build-deploy.yml

name: Build and deploy site

on:
  repository_dispatch:
  schedule:
    - cron: '29 11 * * *'
  pull_request:
  push:
    branches: [main]

jobs:
  cancel-superseded:
    name: Cancel superseded
    runs-on: ubuntu-24.04
    steps:
        - name: Cancel Previous Runs
          uses: styfle/cancel-workflow-action@0.12.1
          with:
            access_token: ${{ github.token }}

  build-core-site:
    needs: cancel-superseded
    name: Build core site
    runs-on: ubuntu-24.04
    steps:
      - name: Cancel Previous Runs
        uses: styfle/cancel-workflow-action@0.12.1
        with:
          access_token: ${{ github.token }}

      - name: Checkout
        uses: actions/checkout@v4.2.2

      - name: Set up Ruby 2.7
        uses: ruby/setup-ruby@v1.203.0
        with:
          ruby-version: '2.7'
          bundler-cache: true # runs 'bundle install' and caches installed gems automatically

      - uses: actions/setup-node@v4.1.0
        with:
          node-version: 14
          cache: 'npm'

      - name: Install deps
        run: npm ci

      - name: Build site
        run: GITHUB_TOKEN=${{ github.token }} grunt build

      - name: Debug
        run: |
          cat Gemfile.lock
          bundle info jekyll
          bundle info jekyll-theme-cayman
          ls
          cat dist/index.html

      - name: Upload built site
        uses: actions/upload-artifact@v4.4.3
        with:
          name: core-site
          path: dist/*

  build-msprime-docs:
    name: Build msprime docs
    needs: cancel-superseded
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4.2.2
        name: Checkout msprime
        with:
          ref: main
          repository: tskit-dev/msprime
          submodules: true
          fetch-depth: 0 # Needed for setuptools_scm to work correctly

      - name: Get commit SHA1 for cache
        run: git rev-parse HEAD > SHA1

      - uses: actions/cache@v4.2.0
        id: docs-cache
        name: Docs cache
        with:
          path: dist
          key: msprime-docs-v11-${{ hashFiles('SHA1') }}

      - name: Install GSL
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: sudo apt-get install -y libgsl0-dev

      - uses: actions/setup-python@v5.3.0
        if: steps.docs-cache.outputs.cache-hit != 'true'
        name: Setup Python
        with:
          python-version: "3.10"

      - name: Build virtualenv
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: python -m venv venv-latest

      - name: Install deps
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate && pip install -r requirements/CI-docs/requirements.txt

      - name: Build C module
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: venv-latest/bin/activate && make

      - name: Build Latest Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate
          cd docs
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          mkdir -p dist
          cp -r docs/_build/html dist/latest

      - name: Checkout latest stable tag
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          git fetch --tags --recurse-submodules=no
          git checkout `git tag --list --sort=creatordate | grep -vi "[baC]" | tail -n1`
          git submodule update --init --recursive
          git status

#      - name: Build virtualenv
#        if: steps.docs-cache.outputs.cache-hit != 'true'
#        run: python -m venv venv-stable
#
#      - name: Install deps
#        if: steps.docs-cache.outputs.cache-hit != 'true'
#        run: |
#          venv-stable/bin/activate
#          [ -f requirements/CI-docs/requirements.txt ] && pip install -r requirements/CI-docs/requirements.txt
#          [ -f requirements/development.txt ] && pip install -r requirements/development.txt
      - name: Build C module
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: venv-latest/bin/activate && make

      - name: Build Stable Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          rm -rf docs/_build
          venv-latest/bin/activate
          cd docs
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .
          
      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run:
          cp -r docs/_build/html dist/stable

      - name: Upload msprime docs
        uses: actions/upload-artifact@v4.4.3
        with:
          name: msprime-docs
          path: dist/*

  build-tsinfer-docs:
    name: Build tsinfer docs
    needs: cancel-superseded
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4.2.2
        name: Checkout tsinfer
        with:
          ref: main
          repository: tskit-dev/tsinfer
          submodules: true
          fetch-depth: 0 # Needed for setuptools_scm to work correctly

