Merge pull request #40 from MODFLOW-USGS/v0.2.0

Release 0.2.0
MODFLOW-USGS · Feb 8, 2024 · 31e90fd · 31e90fd
2 parents 400780e + 9de3c7f
commit 31e90fd
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -128,16 +128,58 @@ jobs:
       - name: Install modflow executables
         uses: modflowpy/install-modflow-action@v1
         with:
-          path: ~/work/modflowapi/modflowapi/autotest
+          path: ${{ github.workspace }}/autotest
           repo: modflow6-nightly-build
 
       - name: Run autotests
         working-directory: ./autotest
         shell: bash -l {0}
+        run: pytest -v -n auto -m "not mf6"
+
+  autotest_preidm_extensions:
+    name: modflowapi pre-idm extensions autotests
+    needs: lint
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, macos-latest, windows-latest ]
+        python-version: [ 3.8, 3.9, "3.10", "3.11" ]
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+      # check out repo
+      - name: Checkout repo
+        uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: pyproject.toml
+
+      - name: Install Python dependencies
         run: |
-          # chmod a+x libmf6*
-          pytest -n auto -m "not mf6"
-          
+          python -m pip install --upgrade pip
+          pip install git+https://[email protected]/Deltares/xmipy@develop
+          pip install git+https://[email protected]/MODFLOW-USGS/modflow-devtools@develop
+          pip install .[test]
+
+      - name: Install modflow executables
+        uses: modflowpy/install-modflow-action@v1
+        with:
+          path: ${{ github.workspace }}/autotest
+          repo: executables
+          tag: "14.0"
+
+      - name: Run autotests
+        working-directory: ./autotest
+        shell: bash -l {0}
+        run: pytest -v -n auto -m "not mf6"     
+
   autotest_mf6_examples:
     name: modflowapi mf6 examples autotests
     needs: lint
@@ -173,12 +215,10 @@ jobs:
       - name: Install modflow executables
         uses: modflowpy/install-modflow-action@v1
         with:
-          path: ~/work/modflowapi/modflowapi/autotest
+          path: ${{ github.workspace }}/autotest
           repo: modflow6-nightly-build
 
