documentation builder bug fixes and general overhaul

Following extensive investigation in #2619 this PR finally fixes the documentation build and modernizes the workflow a bit:
 - runs the workflow on a schedule so that we can catch future errors once a week instead of whenever we update the docs
 - fixes the incorrect installation order by copying from the CI setup steps
 - fixes the path error in the docs building/commiting
 - reorders the steps somewhat to improve clarity of the actual doc build

.github/workflows/docs.yml

@@ -5,17 +5,25 @@ on:
  branches:
  - main
  pull_request:
+ schedule:
+ # * is a special character in YAML so you have to quote this string
+ - cron: "0 8 * * 1"
 
 jobs:
  build-documentation:
  runs-on: ubuntu-latest
- strategy:
- max-parallel: 5
  defaults:
  run:
  shell: bash -l {0}
  steps:
- - uses: actions/checkout@v2
+ - name: Sign into GitHub Actions Bot
+ run: |
+ git config --global user.name "github-actions"
+ git config --global user.email "github-actions@github.com"
+
+ - name: Clone RMG-Py
+ uses: actions/checkout@v2
+
  - name: Setup Mambaforge Python 3.7
  uses: conda-incubator/setup-miniconda@v2
  with:
@@ -25,51 +33,61 @@ jobs:
  python-version: 3.7
  activate-environment: rmg_env
  use-mamba: true
+
  - name: Install sphinx
  run: mamba install -y sphinx
+
  - name: Mamba info
  run: |
  mamba info
  mamba list
- - name: Install and link Julia dependencies 
- run: |
- julia -e "using Pkg; Pkg.add(PackageSpec(url=\"https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl\", rev=\"main\"))"
- julia -e "using Pkg; Pkg.add(\"PyCall\"); Pkg.add(\"DifferentialEquations\")"
- python -c "import julia; julia.install()"
- - name: Install and compile RMG
+
+ - name: Clone RMG-database
  run: |
  cd ..
- git clone https://github.com/ReactionMechanismGenerator/RMG-database.git
- cd RMG-Py
- sed -i '/embedsignature/s/# //g' setup.py
+ git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git
+
+ - name: Set Environment Variables
+ run: |
+ RUNNER_CWD=$(pwd)
+ echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV
+ echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH
+
+ - name: make RMG
+ run: |
+ make clean
  make
- - uses: actions/checkout@v2
+
+ - name: Install and link Julia dependencies
+ timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
+ run: |
+ python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
+ julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator'
+
+ - name: Checkout gh-pages Branch
+ uses: actions/checkout@v2
  with:
  ref: gh-pages
  path: build/html
- - name: Make documentation - for testing
- if: ${{ github.event_name != 'push' || github.repository != 'ReactionMechanismGenerator/RMG-Py' }}
- run: |
- cd documentation
- sphinx-build -b html -d build/doctrees/ source/ build/html -w errors.log -W --keep-going
- - name: Report documentation errors
- if: ${{ failure() }}
- run: |
- cat documentation/errors.log
- - name: Make documentation - to publish
- if: ${{ github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
+ clean: false
+
+ - name: Build Documentation
  run: |
- git config --global user.name "github-actions"
- git config --global user.email "github-actions@github.com"
  cd documentation
  make html
+ cd build/html
+ touch .nojekyll
+ git add -A .
+ git commit -m "Automated documentation rebuild"
+
  - name: Check documentation links
  continue-on-error: true
  run: |
  cd documentation
  sphinx-build -b linkcheck -d build/doctrees/ source/ build/linkcheck | grep -e broken -e redirect | grep -v -e 'redirect https://doi.org/' -e 'broken https://doi.org/.* 403 Client Error: Forbidden'
- - name: Publish documentation
+
+ - name: Publish Updated Documentation
  if: ${{ github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
  run: |
- touch build/html/.nojekyll
- cd build/html; git add -A .; git commit -m "Automated documentation rebuild"; git push origin gh-pages
+ cd documentation/build/html
+ git push origin gh-pages