Merge branch 'main' into 130-create-musicbox-configuration-for-ts1cap…

…ram-24-reduced-mechanism

.github/workflows/CI_Tests.yml

@@ -0,0 +1,43 @@
+name: CI Tests
+
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build:
+    continue-on-error: true
+    strategy:
+        matrix:
+          os: [ubuntu-latest, macos-latest, windows-latest]
+
+    runs-on: ${{ matrix.os }}
+    steps:
+
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+        cache: 'pip' 
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+
+    - name: Install this package
+      run: pip install -e .
+
+    - name: Run pytest
+      run: cd tests && pytest
+
+    - name: Run the smoke tests
+      run: |
+        music_box configFile=tests/configs/analytical_config/my_config.json outputDir=tests/configs/analytical_config
+

.github/workflows/gh_pages.yml

@@ -0,0 +1,132 @@
+# Build and deploy documentation to GitHub Pages
+name: GitHub Pages
+
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+env:
+  DEFAULT_BRANCH: "release"
+
+jobs:
+  build-and-deploy:
+    name: Build and deploy to gh-pages
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          lfs: true
+
+      - name: Debugging information
+        run: |
+          echo "github.ref:" ${{github.ref}}
+          echo "github.event_name:" ${{github.event_name}}
+          echo "github.head_ref:" ${{github.head_ref}}
+          echo "github.base_ref:" ${{github.base_ref}}
+          set -x
+          git rev-parse --abbrev-ref HEAD
+          git branch
+          git branch -a
+          git remote -v
+          python -V
+          pip list --not-required
+          pip list
+
+      # Clone and set up the old gh-pages branch
+      - name: Clone old gh-pages
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          set -x
+          git fetch
+          ( git branch gh-pages remotes/origin/gh-pages && git clone . --branch=gh-pages _gh-pages/ ) || mkdir _gh-pages
+          rm -rf _gh-pages/.git/
+          mkdir -p _gh-pages/branch/
+
+      # If a push and default branch, copy build to _gh-pages/ as the "main"
+      # deployment.
+      - name: Build and copy documentation (default branch)
+        if: |
+          contains(github.event_name, 'push') &&
+          contains(github.ref, env.DEFAULT_BRANCH)
+        run: |
+          set -x
+          mkdir -p _build/html/versions
+
+          # create two copies of the documentation
+          # 1. the frozen version, represented as vX.X in the version switcher
+          docker build -t music_box -f docker/Dockerfile.docs .
+          id=$(docker create music_box)
+          docker cp $id:/build/docs/build/html tmpdocs
+          docker rm -v $id
+          version=$(sed -nr "s/^release = f'v(.+)\{suffix\}'.*$/\1/p" docs/source/conf.py)
+          mv tmpdocs _build/html/versions/${version}
+
+          # 2. stable, represented as vX.X (stable) in the version switcher
+          # edit conf.py to produce a version string that looks like vX.X (stable)
+          docker build -t music_box -f docker/Dockerfile.docs --build-arg SUFFIX=" (stable)" .
+          id=$(docker create music_box)
+          docker cp $id:/build/docs/build/html tmpdocs
+          docker rm -v $id
+          mv tmpdocs _build/html/versions/stable
+          # Delete everything under _gh-pages/ that is from the
+          # primary branch deployment.  Excludes the other branches
+          # _gh-pages/branch-* paths, and not including
+          # _gh-pages itself.
+          find _gh-pages/ -mindepth 1 ! -path '_gh-pages/branch*' ! -path '_gh-pages/versions*' -delete
+          rsync -a _build/html/versions/stable/* _gh-pages/
+          mkdir -p _gh-pages/versions
+          rsync -a _build/html/versions/* _gh-pages/versions
+          # mv docs/switcher.json _gh-pages
+
+      # If a push and not on default branch, then copy the build to
+      # _gh-pages/branch/$brname (transforming '/' into '--')
+      - name: Build and copy documentation (branch)
+        if: |
+          contains(github.event_name, 'push') &&
+          !contains(github.ref, env.DEFAULT_BRANCH)
+        run: |
+          set -x
+          docker build -t music_box -f docker/Dockerfile.docs .
+          id=$(docker create music_box)
+          docker cp $id:/music-box/docs/build/html tmpdocs
+          docker rm -v $id
+          brname="${{github.ref}}"
+          brname="${brname##refs/heads/}"
+          brdir=${brname//\//--}   # replace '/' with '--'
+          rm -rf   _gh-pages/branch/${brdir}
+          rsync -a tmpdocs/ _gh-pages/branch/${brdir}
+
+      # Go through each branch in _gh-pages/branch/, if it's not a
+      # ref, then delete it.
+      - name: Delete old feature branches
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          set -x
+          for brdir in `ls _gh-pages/branch/` ; do
+              brname=${brdir//--/\/}   # replace '--' with '/'
+              if ! git show-ref remotes/origin/$brname ; then
+                  echo "Removing $brdir"
+                  rm -r _gh-pages/branch/$brdir/
+              fi
+          done
+
+      # Add the .nojekyll file
+      - name: nojekyll
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          touch _gh-pages/.nojekyll
+
+      # Deploy
+      # https://github.com/peaceiris/actions-gh-pages
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _gh-pages/
+          force_orphan: true

