Update documentation links and installation instructions

Updated documentation URLs to point to rosettacommons.github.io instead of baker-laboratory.github.io. Clarified installation instructions for Open Babel and updated contributor guide to use a requirements file for documentation dependencies. Removed outdated Apptainer instructions and improved clarity in installation steps.

Author: rclune

README.md

@@ -1,7 +1,7 @@
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![PyPI version](https://img.shields.io/pypi/v/atomworks.svg)](https://pypi.org/project/atomworks/)
 [![Python versions](https://img.shields.io/pypi/pyversions/atomworks.svg)](https://pypi.org/project/atomworks/)
-[![Documentation Status](https://img.shields.io/badge/docs-latest-brightgreen.svg)](https://baker-laboratory.github.io/atomworks-dev/latest/index.html)
+[![Documentation Status](https://img.shields.io/badge/docs-latest-brightgreen.svg)](https://rosettacommons.github.io/atomworks/latest/)
 [![License: BSD 3-Clause](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
 <div align="center">
@@ -78,7 +78,8 @@ We have found that `atomworks.ml` **dramatically** reduces the overhead of start
 pip install atomworks # base installation version without torch (for only atomworks.io)
 pip install "atomworks[ml]" # with torch and ML dependencies (for atomworks.io plus atomworks.ml)
 pip install "atomworks[dev]" # with development dependencies
-pip install "atomworks[ml,dev]" # with all dependencies
+pip install "atomworks[openbabel]" # with [Open Babel](https://openbabel.org/) and its dependencies
+pip install "atomworks[ml,openbabel,dev]" # with all dependencies
 ```
 *Running multiple of these installations will just add to the installed dependencies and will not install multiple installations of atomworks.*
 
@@ -88,7 +89,7 @@ If you are using [uv](https://docs.astral.sh/uv/reference/policies/versioning/)
 uv pip install "atomworks[ml,openbabel,dev]"
 ```
 
-For more advanced setup options (including how to run workflows via apptainers) see the [full documentation](https://baker-laboratory.github.io/atomworks-dev/latest).
+For more advanced setup options (including how to run workflows via apptainers) see the [full documentation](https://rosettacommons.github.io/atomworks/latest/index.html).
 
 ---
 
@@ -100,7 +101,7 @@ This section contains information for how to get atomworks set up and a quick gu
 
 To parse a pdb file (parse = load, clean, annotate relevant metadata such as entities, molecules, etc) you can use the `parse` function:
 
-> Note: To run the code in this section you will need to download the 3nez.cif.gz file yourself. See the [examples](https://baker-laboratory.github.io/atomworks-dev/latest/auto_examples/) for how to download files from the PDB within a Python script. 
+> Note: To run the code in this section you will need to download the 3nez.cif.gz file yourself. See the [examples](https://rosettacommons.github.io/atomworks/latest/auto_examples/index.html) for how to download files from the PDB within a Python script. 
 
 ```python
 
@@ -125,7 +126,7 @@ The output of `parse` includes:
 - **assemblies** — Built biological assemblies (each are their own `AtomArrayStack`)
 - **metadata** — Experimental and source information
 
-See [usage examples](https://baker-laboratory.github.io/atomworks-dev/latest/auto_examples/) for more examples of the use of `parse()`. All of the provided examples make use of this method. 
+See [usage examples](https://rosettacommons.github.io/atomworks/latest/auto_examples/index.html) for more examples of the use of `parse()`. All of the provided examples make use of this method. 
 See [API reference documentation](https://rosettacommons.github.io/atomworks/latest/io/parser.html) for more information on this method.
 
 If you just want to load a file, you can use the `load_any` function:

docs/contributor_guide.rst

@@ -47,14 +47,11 @@ As you review
 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, you will need to have the following installed to build the documentation locally:
+Aside from having AtomWorks and its dependencies installed, to build the documentation locally, you will need to install the documentation requirements:
 
-* Sphinx (``pip install sphinx``)
-
-* Sphinx gallery (``pip install sphinx-gallery``)
-
-* Pydata Sphinx Theme (``pip install pydata-sphinx-theme``)
+.. code-block:: bash
 
+   uv pip install -r docs/docs_requirements.txt
 
 To build the documentation, navigate to the ``docs`` directory and run:
 

docs/installation.rst

@@ -14,19 +14,19 @@ This is the easiest way to get started with atomworks.
    pip install "atomworks[dev]" # with development dependencies
    pip install "atomworks[ml,dev]" # with all dependencies
 
+You can also install AtomWorks with `Open Babel <https://openbabel.org/>`_, an alternative to RDKit:
 
-2. Using the Standalone Apptainer
------------------------------------------------
-This is ideal for dataset parsing and generation in a controlled environment.
+.. code-block:: bash
+
+   pip install "atomworks[openbabel]"
+
+or for all possible dependencies: 
 
 .. code-block:: bash
 
-   # Set up IPD-specific environment variables
-   source ./.ipd/setup.sh
-   # Use the provided apptainer image
-   ./.ipd/atomworks.sif
+   pip install "atomworks[ml,openbabel,dev]"
 
-.. _local-conda_environment:
+Open Babel is not automatically installed with AtomWorks due to its larger size and additional dependencies, only install it if you plan to use it.
 
 2. Local Conda Environment
 --------------------------
@@ -60,11 +60,3 @@ Add `atomworks.io/src` to your apptainer's PYTHONPATH:
 .. code-block:: bash
 
    export PYTHONPATH=$PWD/src:$PYTHONPATH
-
-Or, if at IPD:
-
-.. code-block:: bash
-
-   source ./.ipd/setup.sh
-
-For new apptainers, see the apptainer.spec file for integration details.