From 3d2c580aad9ae5ff3eac0a45d7aa30468ac304fb Mon Sep 17 00:00:00 2001 From: Paula Ruiz-Rodriguez <50167687+Paururo@users.noreply.github.com> Date: Sun, 18 Oct 2026 09:51:42 +0200 Subject: [PATCH] docs: point to the Zenodo archive from the README, the citation file and the website Recore 1.0.0 is archived on Zenodo, so the README carries the DOI badge and both DOIs, CITATION.cff holds them, the citation page has a BibTeX entry for the software and the footer links the archive. check_site.py fails if the DOI in CITATION.cff goes missing from any of those places. --- CHANGELOG.md | 8 ++++++++ CITATION.cff | 8 ++++++++ README.md | 4 ++++ docs/about/citation.html | 11 +++++++++++ docs/about/citation.md | 17 +++++++++++++++++ docs/about/contributing.html | 1 + docs/assets/search-index.js | 2 +- docs/assets/site.css | 4 ++++ docs/documentation.html | 1 + docs/getting-started/inputs.html | 1 + docs/getting-started/tutorial.html | 1 + docs/guide/matrix-policies.html | 1 + docs/guide/outputs.html | 1 + docs/guide/parameters.html | 1 + docs/guide/report.html | 1 + docs/how-it-works.html | 1 + docs/how-it-works/algorithm.html | 1 + docs/how-it-works/evidence-states.html | 1 + docs/how-it-works/evolutionary-events.html | 1 + docs/how-it-works/limits.html | 1 + docs/how-it-works/rescue-types.html | 1 + docs/index.html | 1 + docs/reference.html | 1 + tools/build_docs.py | 3 ++- tools/check_site.py | 12 +++++++++++- 25 files changed, 82 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9ee9b9f..14da29a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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. diff --git a/CITATION.cff b/CITATION.cff index 963944f..71b6be4 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -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: diff --git a/README.md b/README.md index 620e4ea..15975a3 100644 --- a/README.md +++ b/README.md @@ -23,6 +23,7 @@ puts back the genes that are really there, and keeps the evidence for each one. CI License: AGPLv3 Rust 1.85+ +DOI 10.5281/zenodo.23448590 @@ -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. + AGPL-3.0, see [LICENSE](LICENSE) · [PathoGenOmics Lab](https://github.com/PathoGenOmics-Lab) · Paula Ruiz-Rodriguez, paula.ruiz.rodriguez@csic.es --- diff --git a/docs/about/citation.html b/docs/about/citation.html index 31accaa..605226a 100644 --- a/docs/about/citation.html +++ b/docs/about/citation.html @@ -81,6 +81,16 @@

Citation

note = {In preparation}, howpublished = {\url{https://github.com/PathoGenOmics-Lab/recore}} } +

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:

+
@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:

Contact#

@@ -98,6 +108,7 @@

LicenseSoftware: doi:10.5281/zenodo.23448590

Learn more

diff --git a/docs/about/citation.md b/docs/about/citation.md index ab0cc29..5d5d329 100644 --- a/docs/about/citation.md +++ b/docs/about/citation.md @@ -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: diff --git a/docs/about/contributing.html b/docs/about/contributing.html index 0f523eb..d0309f2 100644 --- a/docs/about/contributing.html +++ b/docs/about/contributing.html @@ -124,6 +124,7 @@

Reporting a problemSoftware: doi:10.5281/zenodo.23448590

Learn more

diff --git a/docs/assets/search-index.js b/docs/assets/search-index.js index 2873628..9faac1a 100644 --- a/docs/assets/search-index.js +++ b/docs/assets/search-index.js @@ -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", diff --git a/docs/assets/site.css b/docs/assets/site.css index c0b0436..afe6583 100644 --- a/docs/assets/site.css +++ b/docs/assets/site.css @@ -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); diff --git a/docs/documentation.html b/docs/documentation.html index 3bbf717..c470a72 100644 --- a/docs/documentation.html +++ b/docs/documentation.html @@ -104,6 +104,7 @@

About

Cite

Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation.
+

Software: doi:10.5281/zenodo.23448590

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diff --git a/docs/getting-started/inputs.html b/docs/getting-started/inputs.html index 10daec7..85dec25 100644 --- a/docs/getting-started/inputs.html +++ b/docs/getting-started/inputs.html @@ -95,6 +95,7 @@

Choosing the optional inputsSoftware: doi:10.5281/zenodo.23448590

Learn more

diff --git a/docs/getting-started/tutorial.html b/docs/getting-started/tutorial.html index 059897c..fb66564 100644 --- a/docs/getting-started/tutorial.html +++ b/docs/getting-started/tutorial.html @@ -168,6 +168,7 @@

