settylab · katosh · May 13, 2024 · May 14, 2024 · May 14, 2024 · May 14, 2024
diff --git a/.github/workflows/make-json.yml b/.github/workflows/make-json.yml
@@ -15,7 +15,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: setup-yq
         run: |
           sudo curl -L "https://github.com/mikefarah/yq/releases/download/v4.28.2/yq_linux_amd64" > /usr/local/bin/yq
@@ -27,7 +27,7 @@ jobs:
           cat packages/**/meta.yaml
           yq -o=json packages/**/meta.yaml | jq -s . > build/ecosystem.json
       - name: Upload GitHub Pages artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v3
         with:
           path: "build"
 
@@ -48,7 +48,7 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v1
+        uses: actions/deploy-pages@v4
       - name: Trigger website build
         run: |
           curl -XPOST \

diff --git a/.github/workflows/register-template-repos.yml b/.github/workflows/register-template-repos.yml
@@ -10,11 +10,11 @@ jobs:
   register-template-repos:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.BOT_GH_TOKEN }}
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
           cache: "pip"

diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,5 @@
 .DS_STORE
 __pycache__/
-.ruff_cache/
+.*cache/
 
 /.vscode/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,13 +2,13 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
   # all files
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast
@@ -23,13 +23,13 @@ repos:
       - id: prettier
   # package metadata
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.28.2
+    rev: 0.33.3
     hooks:
       - id: check-jsonschema
         files: "schema.json"
         args: ["--check-metaschema"]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.28.2
+    rev: 0.33.3
     hooks:
       - id: check-jsonschema
         files: "packages/.*/meta.yaml"
@@ -45,7 +45,7 @@ repos:
         exclude: "^packages/.*/meta.yaml$"
   # template repo registry
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    rev: v0.13.0
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

diff --git a/README.md b/README.md
@@ -1,9 +1,10 @@
 # Scverse Ecosystem Packages
 
-This repository contains the list of scverse ecosystem packages that are displayed on scverse.org.
+This repository contains the list of scverse ecosystem packages that are displayed on scverse.org and are part of
+the scverse® project.
 The goal is to increase visibility of ecosystem packages and make it easier for users to find appropriate software.
 Registered ecosystem packages can also get their own tag to use on the [scverse forum](https://discourse.scverse.org) for user discussion.
-Authors of these packages can be added the [scverse github organization](https://github.com/scverse).
+Authors of these packages can be added to the [scverse github organization](https://github.com/scverse).
 In the future, we may also test releases of core packages against the test suites of ecosystem packages.
 
 If a package is part of this list, it means it fulfills certain minimum requirements as outlined below.
@@ -15,9 +16,9 @@ It **does not** imply endorsement or that an in-depth review has been performed.
 
 Submit a pull-request adding a `meta.yaml` file for your package to the `packages` directory.
 
--   Please refer to other entries for examples
--   The full definition of available fields is available in [`schema.json`](schema.json)
--   Please copy the checklist from below into the pull request description and answer all questions.
+- Please refer to other entries for examples
+- The full definition of available fields is available in [`schema.json`](schema.json)
+- Please copy the checklist from below into the pull request description and answer all questions.
 
 ## What are the requirements for an ecosystem package?
 
@@ -37,21 +38,30 @@ Short description: XXX
 
 How does the package use scverse data structures (please describe in a few sentences): XXX
 
--   [ ] The code is publicly available under an [OSI-approved](https://opensource.org/licenses/alphabetical) license
--   [ ] The package provides versioned releases
--   [ ] The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda)
--   [ ] The package uses automated software tests and runs them via continuous integration (CI)
--   [ ] The package provides API documentation via a website or README
--   [ ] The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions)
--   [ ] I am an author or maintainer of the tool and agree on listing the package on the scverse website
+- [ ] The code is publicly available under an [OSI-approved](https://opensource.org/licenses/alphabetical) license
+- [ ] The package provides versioned releases
+- [ ] The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda)
+- [ ] Automated tests cover essential functions of the package and a reasonable range of inputs and conditions [^1]
+- [ ] Continuous integration (CI) automatically executes these tests on each push or pull request [^2]
+- [ ] The package provides API documentation via a website or README[^3]
+- [ ] The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions)
+- [ ] I am an author or maintainer of the tool and agree on listing the package on the scverse website
 
