From 176622d9aee4835e9b22cc37679450dcae6311a9 Mon Sep 17 00:00:00 2001 From: Dominik Date: Mon, 13 May 2024 13:18:50 -0700 Subject: [PATCH 001/126] add Palantir --- packages/palantir/meta.yaml | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 packages/palantir/meta.yaml diff --git a/packages/palantir/meta.yaml b/packages/palantir/meta.yaml new file mode 100644 index 00000000..07a562d4 --- /dev/null +++ b/packages/palantir/meta.yaml @@ -0,0 +1,31 @@ +name: Palantir +description: | + Palantir is an algorithm to align cells along differentiation trajectories. + Palantir models differentiation as a stochastic process where stem cells + differentiate to terminally differentiated cells by a series of steps through + a low dimensional phenotypic manifold. Palantir effectively captures the + continuity in cell states and the stochasticity in cell fate determination. + Palantir has been designed to work with multidimensional single cell data from + diverse technologies such as Mass cytometry and single cell RNA-seq. +project_home: https://github.com/dpeerlab/Palantir +documentation_home: https://palantir.readthedocs.io +publications: + - 10.1038/s41587-019-0068-4 +install: + pypi: palantir +tags: + - markov-chain + - dimensionality-reduction + - scrna-seq + - trajectory-generation + - diffusion-maps + - differentiation + - manifold-learning + - single-cell-genomics + - cell-fate-transitions + - scrna-seq-analysis +license: GPL-2.0-or-later +version: v1.3.3 +authors: + - ManuSetty +test_command: pip install -e '.' && pip install flake8 pytest coverage typing-extensions && pytest From 8abdd641512c9070a2144353aa963b41e3c3c069 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 14 May 2024 10:36:21 +0200 Subject: [PATCH 002/126] [pre-commit.ci] pre-commit autoupdate (#170) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/python-jsonschema/check-jsonschema: 0.28.2 → 0.28.3](https://github.com/python-jsonschema/check-jsonschema/compare/0.28.2...0.28.3) - [github.com/python-jsonschema/check-jsonschema: 0.28.2 → 0.28.3](https://github.com/python-jsonschema/check-jsonschema/compare/0.28.2...0.28.3) - [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.3...v0.4.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3810e820..119bd286 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.28.2 + rev: 0.28.3 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.28.2 + rev: 0.28.3 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: v0.4.4 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From b01c0f4aa8fad5c43b9e8d32383a3299221a15cc Mon Sep 17 00:00:00 2001 From: Benjamin Rombaut Date: Tue, 14 May 2024 17:08:59 +0200 Subject: [PATCH 003/126] add flowsom meta.yaml (#168) --- packages/flowsom/meta.yaml | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 packages/flowsom/meta.yaml diff --git a/packages/flowsom/meta.yaml b/packages/flowsom/meta.yaml new file mode 100644 index 00000000..3ddec752 --- /dev/null +++ b/packages/flowsom/meta.yaml @@ -0,0 +1,27 @@ +name: flowsom +description: | + The complete FlowSOM package known from R, now available in Python! + Analyze high-dimensional cytometry data using FlowSOM, + a clustering and visualization algorithm based on a self-organizing map (SOM). + FlowSOM is used to distinguish cell populations from cytometry data in an unsupervised way and + can help to gain deeper insights in fields such as immunology and oncology. +project_home: https://github.com/saeyslab/FlowSOM_Python +documentation_home: https://flowsom.readthedocs.io/en/latest/ +tutorials_home: https://flowsom.readthedocs.io/en/latest/notebooks/example.html +publications: + - 10.1093/bioinformatics/btae179 + - 10.1002/cyto.a.22625 + - 10.1038/s41596-021-00550-0 +install: + conda: conda-forge::flowsom +tags: + - clustering + - flowcytometry +license: GPL-3.0-only +version: v0.0.1 +authors: + - artuurC + - berombau + - ysaeys + - SofieVG +test_command: pip install "." && pytest From a3aad875067ed48c70f9c90ce0b3fd50896f064c