From e07eed7de6e0290f8fd3021ea592ae3e8eb157b7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sat, 10 Aug 2024 13:43:20 +0200 Subject: [PATCH 01/21] Create meta.yaml --- packages/scPRINT/meta.yaml | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 packages/scPRINT/meta.yaml diff --git a/packages/scPRINT/meta.yaml b/packages/scPRINT/meta.yaml new file mode 100644 index 00000000..7ec87237 --- /dev/null +++ b/packages/scPRINT/meta.yaml @@ -0,0 +1,26 @@ +name: scPRINT +description: | + A single cell foundation model for Gene network inference and more... +project_home: https://github.com/cantinilab/scPRINT +documentation_home: https://jkobject.com/scPRINT +publications: + - 10.1101/2024.07.29.605556 +install: + pypi: scprint +tags: + - foundation model + - single cell + - RNAseq + - gene network inference + - denoising + - zero imputation + - label prediction + - zero shot + - embedding + - pytorch + - lightning +license: MIT +version: v1.0.12 +authors: + - jkobject (jeremie kalfon) +test_command: pip install . && make test From 16dcf19fd5fe1094f79778afbbfb3d76f80e5d56 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sat, 10 Aug 2024 13:43:42 +0200 Subject: [PATCH 02/21] Create meta.yaml --- packages/scDataLoader/meta.yaml | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 packages/scDataLoader/meta.yaml diff --git a/packages/scDataLoader/meta.yaml b/packages/scDataLoader/meta.yaml new file mode 100644 index 00000000..02d5a92a --- /dev/null +++ b/packages/scDataLoader/meta.yaml @@ -0,0 +1,24 @@ +name: scDataLoader +description: | + A dataloader for large single cell databases like cellxgene. + Does weighted random sampling, downloading and preprocessing. + works with anndata, zarr, and h5ad files. +project_home: https://github.com/jkobject/scDataLoader +documentation_home: https://jkobject.com/scDataLoader +publications: + - 10.1101/2024.07.29.605556 +install: + pypi: scdataloader +tags: + - dataloader + - single cell + - RNAseq + - pytorch + - lightning + - cellxgene + - preprocessing +license: MIT +version: v1.0.1 +authors: + - jkobject (jeremie kalfon) +test_command: pip install . && make test From 2104287d01475ad2324ce48953d398237622230c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sat, 10 Aug 2024 13:46:47 +0200 Subject: [PATCH 03/21] Create meta.yaml --- packages/benGRN/meta.yaml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 packages/benGRN/meta.yaml diff --git a/packages/benGRN/meta.yaml b/packages/benGRN/meta.yaml new file mode 100644 index 00000000..2c1948fb --- /dev/null +++ b/packages/benGRN/meta.yaml @@ -0,0 +1,20 @@ +name: benGRN +description: | + Benchmarking tool for gene network inference from single cell RNAseq methods. + It uses the grnndata/anndata modality and only contains biological ground truth networks +project_home: https://github.com/jkobject/benGRN +documentation_home: https://jkobject.com/benGRN +publications: + - 10.1101/2024.07.29.605556 +install: + pypi: bengrn +tags: + - single cell + - RNAseq + - gene network inference + - benchmark +license: MIT +version: v1.0.1 +authors: + - jkobject (jeremie kalfon) +test_command: pip install . && make test From ee979425b858af3cec514c6775a448ddf91c0894 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sat, 10 Aug 2024 13:47:27 +0200 Subject: [PATCH 04/21] Create meta.yaml --- packages/GRnnData/meta.yaml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 packages/GRnnData/meta.yaml diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml new file mode 100644 index 00000000..0a4ebbfe --- /dev/null +++ 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://jkobject.com/GRnnData +publications: + - 10.1101/2024.07.29.605556 +install: + pypi: grnndata +tags: + - single cell + - RNAseq + - gene networks + - format + - utilities +license: MIT +version: v1.0.0 +authors: + - jkobject (jeremie kalfon) +test_command: pip install . && make test From a86f3e2dd654479c793dd802bce1a1cd47a2c76f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Wed, 13 Nov 2024 14:55:14 +0100 Subject: [PATCH 05/21] Update meta.yaml --- packages/benGRN/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/benGRN/meta.yaml