test no docker (#250)

sosiristseng · Aug 31, 2024 · f35fabb · f35fabb
1 parent 21b81b1
commit f35fabb
Show file tree

Hide file tree

Showing 8 changed files with 89 additions and 100 deletions.
diff --git a/.dockerignore b/.dockerignore
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -8,9 +8,3 @@ updates:
     directory: "/"
     schedule:
       interval: daily
-  - package-ecosystem: docker
-    directory: "/"
-    schedule:
-      interval: daily
-    labels:
-      - automerge
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -14,34 +14,60 @@ concurrency:
 env:
   ALLOWERRORS: 'false'
   NBCACHE: '.cache'
+  CACHE_NUM: '1'
+  JULIA_CONDAPKG_BACKEND: 'Null'
+  JULIA_NUM_THREADS: 'auto'
+  JULIA_CI: 'true'
+  UV_SYSTEM_PYTHON: 1
 
 jobs:
   setup:
-    permissions:
-      packages: write
     runs-on: ubuntu-latest
     outputs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
-      hash: ${{ steps.img.outputs.hash }}
+      hash: ${{ steps.hash.outputs.value }}
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
-    - name: Login to ghcr.io
-      uses: docker/login-action@v3
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      id: setup-python
+      with:
+        python-version: '3.x'
+    - 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@v2
       with:
-        registry: ghcr.io
-        username: ${{ github.repository_owner	}}
-        password: ${{ github.token }}
-    - name: Get docker image hash
-      id: img
-      run: echo "hash=${{ hashFiles('requirements.txt', 'Project.toml', 'Manifest.toml', 'src/**', 'env.Dockerfile') }}" >> "$GITHUB_OUTPUT"
-    - name: Build Docker container
-      env:
-        IMG: ghcr.io/${{ github.repository }}:${{ steps.img.outputs.hash }}
+        version: ${{ steps.read_toml.outputs.value }}
+    - name: Get environment hash
+      id: hash
+      run: echo "value=${{ hashFiles('Project.toml', 'Manifest.toml', 'src/**') }}" >> "$GITHUB_OUTPUT"
+    - name: Cache Julia packages
+      if: ${{ contains(runner.name, 'GitHub Actions') }}
+      uses: actions/cache@v4
+      id: cache-julia
+      with:
+        path: |
+          ~/.julia
+          !~/.julia/registries
+        key: ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-${{ steps.read_toml.outputs.value }}-${{ steps.hash.outputs.value }}
+        restore-keys: |
+          ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-${{ steps.read_toml.outputs.value }}-
+    - name: Install Julia packages
+      if: ${{ !contains(runner.name, 'GitHub Actions') || steps.cache-julia.outputs.cache-hit != 'true' }}
+      shell: julia --color=yes {0}
       run: |
-        docker manifest inspect ${IMG} && exit 0
-        docker build -f env.Dockerfile -t ${IMG} .
-        docker push ${IMG}
+        using Pkg, Dates
+        Pkg.add(["IJulia", "Literate", "PrettyTables", "JSON"])
+        Pkg.activate(".")
+        Pkg.instantiate()
+        Pkg.precompile()
+        Pkg.gc(collect_delay=Day(0))
     - name: List notebooks as a JSON array
       id: set-matrix
       run: echo "matrix=$(python -c 'import glob, json; print(json.dumps(glob.glob("**/*.ipynb", root_dir="docs", recursive=True) + glob.glob("**/*.jl", root_dir="docs",recursive=True)))')" >> "$GITHUB_OUTPUT"
@@ -57,7 +83,6 @@ jobs:
     runs-on: ubuntu-latest
     env:
       NB: docs/${{ matrix.notebook }}
-      IMG: ghcr.io/${{ github.repository }}:${{ needs.setup.outputs.hash }}
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -67,25 +92,42 @@ jobs:
         with:
           path: ${{ env.NBCACHE }}
           key: ${{ runner.os }}-notebook-${{ hashFiles(env.NB) }}-${{ needs.setup.outputs.hash }}
-      - name: Pull docker image
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        if: ${{ steps.nb-cache.outputs.cache-hit != 'true' }}
+        with:
+          python-version: '3.x'
+      - name: Install uv
         if: ${{ steps.nb-cache.outputs.cache-hit != 'true' }}
-        run: |
-          docker pull ${{ env.IMG }}
-          docker images ${{ env.IMG }}
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+      - name: Install Python dependencies
+        if: ${{ steps.nb-cache.outputs.cache-hit != 'true' }}
+        run: uv pip install -r requirements.txt
+      - name: Read Julia version
+        if: ${{ steps.nb-cache.outputs.cache-hit != 'true' }}
+        uses: SebRollen/[email protected]
+        id: read_toml
+        with:
+          file: 'Manifest.toml'
+          field: 'julia_version'
+      - name: Setup Julia
+        if: ${{ steps.nb-cache.outputs.cache-hit != 'true' }}
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ steps.read_toml.outputs.value }}
+      - name: Restore Julia packages
+        if: ${{ steps.nb-cache.outputs.cache-hit != 'true' && contains(runner.name, 'GitHub Actions')}}
+        uses: actions/cache/restore@v4
+        with:
+          path: |
+            ~/.julia
+            !~/.julia/registries
+          key: ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-${{ steps.read_toml.outputs.value }}-${{ needs.setup.outputs.hash }}
+          restore-keys: |
+            ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-${{ steps.read_toml.outputs.value }}-
       - name: Execute notebook
         if: ${{ steps.nb-cache.outputs.cache-hit != 'true' }}
-        run: >
-          docker run -w /tmp -v ${{ github.workspace }}:/tmp
-          -e NB=${{ env.NB }}
-          -e NBCACHE=${{ env.NBCACHE }}
-          -e WORKSPACE=${{ github.workspace }}
-          -e ALLOWERRORS=${{ env.ALLOWERRORS }}
-          ${{ env.IMG }}
-          julia execute.jl
-      - name: Claim output cache folder
-        run: |
-          sudo chown -R $USER ${{ env.NBCACHE }}
-          ls -R ${{ env.NBCACHE }}
+        run: julia execute.jl
       - name: Cache notebook
         uses: actions/cache/save@v4
         if: ${{ steps.nb-cache.outputs.cache-hit != 'true' }}
@@ -122,7 +164,6 @@ jobs:
         run: cp --verbose -rf ${{ env.NBCACHE }}/docs/* docs/
       - name: Setup Python
         uses: actions/setup-python@v5
-        id: setup-python
         with:
           python-version: '3.x'
       - name: Install uv

diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml
@@ -49,6 +49,6 @@ jobs:
       - name: Install uv
         run: curl -LsSf https://astral.sh/uv/install.sh | sh
       - name: Install Python dependencies
-        run: uv pip install -r requirements-jb.txt
+        run: uv pip install -r requirements.txt
       - name: Build website
         run: jupyter-book build ${DIR} --builder linkcheck
diff --git a/.github/workflows/rm-old-image.yml b/.github/workflows/rm-old-image.yml
diff --git a/.github/workflows/update-manifest.yml b/.github/workflows/update-manifest.yml
@@ -26,13 +26,14 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
       - name: Update Julia dependencies
-        run: >
-          docker run --rm -w /tmp
-          -v ${{ github.workspace }}:/tmp
-          -e JULIA_PKG_PRECOMPILE_AUTO=0
-          julia:latest
-          julia --project=@. --color=yes -e 'import Pkg; Pkg.update()'
+        env:
+          JULIA_PKG_PRECOMPILE_AUTO: '0'
+        run: julia --project=@. --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

diff --git a/env.Dockerfile b/env.Dockerfile
diff --git a/execute.jl b/execute.jl
@@ -1,16 +1,17 @@
 using Literate
 using JSON
 using Pkg
+using IJulia
 Pkg.activate(Base.current_project())
 
 ENV["GKSwstype"] = "100"
-file = get(ENV, "NB", "test.ipynb")
-cachedir = get(ENV, "NBCACHE", ".cache")
 
 function main(; rmsvg=true)
+    file = get(ENV, "NB", "test.ipynb")
     if endswith(file, ".jl")
         run_literate(file; rmsvg)
     elseif endswith(file, ".ipynb")
+        IJulia.installkernel("Julia", "--project=@.")
         run_ipynb(file)
     else
         error("$(file) is not a valid notebook file!")
@@ -40,6 +41,7 @@ function strip_svg(ipynb)
 end
 
 function run_literate(file; rmsvg=true)
+    cachedir = get(ENV, "NBCACHE", ".cache")
     outpath = joinpath(abspath(pwd()), cachedir, dirname(file))
     mkpath(outpath)
     ipynb = Literate.notebook(file, outpath; mdstrings=true, execute=true)
@@ -48,6 +50,7 @@ function run_literate(file; rmsvg=true)
 end
 
 function run_ipynb(file)
+    cachedir = get(ENV, "NBCACHE", ".cache")
     outpath = joinpath(abspath(pwd()), cachedir, file)
     mkpath(dirname(outpath))
     kernelname = "--ExecutePreprocessor.kernel_name=julia-1.$(VERSION.minor)"