doc: add sphinx

.github/workflows/doc.yml

@@ -0,0 +1,42 @@
+name: Build-sphinx-doc
+
+on:
+  push:
+    # branches: [main]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[doc]
+          pip install ghp-import
+
+      - name: Build HTML
+        env:
+          TOKEN: ${{ secrets.TOKEN }}
+        run: |
+          sed -i '/nb_execution_mode = "off"/d' doc/source/conf.py # enable executing jupyter notebook
+          cd doc
+          make html
+
+      - name: Remove ampersand encoding and token in the generated html
+        run: |
+          # See issues about ampersand encoding at https://github.com/executablebooks/MyST-Parser/issues/760
+          sed -i 's/amp;//g' doc/build/html/Tutorial/Oceans_3.0_API_Tutorial.html
+          sed -i 's/token=[a-zA-Z0-9-]\+/token=YOUR_TOKEN/g' doc/build/html/Tutorial/onc_Library_Tutorial.html
+
+      - name: Run ghp-import to generate GitHub Pages
+        run: |
+          ghp-import -npfo doc/build/html

CONTRIBUTING.md

@@ -90,7 +90,7 @@ $ isort src tests
 Or use tox
 
 ```shell
-$ tox -e format
+$ tox -e format # This also formats doc folder
 ```
 
 ### Linter
@@ -121,7 +121,68 @@ $ tox -e lint -- --fix src tests
 
 ## Set up a development environment for documentation
 
-WIP.
+[Sphinx](https://www.sphinx-doc.org) is used for documentation, with several extensions.
+
+- [MyST](https://myst-parser.readthedocs.io): Parse markdown files.
+- [MyST_NB](https://myst-nb.readthedocs.io): Compile jupyter notebooks.
+- [AutoAPI](https://sphinx-autoapi.readthedocs.io/): Auto generate API documentation.
+- [napoleon](https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html): Support NumPy style docstrings.
+- [viewcode](https://www.sphinx-doc.org/en/master/usage/extensions/viewcode.html): Add links to source code.
+- [copybutton](https://sphinx-copybutton.readthedocs.io/): Add a copy button for code blocks.
+
+### Creating a virtual environment for documentation
+
+Follow the same step in "Set up a development environment", and install dependencies for doc instead of dev.
+
+```shell
+# Install onc library and doc dependencies in editable mode
+$ pip install -e .[doc]
+```
+
+### Building doc
+
+```shell
+$ cd doc
+$ make html
+# For Windows, use ".\make html" or "doc\make html" without cd
+```
+
+Sometimes you need to clean the build folder to force a rebuild.
+
+```shell
+$ make clean
+# For Windows, use ".\make clean" or "doc\make html" without cd
+```
+
+There is a Sphinx extension called [sphinx-autobuild](https://github.com/executablebooks/sphinx-autobuild) to watch a Sphinx directory and rebuild the documentation when a change is detected. It also includes a livereload enabled web server.
+
+```shell
+$ sphinx-autobuild doc/source doc/build/html --watch "*.md" --watch src
+```
+
+Or use tox
+
+```shell
+tox -e doc-autobuild
+```
+
+### Jupyter notebooks
+
+Jupyter notebooks are formatted using [black](https://black.readthedocs.io/en/stable/).
+
+```shell
+$ black doc
+```
+
+Or use tox
+
+```shell
+$ tox -e format # This also formats src and tests folder
+```
+
+[MyST_NB](https://myst-nb.readthedocs.io) supports executing jupyter notebooks when building the documentation. This is turned off in `conf.py` for faster local development, and enabled in GitHub Actions. Currently only `onc_Library_Tutorial.ipynb` will be run during the build.
+
+For a better git diff, all the outputs are cleared in the jupyter notebooks.
 
 ## Make a pull request
 
@@ -172,6 +233,8 @@ $ tox
 
 3. If you are working on a fork, add an Actions secret called TOKEN, and manually trigger the the "Formatting, Linting and Testing" workflow for your feature branch after pushing your commits.
 
+4. If you make changes to any jupyter notebooks, make sure to clear all the outputs and run `$ black doc`.
+
 ### After making the pull request
 
 If you find that some GitHub checks failed, you can check the log in the Actions tab to see what went wrong.

LICENSE.txt

@@ -1,13 +1,190 @@
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