NextSoftware: doi:10.5281/zenodo.23448590

Learn more

diff --git a/docs/guide/matrix-policies.html b/docs/guide/matrix-policies.html index 571285c..d4cdd97 100644 --- a/docs/guide/matrix-policies.html +++ b/docs/guide/matrix-policies.html @@ -99,6 +99,7 @@

Reporting it

Cite

Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation.
+

Software: doi:10.5281/zenodo.23448590

Learn more

diff --git a/docs/guide/outputs.html b/docs/guide/outputs.html index 15ee1da..cc51eb2 100644 --- a/docs/guide/outputs.html +++ b/docs/guide/outputs.html @@ -293,6 +293,7 @@

Common debug messages and their

Cite

Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation.
+

Software: doi:10.5281/zenodo.23448590

Learn more

diff --git a/docs/guide/parameters.html b/docs/guide/parameters.html index af7000d..86871e3 100644 --- a/docs/guide/parameters.html +++ b/docs/guide/parameters.html @@ -151,6 +151,7 @@

--nsc-threshold (NSC simila

Cite

Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation.
+

Software: doi:10.5281/zenodo.23448590

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diff --git a/docs/guide/report.html b/docs/guide/report.html index 0297efe..73e333c 100644 --- a/docs/guide/report.html +++ b/docs/guide/report.html @@ -142,6 +142,7 @@

If you did not use --write

Cite

Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation.
+

Software: doi:10.5281/zenodo.23448590

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diff --git a/docs/how-it-works.html b/docs/how-it-works.html index 31331c9..6a4fa1e 100644 --- a/docs/how-it-works.html +++ b/docs/how-it-works.html @@ -97,6 +97,7 @@

Go deeper

Cite

Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation.
+

Software: doi:10.5281/zenodo.23448590

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diff --git a/docs/how-it-works/algorithm.html b/docs/how-it-works/algorithm.html index e2d638a..98a4ed5 100644 --- a/docs/how-it-works/algorithm.html +++ b/docs/how-it-works/algorithm.html @@ -235,6 +235,7 @@

Computational Complexity

Cite

Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation.
+

Software: doi:10.5281/zenodo.23448590

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diff --git a/docs/how-it-works/evidence-states.html b/docs/how-it-works/evidence-states.html index cf965e9..5e9a5f4 100644 --- a/docs/how-it-works/evidence-states.html +++ b/docs/how-it-works/evidence-states.html @@ -93,6 +93,7 @@

Which policy corrects which state

Cite

Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation.
+

Software: doi:10.5281/zenodo.23448590

Learn more

diff --git a/docs/how-it-works/evolutionary-events.html b/docs/how-it-works/evolutionary-events.html index 2b0a3b5..23678dc 100644 --- a/docs/how-it-works/evolutionary-events.html +++ b/docs/how-it-works/evolutionary-events.html @@ -106,6 +106,7 @@

Where the fields liveSoftware: doi:10.5281/zenodo.23448590

Learn more

diff --git a/docs/how-it-works/limits.html b/docs/how-it-works/limits.html index dbbac0a..578b0f4 100644 --- a/docs/how-it-works/limits.html +++ b/docs/how-it-works/limits.html @@ -115,6 +115,7 @@

Reproducible reviewSoftware: doi:10.5281/zenodo.23448590

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diff --git a/docs/how-it-works/rescue-types.html b/docs/how-it-works/rescue-types.html index 87be91e..bf98352 100644 --- a/docs/how-it-works/rescue-types.html +++ b/docs/how-it-works/rescue-types.html @@ -174,6 +174,7 @@

Rescue Type Priority in Con

Cite

Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation.
+

Software: doi:10.5281/zenodo.23448590

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diff --git a/docs/index.html b/docs/index.html index db27bbd..6b141b8 100644 --- a/docs/index.html +++ b/docs/index.html @@ -315,6 +315,7 @@

Open source, on GitHub

Cite

Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation.
+

Software: doi:10.5281/zenodo.23448590

Learn more

diff --git a/docs/reference.html b/docs/reference.html index 400b283..d0e2e72 100644 --- a/docs/reference.html +++ b/docs/reference.html @@ -230,6 +230,7 @@

Go deeper

Cite

Ruiz-Rodriguez P, Coscolla M. (2026). Recore: post-hoc rescue and quality control of pangenome presence/absence matrices. In preparation.
+

Software: doi:10.5281/zenodo.23448590

Learn more

diff --git a/tools/build_docs.py b/tools/build_docs.py index 469bc3d..10e56ae 100644 --- a/tools/build_docs.py +++ b/tools/build_docs.py @@ -427,7 +427,8 @@ def footer(root: str) -> str: return ( '