CI (#299)

* CI * workaround for steady state * fix
ntumitolab · Jan 25, 2024 · bf2999e · bf2999e
1 parent b9a8676
commit bf2999e
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diff --git a/.github/read_toml.py b/.github/read_toml.py
@@ -0,0 +1,3 @@
+import tomllib
+with open("Manifest.toml", "rb") as f:
+    print(tomllib.load(f)["julia_version"])
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,101 +1,92 @@
-name: Build notebooks and publish
-
-on:
-  workflow_dispatch:
-  push:
-    branches: [main]
-  pull_request:
-    branches: [main]
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
-env:
-  NPROC: '2' # Number of Julia processes to run the notebooks
-  CACHE_NUM: '1'
-  PY_VER: '3.12'
-  JULIA_CONDAPKG_BACKEND: 'Null'
-  JULIA_CI: 'true'
-  JULIA_NUM_THREADS: '2'
-
-jobs:
-  CI:
-    runs-on: ubuntu-latest
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-    - name: Setup Python
-      uses: actions/setup-python@v5
-      id: cp
-      with:
-        python-version: ${{ env.PY_VER }}
-    - name: Cache pip
-      uses: actions/cache@v4
-      id: cache-pip
-      with:
-        path: ${{ env.pythonLocation }}
-        key: ${{ runner.os }}-pip-${{ steps.cp.outputs.python-version }}-${{ hashFiles('requirements.txt') }}
-    - name: Install python packages
-      if: ${{ steps.cache-pip.outputs.cache-hit != 'true' }}
-      run: pip install -r requirements.txt
-    - name: Read Julia version
-      uses: SebRollen/[email protected]
-      id: read_toml
-      with:
-        file: 'Manifest.toml'
-        field: 'julia_version'
-    - name: Setup Julia
-      uses: julia-actions/setup-julia@v1
-      with:
-        version: ${{ steps.read_toml.outputs.value }}
-        show-versioninfo: 'true'
-    - name: Cache Julia packages
-      uses: actions/cache/restore@v4
-      id: cache-julia
-      with:
-        path: |
-          ~/.julia
-          !~/.julia/registries
-        key: ${{ runner.os }}-julia-${{ steps.read_toml.outputs.value }}-${{ env.CACHE_NUM }}-${{ hashFiles('src/**','Project.toml', 'Manifest.toml')}}
-        restore-keys: |
-          ${{ runner.os }}-julia-${{ steps.read_toml.outputs.value }}-${{ env.CACHE_NUM }}-
-    - name: Install Julia packages
-      if: ${{ steps.cache-julia.outputs.cache-hit != 'true' }}
-      run: |
-        julia --project=@. --color=yes -e 'using Pkg, Dates; Pkg.instantiate(); Pkg.precompile(); Pkg.gc(collect_delay=Day(0))'
-    - name: Save Julia packages
-      uses: actions/cache/save@v4
-      if: ${{ steps.cache-julia.outputs.cache-hit != 'true' }}
-      with:
-        path: |
-          ~/.julia
-          !~/.julia/registries
-        key: ${{ steps.cache-julia.outputs.cache-primary-key }}
-    - name: Run program
-      run: julia --project=@. --color=yes -p ${{ env.NPROC }} literate.jl
-    - name: Build website
-      run: jupyter-book build docs/
-    - name: Upload page artifact
-      if: ${{ github.ref == 'refs/heads/main' }}
-      uses: actions/upload-pages-artifact@v3
-      with:
-        path: docs/_build/html
-
-  # Deploy pages
-  deploy:
-    needs: CI
-    if: ${{ github.ref == 'refs/heads/main' }}
-    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
-    permissions:
-      pages: write # to deploy to Pages
-      id-token: write # to verify the deployment originates from an appropriate source
-      actions: read   # to download an artifact uploaded by `actions/upload-pages-artifact@v3`
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    runs-on: ubuntu-latest
-    steps:
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v4
+name: Build notebooks and publish
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  NPROC: '2' # Number of Julia processes to run the notebooks
+  CACHE_NUM: '1'
+  PY_VER: '3.12'
+  JULIA_CONDAPKG_BACKEND: 'Null'
+  JULIA_CI: 'true'
+  JULIA_NUM_THREADS: '2'
+
+jobs:
+  CI:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      id: cp
+      with:
+        python-version: ${{ env.PY_VER }}
+        cache: 'pip'
+    - name: Install python packages
+      run: pip install -r requirements.txt
+    - name: Read Julia version
+      id: read_toml
+      run: echo "value=$(python .github/read_toml.py)" >> "$GITHUB_OUTPUT"
+    - name: Setup Julia
+      uses: julia-actions/setup-julia@v1
+      with:
+        version: ${{ steps.read_toml.outputs.value }}
+    - name: Cache Julia packages
+      uses: actions/cache@v4
+      id: cache-julia
+      with:
+        save-always: 'true'
+        path: |
+          ~/.julia
+          !~/.julia/registries
+        key: ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-${{ hashFiles('src/**','Project.toml', 'Manifest.toml')}}
+        restore-keys: |
+          ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-
+    - name: Install Julia packages
+      if: ${{ steps.cache-julia.outputs.cache-hit != 'true' }}
+      env:
+        PYTHON: ${{ env.pythonLocation }}/python
+      shell: julia --color=yes {0}
+      run: |
+        using Pkg, Dates
+        Pkg.add(["PrettyTables", "Literate"])
+        Pkg.activate(".")