 ### Recommended
 
--   [ ] Please announce this package on scverse communication channels (zulip, discourse, twitter)
--   [ ] Please tag the author(s) these announcements. Handles (e.g. `@scverse_team`) to include are:
-    -   Twitter:
-    -   Zulip:
-    -   Discourse:
-    -   Mastodon:
--   [ ] The package provides tutorials (or "vignettes") that help getting users started quickly
--   [ ] The package uses the [scverse cookiecutter template](https://github.com/scverse/cookiecutter-scverse).
+- [ ] Please announce this package on scverse communication channels (zulip, discourse, twitter)
+- [ ] Please tag the author(s) these announcements. Handles (e.g. `@scverse_team`) to include are:
+    - Zulip:
+    - Discourse:
+    - Mastodon:
+    - Bluesky:
+    - Twitter:
+
+- [ ] The package provides tutorials (or "vignettes") that help getting users started quickly
+- [ ] The package uses the [scverse cookiecutter template](https://github.com/scverse/cookiecutter-scverse).
+
+[^1]: We recommend thtat tests cover at least all user facing (public) functions. Minimal tests ensure that the function does not fail on an example data set. Ideally, tests also ensure the correctness of the results, e.g. by comparing against a snapshot.
+
+[^2]: Continuous integration means that software tests are automatically executed on every push to the git repository. This guarantees they are always run and that they are run in a clean environment. Scverse ecosystem packages most commonly use [GitHub Actions](https://github.com/features/actions) for CI. For an example, check out our [cookiecutter template](https://github.com/scverse/cookiecutter-scverse).
+
+[^3]: By API documentation, we mean an overview of _all_ public functions provided a package, with documentation of their parameters. For an example, see the [Scanpy documentation](https://scanpy.readthedocs.io/en/stable/api/preprocessing.html). In simple cases, this can be done manually in a README file. For anything more complex, we recommend the [Sphinx Autodoc plugin](https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html)
diff --git a/packages/CellAnnotator/meta.yaml b/packages/CellAnnotator/meta.yaml
@@ -0,0 +1,18 @@
+name: CellAnnotator
+description: |
+  CellAnnotator is a leightweight tool to query large language models for cell type labels in scRNA-seq data. It can incorporate prior knowledge, and it creates consistent labels across samples in your study.
+project_home: https://github.com/quadbio/cell-annotator
+documentation_home: https://cell-annotator.readthedocs.io/en/latest/
+install:
+  pypi: cell-annotator
+tags:
+  - cell type labels
+  - openai
+  - large language models
+  - automatic annotation
+  - cell state
+license: MIT
+version: v0.1.3
+authors:
+  - Marius1311
+test_command: pip install -e '.[test]' && pytest
diff --git a/packages/CellCharter/meta.yaml b/packages/CellCharter/meta.yaml
@@ -0,0 +1,21 @@
+name: CellCharter
+description: |
+  CellCharter is a framework to identify, characterize and compare spatial domains from spatial omics and multi-omics data.
+project_home: https://github.com/CSOgroup/cellcharter
+documentation_home: https://cellcharter.readthedocs.io/
+tutorials_home: https://cellcharter.readthedocs.io/
+publications:
+  - 10.1038/s41588-023-01588-4
+install:
+  pypi: cellcharter
+tags:
+  - spatial omics
+  - spatial clustering
+  - spatial domains
+  - gaussian mixture model
+license: BSD-3-Clause
+version: v0.3.1
+authors:
+  - marcovarrone
+test_command: |
+  pip install ".[test]" && pytest
diff --git a/packages/CellMapper/meta.yaml b/packages/CellMapper/meta.yaml
@@ -0,0 +1,17 @@
+name: CellMapper
+description: |
+  CellMapper is a leightweight tool to transfer labels, expression values and embeddings from reference to query datasets using k-NN mapping. It's fast and versatile, applicable to mapping scenarios in space, across modalities, or from an atlas to a new query dataset.
+project_home: https://github.com/quadbio/cellmapper
+documentation_home: https://cellmapper.readthedocs.io/en/latest/
+install:
+  pypi: cellmapper
+tags:
+  - k-NN based mapping
+  - rapids
+  - faiss
+  - query-to-reference
+license: MIT
+version: v0.1.2
+authors:
+  - Marius1311
+test_command: pip install -e '.[test]' && pytest
diff --git a/packages/GPTBioInsightor/meta.yaml b/packages/GPTBioInsightor/meta.yaml
@@ -0,0 +1,18 @@
+name: GPTBioInsightor
+description: |
+  GPTBioInsightor is a tool designed for single-cell data analysis, particularly beneficial for newcomers to a biological field or those in interdisciplinary areas who may lack sufficient biological background knowledge.
+  GPTBioInsightor utilizes the powerful capabilities of large language models to help people quickly gain knowledge and insight, enhancing their work efficiency.
+project_home: https://github.com/huang-sh/GPTBioInsightor
