Merge pull request #67 from OpenCOMPES/update_python_and_move_package…

…_to_uv

Update python and move package to uv

.cspell/custom-dictionary.txt

@@ -62,9 +62,11 @@ imwrite
 Interp
 ipykernel
 ipympl
+ipynb
 ipython
 ipywidgets
 irfft
+isin
 kernelspec
 kwds
 labview
@@ -104,6 +106,7 @@ pcolormesh
 Phoibos
 polyfit
 polyval
+pydata
 pyenv
 pygments
 pynxtools
@@ -132,6 +135,7 @@ typehints
 TZCYXS
 undoc
 venv
+viewcode
 vline
 vmax
 vmin

.github/workflows/documentation.yml

@@ -4,53 +4,46 @@ on:
   push:
     branches: [ main ]
     paths:
-      - specsanalyzer/**/*
-      - specsscan/**/*
+      - src/specsanalyzer/**/*
+      - src/specsscan/**/*
       - tutorial/**
       - .github/workflows/documentation.yml
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
-
-  # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
-permissions:
-  contents: read
-  pages: write
-  id-token: write
-
-# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
-# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
-concurrency:
-  group: "pages"
-  cancel-in-progress: false
+env:
+  UV_SYSTEM_PYTHON: true
 
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      #  Check out repo and set up Python
-      - name: Check out the repository
-        uses: actions/checkout@v4
+      # Check out repo and set up Python
+      - uses: actions/checkout@v4
         with:
-          lfs: true
+          fetch-depth: 0
 
       # see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions and https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key
-      - name: checkout test data
+      - name: Fetch test data
         run: |
           eval `ssh-agent -s`
           ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}'
           git submodule sync --recursive
-          git submodule update --init --recursive
+          git submodule update --init --recursive --jobs=4
 
-      # Use cached python and dependencies, install poetry
-      - name: "Setup Python, Poetry and Dependencies"
-        uses: packetcoders/action-setup-cache-python-poetry@main
+      # Setup python
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
-          poetry-version: 1.8.5
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
 
-      - name: Install notebook dependencies
-        run: poetry install -E notebook --with docs
+      - name: Install package
+        run: |
+          uv pip install ".[docs,notebook]"
 
       - name: Install pandoc
         run: |
@@ -61,37 +54,80 @@ jobs:
       - name: copy tutorial files to docs
         run: |
           cp -r $GITHUB_WORKSPACE/tutorial $GITHUB_WORKSPACE/docs/
-          cp -r $GITHUB_WORKSPACE/specsscan/config $GITHUB_WORKSPACE/docs/specsscan/
           mkdir $GITHUB_WORKSPACE/docs/tests
           cp -r $GITHUB_WORKSPACE/tests/data $GITHUB_WORKSPACE/docs/tests/
-
-      # To be included later
-      # - name: Cache docs build
-      #   id: cache-docs
-      #   uses: actions/cache@v3
-      #   with:
-      #     path: $GITHUB_WORKSPACE/_build
-      #     key: ${{ runner.os }}-docs
+          mkdir -p $GITHUB_WORKSPACE/docs/src/specsscan
+          cp -r $GITHUB_WORKSPACE/src/specsscan/config $GITHUB_WORKSPACE/docs/src/specsscan
 
       - name: build Sphinx docs
-        run: poetry run sphinx-build -b html $GITHUB_WORKSPACE/docs $GITHUB_WORKSPACE/_build
-
-      - name: Setup Pages
-        uses: actions/configure-pages@v3
+        run: sphinx-build -b html $GITHUB_WORKSPACE/docs $GITHUB_WORKSPACE/_build
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
-          path: '_build'
+          name: sphinx-docs
+          path: _build
 