      - name: Get commit SHA1 for cache
        run: git rev-parse HEAD > SHA1

      - uses: actions/cache@v4.2.0
        id: docs-cache
        name: Docs cache
        with:
          path: dist
          key: tsinfer-docs-v1-${{ hashFiles('SHA1') }}

      - uses: actions/setup-python@v5.3.0
        if: steps.docs-cache.outputs.cache-hit != 'true'
        name: Setup Python
        with:
          python-version: "3.10"

      - name: Build virtualenv
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: python -m venv venv-latest

      - name: Install deps
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate && pip install -r requirements/CI-docs/requirements.txt
          sudo apt-get install tabix

      - name: Build C module
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: venv-latest/bin/activate && make

      - name: Build Latest Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate
          cd docs
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          mkdir -p dist
          cp -r docs/_build/html dist/latest

      - name: Checkout latest stable tag
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          git fetch --tags --recurse-submodules=no
          git checkout `git tag --list --sort=creatordate | grep -vi "[baC]" | tail -n1`
          git submodule update --init --recursive
          git status

      - uses: actions/setup-python@v5.3.0
        if: steps.docs-cache.outputs.cache-hit != 'true'
        name: Setup Python
        with:
          python-version: "3.10"

      - name: Build virtualenv
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: python -m venv venv-stable

      - name: Install deps
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-stable/bin/activate
          [ -f requirements/CI-docs/requirements.txt ] && pip install -r requirements/CI-docs/requirements.txt

      - name: Build C module
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate && make

      - name: Build Stable Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          rm -rf docs/_build
          venv-latest/bin/activate
          cd docs
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run:
          cp -r docs/_build/html dist/stable

      - name: Upload tsinfer docs
        uses: actions/upload-artifact@v4.4.3
        with:
          name: tsinfer-docs
          path: dist/*


  build-tskit-docs:
    name: Build tskit docs
    needs: cancel-superseded
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4.2.2
        name: Checkout tskit
        with:
          ref: main
          repository: tskit-dev/tskit
          submodules: true
          fetch-depth: 0 # Needed for setuptools_scm to work correctly

      - name: Get commit SHA1 for cache
        run: git rev-parse HEAD > SHA1

      - uses: actions/cache@v4.2.0
        id: docs-cache
        name: Docs cache
        with:
          path: dist
          key: tskit-docs-v7-${{ hashFiles('SHA1') }}

      - uses: actions/setup-python@v5.3.0
        if: steps.docs-cache.outputs.cache-hit != 'true'
        name: Setup Python
        with:
          python-version: "3.10"

      - name: Build virtualenv
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: python -m venv venv-latest

      - name: Install deps
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          sudo apt-get install doxygen
          venv-latest/bin/activate && pip install -r python/requirements/CI-docs/requirements.txt

      - name: Build C module
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: venv-latest/bin/activate && make -C python

      - name: Build Latest Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate
          cd docs
          make dist

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          mkdir -p dist
          cp -r docs/_build/html dist/latest

      - name: Checkout latest stable tag
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          git stash
          git fetch --tags --recurse-submodules=no
          git checkout `git tag --list --sort=creatordate | grep -vi "[baC]" | tail -n1`
          git submodule update --init --recursive
          git status

      - uses: actions/setup-python@v5.3.0
        if: steps.docs-cache.outputs.cache-hit != 'true'
        name: Setup Python
        with:
          python-version: "3.10"

      - name: Build virtualenv
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: python -m venv venv-stable

      - name: Downgrade pip (for conflicting dependencies)
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: venv-stable/bin/activate && pip install pip==20.0.2

      - name: Install deps
        if: steps.docs-cache.outputs.cache-hit != 'true'
        # Remove this second line after next release of tskit
        run: |
          venv-stable/bin/activate && pip install -r python/requirements/CI-docs/requirements.txt
          venv-stable/bin/activate && pip install nbclient==0.5.13

      - name: Build C module
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: venv-stable/bin/activate && make -C python

      - name: Build Stable Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          rm -rf docs/_build
          venv-stable/bin/activate
          # Install jsonschema for bugfix
          pip install jsonschema[format-nongpl]==4.17.3
          cd docs
          # A sphinx-book-theme breaking change needs this
          sed -i '/html_theme_options:/a\ \ \ \ \ \ \ \ navigation_with_keys: False' _config.yml
          make dist || make

