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Merge pull request #40 from MODFLOW-USGS/v0.2.0
Release 0.2.0
2 parents 400780e + 9de3c7f commit 31e90fd

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‎.github/workflows/ci.yml

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- name: Install modflow executables
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uses: modflowpy/install-modflow-action@v1
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with:
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path: ~/work/modflowapi/modflowapi/autotest
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path: ${{ github.workspace }}/autotest
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repo: modflow6-nightly-build
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- name: Run autotests
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working-directory: ./autotest
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shell: bash -l {0}
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run: pytest -v -n auto -m "not mf6"
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autotest_preidm_extensions:
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name: modflowapi pre-idm extensions autotests
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needs: lint
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ ubuntu-latest, macos-latest, windows-latest ]
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python-version: [ 3.8, 3.9, "3.10", "3.11" ]
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defaults:
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run:
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shell: bash
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steps:
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# check out repo
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- name: Checkout repo
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uses: actions/checkout@v3
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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cache-dependency-path: pyproject.toml
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- name: Install Python dependencies
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run: |
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# chmod a+x libmf6*
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pytest -n auto -m "not mf6"
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python -m pip install --upgrade pip
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pip install git+https://[email protected]/Deltares/xmipy@develop
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pip install git+https://[email protected]/MODFLOW-USGS/modflow-devtools@develop
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pip install .[test]
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- name: Install modflow executables
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uses: modflowpy/install-modflow-action@v1
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with:
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path: ${{ github.workspace }}/autotest
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repo: executables
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tag: "14.0"
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- name: Run autotests
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working-directory: ./autotest
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shell: bash -l {0}
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run: pytest -v -n auto -m "not mf6"
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autotest_mf6_examples:
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name: modflowapi mf6 examples autotests
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needs: lint
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- name: Install modflow executables
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uses: modflowpy/install-modflow-action@v1
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with:
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path: ~/work/modflowapi/modflowapi/autotest
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path: ${{ github.workspace }}/autotest
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repo: modflow6-nightly-build
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- name: Run autotests
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working-directory: ./autotest
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shell: bash -l {0}
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run: |
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# chmod a+x libmf6*
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pytest -n auto -m "mf6 and not extensions"
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run: pytest -v -n auto -m "mf6 and not extensions"

