docs: MSA documentation #72
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Adds structured citation metadata to enable: - GitHub citation UI - Zenodo automatic archiving on release Also updates README citation with corrected author list.
## [2.1.2](v2.1.1...v2.1.2) (2025-12-09) ### Bug Fixes * add CITATION.cff for Zenodo integration ([fc5b92c](fc5b92c))
…parsing utilities.
…ntroduce a parsing verification script with example data.
… inference in `io_utils.py`.
… data directory fixture
# [2.2.0](v2.1.2...v2.2.0) (2025-12-19) ### Features * add automated mmJSON parsing test and refactor buffer file type inference in `io_utils.py`. ([5db3631](5db3631)) * Add example CIF/JSON data, update dependencies, and modify I/O parsing utilities. ([ba00b49](ba00b49)) * Add mmjson file type support, update file type inference, and introduce a parsing verification script with example data. ([0a995dc](0a995dc))
Added the CLI information to the documentation in its own page. Cleaned up the CLI docstrings and added information about required docstrings. Added the preprocessing/msa functions to the API documentation. Thanks to Hope for helping test and take notes!
partrita
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Jan 19, 2026
…one-to-secondary-structure-group-from-dssp feat: add NONE value to SecondaryStructureGroup enum
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📋 PR Checklist
This PR is tagged as a draft if it is still under development and not ready for review.
I have ensured that all my commits follow angular commit message conventions.
I have run
make formaton the codebase before submitting the PR (this autoformats the code and lints it).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.
ℹ️ PR Description
What changes were made and why?
Added MSA documentation (CLI and API) to the external documentation. Adding the CLI information to the external docs required a new dependency, sphinxcontrib-typer.
How were the changes tested?
Built the documentation locally.
Additional Notes