b/packages/benGRN/meta.yaml index 2c1948fb..43d716b3 100644 --- a/packages/benGRN/meta.yaml +++ b/packages/benGRN/meta.yaml @@ -3,7 +3,7 @@ description: | Benchmarking tool for gene network inference from single cell RNAseq methods. It uses the grnndata/anndata modality and only contains biological ground truth networks project_home: https://github.com/jkobject/benGRN -documentation_home: https://jkobject.com/benGRN +documentation_home: https://www.jkobject.com/benGRN publications: - 10.1101/2024.07.29.605556 install: @@ -14,7 +14,7 @@ tags: - gene network inference - benchmark license: MIT -version: v1.0.1 +version: v1.2.1 authors: - jkobject (jeremie kalfon) test_command: pip install . && make test From aa7a3faac368c3b1644ef27160b0846ca99f27ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Wed, 13 Nov 2024 15:00:14 +0100 Subject: [PATCH 06/21] Update meta.yaml --- packages/GRnnData/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml index 0a4ebbfe..d3983e8a 100644 --- a/packages/GRnnData/meta.yaml +++ b/packages/GRnnData/meta.yaml @@ -3,7 +3,7 @@ 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://jkobject.com/GRnnData +documentation_home: https://cantinilab.github.io/GRnnData/ publications: - 10.1101/2024.07.29.605556 install: @@ -15,7 +15,7 @@ tags: - format - utilities license: MIT -version: v1.0.0 +version: v1.1.4 authors: - jkobject (jeremie kalfon) test_command: pip install . && make test From a68d8e2963c5ea9884a85a80c32af463cdff4a73 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Wed, 13 Nov 2024 15:08:56 +0100 Subject: [PATCH 07/21] Update meta.yaml --- packages/scDataLoader/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/scDataLoader/meta.yaml b/packages/scDataLoader/meta.yaml index 02d5a92a..115553f7 100644 --- a/packages/scDataLoader/meta.yaml +++ b/packages/scDataLoader/meta.yaml @@ -4,7 +4,7 @@ description: | Does weighted random sampling, downloading and preprocessing. works with anndata, zarr, and h5ad files. project_home: https://github.com/jkobject/scDataLoader -documentation_home: https://jkobject.com/scDataLoader +documentation_home: https://www.jkobject.com/scDataLoader/ publications: - 10.1101/2024.07.29.605556 install: @@ -18,7 +18,7 @@ tags: - cellxgene - preprocessing license: MIT -version: v1.0.1 +version: v1.2.2 authors: - jkobject (jeremie kalfon) test_command: pip install . && make test From 81a4a4fd98bd4ca530662561d842f2e67ef86764 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Wed, 13 Nov 2024 15:11:22 +0100 Subject: [PATCH 08/21] Update meta.yaml --- packages/scPRINT/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/scPRINT/meta.yaml b/packages/scPRINT/meta.yaml index 7ec87237..5fbf626a 100644 --- a/packages/scPRINT/meta.yaml +++ b/packages/scPRINT/meta.yaml @@ -2,7 +2,7 @@ name: scPRINT description: | A single cell foundation model for Gene network inference and more... project_home: https://github.com/cantinilab/scPRINT -documentation_home: https://jkobject.com/scPRINT +documentation_home: https://cantinilab.github.io/scPRINT/ publications: - 10.1101/2024.07.29.605556 install: @@ -20,7 +20,7 @@ tags: - pytorch - lightning license: MIT -version: v1.0.12 +version: v1.6.2 authors: - jkobject (jeremie kalfon) test_command: pip install . && make test From 04853c064533a1b0a7c280374a79dc81e187f0f9 Mon Sep 17 00:00:00 2001 From: jkobject Date: Sun, 28 Dec 2025 17:00:16 +0100 Subject: [PATCH 09/21] adding scprint-2 and scprint --- packages/scPRINT-2/meta.yaml | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 packages/scPRINT-2/meta.yaml diff --git a/packages/scPRINT-2/meta.yaml b/packages/scPRINT-2/meta.yaml new file mode 100644 index 00000000..6fa67b5e --- /dev/null +++ b/packages/scPRINT-2/meta.yaml @@ -0,0 +1,29 @@ +name: scPRINT-2 +description: | + A next generation single cell foundation model +project_home: https://github.com/cantinilab/scPRINT-2 +documentation_home: https://cantinilab.github.io/scPRINT-2/ +publications: + - 10.64898/2025.12.11.693702v2 +install: + pypi: scprint2 +tags: + - foundation model + - single cell + - RNAseq + - gene network inference + - denoising + - zero imputation + - label prediction + - zero shot + - embedding + - pytorch + - lightning + - species integration + - expression imputation + - counterfactual predictions +license: GPL-3.0-or-later +version: v1.0.0 +authors: + - jkobject (jeremie kalfon) +test_command: pip install . && make test From 9e42b5baecef17c14615a8d7be665b2c597e630f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sun, 28 Dec 2025 17:45:45 +0100 Subject: [PATCH 10/21] Add contact information to authors in meta.yaml Updated authors section to include contact information. --- packages/scPRINT-2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/scPRINT-2/meta.yaml b/packages/scPRINT-2/meta.yaml index 6fa67b5e..52d52b88 100644 --- a/packages/scPRINT-2/meta.yaml +++ b/packages/scPRINT-2/meta.yaml @@ -24,6 +24,6 @@ tags: - counterfactual predictions license: GPL-3.0-or-later version: v1.0.0 -authors: +contact: - jkobject (jeremie kalfon) test_command: pip install . && make test From 65666a98dcd8bc8cd3d1a9bb61d04c3ce6a18ab2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sun, 28 Dec 2025 17:47:10 +0100 Subject: [PATCH 11/21] Apply suggestions from code review Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- packages/GRnnData/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml index dda919bc..85b63c06 100644 --- a/packages/GRnnData/meta.yaml +++ b/packages/GRnnData/meta.yaml @@ -1,7 +1,7 @@ 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. + Allows easy conversion between anndata and grnndata and provide loads of useful utilities functions. project_home: https://github.com/cantinilab/GRnnData documentation_home: https://cantinilab.github.io/GRnnData/ publications: From 6e78a97ef5672af51c07f99778196297bd614b50 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sun, 28 Dec 2025 17:47:18 +0100 Subject: [PATCH 12/21] Apply suggestion from @Copilot Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- packages/GRnnData/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml index 85b63c06..6e07988d 100644 --- a/packages/GRnnData/meta.yaml +++ b/packages/GRnnData/meta.yaml @@ -1,6 +1,6 @@ name: GRnnData description: | - An onverload of anndata to more easily work with gene networks. + An overload of anndata to more easily work with gene networks. Allows easy conversion between anndata and grnndata and provide loads of useful utilities functions. project_home: https://github.com/cantinilab/GRnnData documentation_home: https://cantinilab.github.io/GRnnData/ From 6b43e16e5bb483d32d8086114bd3bef993f7db67 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Sat, 21 Mar 2026 20:11:52 +0100 Subject: [PATCH 13/21] Add category --- packages/scPRINT-2/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/packages/scPRINT-2/meta.yaml b/packages/scPRINT-2/meta.yaml index 52d52b88..f27c497c 100644 --- a/packages/scPRINT-2/meta.yaml +++ b/packages/scPRINT-2/meta.yaml @@ -27,3 +27,4 @@ version: v1.0.0 contact: - jkobject (jeremie kalfon) test_command: pip install . && make test +category: ecosystem From d02af7559a86422bb1ad8a9da26ea1c678a61115 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Wed, 8 Apr 2026 10:04:21 +0200 Subject: [PATCH 14/21] Update meta.yaml --- packages/benGRN/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/benGRN/meta.yaml b/packages/benGRN/meta.yaml index 3ea2a9bd..dc768cb1 100644 --- a/packages/benGRN/meta.yaml +++ b/packages/benGRN/meta.yaml @@ -16,6 +16,6 @@ tags: license: MIT version: v1.2.1 contact: - - jkobject (jeremie kalfon) + - jkobject test_command: pip install . && make test category: ecosystem From cec07cd302a8fa9dbaf4e40f5dbf6dcbf7cb9787 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Wed, 8 Apr 2026 10:04:46 +0200 Subject: [PATCH 15/21] Update meta.yaml --- packages/scDataLoader/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/scDataLoader/meta.yaml b/packages/scDataLoader/meta.yaml index 7dc789cc..bb77545f 100644 --- a/packages/scDataLoader/meta.yaml +++ b/packages/scDataLoader/meta.yaml @@ -20,6 +20,6 @@ tags: license: MIT version: v1.2.2 contact: - - jkobject (jeremie kalfon) + - jkobject test_command: pip install . && make test category: ecosystem From 