Basic CitationCompass integration

[mtauraso]

Codex generated this pull request, but encountered an unexpected error after generation. This is a placeholder PR message.

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Codex Task

[Copilot]

Pull request overview

Adds first-class citation metadata for Hyrax and a curated dependency-citation workflow via Citation Compass, with lightweight validation and user-facing documentation.

Changes:

• Add CITATION.cff for citing Hyrax itself.
• Add citation_compass.toml to curate “methodologically central” dependency citations and document the canonical generation command.
• Add tests and docs updates to ensure citation artifacts remain present and discoverable.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/hyrax/test_citation_metadata.py	Adds basic tests to assert citation files exist and contain expected content.
README.md	Documents how to cite Hyrax and how to generate dependency citations.
docs/reference_and_faq.rst	Adds a reference/FAQ section describing citation and attribution workflows.
CITATION.cff	Introduces repository-root citation metadata for Hyrax.
citation_compass.toml	Adds curated Citation Compass configuration for key dependencies.
CITATION_COMPASS_IMPLEMENTATION_PLAN.md	Adds a short implementation plan and maintenance policy for the citation workflow.

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[github-actions]

Before [6148393]	After [a06c126]	Ratio	Benchmark (Parameter)
1.97±0.03s	2.06±0.03s	1.05	benchmarks.time_database_connection_help
296±3ms	310±5ms	1.05	benchmarks.time_import
15.465946515928916	16.203467288067017	1.05	data_cache_benchmarks.DataCacheBenchmarks.track_cache_hsc1k_hyrax_size_undercount
2.02±0.02s	2.09±0.03s	1.03	benchmarks.time_help
2.04±0.01s	2.11±0.04s	1.03	benchmarks.time_infer_help
1.47G	1.52G	1.03	vector_db_benchmarks.VectorDBInsertBenchmarks.peakmem_load_vector_db(16384, 'chromadb')
1.98±0.04s	2.03±0.02s	1.02	benchmarks.time_lookup_help
40.2±0.5ms	40.9±1ms	1.02	benchmarks.time_nb_obj_dir
3.71±0.01s	3.77±0.01s	1.02	vector_db_benchmarks.VectorDBInsertBenchmarks.time_load_vector_db(256, 'chromadb')
5.26±0.02s	5.37±0.04s	1.02	vector_db_benchmarks.VectorDBInsertBenchmarks.time_load_vector_db(64, 'qdrant')

Click here to view all benchmarks.

[mtauraso]

@copilot Can you resolve the pre-commit error in CI on this? It appears to be a ruff formatting thing.

[Copilot]

@mtauraso I've opened a new pull request, #794, to work on those changes. Once the pull request is ready, I'll request review from you.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 64.93%. Comparing base (7e4b1fa) to head (273ab83).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #793      +/-   ##
==========================================
+ Coverage   64.84%   64.93%   +0.09%     
==========================================
  Files          61       61              
  Lines        5896     5912      +16     
==========================================
+ Hits         3823     3839      +16     
  Misses       2073     2073              

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[jeremykubica]

I don't think the command

python -m citation_compass --config citation_compass.toml

in your PR will work. Currently citation compass doesn't have a main, so it can't be run. It also doesn't process toml files. We could add this to citation-compass if it would be useful though.

[mtauraso]

Given this feedback and a closer look at citation-compass I'm going to have a re-think about this PR.