ntumitolab · sosiristseng · Jun 10, 2024 · Jun 10, 2024 · Jun 10, 2024
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
diff --git a/.github/renovate.json b/.github/renovate.json
@@ -0,0 +1,21 @@
+{
+  "$schema": "https://docs.renovatebot.com/renovate-schema.json",
+  "extends": [
+      "config:best-practices"
+  ],
+  "packageRules": [
+      {
+        "matchUpdateTypes": ["minor", "patch", "pin", "digest"],
+        "automerge": true
+      }
+  ],
+  "lockFileMaintenance": {
+    "enabled": true,
+    "automerge": true
+  },
+  "git-submodules": {
+    "enabled": true
+  },
+  "platformAutomerge": true,
+  "automergeStrategy": "squash"
+}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -25,54 +25,59 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
     - name: Setup Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
       id: setup-python
       with:
         python-version: '3.x'
-    - name: Cache python
-      uses: actions/cache@v4
+    - name: Cache python venv
+      uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
       if: ${{ contains(runner.name, 'GitHub Actions') }}
-      id: cache-py
+      id: cache-venv
       with:
-        key: ${{ runner.os }}-pip-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}
-        path: |
-          ${{ env.pythonLocation }}/lib
-          ${{ env.pythonLocation }}/bin
+        key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}
+        path: .venv
     - name: Install Python dependencies
-      if: ${{ !contains(runner.name, 'GitHub Actions') || steps.cache-py.outputs.cache-hit != 'true' }}
-      run: pip install -r requirements.txt
+      run: |
+        python -m venv .venv
+        source .venv/bin/activate
+        python -m pip install -r requirements.txt
+        echo "${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
     - name: Cache executed notebooks
-      uses: actions/cache@v4
+      uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
       id: cache-nb
       with:
         path: ${{ env.NBCACHE }}
-        key: ${{ runner.os }}-nb-${{ env.CACHE_NUM }}-${{ hashFiles('src/**', 'Project.toml', 'Manifest.toml') }}-${{ hashFiles('docs/**/*.ipynb', 'docs/**/*.jl') }}
+        key: ${{ runner.os }}-nb-${{ env.CACHE_NUM }}-${{ hashFiles('src/**', 'Project.toml', 'Manifest.toml', 'requirements.txt') }}-${{ hashFiles('docs/**/*.ipynb', 'docs/**/*.jl') }}
         restore-keys: |
-          ${{ runner.os }}-nb-${{ env.CACHE_NUM }}-${{ hashFiles('src/**', 'Project.toml', 'Manifest.toml') }}-
+          ${{ runner.os }}-nb-${{ env.CACHE_NUM }}-${{ hashFiles('src/**', 'Project.toml', 'Manifest.toml', 'requirements.txt') }}-
     - name: Read Julia version
+      uses: SebRollen/toml-action@b1b3628f55fc3a28208d4203ada8b737e9687876 # v1.2.0
       id: read_toml
-      run: echo "value=$(python -c 'import tomllib; from pathlib import Path; print(tomllib.loads(Path("Manifest.toml").read_text())["julia_version"])')" >> "$GITHUB_OUTPUT"
+      with:
+        file: 'Manifest.toml'
+        field: 'julia_version'
     - name: Setup Julia
-      uses: julia-actions/setup-julia@v2
+      uses: julia-actions/setup-julia@f2258781c657ad9b4b88072c5eeaf9ec8c370874 # v2
       with:
         version: ${{ steps.read_toml.outputs.value }}
     - name: Restore Julia packages
-      uses: actions/cache/restore@v4
+      uses: actions/cache/restore@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
       if: ${{ contains(runner.name, 'GitHub Actions') }}
       id: cache-julia
       with:
         path: |
           ~/.julia
           !~/.julia/registries
-        key: ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-${{ hashFiles('src/**', 'Project.toml', 'Manifest.toml') }}
+        key: ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-${{ steps.read_toml.outputs.value }}-${{ hashFiles('src/**', 'Project.toml', 'Manifest.toml') }}
         restore-keys: |
-          ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-