44c5c3d3ff3773e950429e237b21e43b297c640a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Wed, 8 Apr 2026 10:05:07 +0200 Subject: [PATCH 16/21] Update contact information in meta.yaml --- packages/GRnnData/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml index 6e07988d..69164181 100644 --- a/packages/GRnnData/meta.yaml +++ b/packages/GRnnData/meta.yaml @@ -17,6 +17,6 @@ tags: license: MIT version: v1.1.4 contact: - - jkobject (jeremie kalfon) + - jkobject test_command: pip install . && make test category: ecosystem From 47ddf274bbc4a900765a8da57825c8d3b1bd7191 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Wed, 8 Apr 2026 10:05:25 +0200 Subject: [PATCH 17/21] Simplify contact name in meta.yaml Removed the full name from the contact field in meta.yaml. --- packages/scPRINT/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/scPRINT/meta.yaml b/packages/scPRINT/meta.yaml index fef885ac..ab50d3bf 100644 --- a/packages/scPRINT/meta.yaml +++ b/packages/scPRINT/meta.yaml @@ -22,6 +22,6 @@ tags: license: MIT version: v1.6.2 contact: - - jkobject (jeremie kalfon) + - jkobject test_command: pip install . && make test category: ecosystem From e1182fda39689e8f7889cfec0a3cff722a7bc052 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sun, 7 Jun 2026 19:02:53 +0200 Subject: [PATCH 18/21] Update README checklist for scPRINT-2 package Updated the checklist for adding packages, replacing placeholders with actual information for the tool 'scPRINT-2'. Marked mandatory items as completed. --- README.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 8c3ca50d..58d08a62 100644 --- a/README.md +++ b/README.md @@ -33,32 +33,32 @@ If you cannot or do not want to comply with these requirements, you are still fr ### Mandatory -Name of the tool: XXX +Name of the tool: scPRINT-2 -Short description: XXX +Short description: A next generation single cell foundation model 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) -- [ ] 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 +- [x] The code is publicly available under an [OSI-approved](https://opensource.org/licenses/alphabetical) license +- [x] The package provides versioned releases +- [x] The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda) +- [x] Automated tests cover essential functions of the package and a reasonable range of inputs and conditions [^1] +- [x] Continuous integration (CI) automatically executes these tests on each push or pull request [^2] +- [x] The package provides API documentation via a website or README[^3] +- [x] The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions) +- [x] 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: +- [x] Please announce this package on scverse communication channels (zulip, discourse, twitter) +- [x] 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 +- [x] 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. From f103940ea3815b5ed413a5ea1422a38ab67ad4cf Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Mon, 29 Jun 2026 20:24:17 +0200 Subject: [PATCH 19/21] Delete README.md --- README.md | 68 ------------------------------------------------------- 1 file changed, 68 deletions(-) delete mode 100644 README.md diff --git a/README.md b/README.md deleted file mode 100644 index 58d08a62..00000000 --- a/README.md +++ /dev/null @@ -1,68 +0,0 @@ -# Scverse Ecosystem Packages - -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 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. -It **does not** imply endorsement or that an in-depth review has been performed. - -**Hint:** If you want to receive notifications about new ecosystem packages, simply use GitHub's "watch" functionality for this repository. - -## How can my package become part of the list? - -Submit a pull-request adding a `meta.yaml` file for your package to the `packages` directory. - -- 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`](scripts/src/ecosystem_scripts/schema.json) -- You can add a logo in svg/png/webp format if you like. Currently it is not used on our website, though. - -## What are the requirements for an ecosystem package? - -For a package to become an approved ecosystem package, it must fulfill all mandatory