+        Pkg.instantiate()
+        Pkg.precompile()
+        Pkg.gc(collect_delay=Day(0))
+    - name: Run program
+      run: julia --color=yes -p ${{ env.NPROC }} literate.jl
+    - name: Build website
+      run: jupyter-book build docs/
+    - name: Upload page artifact
+      if: ${{ github.ref == 'refs/heads/main' }}
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: docs/_build/html
+
+  # Deploy pages
+  deploy:
+    needs: CI
+    if: ${{ github.ref == 'refs/heads/main' }}
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      pages: write # to deploy to Pages
+      id-token: write # to verify the deployment originates from an appropriate source
+      actions: read   # to download an artifact uploaded by `actions/upload-pages-artifact@v3`
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml
@@ -1,57 +1,55 @@
-name: Check markdown links
-
-on:
-  workflow_dispatch:
-  schedule:
-    - cron: '0 0 1 * *' # Every month
-  push:
-    branches:
-      - main
-    paths:
-      - 'docs/**'
-      - '.lycheeignore'
-      - '.github/workflows/linkcheck.yml'
-
-env:
-  DIR: 'docs'
-  PY_VER: '3.12'
-
-jobs:
-  linkcheck:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Setup Python
-        uses: actions/setup-python@v5
-        id: cp
-        with:
-          python-version: ${{ env.PY_VER }}
-      - name: Cache pip
-        uses: actions/cache@v4
-        id: cache-pip
-        with:
-          path: ${{ env.pythonLocation }}
-          key: ${{ runner.os }}-pip-${{ steps.cp.outputs.python-version }}-${{ hashFiles('requirements.txt') }}
-      - name: Install python packages
-        if: ${{ steps.cache-pip.outputs.cache-hit != 'true' }}
-        run: pip install -r requirements.txt
-      - name: Setup Julia
-        uses: julia-actions/setup-julia@v1
-      - name: Convert literate notebooks to markdown files
-        shell: julia --color=yes {0}
-        working-directory: ${{ env.DIR }}
-        run: |
-          import Pkg
-          Pkg.add("Literate")
-          using Literate
-          for (root, dirs, files) in walkdir(pwd())
-            for file in files
-              if endswith(file, ".jl")
-                nb = joinpath(root, file)
-                Literate.notebook(nb, dirname(nb); mdstrings=true, execute=false)
-              end
-            end
-          end
-      - name: Check links
-        run: jupyter-book build ${DIR} --builder linkcheck
+name: Check markdown links
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 1 * *' # Every month
+  push:
+    branches:
+      - main
+    paths:
+      - 'docs/**'
+      - '.lycheeignore'
+      - '.github/workflows/linkcheck.yml'
+
+env:
+  DIR: 'docs'
+
+jobs:
+  linkcheck:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v1
+      - name: Convert literate notebooks to markdown files
+        shell: julia --color=yes {0}
+        working-directory: ${{ env.DIR }}
+        run: |
+          import Pkg
+          Pkg.add("Literate")
+          using Literate
+          for (root, dirs, files) in walkdir(pwd())
+            for file in files
+              if endswith(file, ".jl")
+                Literate.markdown(joinpath(root, file); mdstrings=true, flavor = Literate.CommonMarkFlavor())
+              end
+            end
+          end
+      - name: Restore lychee cache
+        id: restore-cache
+        uses: actions/cache@v4
+        with:
+          save-always: 'true'
+          path: .lycheecache
+          key: cache-lychee-${{ github.sha }}
+          restore-keys: cache-lychee-
+      - name: Lychee Checker
+        uses: lycheeverse/[email protected]
+        id: lychee
+        with:
+          fail: true
+          args: '--accept 200,204,429 --verbose --no-progress --cache --max-cache-age 1d ${{ env.DIR }}'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}