       - name: Run autotests
         working-directory: ./autotest
         shell: bash -l {0}
-        run: |
-          # chmod a+x libmf6*
-          pytest -n auto -m "mf6 and not extensions"
+        run: pytest -v -n auto -m "mf6 and not extensions"
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -0,0 +1,207 @@
+name: Release
+on:
+  push:
+    branches:
+      - main
+      - v[0-9]+.[0-9]+.[0-9]+*
+  release:
+    types:
+      - published
+jobs:
+  prep:
+    name: Prepare release
+    runs-on: ubuntu-latest
+    if: ${{ github.event_name == 'push' && github.ref_name != 'main' }}
+    permissions:
+      contents: write
+      pull-requests: write
+    defaults:
+      run:
+        shell: bash
+    steps:
+
+      - name: Checkout release branch
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.8
+          cache: 'pip'
+          cache-dependency-path: pyproject.toml
+
+      - name: Install Python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install build twine
+          pip install .
+          pip install ".[lint, test]"
+
+      - name: Update version
+        id: version
+        run: |
+          ref="${{ github.ref_name }}"
+          version="${ref#"v"}"
+          python scripts/update_version.py -v "$version"
+          python -c "import modflowapi; print('Version: ', modflowapi.__version__)"
+          echo "version=$version" >> $GITHUB_OUTPUT
+
+      - name: Touch changelog
+        run: touch HISTORY.md
+
+      - name: Generate changelog
+        id: cliff
+        uses: orhun/git-cliff-action@v1
+        with:
+          config: cliff.toml
+          args: --verbose --unreleased --tag ${{ steps.version.outputs.version }}
+        env:
+          OUTPUT: CHANGELOG.md
+
+      - name: Update changelog
+        run: |
+          # substitute full group names
+          sed -i 's/#### Ci/#### Continuous integration/' CHANGELOG.md
+          sed -i 's/#### Feat/#### New features/' CHANGELOG.md
+          sed -i 's/#### Fix/#### Bug fixes/' CHANGELOG.md
+          sed -i 's/#### Refactor/#### Refactoring/' CHANGELOG.md
+          sed -i 's/#### Test/#### Testing/' CHANGELOG.md
+          
+          # prepend release changelog to cumulative changelog
+          clog="HISTORY.md"
+          temp="temp.md"
+          echo "$(tail -n +2 $clog)" > $clog
+          cat CHANGELOG.md $clog > $temp
+          sudo mv $temp $clog
+          sed -i '1i # Changelog' $clog
+
+      - name: Upload changelog
+        uses: actions/upload-artifact@v3
+        with:
+          name: changelog
+          path: CHANGELOG.md
+
+      - name: Format Python files
+        run: python scripts/pull_request_prepare.py
+
+      - name: Push release branch
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: |
+          ver="${{ steps.version.outputs.version }}"
+          changelog=$(cat CHANGELOG.md | grep -v "### Version $ver")
+          
+          # remove this release's changelog so we don't commit it
+          # the changes have already been prepended to HISTORY.md
+          rm -f CHANGELOG.md
+          
+          # commit and push changes
+          git config core.sharedRepository true
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add -A
+          git commit -m "ci(release): set version to ${{ steps.version.outputs.version }}, update changelog"
+          git push origin "${{ github.ref_name }}"
+
+          title="Release $ver"
+          body='
+          # Release '$ver'
+          
+          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.
+          
+          ## Changelog
+          
+          '$changelog'
+          '
+          gh pr create -B "main" -H "${{ github.ref_name }}" --title "$title" --draft --body "$body"
+
+  release:
+    name: Draft release
+    # runs only when changes are merged to main
+    if: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+    steps:
+
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          ref: main
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.8
+
+      - name: Install Python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install .
+          pip install ".[test]"
+
+      # actions/download-artifact won't look at previous workflow runs but we need to in order to get changelog
+      - name: Download artifacts
+        uses: dawidd6/action-download-artifact@v2
+
+      - name: Draft release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: |
+          version=$(python scripts/update_version.py -g)
+          title="modflowapi $version"
+          notes=$(cat "changelog/CHANGELOG.md" | grep -v "### Version $version")
+          gh release create "$version" \
+            --target main \
+            --title "$title" \
+            --notes "$notes" \
+            --draft \
+            --latest
+
+  publish:
+    name: Publish package
+    # runs only after release is published (manually promoted from draft)
+    if: github.event_name == 'release' && github.repository_owner == 'MODFLOW-USGS'
+    runs-on: ubuntu-22.04
+    permissions:
+      contents: write
+      pull-requests: write
+      id-token: write
+    environment:  # requires a 'release' environment in repo settings
+      name: release
+      url: https://pypi.org/p/modflowapi
+    steps:
+
+      - name: Checkout main branch
+        uses: actions/checkout@v3
+        with:
+          ref: main
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.8
+
+      - name: Install Python dependencies
+        run: |
+          pip install --upgrade pip
+          pip install build twine
+          pip install .
+
+      - name: Build package
+        run: python -m build
+
+      - name: Check package
+        run: twine check --strict dist/*
+
+      - name: Upload package
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/CITATION.cff b/CITATION.cff
@@ -3,7 +3,7 @@ message: If you use this software, please cite both the article from preferred-c
   and the software itself.
 type: software
 title: MODFLOW API
-version: 0.1.0
+version: 0.2.0
 date-released: '2023-04-19'
 abstract: An extension to xmipy for the MODFLOW API.
 repository-artifact: https://pypi.org/project/modflowapi