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          cp -r docs/_build/html dist/stable

      - name: Upload tskit docs
        uses: actions/upload-artifact@v4.4.3
        with:
          name: tskit-docs
          path: dist/*


  build-pyslim-docs:
    name: Build pyslim docs
    needs: cancel-superseded
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4.2.2
        name: Checkout pyslim
        with:
          ref: main
          repository: tskit-dev/pyslim
          submodules: true
          fetch-depth: 0 # Needed for setuptools_scm to work correctly

      - name: Get commit SHA1 for cache
        run: git rev-parse HEAD > SHA1

      - uses: actions/cache@v4.2.0
        id: docs-cache
        name: Docs cache
        with:
          path: dist
          key: pyslim-docs-v6-${{ hashFiles('SHA1') }}

      - uses: actions/setup-python@v5.3.0
        if: steps.docs-cache.outputs.cache-hit != 'true'
        name: Setup Python
        with:
          python-version: "3.10"

      - name: Build latest SLiM
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          git clone https://github.com/messerlab/SLiM.git
          mkdir -p SLiM/Release
          cd SLiM/Release
          cmake -D CMAKE_BUILD_TYPE=Release ..
          make -j 2

      - name: Build virtualenv
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: python -m venv venv-latest

      - name: Install deps
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate
          pip install -r requirements/CI-docs/requirements.txt

      - name: Build Latest Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate
          export PATH=$PATH:$PWD/SLiM/Release
          cd docs
          # don't re-generate these which require tricky prerequisites (inkscape, xmlstarlet)
          touch _static/{pedigree0.svg,pedigree1.svg,pedigree2.svg,pedigree_recapitate.svg,pedigree_simplify.svg,pedigree_mutate.svg}
          touch _static/{pedigree01.png,pedigree0.png,pedigree1.png,pedigree2.png,pedigree_recapitate.png,pedigree_simplify.png,pedigree_mutate.png}
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          mkdir -p dist
          cp -r docs/_build/html dist/latest

      - name: Build stable SLiM
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          mkdir -p SLiM/Stable
          cd SLiM/Stable
          git fetch --tags --recurse-submodules=no
          git checkout `git tag --list --sort=creatordate | grep -vi "[baC]" | tail -n1`
          git status
          cmake -D CMAKE_BUILD_TYPE=Release ..
          make -j 2

      - name: Checkout latest stable tag
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          git fetch --tags --recurse-submodules=no
          git checkout `git tag --list --sort=creatordate | grep -vi "[baC]" | tail -n1`
          git submodule update --init --recursive
          git status

# As docs build has had issues with dependancies, just use venv-latest for now
#      - name: Build virtualenv
#        if: steps.docs-cache.outputs.cache-hit != 'true'
#        run: python -m venv venv-stable
#
#      - name: Install deps
#        if: steps.docs-cache.outputs.cache-hit != 'true'
#        run: |
#          venv-stable/bin/activate
#          pip install -r requirements/CI-docs/requirements.txt

      - name: Build Stable Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          rm -rf docs/_build
          venv-latest/bin/activate
          export PATH=$PWD/SLiM/Stable:$PATH
          cd docs
          # A sphinx-book-theme breaking change needs this
          sed -i '/html_theme_options:/a\ \ \ \ \ navigation_with_keys: False' _config.yml
          
          # don't re-generate these which require tricky prerequisites (inkscape, xmlstarlet)
          touch _static/{pedigree0.svg,pedigree1.svg,pedigree2.svg,pedigree_recapitate.svg,pedigree_simplify.svg,pedigree_mutate.svg}
          touch _static/{pedigree01.png,pedigree0.png,pedigree1.png,pedigree2.png,pedigree_recapitate.png,pedigree_simplify.png,pedigree_mutate.png}
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run:
          cp -r docs/_build/html dist/stable

      - name: Upload pyslim docs
        uses: actions/upload-artifact@v4.4.3
        with:
          name: pyslim-docs
          path: dist/*

  build-tstrait-docs:
    name: Build tstrait docs
    needs: cancel-superseded
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4.2.2
        name: Checkout tstrait
        with:
          ref: main
          repository: tskit-dev/tstrait

