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Paururo merged 1 commit into from
Oct 18, 2026
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docs: point to the Zenodo archive from the README, the citation file and the website #29

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8 changes: 8 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,14 @@ and Recore uses semantic versioning.

## [Unreleased]

### Added

- Recore is archived on Zenodo. The README carries the DOI badge and both DOIs
(10.5281/zenodo.23448590 for every version, 10.5281/zenodo.23448591 for 1.0.0), `CITATION.cff` holds
them, the citation page has a BibTeX entry for the software, and the
website's footer links the archive. `tools/check_site.py` fails if the DOI in
`CITATION.cff` is missing from the README, the citation page or the footer.

## [1.0.0] - 2026-10-18

The first public release, under the GNU Affero General Public License v3.0.
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8 changes: 8 additions & 0 deletions CITATION.cff
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Expand Up @@ -16,6 +16,14 @@ authors:
repository-code: "https://github.com/PathoGenOmics-Lab/recore"
url: "https://pathogenomics-lab.github.io/recore/"
version: 1.0.0
doi: 10.5281/zenodo.23448590
identifiers:
- type: doi
value: 10.5281/zenodo.23448590
description: "Every version; resolves to the latest"
- type: doi
value: 10.5281/zenodo.23448591
description: "Version 1.0.0"
date-released: "2026-10-18"
license: AGPL-3.0-only
keywords:
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4 changes: 4 additions & 0 deletions README.md
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Expand Up @@ -23,6 +23,7 @@ puts back the genes that are really there, and keeps the evidence for each one.
<a href="https://github.com/PathoGenOmics-Lab/recore/actions/workflows/ci.yml"><img src="https://github.com/PathoGenOmics-Lab/recore/actions/workflows/ci.yml/badge.svg" alt="CI"></a>
<a href="LICENSE"><img src="https://img.shields.io/badge/license-AGPLv3-blue.svg" alt="License: AGPLv3"></a>
<img src="https://img.shields.io/badge/Rust-1.85%2B-orange.svg" alt="Rust 1.85+">
<a href="https://doi.org/10.5281/zenodo.23448590"><img src="https://img.shields.io/badge/doi-10.5281%2Fzenodo.23448590-%23ff0077" alt="DOI 10.5281/zenodo.23448590"></a>

</div>

Expand Down Expand Up @@ -146,6 +147,9 @@ here as well:
> Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality
> control of pangenome presence/absence matrices. *In preparation.*

The software itself is archived on Zenodo: [doi:10.5281/zenodo.23448590](https://doi.org/10.5281/zenodo.23448590)
for every version, or [doi:10.5281/zenodo.23448591](https://doi.org/10.5281/zenodo.23448591) for 1.0.0.

<sub>AGPL-3.0, see [LICENSE](LICENSE) · [PathoGenOmics Lab](https://github.com/PathoGenOmics-Lab) · Paula Ruiz-Rodriguez, paula.ruiz.rodriguez@csic.es</sub>