-  # Deployment job
-  deploy:
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
+  # this job pushes the built documentation to the docs repository
+  push:
     runs-on: ubuntu-latest
     needs: build
     steps:
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v2
+      - name: Checkout docs repo
+        uses: actions/checkout@v2
+        with:
+          repository: ${{ github.repository_owner }}/docs
+          token: ${{ secrets.GITHUB_TOKEN }}
+          path: 'docs-repo'
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Setup SSH
+        uses: webfactory/[email protected]
+        with:
+          ssh-private-key: ${{ secrets.SSH_DOCS_DEPLOY_KEY }}
+
+      - name: Download artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: sphinx-docs
+          path: sphinx-docs
+
+      - name: Determine version folder
+        id: version-folder
+        run: |
+          if [[ $GITHUB_REF == refs/tags/* ]]; then
+            VERSION=${GITHUB_REF#refs/tags/}
+            echo "folder=specsanalyzer/$VERSION" >> $GITHUB_OUTPUT
+            rm docs-repo/specsanalyzer/stable
+            ln -s -r docs-repo/specsanalyzer/$VERSION docs-repo/specsanalyzer/stable
+          elif [[ $GITHUB_REF == refs/heads/main ]]; then
+            echo "folder=specsanalyzer/latest" >> $GITHUB_OUTPUT
+          else
+            echo "folder=specsanalyzer/develop" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Update switcher.json
+        run: |
+          VERSION=`grep "<title>" sphinx-docs/index.html | sed -n 's/.*specsanalyzer \(.*\) documentation.*/\1/p'`
+          echo "python docs-repo/specsanalyzer/update_switcher.py docs-repo/specsanalyzer/switcher.json $GITHUB_REF $VERSION"
+          python docs-repo/specsanalyzer/update_switcher.py docs-repo/specsanalyzer/switcher.json $GITHUB_REF $VERSION
+
+      - name: Copy documentation to the right version folder
+        run: |
+          mkdir -p docs-repo/${{ steps.version-folder.outputs.folder }}
+          cp -r sphinx-docs/* docs-repo/${{ steps.version-folder.outputs.folder }}
+          rm -rf docs-repo/${{ steps.version-folder.outputs.folder }}/.doctrees
+          rm -rf docs-repo/${{ steps.version-folder.outputs.folder }}/tutorial/*.ipynb
+
+      - name: Push changes
+        run: |
+          cd docs-repo
+          git config user.name github-actions
+          git config user.email [email protected]
+          git add .
+          git commit -m "Update documentation"
+          git push

.github/workflows/linting.yml

@@ -6,42 +6,49 @@ on:
     paths-ignore:
       pyproject.toml
 
+env:
+  UV_SYSTEM_PYTHON: true
+
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
       # Check out repo and set up Python
-      - uses: actions/checkout@v3
-        with:
-          lfs: true
+      - uses: actions/checkout@v4
 
 # see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions and https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key
-      - name: checkout test data
+      - name: Fetch test data
         run: |
           eval `ssh-agent -s`
           ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}'
           git submodule sync --recursive
-          git submodule update --init --recursive
+          git submodule update --init --recursive --jobs=4
 
-      # Use cached python and dependencies, install poetry
-      - name: "Setup Python, Poetry and Dependencies"
-        uses: packetcoders/action-setup-cache-python-poetry@main
+      # Setup python
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
-          poetry-version: 1.8.5
+          python-version: "3.10"
 
+      - name: Install dependencies
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+
+      - name: Install package
+        run: |
+          uv pip install ".[dev]"
       # Linting steps, execute all linters even if one fails
       - name: ruff
         run:
-          poetry run ruff specsanalyzer specsscan tests
+          ruff check src/specsanalyzer src/specsscan tests
       - name: ruff formatting
         if: ${{ always() }}
         run:
-          poetry run ruff format --check specsanalyzer specsscan tests
+          ruff format --check src/specsanalyzer src/specsscan tests
       - name: mypy
         if: ${{ always() }}
         run:
-          poetry run mypy specsanalyzer specsscan tests
+          mypy src/specsanalyzer src/specsscan tests
       - name: spellcheck
         if: ${{ always() }}
         uses: streetsidesoftware/cspell-action@v6