requirements from the checklist below. - -Ecosystem packages can be written in non-Python languages as long as they fulfill the above requirements. - -If you cannot or do not want to comply with these requirements, you are still free to make your package interoperable with scverse by using our datastructures, but we will not list your package on our ecosystem page. - -## Checklist for adding packages - -### Mandatory - -Name of the tool: scPRINT-2 - -Short description: A next generation single cell foundation model - -How does the package use scverse data structures (please describe in a few sentences): XXX - -- [x] The code is publicly available under an [OSI-approved](https://opensource.org/licenses/alphabetical) license -- [x] The package provides versioned releases -- [x] The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda) -- [x] Automated tests cover essential functions of the package and a reasonable range of inputs and conditions [^1] -- [x] Continuous integration (CI) automatically executes these tests on each push or pull request [^2] -- [x] The package provides API documentation via a website or README[^3] -- [x] The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions) -- [x] I am an author or maintainer of the tool and agree on listing the package on the scverse website - -### Recommended - -- [x] Please announce this package on scverse communication channels (zulip, discourse, twitter) -- [x] Please tag the author(s) these announcements. Handles (e.g. `@scverse_team`) to include are: - - Zulip: - - Discourse: - - Mastodon: - - Bluesky: - - Twitter: - -- [x] 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/page/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) From c0fa65a5ee781a3ec4a6920deededcb61e29514a Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Mon, 29 Jun 2026 20:27:08 +0200 Subject: [PATCH 20/21] restore README --- README.md | 68 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 00000000..8c3ca50d --- /dev/null +++ b/README.md @@ -0,0 +1,68 @@ +# Scverse Ecosystem Packages + +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 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. +It **does not** imply endorsement or that an in-depth review has been performed. + +**Hint:** If you want to receive notifications about new ecosystem packages, simply use GitHub's "watch" functionality for this repository. + +## How can my package become part of the list? + +Submit a pull-request adding a `meta.yaml` file for your package to the `packages` directory. + +- 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`](scripts/src/ecosystem_scripts/schema.json) +- You can add a logo in svg/png/webp format if you like. Currently it is not used on our website, though. + +## What are the requirements for an ecosystem package? + +For a package to become an approved ecosystem package, it must fulfill all mandatory requirements from the checklist below. + +Ecosystem packages can be written in non-Python languages as long as they fulfill the above requirements. + +If you cannot or do not want to comply with these requirements, you are still free to make your package interoperable with scverse by using our datastructures, but we will not list your package on our ecosystem page. + +## Checklist for adding packages + +### Mandatory + +Name of the tool: XXX + +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) +- [ ] 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: + - 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/page/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) From 152e48795c531c39f24301c35129fe7a5cae76cf Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Tue, 30 Jun 2026 20:35:08 +0200 Subject: [PATCH 21/21] fix github user --- packages/scPRINT-2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/scPRINT-2/meta.yaml b/packages/scPRINT-2/meta.yaml index f27c497c..7033538d 100644 --- a/packages/scPRINT-2/meta.yaml +++ b/packages/scPRINT-2/meta.yaml @@ -25,6 +25,6 @@ tags: license: GPL-3.0-or-later version: v1.0.0 contact: - - jkobject (jeremie kalfon) + - jkobject test_command: pip install . && make test category: ecosystem