‎.github/workflows/release.yml

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name: Release
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on:
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push:
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branches:
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- main
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- v[0-9]+.[0-9]+.[0-9]+*
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release:
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types:
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- published
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jobs:
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prep:
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name: Prepare release
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runs-on: ubuntu-latest
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if: ${{ github.event_name == 'push' && github.ref_name != 'main' }}
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permissions:
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contents: write
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pull-requests: write
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defaults:
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run:
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shell: bash
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steps:
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- name: Checkout release branch
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uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: 3.8
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cache: 'pip'
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cache-dependency-path: pyproject.toml
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- name: Install Python dependencies
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run: |
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pip install --upgrade pip
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pip install build twine
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pip install .
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pip install ".[lint, test]"
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- name: Update version
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id: version
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run: |
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ref="${{ github.ref_name }}"
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version="${ref#"v"}"
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python scripts/update_version.py -v "$version"
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python -c "import modflowapi; print('Version: ', modflowapi.__version__)"
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echo "version=$version" >> $GITHUB_OUTPUT
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- name: Touch changelog
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run: touch HISTORY.md
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- name: Generate changelog
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id: cliff
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uses: orhun/git-cliff-action@v1
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with:
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config: cliff.toml
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args: --verbose --unreleased --tag ${{ steps.version.outputs.version }}
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env:
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OUTPUT: CHANGELOG.md
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- name: Update changelog
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run: |
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# substitute full group names
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sed -i 's/#### Ci/#### Continuous integration/' CHANGELOG.md
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sed -i 's/#### Feat/#### New features/' CHANGELOG.md
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sed -i 's/#### Fix/#### Bug fixes/' CHANGELOG.md
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sed -i 's/#### Refactor/#### Refactoring/' CHANGELOG.md
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sed -i 's/#### Test/#### Testing/' CHANGELOG.md
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# prepend release changelog to cumulative changelog
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clog="HISTORY.md"
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temp="temp.md"
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echo "$(tail -n +2 $clog)" > $clog
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cat CHANGELOG.md $clog > $temp
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sudo mv $temp $clog
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sed -i '1i # Changelog' $clog
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- name: Upload changelog
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uses: actions/upload-artifact@v3
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with:
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name: changelog
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path: CHANGELOG.md
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- name: Format Python files
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run: python scripts/pull_request_prepare.py
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- name: Push release branch
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env:
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GITHUB_TOKEN: ${{ github.token }}
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run: |
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ver="${{ steps.version.outputs.version }}"
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changelog=$(cat CHANGELOG.md | grep -v "### Version $ver")
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# remove this release's changelog so we don't commit it
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# the changes have already been prepended to HISTORY.md
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rm -f CHANGELOG.md
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# commit and push changes
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git config core.sharedRepository true
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git config user.name "github-actions[bot]"
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git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
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git add -A
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git commit -m "ci(release): set version to ${{ steps.version.outputs.version }}, update changelog"
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git push origin "${{ github.ref_name }}"
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title="Release $ver"
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body='
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# Release '$ver'
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The release can be approved by merging this pull request into `main`. This will trigger jobs to publish the release to PyPI and reset `develop` from `main`, incrementing the minor version number.
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## Changelog
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'$changelog'
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'
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gh pr create -B "main" -H "${{ github.ref_name }}" --title "$title" --draft --body "$body"
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release:
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name: Draft release
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# runs only when changes are merged to main
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if: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
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runs-on: ubuntu-latest
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permissions:
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contents: write
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pull-requests: write
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steps:
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- name: Checkout repo
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uses: actions/checkout@v3
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with:
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ref: main
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: 3.8
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- name: Install Python dependencies
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run: |
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pip install --upgrade pip
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pip install .
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pip install ".[test]"
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# actions/download-artifact won't look at previous workflow runs but we need to in order to get changelog
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- name: Download artifacts
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uses: dawidd6/action-download-artifact@v2
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- name: Draft release
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env:
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GITHUB_TOKEN: ${{ github.token }}
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run: |
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version=$(python scripts/update_version.py -g)
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title="modflowapi $version"
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notes=$(cat "changelog/CHANGELOG.md" | grep -v "### Version $version")
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gh release create "$version" \
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--target main \
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--title "$title" \
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--notes "$notes" \
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--draft \
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--latest
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publish:
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name: Publish package
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# runs only after release is published (manually promoted from draft)
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if: github.event_name == 'release' && github.repository_owner == 'MODFLOW-USGS'
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runs-on: ubuntu-22.04
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permissions:
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contents: write
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pull-requests: write
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id-token: write
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environment: # requires a 'release' environment in repo settings
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name: release
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url: https://pypi.org/p/modflowapi
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steps:
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- name: Checkout main branch
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uses: actions/checkout@v3
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with:
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ref: main
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: 3.8
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- name: Install Python dependencies
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run: |
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pip install --upgrade pip
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pip install build twine
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pip install .
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- name: Build package
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run: python -m build
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- name: Check package
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run: twine check --strict dist/*
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- name: Upload package
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uses: actions/upload-artifact@v4
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with:
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name: dist
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path: dist
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎CITATION.cff

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and the software itself.
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type: software
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title: MODFLOW API
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version: 0.1.0
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version: 0.2.0
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date-released: '2023-04-19'
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abstract: An extension to xmipy for the MODFLOW API.
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repository-artifact: https://pypi.org/project/modflowapi