Mon Sep 17 00:00:00 2001 From: Dominik Date: Tue, 14 May 2024 12:38:15 -0700 Subject: [PATCH 004/126] add authors to palantir --- packages/palantir/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/packages/palantir/meta.yaml b/packages/palantir/meta.yaml index 07a562d4..454b9bda 100644 --- a/packages/palantir/meta.yaml +++ b/packages/palantir/meta.yaml @@ -28,4 +28,6 @@ license: GPL-2.0-or-later version: v1.3.3 authors: - ManuSetty + - dpeerlab + - katosh test_command: pip install -e '.' && pip install flake8 pytest coverage typing-extensions && pytest From 5082626285c7d1d71b36e481581996f15d14c173 Mon Sep 17 00:00:00 2001 From: "Dominik J. Otto" Date: Fri, 24 May 2024 02:13:11 -0700 Subject: [PATCH 005/126] Add palantir to the scverse (#171) * add Palantir * add authors to palantir --- packages/palantir/meta.yaml | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 packages/palantir/meta.yaml diff --git a/packages/palantir/meta.yaml b/packages/palantir/meta.yaml new file mode 100644 index 00000000..454b9bda --- /dev/null +++ b/packages/palantir/meta.yaml @@ -0,0 +1,33 @@ +name: Palantir +description: | + Palantir is an algorithm to align cells along differentiation trajectories. + Palantir models differentiation as a stochastic process where stem cells + differentiate to terminally differentiated cells by a series of steps through + a low dimensional phenotypic manifold. Palantir effectively captures the + continuity in cell states and the stochasticity in cell fate determination. + Palantir has been designed to work with multidimensional single cell data from + diverse technologies such as Mass cytometry and single cell RNA-seq. +project_home: https://github.com/dpeerlab/Palantir +documentation_home: https://palantir.readthedocs.io +publications: + - 10.1038/s41587-019-0068-4 +install: + pypi: palantir +tags: + - markov-chain + - dimensionality-reduction + - scrna-seq + - trajectory-generation + - diffusion-maps + - differentiation + - manifold-learning + - single-cell-genomics + - cell-fate-transitions + - scrna-seq-analysis +license: GPL-2.0-or-later +version: v1.3.3 +authors: + - ManuSetty + - dpeerlab + - katosh +test_command: pip install -e '.' && pip install flake8 pytest coverage typing-extensions && pytest From 02eb1f0434304b3e81b226c1c75d6bd03a971606 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 31 May 2024 08:40:17 +0200 Subject: [PATCH 006/126] [pre-commit.ci] pre-commit autoupdate (#172) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/python-jsonschema/check-jsonschema: 0.28.3 → 0.28.4](https://github.com/python-jsonschema/check-jsonschema/compare/0.28.3...0.28.4) - [github.com/python-jsonschema/check-jsonschema: 0.28.3 → 0.28.4](https://github.com/python-jsonschema/check-jsonschema/compare/0.28.3...0.28.4) - [github.com/astral-sh/ruff-pre-commit: v0.4.4 → v0.4.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.4...v0.4.5) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 119bd286..d7230d0f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.28.3 + rev: 0.28.4 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.28.3 + rev: 0.28.4 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: v0.4.4 + rev: v0.4.5 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 4ec23f35f35ab94c4c4563998b1aac646e6a0bb3 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 3 Jun 2024 14:37:56 -0700 Subject: [PATCH 007/126] [pre-commit.ci] pre-commit autoupdate (#174) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.5 → v0.4.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.5...v0.4.