update docs readme

docs/README.md

@@ -1,23 +1,33 @@
-# Compiling gninatorch's Documentation
+# Compiling spyrmsd's Documentation
 
 The docs for this project are built with [Sphinx](http:https://www.sphinx-doc.org/en/master/).
-To compile the docs, first ensure that Sphinx and the ReadTheDocs theme are installed.
 
+## Installation
+
+Ensure that Sphinx and the ReadTheDocs theme are installed:
 
 ```bash
 conda install sphinx sphinx_rtd_theme
 ```
 
+## Documentation
+
+### Automatic API Documentation
+
+Create API documentation automatically with `sphinx-apidoc`:
 
-Once installed, you can use the `Makefile` in this directory to compile static HTML pages by
 ```bash
-make html
+sphinx-apidoc -f -M -e -T -o source/api ../gninatorch
 ```
 
-The compiled docs will be in the `_build` directory and can be viewed by opening `index.html` (which may itself
-be inside a directory called `html/` depending on what version of Sphinx is installed).
+### Build Documentation
 
+Use the `Makefile` to compile static HTML pages:
+
+```bash
+make html
+```
 
-A configuration file for [Read The Docs](https://readthedocs.org/) (readthedocs.yaml) is included in the top level of the repository. To use Read the Docs to host your documentation, go to https://readthedocs.org/ and connect this repository. You may need to change your default branch to `main` under Advanced Settings for the project.
+### Visualize Documentation
 
-If you would like to use Read The Docs with `autodoc` (included automatically) and your package has dependencies, you will need to include those dependencies in your documentation yaml file (`docs/requirements.yaml`).
+The compiled docs will be in the `build` directory and can be viewed by opening `index.html` (which may itself be inside a directory called `html/` depending on what version of Sphinx is installed).

docs/_static/README.md → docs/source/_static/README.md

@@ -1,11 +1,11 @@
 # Static Doc Directory
 
 Add any paths that contain custom static files (such as style sheets) here,
-relative to the `conf.py` file's directory. 
+relative to the `conf.py` file's directory.
 They are copied after the builtin static files,
 so a file named "default.css" will overwrite the builtin "default.css".
 
-The path to this folder is set in the Sphinx `conf.py` file in the line: 
+The path to this folder is set in the Sphinx `conf.py` file in the line:
 ```python
 templates_path = ['_static']
 ```

docs/_templates/README.md → docs/source/_templates/README.md

@@ -1,11 +1,11 @@
 # Templates Doc Directory
 
-Add any paths that contain templates here, relative to 
+Add any paths that contain templates here, relative to
 the `conf.py` file's directory.
 They are copied after the builtin template files,
 so a file named "page.html" will overwrite the builtin "page.html".
 
-The path to this folder is set in the Sphinx `conf.py` file in the line: 
+The path to this folder is set in the Sphinx `conf.py` file in the line:
 ```python
 html_static_path = ['_templates']
 ```