: 0 + - name: Setup uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.5.18" + - name: Setup Python uses: actions/setup-python@v5 with: - python-version: 3.9 - cache: 'pip' - cache-dependency-path: pyproject.toml + python-version-file: pyproject.toml - name: Install Python dependencies - run: | - pip install --upgrade pip - pip install build twine - pip install . - pip install ".[lint, test, optional]" + run: uv sync --all-extras - name: Install MODFLOW run: | mkdir -p ~/.local/bin - get-modflow ~/.local/bin + uv run get-modflow ~/.local/bin env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -54,23 +53,23 @@ jobs: # update version files if [[ "$ver" == *"rc"* ]]; then - python scripts/update_version.py -v "${ver%"rc"}" + uv run python scripts/update_version.py -v "${ver%"rc"}" else - python scripts/update_version.py -v "$ver" + uv run python scripts/update_version.py -v "$ver" fi # show version and set output - python -c "import flopy; print(f'FloPy version: {flopy.__version__}')" + uv run python -c "import flopy; print(f'FloPy version: {flopy.__version__}')" echo "version=${ver#"v"}" >> $GITHUB_OUTPUT - name: Lint and format Python files run: | - ruff check . --fix - ruff format . + uv run ruff check . --fix + uv run ruff format . - 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: uv run pytest -v -m="not example and not regression" -n=auto --durations=0 --keep-failed=.failed --dist loadfile env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/pyproject.toml b/pyproject.toml index ade0dbaf1..59a552d39 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,7 +36,8 @@ dependencies = [ dynamic = ["version", "readme"] 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