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Add LaTeX paper skeleton for Bioinformatics Application Note - #21
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Introduce paper/ with a Bioinformatics-oriented draft (main.tex, BibTeX, Makefile, figure/table placeholders, build README) and ignore LaTeX build artifacts. Paper-prep only; no product changes. Co-authored-by: ehsan.estaji <ehsan.estaji@gmail.com> Signed-off-by: Cursor Agent <cursoragent@cursor.com>
Complete a full Application Note first draft (claims, gates, packaging, TikZ overview figure, v0.6 evidence table) and add paper/HANDOFF.md plus README updates so cold-start agents can resume the paper track. Signed-off-by: Cursor Agent <cursoragent@cursor.com> Co-authored-by: ehsan.estaji <ehsan.estaji@gmail.com>
Reuse author/ORCID/Umeå affiliation, WIFORCE funding, COI, AI disclosure, CRediT, and acknowledgements from the VariantFlow Bioinformatics note. Keep FastaGuard-specific evidence, claims, and bibliography; expand handoff docs for cold-start agents. Signed-off-by: Cursor Agent <cursoragent@cursor.com> Co-authored-by: ehsan.estaji <ehsan.estaji@gmail.com>
Prepare format-free Bioinformatics submission: submission.yml, check script, paper-readiness checklist, cover letter, Zenodo/bioRxiv prep without fake DOIs, pin Availability to v1.0.0 and Table 1 to the v0.6 evidence TSV. Signed-off-by: Cursor Agent <cursoragent@cursor.com> Co-authored-by: ehsan.estaji <ehsan.estaji@gmail.com>
Minted version DOI 10.5281/zenodo.23622311 (concept 10.5281/zenodo.23622310) from the existing v1.0.0 release via Zenodo GitHub integration.
Claims re-tested against a binary built from the v1.0.0 tag; related work and references audited against Crossref/DataCite. - Table 1: state --min-contig-length 1 (default => synthetic fixture WARNs), note N. crassa count includes mitochondrion NC_026614.1, report that v1.0.0 reproduces the two local fixtures - Remove unsupported benchmark sentence, "fast", SNIC/HPC2N acknowledgement, and the paper/ supplementary pointer (not in the v1.0.0 tree) - Correct gate blockers, release-binary platforms, determinism wording and the NCBI policy description - Add related work (py_fasta_validator, fa-lint, AssemblyQC, SeqFu, gfastats) and missing citations; 24 verified bib entries, 0 BibTeX warnings - Fix --flag en-dash ligature, PDF metadata, Fig. 1 label overlap - Cover letter: preprint, AI-use and archive-DOI disclosures (OUP policy) - Handoff docs, manifest and bioRxiv checklist updated Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
The Rust quality gate runs `git grep -nI -E '[[:blank:]]$'` over the repo and has failed on this branch since the cover letter was added. Replace Markdown two-space hard breaks with blank-line-separated lines in paper/cover-letter.md, paper/README.md and docs/paper-readiness.md. No wording changes. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…tle disclosures - Table 2 and paper/comparison/: capability comparison of py_fasta_validator 0.6, fa-lint 1.2.0, table2asn 1.29.324, SeqKit 2.14.0 and FastaGuard v1.0.0 on 30 author-constructed FASTA files (expectations fixed before running) and the two RefSeq assemblies; tool versions and SHA-256 checksums recorded. Generated results are byte-reproducible; the corpus favours FastaGuard and the paper says so. - docs/evidence/results/v1.0.0-rerun/: all five evidence-pack rows re-run with a build of the v1.0.0 tag; verdicts, gates, blockers, lengths, sequence counts, input SHA-256 and exit codes match the frozen v0.6.0 rows (timings differ). - AI-use disclosure rewritten per the authors (software and benchmarks first, manuscript drafted solely from them; Cursor agents and Claude Code named) in both the manuscript and the cover letter. Funding unchanged (matches the three related preprints); SNIC/HPC2N acknowledgement stays removed. - Record co-author confirmation (reported by the corresponding author), update the manifest and handoff docs, add the table2asn reference. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
… manifest and handoff The preprint was submitted on 2026-10-24 and bioRxiv acknowledged it; it is in screening and has no DOI yet. Update biorxiv_status, the human-blocker list, the handoff status table (with the form notes learned during submission) and the readiness file so a resuming agent starts from the real state. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
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Signed-off-by: Ehsan ESTAJI <71376358+ehsanestaji@users.noreply.github.com>
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Scoped change description
Paper-only completion of the format-free first-submission package for the user-confirmed Bioinformatics (OUP) Application Note.
Machine-ready now
docs/evidence/results/v0.6/evidence_summary.tsv; Availability cites GitHubv1.0.0paper/submission.yml,paper/check_submission.py,make checkdocs/paper-readiness.md(DONE vs USER-ACTION).zenodo.json,paper/ZENODO.md, bioRxiv checklist/make biorxivStill USER-ACTION (Ehsan) — ScholarOne upload, Zenodo DOI mint from existing
v1.0.0, co-author OK, APC/R&P. This PR does not claim ScholarOne submitted.Tests
make checkexits 0 (~2.3k tokens; human blockers listed only).Contract impact
Documentation impact
paper/,docs/paper-readiness.md,.zenodo.json)Review checklist
Signed-off-by:line.