Convert md tutorials to rst and copy them to the website (#95)

* tutorials are now build and cc to the website

* Same action for building docs and website

* Fixing rendering

* Correct use of artifacts upload/download

* Adding back index for tutorials

* The sphinx-tutorial formula is not required anymore [skip ci]

* Chrome present in GHA allows rendering mermaid

* Fixed figures

* Improving readability

* Updating lock file

* Update model/src/pyrenew/latent/hospitaladmissions.py

Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>

* Fixing pre-commit

---------

Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>

.github/workflows/website.yaml

@@ -15,7 +15,46 @@ permissions:
   id-token: write
 
 jobs:
+  render-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: quarto-dev/quarto-actions/setup@v2
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: cache poetry
+        uses: actions/cache@v4
+        with:
+          path: ~/.local
+          key: ${{ runner.os }}-poetry
+
+      - name: install poetry
+        run: pip install poetry
+
+      - name: install package
+        run: poetry install --with dev -C model
+
+      - name: Render documents
+        run: |
+            cd model
+            mkdir _compiled
+            for file in $(find docs -name '*.qmd'); do
+                poetry run quarto render $file --to rst --output-dir ../_compiled
+            done
+
+      # Upload
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: tutorials
+          path: model/_compiled/
+
   build:
+    needs: render-docs
     runs-on: ubuntu-latest
     permissions:
       contents: write
@@ -26,6 +65,13 @@ jobs:
     - name: Setup Pages
       uses: actions/configure-pages@v4
 
+    # Load the artifact github-pages-tutorials
+    - name: Download artifacts
+      uses: actions/download-artifact@v3
+      with:
+        name: tutorials
+        path: docs/source/tutorials/
+
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
@@ -67,4 +113,4 @@ jobs:
       uses: actions/deploy-pages@v4
       with:
         artifact_name: github-pages
-        preview: false # Not yet available to the public.
+        preview: true # Not yet available to the public.

README.md

@@ -7,7 +7,6 @@
 [![installation and testing pipeline](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pipeline.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pipeline.yaml)
 [![Docs: model](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/website.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/website.yaml)
 [![codecov (model)](https://codecov.io/gh/CDCgov/multisignal-epi-inference/graph/badge.svg?token=7Z06HOMYR1)](https://codecov.io/gh/CDCgov/multisignal-epi-inference)
-[![Quarto documents](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/docs.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/docs.yaml)
 
 
 This repo hosts the multisignal (*a.k.a.* signal fusion) renewal project: an internal forecasting model that leverages multiple data sources for enhancing epidemiological modeling of infectious disease outbreaks.