diff --git a/HISTORY.md b/HISTORY.md
@@ -0,0 +1,67 @@
+# Changelog
+### Version 0.2.0
+
+#### Refactoring
+
+* [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.
+* [refactor(Quickstart.ipynb)](https://github.com/MODFLOW-USGS/modflowapi/commit/3b6675aa687f5af01813abfdb143c7ddd4343646): Fix error in callback_function. Committed by Joshua Larsen on 2023-07-17.
+* [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.
+* [refactor](https://github.com/MODFLOW-USGS/modflowapi/commit/e693282611d5863bafeece362230a4aadd02311f): Update libmf6 path handling (#27). Committed by w-bonelli on 2023-08-03.
+* [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.
+* [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.
+* [refactor(extensions)](https://github.com/MODFLOW-USGS/modflowapi/commit/c97339d06e7386055e486f6354825ec15cea4638): Add support for IDM changes. Committed by Joshua Larsen on 2023-12-21.
+* [refactor(extensions)](https://github.com/MODFLOW-USGS/modflowapi/commit/de0aff9c21d5d925235f306fd2b3d148c3281efa): Add support for IDM changes. Committed by Joshua Larsen on 2023-12-21.
+
+### Version 0.1.0
+
+* Fix typo in README (https://github.com/MODFLOW-USGS/modflowapi/pull/4)
+* modflowapi interface (https://github.com/MODFLOW-USGS/modflowapi/pull/8)
+* update package: manual variable address assembly updated to use xmipy get_variable_addr()
+* update additional manual variable address assembly statements
+* Refactor code and added functionality:
+* add stress_period_start, stress_period_end Callbacks
+* fix ApiModel __repr__
+* added Exchanges, TDIS, ATS, and SLN support
+* added ScalarInput and ScalarPackage support
+* update autotests
+* added parallel testing support through pytest-xdist
+* updated markers and split the extensions tests from the mf6 examples tests
+* added a test for ATS
+* update setup.cfg
+* update ci.yml
+* update(ListInput): add auxvar to stress_period_data when auxiliary variables are used
+* Allow None to be passed to stress_period_data.values to disable stresses for a package
+* updates: ApiModel, ApiSimulation, run_simulation
+* added a `totim` property on `ApiSimulation` and `ApiModel`
+* added docstrings to ApiModel property methods
+* updated termination message in run_simulation
+* added a finalize callback to Callbacks and run_simulation
+* add support for AUXNAME_CST
+* add(Head Monitor Example): Add a head monitor example application
+* ApiModel: adjust X based on nodetouser
+* ApiPackage: enforce lower cased variable names in get_advanced_var
+* ArrayPointer: trap for arrays that are not adjusted by reduced node numbers (ex. idomain)
+* update setup.cfg
+* try reformatting the xmipy installation instructions
+* 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)
+Co-authored-by: scottrp <[email protected]>
+* update(rhs, hcof, AdvancedInput): bug fixes for setting variable values for advanced inputs
+* update rhs and hcof to copy values to pointer instead of overwriting the pointer
+* add a check for AdvancedInput variables that do not have pointer support in xmipy
+* update setting routine for AdvancedInput
+* refactor(EOL): change CRLF to LF line endings for source files (https://github.com/MODFLOW-USGS/modflowapi/pull/12)
+* Use pyproject.toml for project metadata, add citation info (https://github.com/MODFLOW-USGS/modflowapi/pull/11)
+* add(test_rhs_hcof_advanced): add additional test  (https://github.com/MODFLOW-USGS/modflowapi/pull/13)
+* added test for getting and setting rhs, hcof, and advanced variable values
+* update project to use unix line separators
+* use np.testing.assert_allclose() instead of AssertionError
+* Add missing RIV support to modflowapi (https://github.com/MODFLOW-USGS/modflowapi/pull/16)
+* add(test_rhs_hcof_advanced): add additional test
+* added test for getting and setting rhs, hcof, and advanced variable values
+* update project to use unix line separators
+* use np.testing.assert_allclose() instead of AssertionError
+* Add missing riv package to modflowapi
+
+### Version 0.0.1
+
+Initial release.
diff --git a/autotest/__init__.py b/autotest/__init__.py
@@ -1 +1 @@
-# init file for pytest
+# init file for pytest
diff --git a/autotest/conftest.py b/autotest/conftest.py
@@ -31,6 +31,7 @@ def get_mf6_examples_path() -> Path:
     finally:
         __mf6_examples_lock.release()
 
+
 def is_nested(namfile) -> bool:
     p = Path(namfile)
     if not p.is_file() or not p.name.endswith(".nam"):