      - name: Get commit SHA1 for cache
        run: git rev-parse HEAD > SHA1

      - uses: actions/cache@v4.2.0
        id: docs-cache
        name: Docs cache
        with:
          path: dist
          key: tstrait-docs-v3-${{ hashFiles('SHA1') }}

      - uses: actions/setup-python@v5.3.0
        if: steps.docs-cache.outputs.cache-hit != 'true'
        name: Setup Python
        with:
          python-version: "3.10"

      - name: Build virtualenv
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: python -m venv venv-latest

      - name: Install deps
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate && pip install -r requirements/CI-docs/requirements.txt

      - name: Build Latest Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate
          cd docs
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          mkdir -p dist
          cp -r docs/_build/html dist/latest

      - name: Checkout latest stable tag
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          git fetch --tags --recurse-submodules=no
          git checkout `git tag --list --sort=creatordate | grep -vi "[baC]" | tail -n1`
          git status

      - name: Build Stable Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          rm -rf docs/_build
          venv-latest/bin/activate
          cd docs
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run:
          cp -r docs/_build/html dist/stable

      - name: Upload tstrait docs
        uses: actions/upload-artifact@v4.4.3
        with:
          name: tstrait-docs
          path: dist/*

  build-tscompare-docs:
    name: Build tscompare docs
    needs: cancel-superseded
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4.2.2
        name: Checkout tscompare
        with:
          ref: main
          repository: tskit-dev/tscompare

      - name: Get commit SHA1 for cache
        run: git rev-parse HEAD > SHA1

      - uses: actions/cache@v4.2.0
        id: docs-cache
        name: Docs cache
        with:
          path: dist
          key: tscompare-docs-v3-${{ hashFiles('SHA1') }}

      - uses: actions/setup-python@v5.3.0
        if: steps.docs-cache.outputs.cache-hit != 'true'
        name: Setup Python
        with:
          python-version: "3.10"

      - name: Build virtualenv
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: python -m venv venv-latest

      - name: Install deps
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate && pip install -r requirements/CI-docs-pip/requirements.txt

      - name: Build Latest Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate
          cd docs
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          mkdir -p dist
          cp -r docs/_build/html dist/latest

      - name: Checkout latest stable tag
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          git fetch --tags --recurse-submodules=no
          git checkout `git tag --list --sort=creatordate | grep -vi "[baC]" | tail -n1`
          git status

      - name: Build Stable Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          rm -rf docs/_build
          venv-latest/bin/activate
          cd docs
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run:
          cp -r docs/_build/html dist/stable

      - name: Upload tscompare docs
        uses: actions/upload-artifact@v4.4.3
        with:
          name: tscompare-docs
          path: dist/*


  build-tsdate-docs:
    name: Build tsdate docs
    needs: cancel-superseded
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4.2.2
        name: Checkout tsdate
        with:
          ref: main
          repository: tskit-dev/tsdate

      - name: Get commit SHA1 for cache
        run: git rev-parse HEAD > SHA1

      - uses: actions/cache@v4.2.0
        id: docs-cache
        name: Docs cache
        with:
          path: dist
          key: tsdate-docs-v2-${{ hashFiles('SHA1') }}

      - uses: actions/setup-python@v5.3.0
        if: steps.docs-cache.outputs.cache-hit != 'true'
        name: Setup Python
        with:
          python-version: "3.10"

      - name: Build virtualenv
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: python -m venv venv-latest

      - name: Install deps
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate && pip install -r docs/requirements.txt

      - name: Build Latest Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate
          cd docs
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          mkdir -p dist
          cp -r docs/_build/html dist/latest

      - name: Checkout latest stable tag
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          git fetch --tags --recurse-submodules=no
          git checkout `git tag --list --sort=creatordate | grep -vi "[baC]" | tail -n1`
          git status

      - name: Build Stable Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          rm -rf docs/_build
          venv-latest/bin/activate
          python -m pip install "numpy<2"
          cd docs
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run:
          cp -r docs/_build/html dist/stable

      - name: Upload tsdate docs
        uses: actions/upload-artifact@v4.4.3
        with:
          name: tsdate-docs
          path: dist/*

  build-tszip-docs:
    name: Build tszip docs
    needs: cancel-superseded
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4.2.2
        name: Checkout tszip
        with:
          ref: main
          repository: tskit-dev/tszip

