Update documentation for installation and config

Added prerequisites section to installation guide, updated references to AtomWorks, and clarified instructions. Updated Sphinx config to exclude preprocessing.rst and changed dark logo path. Minor formatting improvements in contributor guide.

Author: rclune

docs/conf.py

@@ -47,7 +47,7 @@
 ]
 
 templates_path = ["_templates"]
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "examples/GALLERY_HEADER.rst"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "examples/GALLERY_HEADER.rst", "ml/preprocessing.rst"]
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
@@ -67,7 +67,7 @@
     "navbar_end": ["theme-switcher", "navbar-icon-links"],
     "logo": {
         "image_light": "_static/atomworks_logo_light.svg",
-        "image_dark": "_static/atomworks_logo_color.svg",
+        "image_dark": "_static/atomworks_logo_dark.svg",
     },
     "navbar_start": ["navbar-logo", "version-switcher"],
     "switcher": {

docs/contributor_guide.rst

@@ -49,7 +49,7 @@ As you review
 3. Keep review time <1h and <500 LOC for focus.
 
 Contributing to the documentation
---------------------------------
+---------------------------------
 The external AtomWorks documentation is built using `Sphinx <https://www.sphinx-doc.org/en/master/#>`_ and hosted on `GitHub Pages <https://docs.github.com/en/pages>`_.
 Aside from having AtomWorks and its dependencies installed, to build the documentation locally, you will need to install the documentation requirements:
 
@@ -92,5 +92,3 @@ When contributing to this repository, please follow these steps:
    - Example: ``git commit -m "docs: add contributing guidelines"``
 5. Open a pull request to ``staging`` and describe your changes.
 6. Wait for review and merge your changes.
-
-For more details, see the README or contact the maintainers. 

docs/installation.rst

@@ -1,11 +1,19 @@
 Installation
 ============
 
-atomworks can be installed in several ways, depending on your workflow and environment. Below are the recommended methods:
+AtomWorks can be installed in several ways, depending on your workflow and environment. Below are the recommended methods:
+
+0. Prerequisites
+-----------------
+
+Before installing AtomWorks, ensure you have the following prerequisites:
+
+* Python 3.12 or higher
+* `dotenv <https://www.npmjs.com/package/dotenv>`_
 
 1. Installing via pip (recommended)
-----------------------
-This is the easiest way to get started with atomworks.
+-----------------------------------
+This is the easiest way to get started with AtomWorks.
 
 .. code-block:: bash
 
@@ -53,10 +61,10 @@ To install in a fresh environment:
    make env
    pytest tests
 
-3. As a Dependency in Your Apptainer
-------------------------------------
-Add `atomworks.io/src` to your apptainer's PYTHONPATH:
-
-.. code-block:: bash
-
-   export PYTHONPATH=$PWD/src:$PYTHONPATH
+#3. As a Dependency in Your Apptainer
+#------------------------------------
+#Add `atomworks.io/src` to your apptainer's PYTHONPATH:
+#
+#.. code-block:: bash
+#
+#   export PYTHONPATH=$PWD/src:$PYTHONPATH