Merge pull request #17 from ntumitolab/neonatal

ntumitolab · Sep 10, 2024 · 524da01 · 524da01
2 parents 0da0f13 + 17f7965
commit 524da01
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -1,10 +1,10 @@
 version: 2
 updates:
-  - package-ecosystem: github-actions
+  - package-ecosystem: pip
     directory: "/"
     schedule:
       interval: daily
-  - package-ecosystem: pip
+  - package-ecosystem: github-actions
     directory: "/"
     schedule:
       interval: daily
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -12,17 +12,18 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  NBCONVERT_JOBS: '4'
-  LITERATE_PROC: '3'
+  NBCONVERT_JOBS: '2'
+  LITERATE_PROC: '4'
   ALLOWERRORS: 'false'
   CACHE_NUM: '1'
   JULIA_CONDAPKG_BACKEND: 'Null'
   JULIA_CI: 'true'
   NBCACHE: '.cache'
+  UV_SYSTEM_PYTHON: 1
 
 jobs:
   CI:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
@@ -31,71 +32,58 @@ jobs:
       id: setup-python
       with:
         python-version: '3.x'
-    - name: Cache python venv
-      uses: actions/cache@v4
-      if: ${{ contains(runner.name, 'GitHub Actions') }}
-      id: cache-venv
-      with:
-        key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}
-        path: .venv
     - name: Install Python dependencies
+      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: Get environment hash
+      id: hash
       run: |
-        python -m venv .venv
-        source .venv/bin/activate
-        python -m pip install -r requirements.txt
-        echo "${VIRTUAL_ENV}/bin" >> $GITHUB_PATH
-        echo "VIRTUAL_ENV=${VIRTUAL_ENV}" >> $GITHUB_ENV
-        echo "PYTHON=${VIRTUAL_ENV}/bin/python" >> $GITHUB_ENV
-        echo "JULIA_PYTHONCALL_EXE=${VIRTUAL_ENV}/bin/python">> $GITHUB_ENV
+        echo "value=${{ hashFiles('Project.toml', 'Manifest.toml', 'src/**') }}" >> "$GITHUB_OUTPUT"
+        echo "ver=${{ runner.os }}-julia-${{ env.CACHE_NUM }}-${{ steps.read_toml.outputs.value }}" >> "$GITHUB_OUTPUT"
     - name: Cache executed notebooks
       uses: actions/cache@v4
       id: cache-nb
       with:
         path: ${{ env.NBCACHE }}
-        key: ${{ runner.os }}-nb-${{ env.CACHE_NUM }}-${{ hashFiles('src/**', 'Project.toml', 'Manifest.toml', 'requirements.txt') }}-${{ hashFiles('docs/**/*.ipynb', 'docs/**/*.jl') }}
+        key: ${{ steps.hash.outputs.ver }}-${{ steps.hash.outputs.value }}-${{ hashFiles('docs/**/*.ipynb', 'docs/**/*.jl') }}
         restore-keys: |
-          ${{ runner.os }}-nb-${{ env.CACHE_NUM }}-${{ hashFiles('src/**', 'Project.toml', 'Manifest.toml', 'requirements.txt') }}-
-    - name: Read Julia version
-      uses: SebRollen/[email protected]
-      id: read_toml
-      with:
-        file: 'Manifest.toml'
-        field: 'julia_version'
+          ${{ steps.hash.outputs.ver }}-${{ steps.hash.outputs.value }}-
     - name: Setup Julia
       uses: julia-actions/setup-julia@v2
       with:
         version: ${{ steps.read_toml.outputs.value }}
     - name: Restore Julia packages
       uses: actions/cache/restore@v4
-      if: ${{ contains(runner.name, 'GitHub Actions') }}
+      if: ${{ runner.environment == 'github-hosted' }}
       id: cache-julia
       with:
-        path: |
-          ~/.julia
-          !~/.julia/registries
-        key: ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-${{ steps.read_toml.outputs.value }}-${{ hashFiles('src/**', 'Project.toml', 'Manifest.toml') }}
+        path: ~/.julia
+        key: ${{ steps.hash.outputs.ver }}-${{ steps.hash.outputs.value }}
         restore-keys: |
-          ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-${{ steps.read_toml.outputs.value }}-
+          ${{ steps.hash.outputs.ver }}-
     - name: Install Julia packages
-      if: ${{ !contains(runner.name, 'GitHub Actions') || steps.cache-julia.outputs.cache-hit != 'true' }}
+      if: ${{ runner.environment == 'self-hosted' || steps.cache-julia.outputs.cache-hit != 'true' }}
       shell: julia --color=yes {0}
       run: |
         using Pkg, Dates
         Pkg.add(["IJulia", "Literate", "PrettyTables", "JSON"])
         Pkg.activate(".")
         Pkg.instantiate()
         Pkg.precompile()
-        Pkg.gc(collect_delay=Day(0))
     - name: Save Julia packages
       uses: actions/cache/save@v4
-      if: ${{ contains(runner.name, 'GitHub Actions') && steps.cache-julia.outputs.cache-hit != 'true' }}
+      if: ${{ runner.environment == 'github-hosted' && steps.cache-julia.outputs.cache-hit != 'true' }}
       with:
-        path: |
-          ~/.julia
-          !~/.julia/registries
+        path: ~/.julia
         key: ${{ steps.cache-julia.outputs.cache-primary-key }}
     - name: Run notebooks
-      run: julia --color=yes -p ${{ env.LITERATE_PROC }} --heap-size-hint=4G run.jl
+      if: ${{ steps.cache-nb.outputs.cache-hit != 'true' }}
+      run: julia --color=yes -p ${{ env.LITERATE_PROC }} --heap-size-hint=3G run.jl
     - name: Copy back built notebooks
       run: cp --verbose -rf ${{ env.NBCACHE }}/docs/* docs/
     - name: Build website

diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml
@@ -19,6 +19,7 @@ jobs:
   linkcheck:
     env:
       DIR: 'docs'
+      UV_SYSTEM_PYTHON: 1
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -45,19 +46,9 @@ jobs:
         id: setup-python
         with:
           python-version: '3.x'
-      - name: Cache python venv
-        uses: actions/cache@v4
-        if: ${{ contains(runner.name, 'GitHub Actions') }}
-        id: cache-venv
-        with:
-          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}
-          path: .venv
+      - name: Install uv
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
       - name: Install Python dependencies
-        run: |
-          python -m venv .venv
-          source .venv/bin/activate
-          python -m pip install -r requirements.txt
-          echo "${VIRTUAL_ENV}/bin" >> $GITHUB_PATH
-          echo "VIRTUAL_ENV=${VIRTUAL_ENV}" >> $GITHUB_ENV
+        run: uv pip install -r requirements.txt
       - name: Build website
         run: jupyter-book build ${DIR} --builder linkcheck
diff --git a/.github/workflows/update-manifest.yml b/.github/workflows/update-manifest.yml
@@ -44,7 +44,7 @@ jobs:
           private_key: ${{ secrets.APP_PRIVATE_KEY }}
       - name: Create Pull Request
         id: cpr
-        uses: peter-evans/create-pull-request@v6
+        uses: peter-evans/create-pull-request@v7
         with:
           title: Julia Dependency Update
           token: ${{ steps.generate-token.outputs.token }}

diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,6 +1 @@
-{
-    "cSpell.words": [
-        "cardiomyocyte",
-        "myocyte"
-    ]
-}
+{}