Merge pull request #2 from NREL/sksundae

sksundae
NREL · Nov 11, 2024 · 5204d3f · 5204d3f
2 parents e23c457 + 47c3457
commit 5204d3f
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diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,5 +1,5 @@
 blank_issues_enabled: true
 contact_links:
   - name: I just have a question...
-    url: https://github.com/ROVI-org/thevenin/discussions
+    url: https://github.com/NREL/thevenin/discussions
     about: Join our discussion instead. Search for existing questions, or ask a new one!
diff --git a/.github/linters/.codespellrc b/.github/linters/.codespellrc
@@ -1,3 +1,3 @@
 [codespell]
-skip = build,docs,images,reports,sphinx,references
+skip = build,docs,images,reports,references
 ignore-words-list = thev
diff --git a/.github/linters/.flake8 b/.github/linters/.flake8
@@ -15,4 +15,4 @@
 
 max-line-length = 80
 extend-ignore = E121,E122,E126,E127,E128,E131,E201,E202,E226,E241,E731
-exclude = build,docs,sphinx,images,reports
+exclude = build,docs,images,reports,references
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -4,7 +4,7 @@ Please include a summary of the change and which issue is fixed. Please also inc
 Fixes # (issue)
 
 ## Type of change
-Please add a line in the relevant section of [CHANGELOG.md](https://github.com/ROVI-org/thevenin/blob/main/CHANGELOG.md) to document the change (include PR #) - note reverse order of PR #s. If necessary, also add to the list of breaking changes.
+Please add a line in the relevant section of [CHANGELOG.md](https://github.com/NREL/thevenin/blob/main/CHANGELOG.md) to document the change (include PR #) - note reverse order of PR #s. If necessary, also add to the list of breaking changes.
 
 - [ ] New feature (non-breaking change which adds functionality)
 - [ ] Optimization (back-end change that improves speed/readability/etc.)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -9,6 +9,7 @@ on:
       - 'CHANGELOG*'
       - 'docs/*'
       - 'images/*'
+      - 'LICENSE'
       - '.github/ISSUE_TEMPLATE/*'
 
   pull_request:
@@ -20,33 +21,38 @@ on:
       - 'CHANGELOG*'
       - 'docs/*'
       - 'images/*'
+      - 'LICENSE'
       - '.github/ISSUE_TEMPLATE/*'
 
 jobs:
   lint:
     name: (Lint ${{ matrix.python-version }}, ${{ matrix.os }})
-
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest']
-        python-version: ['3.12']
+        os: [ubuntu-latest]
+        python-version: ['3.13']
 
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup python
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+
       - name: Spell check
         run: |
           pip install codespell
           codespell --config .github/linters/.codespellrc
+
       - name: Code format
         run: |
           pip install flake8
@@ -55,34 +61,44 @@ jobs:
 
   tests:
     name: (Test ${{ matrix.python-version }}, ${{ matrix.os }})
-
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest', 'windows-latest', 'macos-13', 'macos-latest']
-        python-version: ['3.9', '3.12']
+        os: [macos-13, macos-latest, windows-latest, ubuntu-latest]
+        python-version: ['3.9', '3.13']
 