      - name: Get commit SHA1 for cache
        run: git rev-parse HEAD > SHA1

      - uses: actions/cache@v4.2.0
        id: docs-cache
        name: Docs cache
        with:
          path: dist
          key: tszip-docs-v2-${{ hashFiles('SHA1') }}

      - uses: actions/setup-python@v5.3.0
        if: steps.docs-cache.outputs.cache-hit != 'true'
        name: Setup Python
        with:
          python-version: "3.10"

      - name: Build virtualenv
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: python -m venv venv-latest

      - name: Install deps
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate && pip install -r requirements/CI-docs.txt

      - name: Build Latest Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate
          cd docs
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          mkdir -p dist
          cp -r docs/_build/html dist/latest

# Disabled until next tszip release - also reinstate redirect on line 917
#      - name: Checkout latest stable tag
#        if: steps.docs-cache.outputs.cache-hit != 'true'
#        run: |
#          git fetch --tags --recurse-submodules=no
#          git checkout `git tag --list --sort=creatordate | grep -vi "[baC]" | tail -n1`
#          git status
#
#      - name: Build Stable Docs
#        if: steps.docs-cache.outputs.cache-hit != 'true'
#        run: |
#          rm -rf docs/_build
#          venv-latest/bin/activate
#          cd docs
#          make dist
#          # make dist changes the _conf.yml file to write the version number, so drop the change
#          git checkout .
#
#      - name: Copy docs
#        if: steps.docs-cache.outputs.cache-hit != 'true'
#        run:
#          cp -r docs/_build/html dist/stable

      - name: Upload tszip docs
        uses: actions/upload-artifact@v4.4.3
        with:
          name: tszip-docs
          path: dist/*

  build-tsbrowse-docs:
    name: Build tsbrowse docs
    needs: cancel-superseded
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4.2.2
        name: Checkout tsbrowse
        with:
          ref: main
          repository: tskit-dev/tsbrowse

      - name: Get commit SHA1 for cache
        run: git rev-parse HEAD > SHA1

      - uses: actions/cache@v4.2.0
        id: docs-cache
        name: Docs cache
        with:
          path: dist
          key: tsbrowse-docs-v3-${{ hashFiles('SHA1') }}

      - uses: actions/setup-python@v5.3.0
        if: steps.docs-cache.outputs.cache-hit != 'true'
        name: Setup Python
        with:
          python-version: "3.11"

      - name: Build virtualenv
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: python -m venv venv-latest

      - name: Install deps
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate && pip install -r requirements.txt && playwright install

      - name: Build Latest Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          venv-latest/bin/activate
          cd docs
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          mkdir -p dist
          cp -r docs/_build/html dist/latest

      - name: Checkout latest stable tag
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          git fetch --tags --recurse-submodules=no
          git checkout `git tag --list --sort=creatordate | grep -vi "[baC]" | tail -n1`
          git status

      - name: Build Stable Docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run: |
          rm -rf docs/_build
          venv-latest/bin/activate
          cd docs
          make dist
          # make dist changes the _conf.yml file to write the version number, so drop the change
          git checkout .

      - name: Copy docs
        if: steps.docs-cache.outputs.cache-hit != 'true'
        run:
          cp -r docs/_build/html dist/stable

      - name: Upload tsbrowse docs
        uses: actions/upload-artifact@v4.4.3
        with:
          name: tsbrowse-docs
          path: dist/*


  import-tutorials:
    name: Import tutorials
    needs: cancel-superseded
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4.2.2
        name: Checkout tutorials
        with:
          ref: gh-pages
          repository: tskit-dev/tutorials

      - name: Upload tutorials
        uses: actions/upload-artifact@v4.4.3
        with:
          name: tutorials
          path: .

  import-rust-tutorial:
    name: Import rust tutorials
    needs: cancel-superseded
    runs-on: ubuntu-24.04
    steps:
      - uses: actions/checkout@v4.2.2
        name: Checkout tutorials
        with:
          ref: gh-pages
          repository: tskit-dev/tskit-rust

      - name: Upload tutorials
        uses: actions/upload-artifact@v4.4.3
        with:
          name: rust-tutorials
          path: .