+          ${{ runner.os }}-julia-${{ 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' }}
-      env:
-        PYTHON: ${{ steps.setup-python.outputs.python-path }}
       shell: julia --color=yes {0}
       run: |
         using Pkg, Dates
@@ -82,7 +87,7 @@ jobs:
         Pkg.precompile()
         Pkg.gc(collect_delay=Day(0))
     - name: Save Julia packages
-      uses: actions/cache/save@v4
+      uses: actions/cache/save@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
       if: ${{ contains(runner.name, 'GitHub Actions') && steps.cache-julia.outputs.cache-hit != 'true' }}
       with:
         path: |
@@ -97,7 +102,7 @@ jobs:
       run: jupyter-book build docs/
     - name: Upload pages artifact
       if: ${{ github.ref == 'refs/heads/main' }}
-      uses: actions/upload-pages-artifact@v3
+      uses: actions/upload-pages-artifact@56afc609e74202658d3ffba0e8f6dda462b719fa # v3
       with:
         path: docs/_build/html/
 
@@ -117,4 +122,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e # v4
diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml
@@ -4,12 +4,12 @@ on:
   workflow_dispatch:
   schedule:
     - cron: '0 0 1 * *' # Every month
-  # push:
-  #   branches:
-  #     - main
-  #   paths:
-  #     - 'docs/**'
-  #     - '.github/workflows/linkcheck.yml'
+  push:
+    branches:
+      - main
+    paths:
+      - 'docs/**'
+      - '.github/workflows/linkcheck.yml'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -22,9 +22,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
       - name: Setup Julia
-        uses: julia-actions/setup-julia@v2
+        uses: julia-actions/setup-julia@f2258781c657ad9b4b88072c5eeaf9ec8c370874 # v2
       - name: Convert literate notebooks to ipynb files
         shell: julia --color=yes {0}
         working-directory: ${{ env.DIR }}
@@ -41,21 +41,23 @@ jobs:
             end
           end
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         id: setup-python
         with:
           python-version: '3.x'
-      - name: Cache python
-        uses: actions/cache@v4
+      - name: Cache python venv
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
         if: ${{ contains(runner.name, 'GitHub Actions') }}
-        id: cache-py
+        id: cache-venv
         with:
-          key: ${{ runner.os }}-pip-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}
-          path: |
-            ${{ env.pythonLocation }}/lib
-            ${{ env.pythonLocation }}/bin
+          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}
+          path: .venv
       - name: Install Python dependencies
-        if: ${{ !contains(runner.name, 'GitHub Actions') || steps.cache-py.outputs.cache-hit != 'true' }}
-        run: pip install -r requirements.txt
+        run: |
+          python -m venv .venv
+          source .venv/bin/activate
+          python -m pip install -r requirements.txt
+          echo "${VIRTUAL_ENV}/bin" >> $GITHUB_PATH
+          echo "VIRTUAL_ENV=${VIRTUAL_ENV}" >> $GITHUB_ENV
       - name: Build website
         run: jupyter-book build ${DIR} --builder linkcheck
diff --git a/.github/workflows/update-manifest.yml b/.github/workflows/update-manifest.yml
@@ -25,9 +25,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4
       - name: Setup Julia
-        uses: julia-actions/setup-julia@v2
+        uses: julia-actions/setup-julia@f2258781c657ad9b4b88072c5eeaf9ec8c370874 # v2
         with:
           version: '1'
       - name: Update Julia dependencies
@@ -37,14 +37,14 @@ jobs:
       # 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
+        uses: tibdex/github-app-token@3beb63f4bd073e61482598c45c71c1019b59b73a # v2
         id: generate-token
         with:
           app_id: ${{ env.APP_ID }}
           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@6d6857d36972b65feb161a90e484f2984215f83e # v6
         with:
           title: Julia Dependency Update
           token: ${{ steps.generate-token.outputs.token }}