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Added notes about required file downloads and clarified example usage for parsing PDB files. Updated import statements and corrected file paths in documentation to improve clarity and accuracy for users.
Added a new section clarifying when to use atomworks.io vs atomworks.ml. Improved installation instructions and clarified that multiple installs only add dependencies. Updated the getting started section to reference external documentation and reorganized quick start instructions. Updated contribution link to point to the new contributor guide.
Updated installation instructions to include dotenv dependency.
Expanded the contributor guide with clearer commit and PR instructions, added documentation on building docs with Sphinx, and improved branch naming and workflow details. Added a reference label for the local Conda environment in the installation guide for easier cross-referencing.
rclune
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nscorley
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Oct 13, 2025
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Thank you so much for this PR! A couple minor nits then ready to merge
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 Removed outdated Apptainer instructions and improved clarity in installation steps.
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Added notes about required file downloads and clarified example usage for parsing PDB files. Updated import statements and corrected file paths in documentation to improve clarity and accuracy for users.
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This PR is tagged as a draft if it is still under development and not ready for review.
[ x] I have ensured that all my commits follow angular commit message conventions.
[x ] I have run
make formaton the codebase before submitting the PR (this autoformats the code and lints it).[ x] I have named the PR in angular PR message format as well (c.f. above), with a sensible tag line that summarizes all the changes in the PR.
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