  deploy:
    name: Deploy 🚀 (if on main branch)
    needs:
      - build-core-site
      - build-msprime-docs
      - build-tsinfer-docs
      - build-tskit-docs
      - build-pyslim-docs
      - build-tsdate-docs
      - build-tszip-docs
      - build-tstrait-docs
      - build-tscompare-docs
      - build-tsbrowse-docs
      - import-tutorials
      - import-rust-tutorial
    runs-on: ubuntu-24.04
    steps:
      - name: Checkout
        uses: actions/checkout@v4.2.2
      - name: Download core site
        uses: actions/download-artifact@v4.1.8
        with:
          name: core-site
          path: site

      - name: Download msprime-docs
        uses: actions/download-artifact@v4.1.8
        with:
          name: msprime-docs
          path: site/msprime/docs

      - name: Download tsinfer-docs
        uses: actions/download-artifact@v4.1.8
        with:
          name: tsinfer-docs
          path: site/tsinfer/docs

      - name: Download tskit-docs
        uses: actions/download-artifact@v4.1.8
        with:
          name: tskit-docs
          path: site/tskit/docs

      - name: Download tstrait-docs
        uses: actions/download-artifact@v4.1.8
        with:
          name: tstrait-docs
          path: site/tstrait/docs

      - name: Download tscompare-docs
        uses: actions/download-artifact@v4.1.8
        with:
          name: tscompare-docs
          path: site/tscompare/docs

      - name: Download tsbrowse-docs
        uses: actions/download-artifact@v4.1.8
        with:
          name: tsbrowse-docs
          path: site/tsbrowse/docs

      - name: Download pyslim-docs
        uses: actions/download-artifact@v4.1.8
        with:
          name: pyslim-docs
          path: site/pyslim/docs

      - name: Download tsdate-docs
        uses: actions/download-artifact@v4.1.8
        with:
          name: tsdate-docs
          path: site/tsdate/docs

      - name: Download tszip-docs
        uses: actions/download-artifact@v4.1.8
        with:
          name: tszip-docs
          path: site/tszip/docs

      - name: Download tutorials
        uses: actions/download-artifact@v4.1.8
        with:
          name: tutorials
          path: site/tutorials

      - name: Download rust tutorial
        uses: actions/download-artifact@v4.1.8
        with:
          name: rust-tutorials
          path: site/tutorials/rust

      - name: Pages config and tweaks
        run: |
          touch site/.nojekyll
          echo "tskit.dev" > site/CNAME
          echo "<meta http-equiv=\"Refresh\" content=\"0; url=/msprime/docs/stable\" />" > site/msprime/docs/index.html
          echo "<meta http-equiv=\"Refresh\" content=\"0; url=/tsinfer/docs/stable\" />" > site/tsinfer/docs/index.html
          echo "<meta http-equiv=\"Refresh\" content=\"0; url=/tskit/docs/stable\" />" > site/tskit/docs/index.html
          echo "<meta http-equiv=\"Refresh\" content=\"0; url=/pyslim/docs/stable\" />" > site/pyslim/docs/index.html
          echo "<meta http-equiv=\"Refresh\" content=\"0; url=/tstrait/docs/stable\" />" > site/tstrait/docs/index.html
          echo "<meta http-equiv=\"Refresh\" content=\"0; url=/tscompare/docs/stable\" />" > site/tscompare/docs/index.html
          echo "<meta http-equiv=\"Refresh\" content=\"0; url=/tsbrowse/docs/stable\" />" > site/tsbrowse/docs/index.html
          echo "<meta http-equiv=\"Refresh\" content=\"0; url=/tsdate/docs/stable\" />" > site/tsdate/docs/index.html
          echo "<meta http-equiv=\"Refresh\" content=\"0; url=/tszip/docs/latest\" />" > site/tszip/docs/index.html
      - name: List site contents
        run: |
          ls -R

      - name: Upload site (for PR inspection)
        uses: actions/upload-artifact@v4.4.3
        with:
          name: site
          path: .

      - name: Deploy
        if: github.ref == 'refs/heads/main'
        uses: JamesIves/github-pages-deploy-action@v4.7.2
        with:
          token: ${{ secrets.ADMINBOT_TOKEN }}
          branch: gh-pages
          folder: site
          single-commit: true