+documentation_home: https://gptbioinsightor.readthedocs.io/
+install:
+  pypi: gptbioinsightor
+tags:
+  - single-cell
+  - bioinformatics
+  - LLM
+  - AI
+license: BSD-3-Clause
+version: v0.3.0
+authors:
+  - huangsh
+test_command: pip install "." && pytest
diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml
@@ -0,0 +1,21 @@
+name: GRnnData
+description: |
+  An onverload of anndata to more easily work with gene networks.
+  Allows easy conversion between anndata and grnndata and provide loads of usefull utilities functions.
+project_home: https://github.com/cantinilab/GRnnData
+documentation_home: https://cantinilab.github.io/GRnnData/
+publications:
+  - 10.1101/2024.07.29.605556
+install:
+  pypi: grnndata
+tags:
+  - single cell
+  - RNAseq
+  - gene networks
+  - format
+  - utilities
+license: MIT
+version: v1.1.4
+authors:
+  - jkobject (jeremie kalfon)
+test_command: pip install . && make test
diff --git a/packages/LazySlide/meta.yaml b/packages/LazySlide/meta.yaml
@@ -0,0 +1,18 @@
+name: LazySlide
+description: |
+  LazySlide is a Python library for processing whole slide images (WSI) analysis. It provides a simple interface to perform robust preprocessing and advanced analysis for WSI.
+project_home: https://github.com/rendeirolab/lazyslide
+documentation_home: https://lazyslide.readthedocs.io/en/latest/
+install:
+  pypi: lazyslide
+tags:
+  - Pathology
+  - Whole Slide Imaging
+  - PyTorch
+license: MIT
+version: v0.3.0
+authors:
+  - Mr-Milk
+  - eabila
+  - afrendeiro
+test_command: uv run task test
diff --git a/packages/PEAKQC/meta.yaml b/packages/PEAKQC/meta.yaml
@@ -0,0 +1,17 @@
+name: PEAKQC
+description: periodicity evaluation in scATAC-seq data for quality assessment
+project_home: https://github.com/loosolab/PEAKQC
+documentation_home: https://loosolab.pages.gwdg.de/software/peakqc/
+publications:
+  - 10.1101/2025.02.20.639146
+install:
+  pypi: peakqc
+tags:
+  - single cell
+  - ATAC-seq
+  - quality control
+license: MIT
+version: 0.1.3
+authors:
+  - loosolab
+test_command: pip install . && pytest
diff --git a/packages/PILOT/meta.yaml b/packages/PILOT/meta.yaml
@@ -0,0 +1,50 @@
+name: PILOT
+description: |
+  PILOT is a Python library for Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport.
+project_home: https://github.com/CostaLab/PILOT
+documentation_home: https://pilot.readthedocs.io/en/latest/api.html
+tutorials_home: https://pilot.readthedocs.io/en/latest/
+publications:
+  - 10.1038/s44320-023-00003-8
+install:
+  conda_instructions: |
+    # Create a new conda environment with the required Python version and R base
+    conda create --name PILOT python=3.11.5 r-base
+    # Activate the new environment
+    conda activate PILOT
+    # Install the PILOT package from PyPI
+    pip install pilotpy
+  pypi: pilotpy
+tags:
+  - multi-omics
+  - single-cell
+  - trajectory
+  - pathomics-data
+  - ot
+  - patient-level
+license: MIT
+version: v2.0.6
+authors:
+  - Mehdi Joodaki
+  - Mina Shaigan
+  - Victor Parra
+  - Roman D. Bülow
+  - Christoph Kuppe
+  - David L. Hölscher
+  - Mingbo Cheng
+  - James S. Nagai
+  - Michaël Goedertier
+  - Nassim Bouteldja
+  - Vladimir Tesar
+  - Jonathan Barratt
+  - Ian S.D. Roberts
+  - Rosanna Coppo
+  - Rafael Kramann
+  - Peter Boor
+  - Ivan G. Costa
+test_command: |
+  conda create --name PILOT python=3.11.5 r-base
+  conda activate PILOT
+  pip install pilotpy
+  conda install pytest
+  cd test && pytest test_pilot.py
diff --git a/packages/ParTIpy/meta.yaml b/packages/ParTIpy/meta.yaml
@@ -0,0 +1,18 @@
+name: ParTIpy
+description: |
+  Implements Pareto task inference and archetypal analysis for analyzing functional trade-offs in single-cell and spatial omics data.
+project_home: https://github.com/saezlab/ParTIpy
+documentation_home: https://partipy.readthedocs.io/en/latest/
+tutorials_home: https://partipy.readthedocs.io/en/latest/
+install:
+  pypi: partipy
+license: MIT
+tags:
+  - "single cell"
+  - "archetypal analysis"
+  - "division of labor"
+  - "representation learning"
+version: v0.0.04
+authors:
+  - psl-schaefer
+  - leotenshii
diff --git a/packages/Rectangle/meta.yaml b/packages/Rectangle/meta.yaml
@@ -0,0 +1,18 @@
+name: Rectangle
+description: |
+  Rectangle is a python package for computational deconvolution.
+  Rectangle presents a novel approach to second-generation deconvolution, characterized by hierarchical processing, an estimation of unknown cellular content and a significant reduction in data volume during signature matrix computation.
+project_home: https://github.com/ComputationalBiomedicineGroup/Rectangle
+documentation_home: https://rectanglepy.readthedocs.io
+tutorials_home: https://rectanglepy.readthedocs.io/notebooks/example.html
+install:
+  pypi: rectanglepy
+license: MIT
+tags:
+  - rna-seq
+  - deconvolution
+version: v0.1.6
+authors:
+  - bernheder
+test_command: |
+  pip install ."[dev,test]" && pytest