Ci (#260)

* CI

* CI

.github/workflows/ci.yml

@@ -11,41 +11,80 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-permissions:
-  packages: write
-
 env:
-  NPROC: '2'                      # Number of Julia processes to run the notebooks
-  IMAGE: 'app:test'
+  NPROC: '2' # Number of Julia processes to run the notebooks
+  PYTHON_VER: '3.11'
+  JULIA_CPU_TARGET: 'generic;haswell,clone_all'
+  JULIA_NUM_THREADS: 'auto'
+  JULIA_CONDAPKG_BACKEND: 'Null'
+  GKSwstype: '100'
 
 jobs:
-  CI:
+  execute:
+    container:
+      image: julia:1.9.3
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-      - name: Build and cache Docker container
-        uses: docker/build-push-action@v5
+      - name: Setup Python
+        uses: actions/setup-python@v4
         with:
-          context: .
-          file: '.github/Dockerfile'
-          tags: ${{ env.IMAGE }}
-          load: true
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
+          python-version: ${{ env.PYTHON_VER }}
+      - name: Install Python deps
+        run: python -m pip install --no-cache-dir -r requirements.txt
+      - name: Cache Julia deps
+        uses: actions/cache@v3
+        with:
+          path: |
+            ~/.julia/artifacts
+            ~/.julia/compiled
+            ~/.julia/packages
+          key: ${{ runner.os }}-juliacontainer-${{ hashFiles('Manifest.toml')}}
+          restore-keys: |
+            ${{ runner.os }}-juliacontainer-
+      - name: Install Julia packages
+        env:
+          PYTHON: ${{ env.pythonLocation }}/python
+          JULIA_PYTHONCALL_EXE: ${{ env.pythonLocation }}/python
+        run: julia --color=yes setup.jl
       - name: Build notebooks with ${{ env.NPROC }} processes
-        run: docker run --rm -w /tmp -v ${{ github.workspace }}:/tmp -e JULIA_PROJECT=@. ${{ env.IMAGE }} julia --color=yes -p ${{ env.NPROC }} literate.jl
-      - name: Take ownership
-        run: sudo chown -R $USER docs/
+        env:
+          JULIA_PROJECT: '@.'
+        run: julia --color=yes -p ${{ env.NPROC }} literate.jl
+      - name: Upload notebooks
+        uses: actions/upload-artifact@v3
+        with:
+          name: notebooks
+          path: docs
+          retention-days: 1
+
+  jupyter-book:
+    needs: execute
+    runs-on: ubuntu-latest
+    # store success output flag for the ci job
+    outputs:
+      success: ${{ steps.setoutput.outputs.success }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Download notebooks
+        uses: actions/download-artifact@v3
+        with:
+          name: notebooks
+          path: out/
+      - name: Display structure of downloaded files
+        run: ls -R
+        working-directory: out
+      - name: Copy back built notebooks
+        run: cp --verbose -rf out/* docs/
       - name: Setup micromamba
         uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: jupyterbook.yml
           init-shell: bash
           cache-environment: true
-          post-cleanup: 'all'
+          post-cleanup: all
       - name: Build website
         shell: micromamba-shell {0}
         run: jupyter-book build docs/
@@ -54,10 +93,33 @@ jobs:
         uses: actions/upload-pages-artifact@v2
         with:
           path: docs/_build/html
+      - name: Set output flag
+        id: setoutput
+        run: echo "success=true" >> $GITHUB_OUTPUT
+
+  # CI conclusion for GitHub status check
+  # https://brunoscheufler.com/blog/2022-04-09-the-required-github-status-check-that-wasnt
+  CI:
+    needs: jupyter-book
+    if: always()
+    runs-on: ubuntu-latest
+    steps:
+      # pass step only when output of previous jupyter-book job is set
+      # in case at least one of the execution fails, jupyter-book is skipped
+      # and the output will not be set, which will then cause the ci job to fail
+      - run: |
+          passed="${{ needs.jupyter-book.outputs.success }}"
+          if [[ $passed == "true" ]]; then
+            echo "Tests passed"
+            exit 0
+          else
+            echo "Tests failed"
+            exit 1
+          fi
 
   deploy:
     name: Deploy to GitHub pages
-    needs: CI
+    needs: jupyter-book
     if: ${{ github.ref == 'refs/heads/main'}}
     # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
     permissions:

.github/workflows/update-manifest.yml

@@ -15,40 +15,45 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  DFILE: '.github/Dockerfile'
-  IMAGE_NAME: 'app:test'
+  PYTHON_VER: '3.11'
+  APP_ID: '189113' # https://github.com/apps/wen-wei-s-pr-bot
+  JULIA_CPU_TARGET: 'generic;haswell,clone_all'
+  JULIA_NUM_THREADS: 'auto'
+  JULIA_CONDAPKG_BACKEND: 'Null'
+  JULIA_PKG_PRECOMPILE_AUTO: '0'
+  JULIA_PROJECT: '@.'
 
 jobs:
   update-manifest:
     permissions:
       contents: write
       pull-requests: write
     runs-on: ubuntu-latest
+    container:
+      image: julia:1.9.3
     steps:
+      - name: Install Git
+        run: apt update && apt install -y git
+      - name: Set safe directory
+        run: git config --global --add safe.directory '*'
       - name: Checkout
         uses: actions/checkout@v4
-      - name: Build and cache Docker container
-        uses: docker/build-push-action@v5
+      - name: Setup Python
+        uses: actions/setup-python@v4
         with:
-          target: base
-          context: .
-          file: ${{ env.DFILE }}
-          tags: ${{ env.IMAGE_NAME }}
-          load: true
+          python-version: ${{ env.PYTHON_VER }}
       - name: Update Julia dependencies
-        run: >
-          docker run
-          --workdir=/tmp -v ${{ github.workspace }}:/tmp
-          -e JULIA_PKG_PRECOMPILE_AUTO=0
-          ${{ env.IMAGE_NAME }}
-          julia --color=yes --project=@. -e "import Pkg; Pkg.update()"
+        env:
+          PYTHON: ${{ env.pythonLocation }}/python
+          JULIA_PYTHONCALL_EXE: ${{ env.pythonLocation }}/python
+        run: julia --color=yes -e "import Pkg; Pkg.update()"
       # Authenticate with a custom GitHub APP
       # https://github.com/peter-evans/create-pull-request/blob/main/docs/concepts-guidelines.md#authenticating-with-github-app-generated-tokens
       - name: Generate token for PR
         uses: tibdex/github-app-token@v2
         id: generate-token
         with:
-          app_id: ${{ secrets.APP_ID }} # https://github.com/apps/wen-wei-s-pr-bot
+          app_id: ${{ env.APP_ID }}
           private_key: ${{ secrets.APP_PRIVATE_KEY }}
       - name: Create Pull Request
         id: cpr