baremetal (#271)

.github/dependabot.yml

@@ -1,23 +1,9 @@
 version: 2
 updates:
-  - package-ecosystem: pip
-    directory: "/"
-    open-pull-requests-limit: 1
-    schedule:
-      interval: daily
-    labels:
-      - automerge
   - package-ecosystem: github-actions
     directory: "/"
     open-pull-requests-limit: 1
     schedule:
       interval: daily
     labels:
       - automerge
-  - package-ecosystem: docker
-    directory: "/"
-    open-pull-requests-limit: 1
-    schedule:
-      interval: daily
-    labels:
-      - automerge

.github/workflows/ci.yml

@@ -13,108 +13,70 @@ concurrency:
 
 env:
   NPROC: '2' # Number of Julia processes to run the notebooks
+  JULIA_CPU_TARGET: 'generic;haswell,clone_all'
+  JULIA_NUM_THREADS: 'auto'
+  JULIA_CONDAPKG_BACKEND: 'Current'
+  JULIA_CI: 'true'
+  GKSwstype: '100'
+  JULIA_CACHE_NUM: '1'
 
 jobs:
-  setup:
-    permissions:
-      packages: write
+  CI:
     runs-on: ubuntu-latest
-    outputs:
-      hash: ${{ steps.hash.outputs.id }}
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
-    - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v3
-    - name: Login to Docker Hub
-      uses: docker/login-action@v3
+    - name: Setup micromamba
+      uses: mamba-org/setup-micromamba@v1
       with:
-        registry: ghcr.io
-        username: ${{ github.repository_owner	}}
-        password: ${{ github.token	}}
-    - name: Get docker image hash
-      id: hash
-      run: echo "id=${{ hashFiles('requirements.txt', 'Project.toml', 'Manifest.toml', 'src/**', 'env.Dockerfile') }}" >> "$GITHUB_OUTPUT"
-    - name: Build and cache Docker container
-      uses: docker/build-push-action@v5
+        environment-file: environment.yml
+        cache-environment: true
+        post-cleanup: all
+    - name: Read Julia version
+      uses: SebRollen/[email protected]
+      id: read_toml
       with:
-        context: .
-        file: 'env.Dockerfile'
-        tags: ghcr.io/${{ github.repository }}:${{ steps.hash.outputs.id }}
-        push: true
-        cache-from: type=registry,ref=ghcr.io/${{ github.repository }}:${{ steps.hash.outputs.id }}
-        cache-to: type=inline
-
-  execute:
-    needs: setup
-    runs-on: ubuntu-latest
-    container:
-      image: ghcr.io/${{ github.repository }}:${{ needs.setup.outputs.hash }}
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-      - name: Run program
-        env:
-          JULIA_PROJECT: '@.'
-        run: julia --color=yes -p ${{ env.NPROC }} literate.jl
-      - name: Upload Results
-        uses: actions/upload-artifact@v3
-        with:
-          name: notebooks
-          path: docs/
-          retention-days: 1
-
-  render:
-    needs: execute
-    runs-on: ubuntu-latest
-    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
-      - name: Build website
-        shell: micromamba-shell {0}
-        run: jupyter-book build docs/
-      - name: Upload pages artifact
-        if: ${{ github.ref == 'refs/heads/main' }}
-        uses: actions/upload-pages-artifact@v2
-        with:
-          path: docs/_build/html
-
-  # CI conclusion for GitHub status check
-  # Adaped from https://brunoscheufler.com/blog/2022-04-09-the-required-github-status-check-that-wasnt
-  CI:
-    needs: render
-    if: always()
-    runs-on: ubuntu-latest
-    steps:
-      - run: |
-          if [[ ${{ needs.render.result }} == "success" ]]; then
-            echo "Tests passed"
-            exit 0
-          else
-            echo "Tests failed"
-            exit 1
-          fi
+        file: 'Manifest.toml'
+        field: 'julia_version'
+    - name: Install Julia using jill.sh
+      run: |
+        wget -O /tmp/jill.sh https://raw.githubusercontent.com/abelsiqueira/jill/main/jill.sh
+        bash /tmp/jill.sh --version ${{ steps.read_toml.outputs.value }} -y
+        echo "$HOME/.local/bin" >> $GITHUB_PATH
+    - name: Cache Julia deps
+      uses: actions/cache@v3
+      with:
+        path: |
+          ~/.julia/artifacts
+          ~/.julia/compiled
+          ~/.julia/packages
+          ~/.julia/environments
+          ~/.julia/scratchspaces
+        key: ${{ runner.os }}-jill-${{ env.JULIA_CACHE_NUM }}-${{ hashFiles('src/**','Project.toml', 'Manifest.toml')}}
+        restore-keys: |
+          ${{ runner.os }}-jill-${{ env.JULIA_CACHE_NUM }}-
+    - name: Install Julia deps
+      shell: micromamba-shell {0}
+      run: |
+        julia --color=yes -e 'using Pkg; Pkg.add(["PrettyTables", "Literate"])'
+        julia --project=@. --color=yes -e 'using Pkg, Dates; Pkg.instantiate(); Pkg.precompile(); Pkg.gc(collect_delay=Day(1))'
+    - name: Run program
+      shell: micromamba-shell {0}
+      env:
+        JULIA_PROJECT: '@.'
+      run: julia --color=yes -p ${{ env.NPROC }} literate.jl
+    - name: Build website
+      shell: micromamba-shell {0}
+      run: jupyter-book build docs/
+    - name: Upload pages artifact
+      if: ${{ github.ref == 'refs/heads/main' }}
+      uses: actions/upload-pages-artifact@v2
+      with:
+        path: docs/_build/html
 
   deploy:
     name: Deploy to GitHub pages
-    needs: render
+    needs: CI
     if: ${{ github.ref == 'refs/heads/main'}}
     # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
     permissions:
@@ -125,6 +87,6 @@ jobs:
       url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
     steps:
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v2
+    - name: Deploy to GitHub Pages
+      id: deployment
+      uses: actions/deploy-pages@v2

.github/workflows/update-manifest.yml

@@ -16,7 +16,6 @@ concurrency:
 
 env:
   APP_ID: '189113' # https://github.com/apps/wen-wei-s-pr-bot
-  IMG_NAME: 'app:test'
 
 jobs:
   update-manifest:
@@ -27,19 +26,12 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-      - name: Build and load docker image
-        uses: docker/build-push-action@v5
-        with:
-          context: .
-          file: 'env.Dockerfile'
-          tags: ${{ env.IMG_NAME }}
-          load: true
-          target: base
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v1
       - name: Update Julia dependencies
-        run: >
-          docker run --rm -e JULIA_PKG_PRECOMPILE_AUTO=0
-          ${{ env.IMG_NAME }}
-          julia --color=yes --project=@. -e 'import Pkg; Pkg.update()'
+        env:
+          JULIA_PKG_PRECOMPILE_AUTO: '0'
+        run: julia --color=yes --project=@. -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

environment.yml

@@ -0,0 +1,10 @@
+name: ci
+
+dependencies:
+  - python>=3.11
+  # Jupyter Book
+  - jupyter-book
+  - docutils>=0.17.1,<0.18|>=0.20
+  # PythonPlot
+  # - matplotlib
+  # - libstdcxx-ng<13.0