diff --git a/.github/workflows/sphinx.yaml b/.github/workflows/sphinx.yaml index f3f683c..f236463 100644 --- a/.github/workflows/sphinx.yaml +++ b/.github/workflows/sphinx.yaml @@ -1,79 +1,82 @@ -name: shinx +name: sphinx on: - push: - branches: [main] - pull_request: - branches: [main] - release: - types: [published] - workflow_dispatch: + push: + branches: [main] + pull_request: + branches: [main] + release: + types: [published] + workflow_dispatch: # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages permissions: - contents: read - pages: write - id-token: write + contents: read + pages: write + id-token: write jobs: - build: - runs-on: ubuntu-latest - permissions: - contents: write - steps: - - uses: actions/checkout@v4 - - # Setting up the environment - - name: Setup Pages - uses: actions/configure-pages@v5 - - - name: Set up Quarto - uses: quarto-dev/quarto-actions/setup@v2 - with: - version: 1.4.515 - - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: "3.12" - - # - name: Install Poetry - # run: pip install poetry - - - name: Install the package - run: pip install . - - # Building - - name: Render Quarto File - run: quarto render README.qmd --to rst && mv README.rst docs/index.rst - - - name: Build HTML using Poetry - run: poetry run -C docs sphinx-build -M html docs/source/ docs/build/ - - # Upload - - name: Upload artifacts - uses: actions/upload-pages-artifact@v3 - with: - name: github-pages - path: docs/build/html/ - - deploy: - # Deploy to the github-pages environment - # but not on PRs - if: ${{ github.event_name != 'pull_request' }} - environment: - name: github-pages - url: ${{ steps.deployment.outputs.page_url }} - - needs: build - - # Specify runner + deployment step - runs-on: ubuntu-latest - - steps: - - name: Deploy to GitHub Pages - id: deployment - uses: actions/deploy-pages@v4 - with: - artifact_name: github-pages - preview: true # Not yet available to the public. + build: + runs-on: ubuntu-latest + permissions: + contents: write + steps: + - uses: actions/checkout@v4 + + # Setting up the environment + - name: Setup Pages + uses: actions/configure-pages@v5 + + - name: Set up Quarto + uses: quarto-dev/quarto-actions/setup@v2 + with: + version: 1.4.515 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.12" + + # - name: Install Poetry + # run: pip install poetry + + - name: Install Sphinx + run: pip install sphinx + + - name: Install the package + run: pip install ".[doc]" + + # Building + - name: Render Quarto File + run: quarto render README.qmd --to rst && mv README.rst docs/index.rst + + - name: Build HTML using Sphinx + run: sphinx-build -M html docs docs/build/ + + # Upload + - name: Upload artifacts + uses: actions/upload-pages-artifact@v3 + with: + name: github-pages + path: docs/build/html/ + + deploy: + # Deploy to the github-pages environment + # but not on PRs + if: ${{ github.event_name != 'pull_request' }} + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + + needs: build + + # Specify runner + deployment step + runs-on: ubuntu-latest + + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 + with: + artifact_name: github-pages + preview: true # Not yet available to the public. diff --git a/README.qmd b/README.qmd index 0410406..d598388 100644 --- a/README.qmd +++ b/README.qmd @@ -29,7 +29,7 @@ Here we show how to create a `SEIR` object and add terms to it. We will use the import epiworldpy as epiworld # Create a SEIR model (susceptible, exposed, infectious, recovered), representing COVID-19. -covid19 = epiworld.ModelSEIR( +covid19 = epiworld.ModelSEIRCONN( name = 'covid-19', n = 10000, prevalence = .01, diff --git a/pyproject.toml b/pyproject.toml index 5c87fdd..be7c427 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,6 +28,7 @@ classifiers = [ [project.optional-dependencies] test = ["pytest"] +doc = ["nbformat", "nbclient", "jupyter", "epiworldpy[viz]"] viz = ["ipympl>=0.8", "matplotlib>=3.5.0", "networkx>=3.0", "scipy>=1.0"] [tool.scikit-build]