From 0fd9521a3c0ee3b2a0f771a5601e4b52d7dad901 Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Tue, 25 Aug 2026 10:47:29 +0200 Subject: [PATCH] Move the citation list off the landing page MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Eight dense citation strings closed the landing page, in a section three times the height of the ecosystem, mission and team blocks beside it — each of which is a heading, a paragraph and a link. References now has that shape too. The citations move to where someone asks the question. Each core package row on /packages gains a Paper link, taken from the registry's publications field rather than kept by hand, so the list cannot go stale the way this one had: - anndata still cited the 2021 bioRxiv preprint, though the paper was published in JOSS in 2024 - decoupler, pertpy, SnapATAC2, MuData and rapids-singlecell were missing entirely Eleven of the twelve core packages have a DOI in the registry; rapids-singlecell has none and so gets no link. The scverse paper is not a package and has no row, so it stays on the landing page — as the one citation worth naming there rather than the first of eight. Closes #268 --- assets/main.scss | 21 ------------- content/_index.md | 43 ++------------------------- layouts/index.html | 23 ++++---------- layouts/partials/package-section.html | 5 ++++ 4 files changed, 13 insertions(+), 79 deletions(-) diff --git a/assets/main.scss b/assets/main.scss index e2fc28e..a21c7c7 100644 --- a/assets/main.scss +++ b/assets/main.scss @@ -607,27 +607,6 @@ body { } } } - #references { - #refs-list { - .ref-tile { - display: flex; - margin: 0 -0.8rem; - padding: 0.8rem; - width: 100%; - min-height: 1rem; - align-items: center; - background-color: #ff000000; - color: $tiletext; - transition: all 200ms ease-in-out; - border-radius: 0.5rem; - &:hover { - cursor: pointer; - background-color: $tilebg3; - } - font-size: 0.9rem; - } - } - } } } diff --git a/content/_index.md b/content/_index.md index 61d0227..996bc1e 100644 --- a/content/_index.md +++ b/content/_index.md @@ -29,47 +29,8 @@ Scverse is a community project currently governed by the developers of the core [references] text = """\ -Scverse tools are used in numerous research and industry projects across the globe and are referenced in [thousands](https://scholar.google.ru/scholar?cites=14568046068402025757) of academic publications. Consider consulting the following references for more information about core scverse libraries and citing the relevant articles when using them in your work: +scverse tools are used in research and industry projects across the globe and are cited in [thousands](https://scholar.google.ru/scholar?cites=14568046068402025757) of academic publications. +If they are useful in your work, please cite [the scverse paper](https://www.nature.com/articles/s41587-023-01733-8) along with the individual packages you used. """ -[[references.citations]] - id = "scverse" - url = "https://www.nature.com/articles/s41587-023-01733-8" - text = "Virshup I, Bredikhin D, Heumos L, Palla G, Sturm G, Gayoso A, Kats I, Koutrouli M, scverse community, Berger B, Pe'er D, Regev A, Teichmann S, Finotello F, Wolf F, Yosef N, Stegle O, Theis F: The scverse project provides a computational ecosystem for single-cell omics data analysis. Nature Biotechnology. 2023 April 10" - -[[references.citations]] - id = "scanpy" - url = "https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1382-0" - text = "Wolf F, Angerer P, Theis FJ. SCANPY: large-scale single-cell gene expression data analysis. Genome Biology 19, 15 (2018)" - -[[references.citations]] - id = "muon" - url = "https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02577-8" - text = "Bredikhin D, Kats I, Stegle O. MUON: multimodal omics analysis framework. Genome Biology 23, 42 (2022)" - -[[references.citations]] - id = "anndata" - url = "https://www.biorxiv.org/content/10.1101/2021.12.16.473007" - text = "Virshup I, Rybakov S, Theis FJ, Angerer P, Wolf FA. anndata: Annotated data. bioRxiv. 2021 Dec 19" - -[[references.citations]] - id = "scvi-tools" - url = "https://www.nature.com/articles/s41587-021-01206-w" - text = "Gayoso A, Lopez R, Xing G, Boyeau P, Valiollah Pour Amiri V, Hong J, Wu K, Jayasuriya M, Mehlman E, Langevin M, Liu Y. A Python library for probabilistic analysis of single-cell omics data. Nature Biotechnology. 2022 Feb 7:1-4" - -[[references.citations]] - id = "scirpy" - url = "https://academic.oup.com/bioinformatics/article/36/18/4817/5866543" - text = "Sturm G, Szabo T, Fotakis G, Haider M, Rieder D, Trajanoski Z, Finotello F. Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data. Bioinformatics. 2020 Sep 15;36(18):4817-8" - -[[references.citations]] - id = "squidpy" - url = "https://doi.org/10.1038/s41592-021-01358-2" - text = "Palla G, Spitzer H, Klein M, Fischer D, Schaar AC, Kuemmerle LB, Rybakov S, Ibarra IL, Holmberg O, Virshup I, Lotfollahi M, Richter S, Theis FJ. Squidpy: a scalable framework for spatial omics analysis. Nature Methods 19, 171–178 (2022)" - -[[references.citations]] - id = "spatialdata" - url = "https://doi.org/10.1038/s41592-024-02212-x" - text = "Marconato L, Palla G, Yamauchi KA, Virshup I, Heidari E, Treis T, Vierdag WM, Toth M, Stockhaus S, Shrestha RB, Rombaut B. SpatialData: an open and universal data framework for spatial omics. Nature Methods. 2024 Mar 20:1-5" - +++ diff --git a/layouts/index.html b/layouts/index.html index 813a15d..2c66b13 100644 --- a/layouts/index.html +++ b/layouts/index.html @@ -129,23 +129,12 @@

{{ .Title }}

References
- {{ if .Params.references }} -

- {{ .Params.references.text | markdownify }} -

-
- {{ $refs := .Params.references.citations }} - {{ range $i, $e := $refs }} - -
-
- {{ .text }} -
-
- - {{ end }} -
- {{ end }} +

+ {{ .Params.references.text | markdownify }} +

+ +
Find each package's publication
+
diff --git a/layouts/partials/package-section.html b/layouts/partials/package-section.html index 5b82d36..97968d8 100644 --- a/layouts/partials/package-section.html +++ b/layouts/partials/package-section.html @@ -37,6 +37,11 @@ Conda {{ end }} {{ end }} + {{/* The registry lists every paper a package has; the first is the one to cite. */}} + {{ with $p.publications }} + {{ $doi := index . 0 }} + Paper + {{ end }}