generate_docs.yaml

name: generating documentation

on:
  push:
    branches:
      - main

permissions:
  contents: write

jobs:
  generate:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout this repository
        uses: actions/checkout@v3

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: 3.9

      - name: Install the required python packages
        run: python -m pip install .[docs]

      - name: Other installations
        run: |
          sudo apt-get update
          sudo apt-get install -y build-essential git wget curl

      - name: Create local docs
        run: |
          mkdir docs
          cp -r src/docs/* docs/
          touch docs/.nojekyll
          cp erdiagram-autogen/anatomical_structure.md docs/anatomical_structure.md
          cp erdiagram-autogen/genome_annotation.md docs/genome_annotation.md
          cp erdiagram-autogen/library_generation.md docs/library_generation.md
          gen-doc -d docs linkml-schema/library_generation.yaml
          mv docs/index.md docs/index_library_generation.md
          gen-doc -d docs linkml-schema/anatomical_structure.yaml
          mv docs/index.md docs/index_anatomical_structure.md
          gen-doc -d docs linkml-schema/genome_annotation.yaml
          mv docs/index.md docs/index_genome_annotation.md
          mv docs/index_main.md docs/index.md
          


      - name: Deploy to GitHub Pages
        run: mkdocs gh-deploy --force