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Update packages page hierarchy and scirpy links
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‎content/_index.md

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@@ -32,7 +32,7 @@ description = "Foundational tools for single-cell omics data analysis"
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[[packages]]
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name = "scirpy"
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description = "Single-cell immune sequencing analysis framework"
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url = "https://icbi-lab.github.io/scirpy/latest/"
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url = "https://scirpy.scverse.org/"
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[[packages]]
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name = "squidpy"

‎content/packages/_index.md

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@@ -3,9 +3,10 @@ title = "Packages"
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aliases = ["/projects/"]
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[[sections]]
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core_packages = "These packages are considered foundational in that many other packages build upon them. Joint maintenance by the core team guarantees long-term stability."
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datastructures = "Data structures are the foundational building block for all scverse packages. Building upon common data structures ensures interoperability."
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datastructures_post = "In addition to these packages, we define standards on how to represent certain data types in these data structures. For now, such a specification is available for [Adaptive Immune Receptor Repertoire (AIRR) data](https://scirpy.scverse.org/en/latest/data-structure.html#storing-airr-rearrangement-data-in-anndata). Representations for other data types (e.g. scATAC-seq) will follow."
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core_packages = "These packages are considered foundational in that many other packages build upon them. Joint maintenance by the core team guarantees long-term stability."
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frameworks = ""
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ecosystem = "Many popular packages rely on scverse functionality. For instance, they take advantage of established data format standards such as AnnData and MuData, or are designed to be integrated into the workflow of analysis frameworks. Here, we list ecosystem packages following development best practices (continuous testing, documented, available through standard distribution tools).\n\n *This listing is a work in progress. See [scverse/ecosystem-packages](https://github.com/scverse/ecosystem-packages) for inclusion criteria, and to submit more packages.*"
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[[datastructures]]
@@ -134,15 +135,15 @@ aliases = ["/projects/"]
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[[packages]]
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name = "scirpy"
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description = "Single-cell immune sequencing framework"
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url = "https://icbi-lab.github.io/scirpy/stable/"
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url = "https://scirpy.scverse.org"
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img = "../img/icons/scirpy.svg"
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details = "Scirpy is a scalable toolkit to analyse T-cell receptor or B-cell receptor repertoires from single-cell RNA sequencing data. It seamlessly integrates with scanpy and provides various modules for data import, analysis and visualization."
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[[packages.links]]
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text = "GitHub"
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url = "https://github.com/icbi-lab/scirpy"
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[[packages.links]]
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text = "Documentation and tutorials"
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url = "https://icbi-lab.github.io/scirpy/latest/"
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url = "https://scirpy.scverse.org/"
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[[packages.links]]
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text = "PyPI"
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url = "https://pypi.org/project/scirpy/"

‎layouts/packages/list.html

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@@ -15,39 +15,40 @@ <h1>{{ .Title }}</h1>
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<article class="post">
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{{ $sections := index .Params.sections 0 }}
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<div class="post-content" id="packages-content">
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{{ if .Params.datastructures }}
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<h2 id="datastructures">Data structures</h2>
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{{ $sections.datastructures | markdownify }}
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<div id="packages-list">
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{{ $datastructures := .Params.datastructures }}
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{{ range $i, $e := $datastructures }}
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<div class="package-section">
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<div class="package-img">
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<img src="{{ .img }}" />
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</div>
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<div class="package-info">
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<div class="package-tile" id="{{ .name }}-tile">
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<div class="package-text">
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<span class="package-name">{{ .name }}</span>
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<span class="package-details">{{ .details | markdownify }}</span>
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</div>
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</div>
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<div class="package-links">
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{{ range $k, $v := $e.links }}
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<a href="{{ $v.url }}" target="_blank">{{ $v.text }}</a>
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{{ end }}
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</div>
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</div>
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</div>
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{{ end }}
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</div>
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{{ end }}
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<h3>Modality-specific extensions</h3>
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<p>{{ $sections.datastructures_post | markdownify }}</p>
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{{ if .Params.packages }}
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<h2 id="core-packages">Packages maintained by core team</h2>
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{{ $sections.core_packages | markdownify }}
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{{ if .Params.datastructures }}
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<h3 id="datastructures">Data structures</h3>
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{{ $sections.datastructures | markdownify }}
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<div id="packages-list">
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{{ $datastructures := .Params.datastructures }}
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{{ range $i, $e := $datastructures }}
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<div class="package-section">
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<div class="package-img">
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<img src="{{ .img }}" />
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</div>
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<div class="package-info">
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<div class="package-tile" id="{{ .name }}-tile">
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<div class="package-text">
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<span class="package-name">{{ .name }}</span>
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<span class="package-details">{{ .details | markdownify }}</span>
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</div>
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</div>
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<div class="package-links">
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{{ range $k, $v := $e.links }}
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<a href="{{ $v.url }}" target="_blank">{{ $v.text }}</a>
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{{ end }}
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</div>
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</div>
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</div>
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{{ end }}
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</div>
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{{ end }}
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<h4>Modality-specific extensions</h4>
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<p>{{ $sections.datastructures_post | markdownify }}</p>
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<h3 id="frameworks">Frameworks</h3>
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{{ $sections.frameworks | markdownify }}
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<div id="packages-list">
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{{ $packages := .Params.packages }}
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{{ range $i, $e := $packages }}

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