‎HISTORY.md

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# Changelog
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### Version 0.2.0
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#### Refactoring
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* [refactor(rhs, hcof)](https://github.com/MODFLOW-USGS/modflowapi/commit/c0f681c5b7525388ead4df8c6363c1b4514d6de6): Updates to allow setting values when rhs and hcof have not yet had pointers set.. Committed by Joshua Larsen on 2023-04-28.
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* [refactor(Quickstart.ipynb)](https://github.com/MODFLOW-USGS/modflowapi/commit/3b6675aa687f5af01813abfdb143c7ddd4343646): Fix error in callback_function. Committed by Joshua Larsen on 2023-07-17.
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* [refactor(rhs, hcof)](https://github.com/MODFLOW-USGS/modflowapi/commit/ce4e50286d66da51c6b05f0de29c7c646344f6ce): Allow setting rhs and hcof when pointers have not been previously set. Committed by Joshua Larsen on 2023-07-17.
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* [refactor](https://github.com/MODFLOW-USGS/modflowapi/commit/e693282611d5863bafeece362230a4aadd02311f): Update libmf6 path handling (#27). Committed by w-bonelli on 2023-08-03.
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* [refactor(_ptr_to_recarray)](https://github.com/MODFLOW-USGS/modflowapi/commit/5a631592f2da57bf1564c263e9602c46e5a5a50c): Slice pointers prior to setting data to recarray. Committed by Joshua Larsen on 2023-08-08.
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* [refactor(_ptr_to_recarray)](https://github.com/MODFLOW-USGS/modflowapi/commit/959fe31abda263a52d01262af7dc4c2a878eadb5): Slice pointers prior to setting data to recarray. Committed by Joshua Larsen on 2023-08-08.
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* [refactor(extensions)](https://github.com/MODFLOW-USGS/modflowapi/commit/c97339d06e7386055e486f6354825ec15cea4638): Add support for IDM changes. Committed by Joshua Larsen on 2023-12-21.
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* [refactor(extensions)](https://github.com/MODFLOW-USGS/modflowapi/commit/de0aff9c21d5d925235f306fd2b3d148c3281efa): Add support for IDM changes. Committed by Joshua Larsen on 2023-12-21.
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### Version 0.1.0
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* Fix typo in README (https://github.com/MODFLOW-USGS/modflowapi/pull/4)
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* modflowapi interface (https://github.com/MODFLOW-USGS/modflowapi/pull/8)
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* update package: manual variable address assembly updated to use xmipy get_variable_addr()
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* update additional manual variable address assembly statements
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* Refactor code and added functionality:
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* add stress_period_start, stress_period_end Callbacks
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* fix ApiModel __repr__
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* added Exchanges, TDIS, ATS, and SLN support
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* added ScalarInput and ScalarPackage support
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* update autotests
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* added parallel testing support through pytest-xdist
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* updated markers and split the extensions tests from the mf6 examples tests
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* added a test for ATS
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* update setup.cfg
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* update ci.yml
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* update(ListInput): add auxvar to stress_period_data when auxiliary variables are used
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* Allow None to be passed to stress_period_data.values to disable stresses for a package
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* updates: ApiModel, ApiSimulation, run_simulation
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* added a `totim` property on `ApiSimulation` and `ApiModel`
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* added docstrings to ApiModel property methods
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* updated termination message in run_simulation
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* added a finalize callback to Callbacks and run_simulation
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* add support for AUXNAME_CST
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* add(Head Monitor Example): Add a head monitor example application
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* ApiModel: adjust X based on nodetouser
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* ApiPackage: enforce lower cased variable names in get_advanced_var
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* ArrayPointer: trap for arrays that are not adjusted by reduced node numbers (ex. idomain)
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* update setup.cfg
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* try reformatting the xmipy installation instructions
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* fix(get value): fixed error handling when modflowapi fails to get a pointer to a value from the API (https://github.com/MODFLOW-USGS/modflowapi/pull/9)
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Co-authored-by: scottrp <[email protected]>
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* update(rhs, hcof, AdvancedInput): bug fixes for setting variable values for advanced inputs
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* update rhs and hcof to copy values to pointer instead of overwriting the pointer
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* add a check for AdvancedInput variables that do not have pointer support in xmipy
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* update setting routine for AdvancedInput
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* refactor(EOL): change CRLF to LF line endings for source files (https://github.com/MODFLOW-USGS/modflowapi/pull/12)
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* Use pyproject.toml for project metadata, add citation info (https://github.com/MODFLOW-USGS/modflowapi/pull/11)
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* add(test_rhs_hcof_advanced): add additional test (https://github.com/MODFLOW-USGS/modflowapi/pull/13)
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* added test for getting and setting rhs, hcof, and advanced variable values
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* update project to use unix line separators
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* use np.testing.assert_allclose() instead of AssertionError
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* Add missing RIV support to modflowapi (https://github.com/MODFLOW-USGS/modflowapi/pull/16)
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* add(test_rhs_hcof_advanced): add additional test
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* added test for getting and setting rhs, hcof, and advanced variable values
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* update project to use unix line separators
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* use np.testing.assert_allclose() instead of AssertionError
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* Add missing riv package to modflowapi
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### Version 0.0.1
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Initial release.

‎autotest/__init__.py

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# init file for pytest
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# init file for pytest

‎autotest/conftest.py

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finally:
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__mf6_examples_lock.release()
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def is_nested(namfile) -> bool:
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p = Path(namfile)
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if not p.is_file() or not p.name.endswith(".nam"):

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