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v3
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup conda/python
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          activate-environment: 'rovi'
-          python-version: ${{ matrix.python-version }}
-          miniconda-version: 'latest'
           auto-update-conda: true
-      - name: Conda dependencies
-        run: conda install scikits_odes_sundials -c conda-forge
+          miniconda-version: latest
+          python-version: ${{ matrix.python-version }}
+          activate-environment: rovi
+
+      - name: Verify environment
+        run: |
+          conda info
+          conda list
+
       - name: Pip dependencies
         run: pip install .
-      - name: List packages
-        run: conda list
+
+      - name: List info
+        run: |
+          conda info
+          conda list
+
       - name: Pytest
         run: |
           pip install pytest
-          pytest
+          pytest .
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -0,0 +1,210 @@
+name: release
+
+on:
+  push:
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+'
+      - 'v[0-9]+.[0-9]+.[0-9]+a[0-9]+'
+      - 'v[0-9]+.[0-9]+.[0-9]+b[0-9]+'
+      - 'v[0-9]+.[0-9]+.[0-9]+rc[0-9]+'
+
+env:
+  PACKAGE_NAME: '<PACKAGE_NAME>'
+
+jobs:
+  details:
+    runs-on: ubuntu-latest
+    outputs:
+      tag_version: ${{ steps.release.outputs.tag_version }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Extract tag details
+        id: release
+        run: |
+          if [[ "${{ github.ref_type }}" = "tag" ]]; then
+            TAG_VERSION=${GITHUB_REF#refs/tags/v}
+            echo "tag_version=$TAG_VERSION" >> "$GITHUB_OUTPUT"
+            echo "Tag version is $TAG_VERSION"
+          else
+            echo "No tag found"
+            exit 1
+          fi
+
+  check-version:
+    needs: details
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Fetch info from PyPI
+        run: |
+          response=$(curl -s https://pypi.org/pypi/${{ env.PACKAGE_NAME }}/json || echo "{}")
+          latest_pypi_version=$(echo $response | grep -oP '"releases":\{"\K[^"]+' | sort -rV | head -n 1)
+          if [[ -z "$latest_pypi_version" ]]; then
+            echo "Package not found on PyPI."
+            latest_pypi_version="0.0.0"
+          fi
+          echo "Latest version on PyPI: $latest_pypi_version"
+          echo "latest_pypi_version=$latest_pypi_version" >> $GITHUB_ENV
+
+      - name: Compare version against PyPI and exit if not newer
+        run: |
+          TAG_VERSION=${{ needs.details.outputs.tag_version }}
+          PYPI_VERSION=$latest_pypi_version
+          
+          TAG_BASE=${TAG_VERSION%%[a-z]}
+          PYPI_BASE=${PYPI_VERSION%%[a-z]}
+
+          TAG_SUFFIX=${TAG_VERSION#$TAG_BASE}
+          PYPI_SUFFIX=${PYPI_VERSION#$PYPI_BASE}
+
+          suffix_count=0
+
+          [[ -n "$TAG_SUFFIX" ]] && ((suffix_count++))
+          [[ -n "$PYPI_SUFFIX" ]] && ((suffix_count++))
+
+          if [[ "$TAG_VERSION" == "$PYPI_VERSION" ]]; then
+              echo "The tag $TAG_VERSION matches the PyPI version $PYPI_VERSION."
+              exit 1
+          elif [[ "$suffix_count" == 1 && "$TAG_BASE" == "$PYPI_BASE" ]]; then
+              if [[ -n "$PYPI_SUFFIX" ]]; then 
+                  echo "The tag $TAG_VERSION is newer than PyPI $PYPI_VERSION."
+              else
+                  echo "The tag $TAG_VERSION is older than PyPI $PYPI_VERSION."
+                  exit 1
+              fi
+          else
+              newest=$(printf "%s\n%s" "$TAG_VERSION" "$PYPI_VERSION" | sort -V | tail -n 1)
+              if [[ "$TAG_VERSION" == "$newest" ]]; then
+                  echo "The tag $TAG_VERSION is newer than PyPI $PYPI_VERSION."
+              else
+                  echo "The tag $TAG_VERSION is older than PyPI $PYPI_VERSION."
+                  exit 1
+              fi
+          fi
+
+      - name: Verify tag and pyproject.toml versions match
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools numpy cython
+
+          PKG_VERSION=$(python setup.py --version)
+          TAG_VERSION=${{ needs.details.outputs.tag_version }}
+
+          if [[ "$PKG_VERSION" != "$TAG_VERSION" ]]; then
+            echo "Version mismatch: setup.py has $PKG_VERSION, but tag is $TAG_VERSION."
+            exit 1
+          else
+            echo "Package and tag versions match: $PKG_VERSION == $TAG_VERSION."
+          fi
+
+  build:
+    name: (build ubuntu-latest, 3.13)
+    needs: [details, check-version]
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Install build
+        run: pip install build
+
+      - name: Build distributions
+        run: python -m build
+
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: builds
+          path: dist/*
+
+  test:
+    name: (test ${{ matrix.python-version }}, ${{ matrix.os }})
+    needs: build
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [macos-13, macos-latest, windows-latest, ubuntu-latest]
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: dist/
+          pattern: builds*
+          merge-multiple: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install thevenin
+        run: pip install dist/*.whl -v
+
+      - name: Pytest
+        run: |
+          pip install pytest
+          pytest ./tests
+
+  pypi-publish:
+    name: Upload to PyPI
+    needs: test
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: dist/
+          pattern: builds*
+          merge-multiple: true
+
+      - name: Check files
+        run: ls dist
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Install twine
+        run: pip install twine
+
+      - name: Check builds and upload to PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          twine check dist/*
+          twine upload dist/*
diff --git a/.gitignore b/.gitignore
@@ -81,8 +81,7 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/
-sphinx/
+docs/build
 
 # PyBuilder
 .pybuilder/

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,16 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set OS, Python version, and other tools for the build
+build:
+  os: ubuntu-22.04
+  tools:
+    python: latest
+
+# Location of sphinx configuration file
+sphinx:
+  configuration: docs/source/conf.py