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

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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

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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

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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

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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

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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

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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

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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 ( '