From ef6930b7d4546d3f49f286bb499e17c660cd705c Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Tue, 7 Jul 2026 18:46:43 +0200 Subject: [PATCH] feat: generated llms.txt for AI agents Add a Hugo LLMS output format that renders /llms.txt from the homepage package front matter, plus curated links to other major scverse packages and project resources. Also fix mudata's dead docs URL. Co-Authored-By: Claude Opus 4.8 (1M context) --- config.toml | 8 ++++++ content/_index.md | 2 +- content/packages/_index.md | 4 +-- layouts/index.llms.txt | 54 ++++++++++++++++++++++++++++++++++++++ 4 files changed, 65 insertions(+), 3 deletions(-) create mode 100644 layouts/index.llms.txt diff --git a/config.toml b/config.toml index 6135cba3..360d6a76 100644 --- a/config.toml +++ b/config.toml @@ -8,3 +8,11 @@ description = "Foundational tools for omics data in the life sciences" [markup.goldmark.renderer] unsafe= true + +[outputs] +home = ["HTML", "RSS", "LLMS"] + +[outputFormats.LLMS] +mediaType = "text/plain" +baseName = "llms" +isPlainText = true diff --git a/content/_index.md b/content/_index.md index bdffb6c8..99e4dec5 100644 --- a/content/_index.md +++ b/content/_index.md @@ -12,7 +12,7 @@ description = "Foundational tools for single-cell omics data analysis" [[packages]] name = "mudata" description = "Multimodal data format" - url = "https://mudata.readthedocs.io/en/latest/" + url = "https://mudata.readthedocs.io/" [[packages]] name = "spatialdata" diff --git a/content/packages/_index.md b/content/packages/_index.md index c699cf6d..79d3cc0b 100644 --- a/content/packages/_index.md +++ b/content/packages/_index.md @@ -31,7 +31,7 @@ aliases = ["/projects/"] [[datastructures]] name = "mudata" description = "Multimodal data format" - url = "https://mudata.readthedocs.io/en/latest/" + url = "https://mudata.readthedocs.io/" img = "../img/libs/mudata_flat.svg" details = "MuData is a format for annotated multimodal datasets where each modality is represented by an AnnData object. MuData's reference implementation is in Python, and the cross-language functionality is achieved via HDF5-based .h5mu files with libraries in R and Julia." [[datastructures.links]] @@ -39,7 +39,7 @@ aliases = ["/projects/"] url = "https://github.com/scverse/mudata" [[datastructures.links]] text = "Documentation" - url = "https://mudata.readthedocs.io/en/latest/" + url = "https://mudata.readthedocs.io/" [[datastructures.links]] text = "PyPI" url = "https://pypi.org/project/mudata/" diff --git a/layouts/index.llms.txt b/layouts/index.llms.txt new file mode 100644 index 00000000..b3b6b442 --- /dev/null +++ b/layouts/index.llms.txt @@ -0,0 +1,54 @@ +# scverse + +> scverse is a consortium of foundational, interoperable open-source tools (mostly Python) for single-cell and spatial omics data analysis in the life sciences. + +scverse packages share common data structures (AnnData, MuData, SpatialData) to guarantee interoperability across the ecosystem. +Most package documentation lives on dedicated external sites, linked below. +This site (scverse.org) hosts the package index, tutorials, project governance, events, and the blog. + +## Core packages + +Foundational packages maintained by the scverse core team. +{{ range .Params.packages }} +- [{{ .name }}]({{ .url }}): {{ .description }} +{{- end }} + +## More packages + +Other major packages developed within the scverse GitHub organization. + +- [gget](https://scverse.org/gget/): Efficient querying of genomic reference databases. +- [PyDESeq2](https://pydeseq2.readthedocs.io/en/stable/): Python implementation of the DESeq2 pipeline for bulk RNA-seq differential expression analysis. +- [CellRank](https://cellrank.readthedocs.io/en/latest/): Cell fate and dynamics from multi-view single-cell data. +- [anndataR](https://anndataR.scverse.org): AnnData interoperability in R. +- [spatialdata-io](https://spatialdata.scverse.org/projects/io/en/latest/): Readers and converters for spatial omics formats into SpatialData. +- [napari-spatialdata](https://spatialdata.scverse.org/projects/napari/en/latest/): Interactive napari viewer for SpatialData. +- [spatialdata-plot](https://spatialdata.scverse.org/projects/plot/en/latest/): Static plotting for the SpatialData framework. +- [annbatch](https://annbatch.readthedocs.io): Minibatch loading for on-disk AnnData files, co-developed with Lamin Labs. +- [pytometry](https://pytometry.readthedocs.io/en/latest/): Flow and mass cytometry analytics. +- [rustar-aligner](https://scverse.org/rustar-aligner/): Rust implementation of the STAR RNA-seq aligner. +- [anndata-rs](https://scverse.org/anndata-rs/): Rust implementation of AnnData. + +## Learn +- [Tutorials]({{ absURL "learn/" }}): Getting-started tutorials for the core packages. +- [Package index]({{ absURL "packages/" }}): All core and ecosystem packages with links to docs, source, and distribution. +- [Single-cell best practices](https://www.sc-best-practices.org/): Community book on best practices for single-cell analysis. + +## About +- [Mission]({{ absURL "about/mission/" }}): What scverse is and why it exists. +- [Roles and governance]({{ absURL "about/roles/" }}): Core team, steering council, and how the project is run. +- [Code of conduct]({{ absURL "about/code_of_conduct/" }}): Community standards for participation. +- [AI policy]({{ absURL "about/ai_policy/" }}): Expectations for contributing AI-assisted code to scverse projects. + +## Community +- [GitHub](https://github.com/scverse): Source code for all scverse packages. +- [Discourse](https://discourse.scverse.org/): User forum for questions and discussion. +- [Zulip](https://scverse.zulipchat.com/): Developer chat. +- [Ecosystem packages](https://github.com/scverse/ecosystem-packages): Community packages built on scverse standards, and inclusion criteria. +- [cookiecutter-scverse](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/): Project template for creating new scverse-compatible packages. + +## Optional +- [Blog]({{ absURL "blog/" }}): Announcements and release notes. +- [Events]({{ absURL "events/" }}): Conferences and hackathons. +- [People]({{ absURL "people/" }}): Contributors and core team. +- [YouTube](https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA): Recorded talks and workshops.