[Paururo]

Preparation for making the repository public.

Licence

LICENSE holds the GNU Affero General Public License v3.0, so Cargo.toml (AGPL-3.0-only), the README badge and footer, every website footer and the citation page now say so. The contributing guide states the licence instead of warning that the files disagree. tools/check_site.py reads LICENSE and fails if Cargo.toml, CITATION.cff, the README, the contributing guide or the website name another one.

Citation file

CITATION.cff names Paula Ruiz-Rodriguez and Mireia Coscolla with their ORCIDs and affiliation, for GitHub's "Cite this repository" button and for Zenodo. The version, release date and DOI go in on release day.

Synthetic data, said everywhere the example report appears

• Inside the report, a "Synthetic example data" note sits next to its title, so it shows in the website's frame, full screen and on a phone. Below 900 px it shortens to "Synthetic" so the top bar never overflows (checked at nine widths against the unlabelled report). tools/label_example_report.py adds it after the report is regenerated.
• On the website: the hero button ("Open an example report", tagged synthetic data), the section text, the window bar above the frame and the phone fallback.
• In the README and on the Run report page.

tools/check_site.py fails on an example report without the note, or on a link to it that does not say its data are synthetic.

A benchmark anyone can run

benchmarks/performance_benchmark.py times Recore on any pangenome, given the same inputs as Recore: wall time, peak memory of the process tree, temporary disk and output size. An optional Newick tree keeps only its tips, and --max-clusters keeps a subset for a quick run. It replaces a benchmark that only ran on one local dataset. It was run on the tutorial dataset with the full profile, with a partial tree, with a cluster limit and without annotations, and gave Rescued 11 / Matrix-corrected 8 where the website says so. benchmarks/self_benchmark.py now works in the system's temporary directory instead of a macOS path.

Smaller things

• The Run report page printed a leftover MkDocs button attribute as text. It is gone, and tools/check_site.py fails on MkDocs syntax left in the markdown.
• .gitignore drops an editor-specific entry.

Every new check was broken on purpose and caught it. Locally fmt, clippy, the tests, the build, check_site.py --run-tutorial and the auto-merge gate check all pass.