.github/workflows/pep8_autoformat.yml

@@ -0,0 +1,45 @@
+name: Pep8
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  autopep8:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: autopep8
+        uses: peter-evans/autopep8@v2
+        with:
+          args: --recursive --in-place --aggressive --aggressive .
+
+      - name: Check for changes
+        id: check-changes
+        run: git diff --exit-code
+        continue-on-error: true
+
+      - name: Commit and push changes
+        # a failue of this step means changes were detected
+        if: steps.check-changes.outcome != 'success'
+        run: |
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "[email protected]"
+          git commit -am "Auto-format code using Clang-Format" || echo "No changes to commit"
+
+      - name: Push changes to main-autopep8 branch
+        if: steps.check-changes.outcome != 'success'
+        run: git push origin HEAD:main-autopep8
+
+      - name: Create Pull Request
+        if: steps.check-changes.outcome != 'success'
+        uses: peter-evans/create-pull-request@v6
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: "Auto-format code using autopep8"
+          title: "Auto-format code by autopep8"
+          body: "This is an auto-generated PR with fixes by autopep8."
+          branch: main-autopep8

.github/workflows/publish-package.yml

@@ -1,46 +1,49 @@
-name: Create and publish a Docker image
+name: Publish Python Package
 
 on:
-  push:
-    branches: ['release']
-    tags:
-      - '*'
-
-env:
-  REGISTRY: ghcr.io
-  IMAGE_NAME: ${{ github.repository }}
+  workflow_dispatch:
+  release:
+    types:
+      - published
 
 jobs:
-  build-and-push-image:
+  build_sdist:
+    name: Build
     runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Build SDist and Wheel
+      run: pipx run build --sdist --wheel
+
+    - name: Check metadata
+      run: pipx run twine check dist/*
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: cibw-sdist
+        path: dist/*
+
+  upload_all:
+    name: Upload release
+    needs: [build_sdist]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/acom_music_box
     permissions:
-      contents: read
-      packages: write
+      id-token: write
 
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v2
-        with:
-          submodules: recursive
-
-      - name: Log in to the Container repository
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
-        with:
-          registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
-        with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-
-      - name: Build and push Docker image
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
-        with:
-          context: .
-          platforms: linux/amd64,linux/arm64,linux/arm
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+
+    - uses: actions/download-artifact@v4
+      with:
+        pattern: cibw-*
+        path: dist
+        merge-multiple: true
+
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -5,3 +5,6 @@ CMakeFiles/
 doc/html/
 doc/latex/
 data/
+__pycache__/
+*.pyc
+dist