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Move the citation list off the landing page #274

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Merged
Zethson merged 1 commit into from
Aug 25, 2026
Merged

Move the citation list off the landing page #274

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21 changes: 0 additions & 21 deletions assets/main.scss
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
}
}
}
}
}

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43 changes: 2 additions & 41 deletions content/_index.md
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Expand Up @@ -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"

+++
23 changes: 6 additions & 17 deletions layouts/index.html
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Expand Up @@ -129,23 +129,12 @@ <h2>{{ .Title }}</h2>
<section id="references">
<div class="section-heading">References</div>
<div class="section-content">
{{ if .Params.references }}
<p class="section-paragraph">
{{ .Params.references.text | markdownify }}
</p>
<div class="tiles-list" id="refs-list">
{{ $refs := .Params.references.citations }}
{{ range $i, $e := $refs }}
<a href="{{ .url }}" target="_blank">
<div class="ref-tile" id="{{ .id }}-ref-tile">
<div class="ref-text">
{{ .text }}
</div>
</div>
</a>
{{ end }}
</div>
{{ end }}
<p class="section-paragraph">
{{ .Params.references.text | markdownify }}
</p>
<a href="/packages/">
<div class="more">Find each package's publication</div>
</a>
</div>
</section>
</div>
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5 changes: 5 additions & 0 deletions layouts/partials/package-section.html
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Expand Up @@ -37,6 +37,11 @@
<a href="{{ $url }}" target="_blank">Conda</a>
{{ end }}
{{ end }}
{{/* The registry lists every paper a package has; the first is the one to cite. */}}
{{ with $p.publications }}
{{ $doi := index . 0 }}
<a href="{{ cond (hasPrefix $doi "http") $doi (printf "https://doi.org/%s" $doi) }}" target="_blank">Paper</a>
{{ end }}
</div>
</div>
</div>