---
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11 changes: 11 additions & 0 deletions docs/about/citation.html
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Expand Up @@ -81,6 +81,16 @@ <h1 id="citation">Citation</h1>
note = {In preparation},
howpublished = {\url{https://github.com/PathoGenOmics-Lab/recore}}
}</pre></div>
<p>The software is archived on Zenodo. Cite <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a> for Recore in general (it resolves to the latest version), or the version you ran, such as <a href="https://doi.org/10.5281/zenodo.23448591">doi:10.5281/zenodo.23448591</a> for 1.0.0:</p>
<div class="code" data-lang="bibtex"><pre>@software{recore_software,
author = {Ruiz-Rodriguez, Paula and Coscolla, Mireia},
title = {Recore},
version = {1.0.0},
year = {2026},
publisher = {Zenodo},
doi = {10.5281/zenodo.23448591},
url = {https://doi.org/10.5281/zenodo.23448591}
}</pre></div>
<p>Please also cite the tools Recore depends on for the run you report:</p>
<ul><li><strong>minimap2</strong>, for every sequence search: Li H. (2018). Minimap2: pairwise alignment for nucleotide sequences. <em>Bioinformatics</em> 34(18):3094-3100.</li><li><strong>MMseqs2</strong>, if you used <code>--nsc-engine mmseqs2</code>: Steinegger M, Soeding J. (2017). MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. <em>Nature Biotechnology</em> 35:1026-1028.</li><li>the pangenome tool that produced the input matrix, for example <strong>Panaroo</strong>: Tonkin-Hill G, et al. (2020). Producing polished prokaryotic pangenomes with the Panaroo pipeline. <em>Genome Biology</em> 21:180.</li></ul>
<h2 id="contact">Contact<a class="anchor" href="#contact" aria-label="Link to this section">#</a></h2>
Expand All @@ -98,6 +108,7 @@ <h2 id="license">License<a class="anchor" href="#license" aria-label="Link to th
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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17 changes: 17 additions & 0 deletions docs/about/citation.md
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Expand Up @@ -16,6 +16,23 @@ If you use Recore, please cite:
}
```

The software is archived on Zenodo. Cite
[doi:10.5281/zenodo.23448590](https://doi.org/10.5281/zenodo.23448590) for Recore in general (it
resolves to the latest version), or the version you ran, such as
[doi:10.5281/zenodo.23448591](https://doi.org/10.5281/zenodo.23448591) for 1.0.0:

