Merge pull request #79 from biomarkersParkinson/mixed-improvements

Mixed improvements

.github/workflows/build-and-test.yml

@@ -34,6 +34,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     # Get the version from pyproject.toml
+    # This will be used to tag the release in the publishing workflow
     - name: Install toml package
       run: pip install toml
     - name: Get version from pyproject.toml
@@ -43,22 +44,38 @@ jobs:
         echo Version: $VERSION
         echo "version=$VERSION" >> $GITHUB_OUTPUT
 
+    # Installation
     - name: Install dependencies
       run: |
         python -m pip install poetry
         poetry install
-    - name: Build the docs  # just to see whether the build passes
-      run: |
-        poetry run make html --directory docs
+
+    # Testing and checking
     - name: Test with pytest
       run: |
         poetry run pytest
-    # TODO: run pytype here?
+    - name: Type check
+      run: |
+        poetry run pytype .
+
+    # Build the package
     - name: Build the package
       run: |
         poetry build
     - name: Archive build artifacts
       uses: actions/upload-artifact@v4
+      if: github.ref == 'refs/heads/release'
       with:
         name: build-artifacts
         path: dist/
+
+    # Build the docs
+    - name: Build the docs
+      run: |
+        poetry run make html --directory docs
+    - name: Archive documentation
+      uses: actions/upload-artifact@v4
+      if: github.ref == 'refs/heads/release'
+      with:
+        name: docs-html
+        path: docs/_build/html/

.github/workflows/publish.yml

@@ -0,0 +1,115 @@
+# Sources:
+# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/#workflow-definition
+# https://github.com/marketplace/actions/pypi-publish
+
+name: Publish package and docs
+
+on:
+  push:
+    branches: [ release ]
+
+jobs:
+  build-and-test:
+    uses: ./.github/workflows/build-and-test.yml
+
+  create-tag:
+    name: Create Git Tag
+    needs: build-and-test
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Create Git Tag
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        VERSION: ${{ needs.build-and-test.outputs.version }}
+      run: |
+        git config --global user.name 'github-actions'
+        git config --global user.email '[email protected]'
+        git tag "v${VERSION}"
+        git push origin "v${VERSION}"
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: [build-and-test, create-tag]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/tsdf
+    permissions:
+      id-token: write  # mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: build-artifacts
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+
+  github-release:
+    name: Sign distribution and create GitHub release
+    needs: [build-and-test, create-tag]
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # mandatory for making GitHub Releases
+      id-token: write  # mandatory for sigstore
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: build-artifacts
+        path: dist/
+
+    - name: Sign the dists with Sigstore
+      uses: sigstore/[email protected]
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+        VERSION: ${{ needs.build-and-test.outputs.version }}
+      run: >-
+        gh release create
+        "v${VERSION}"
+        --repo '${{ github.repository }}'
+        --notes ""
+
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+        VERSION: ${{ needs.build-and-test.outputs.version }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        "v${VERSION}" dist/**
+        --repo '${{ github.repository }}'
+
+
+  publish-docs:
+    name: Publish documentation
+    needs: build-and-test
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Download the documentation
+        uses: actions/download-artifact@v4
+        with:
+          name: docs-html
+          path: docs/
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/

docs/basic_reading_and_writing_pandas.ipynb

@@ -154,7 +154,7 @@
     "metadata_samples = metadata_dict[\"ppp_format_samples.bin\"]\n",
     "\n",
     "# Load the data\n",
-    "df = tsdf.load_binaries_to_dataframe([metadata_time, metadata_samples], tsdf.constants.ConcatenationType.columns)\n",
+    "df = tsdf.load_dataframe_from_binaries([metadata_time, metadata_samples], tsdf.constants.ConcatenationType.columns)\n",
     "\n",
     "# Print some info\n",
     "print(f\"Data shape:\\t {df.shape}\")\n",