```bibtex
@software{recore_software,
author = {Ruiz-Rodriguez, Paula and Coscolla, Mireia},
title = {Recore},
version = {1.0.0},
year = {2026},
publisher = {Zenodo},
doi = {10.5281/zenodo.23448591},
url = {https://doi.org/10.5281/zenodo.23448591}
}
```

Please also cite the tools Recore depends on for the run you report:

- **minimap2**, for every sequence search:
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1 change: 1 addition & 0 deletions docs/about/contributing.html
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Expand Up @@ -124,6 +124,7 @@ <h2 id="reporting-a-problem">Reporting a problem<a class="anchor" href="#reporti
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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2 changes: 1 addition & 1 deletion docs/assets/search-index.js
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Expand Up @@ -982,7 +982,7 @@ window.RECORE_DOCS_INDEX = [
"page": "Citation",
"section": "",
"url": "about/citation.html",
"text": "If you use Recore, please cite: Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation. Please also cite the tools Recore depends on for the run you report: minimap2, for every sequence search: Li H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094-3100. MMseqs2, if you used --nsc-engine mmseqs2: Steinegger M, Soeding J. (2017). MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology 35:1026-1028. the pangenome tool "
"text": "If you use Recore, please cite: Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation. The software is archived on Zenodo. Cite doi:10.5281/zenodo.23448590 for Recore in general (it resolves to the latest version), or the version you ran, such as doi:10.5281/zenodo.23448591 for 1.0.0: Please also cite the tools Recore depends on for the run you report: minimap2, for every sequence search: Li H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094-3100. MMseqs2, if you used --"
},
{
"page": "Citation",
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4 changes: 4 additions & 0 deletions docs/assets/site.css
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Expand Up @@ -1504,6 +1504,10 @@ kbd {
color: var(--ink-soft);
}

.foot .doi {
margin: 10px 0 0;
}

@media (max-width: 760px) {
.foot .wrap {
grid-template-columns: minmax(0, 1fr);
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1 change: 1 addition & 0 deletions docs/documentation.html
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Expand Up @@ -104,6 +104,7 @@ <h2 class="docs-group">About</h2>
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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Expand Up @@ -95,6 +95,7 @@ <h2 id="choosing-the-optional-inputs">Choosing the optional inputs<a class="anch
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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Expand Up @@ -168,6 +168,7 @@ <h2 id="next">Next<a class="anchor" href="#next" aria-label="Link to this sectio
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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1 change: 1 addition & 0 deletions docs/guide/matrix-policies.html
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Expand Up @@ -99,6 +99,7 @@ <h2 id="reporting-it">Reporting it<a class="anchor" href="#reporting-it" aria-la
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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Expand Up @@ -293,6 +293,7 @@ <h3 id="common-debug-messages-and-their-meaning">Common debug messages and their
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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Expand Up @@ -151,6 +151,7 @@ <h3 id="--nsc-threshold-nsc-similarity"><code>--nsc-threshold</code> (NSC simila
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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Expand Up @@ -142,6 +142,7 @@ <h2 id="if-you-did-not-use---write-html-report">If you did not use <code>--write
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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1 change: 1 addition & 0 deletions docs/how-it-works.html
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Expand Up @@ -97,6 +97,7 @@ <h2>Go deeper</h2>
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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Expand Up @@ -235,6 +235,7 @@ <h2 id="computational-complexity">Computational Complexity<a class="anchor" href
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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Expand Up @@ -93,6 +93,7 @@ <h2 id="which-policy-corrects-which-state">Which policy corrects which state<a c
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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Expand Up @@ -106,6 +106,7 @@ <h2 id="where-the-fields-live">Where the fields live<a class="anchor" href="#whe
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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Expand Up @@ -115,6 +115,7 @@ <h2 id="reproducible-review">Reproducible review<a class="anchor" href="#reprodu
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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Expand Up @@ -174,6 +174,7 @@ <h2 id="rescue-type-priority-in-conflict-resolution">Rescue Type Priority in Con
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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Expand Up @@ -315,6 +315,7 @@ <h2>Open source, on GitHub</h2>
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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Expand Up @@ -230,6 +230,7 @@ <h2>Go deeper</h2>
<div>
<h3>Cite</h3>
<blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. <i>In preparation.</i></blockquote>
<p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>
</div>
<div>
<h3>Learn more</h3>
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3 changes: 2 additions & 1 deletion tools/build_docs.py
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Expand Up @@ -427,7 +427,8 @@ def footer(root: str) -> str:
return (
'<footer class="foot">\n <div class="wrap">\n <div>\n <h3>Cite</h3>\n'
" <blockquote>Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome "
"presence/absence matrices. <i>In preparation.</i></blockquote>\n </div>\n"
"presence/absence matrices. <i>In preparation.</i></blockquote>\n"
' <p class="doi">Software: <a href="https://doi.org/10.5281/zenodo.23448590">doi:10.5281/zenodo.23448590</a></p>\n </div>\n'
" <div>\n <h3>Learn more</h3>\n <ul>\n"
f' <li><a href="{root}index.html">Get started</a></li>\n'
f' <li><a href="{root}{INDEX}">Documentation</a></li>\n'
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12 changes: 11 additions & 1 deletion tools/check_site.py
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Expand Up @@ -27,7 +27,9 @@
synthetic the example report says its data are made up, next to its title,
and so does every link to it;
version the version in Cargo.toml is the one CITATION.cff and the example
report carry, and the CHANGELOG has a section and a link for it;
report carry, the CHANGELOG has a section and a link for it, and the
DOI in CITATION.cff is shown in the README, on the citation page and
in the footer;
dashes no em-dashes;
try with --run-tutorial, the "Try it" commands are run as written and
summary.txt must give the numbers the page promises.
Expand Down Expand Up @@ -478,6 +480,14 @@ def check_versions() -> list[str]:
problems.append(f"CHANGELOG.md: no dated '## [{version}]' section for the version in Cargo.toml")
if not re.search(rf"^\[{re.escape(version)}\]: https://", changelog, flags=re.M):
problems.append(f"CHANGELOG.md: no link line for [{version}] at the bottom")
# The archive's DOI, once there is one, is the same everywhere it is shown.
doi = re.search(r"^doi:\s*(\S+)", Path("CITATION.cff").read_text(encoding="utf-8"), flags=re.M)
if doi:
for place, text in (("README.md", README.read_text(encoding="utf-8")),
("docs/about/citation.md", (SITE / "about" / "citation.md").read_text(encoding="utf-8")),
("docs/index.html footer", (SITE / "index.html").read_text(encoding="utf-8"))):
if doi.group(1) not in text:
problems.append(f"{place}: does not show the DOI {doi.group(1)} that CITATION.cff holds")
shown = re.search(r"<meta name='generator' content='Recore v([^']+)'>", EXAMPLE_REPORT.read_text(encoding="utf-8"))
if not shown or shown.group(1) != version:
problems.append(
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