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d7230d0f..621efccc 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.5 + rev: v0.4.7 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From f9d569459eeb856a22b818c3857626e177b8f305 Mon Sep 17 00:00:00 2001 From: Malte Kuehl Date: Tue, 4 Jun 2024 16:21:42 +0200 Subject: [PATCH 008/126] Add pytximport (#173) * Add pytximport * Replace tab with spaces to fix prettier error --- packages/pytximport/meta.yaml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 packages/pytximport/meta.yaml diff --git a/packages/pytximport/meta.yaml b/packages/pytximport/meta.yaml new file mode 100644 index 00000000..835808e4 --- /dev/null +++ b/packages/pytximport/meta.yaml @@ -0,0 +1,20 @@ +name: pytximport +description: | + A Python port of the `tximport` R package for importing transcript-level quantification data from various RNA-seq quantification tools such as `salmon` and `kallisto` and summarizing it to the gene level. +project_home: https://github.com/complextissue/pytximport +documentation_home: https://pytximport.readthedocs.io/en/latest/ +tutorials_home: https://pytximport.readthedocs.io/en/latest/ +install: + pypi: pytximport +tags: + - rna-seq + - bulk-rna-seq + - differential-expression +license: GPL-3.0-only +version: v0.2.0 +authors: + - maltekuehl +test_command: | + pip install flit poetry && \ + flit install --deps all && \ + coverage run -m pytest From e92af1ef828fb10f953200e7078914451c874800 Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Fri, 7 Jun 2024 03:00:44 -0700 Subject: [PATCH 009/126] Add pertpy (#175) * Add pertpy Signed-off-by: zethson * rename file Signed-off-by: zethson --------- Signed-off-by: zethson --- packages/pertpy/meta.yaml | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 packages/pertpy/meta.yaml diff --git a/packages/pertpy/meta.yaml b/packages/pertpy/meta.yaml new file mode 100644 index 00000000..cc7689e1 --- /dev/null +++ b/packages/pertpy/meta.yaml @@ -0,0 +1,29 @@ +name: pertpy +description: | + pertpy is a framework for the analysis of multi-condition omics data. +project_home: https://github.com/scverse/pertpy +documentation_home: https://pertpy.readthedocs.io/en/stable/ +tutorials_home: https://pertpy.readthedocs.io/en/stable/tutorials/index.html +install: + pypi: pertpy +tags: + - single-cell + - perturbation + - condition +license: Apache-2.0 +version: v0.7.0 +authors: + - lukas heumos + - Lilly May + - Yuge Ji + - Alejandro Tejada + - Johannes Köster + - Emma Dann + - Xinyue Zhang + - Xichen Wu + - Tessa Green + - Stefan Peidli + - Antonia Schumacher + - Gregor Sturm +test_command: | + pip install ".[dev,test]" && pytest From 39feb475503de057d2998f8ae0ae40b084b4d0bf Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 11 Jun 2024 09:54:41 +0200 Subject: [PATCH 010/126] [pre-commit.ci] pre-commit autoupdate (#176) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 621efccc..8716b237 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.7 + rev: v0.4.8 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From e5ba39f1fe0f4b0538b58c33dc004f4b713bfcde Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Sat, 15 Jun 2024 05:10:02 +0000 Subject: [PATCH 011/126] Updated template-repos.yml --- template-repos.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/template-repos.yml b/template-repos.yml index b104e278..9b648cc1 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -46,6 +46,7 @@ reason: Instance repo gets updated by the bot via the template - url: https://github.com/scverse/genomic-features - url: https://github.com/scverse/multi-condition-comparisions +- url: https://github.com/scverse/pytometry - url: https://github.com/scverse/scirpy - url: https://github.com/scverse/scverse-tutorials - url: https://github.com/scverse/simple-scvi From 521e78c2472710751a11177e864bbec25a5faeff Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 17 Jun 2024 12:22:39 -0700 Subject: [PATCH 012/126] [pre-commit.ci] pre-commit autoupdate (#178) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/python-jsonschema/check-jsonschema: 0.28.4 → 0.28.5](https://github.com/python-jsonschema/check-jsonschema/compare/0.28.4...0.28.5) - [github.com/python-jsonschema/check-jsonschema: 0.28.4 → 0.28.5](https://github.com/python-jsonschema/check-jsonschema/compare/0.28.4...0.28.5) - [github.com/astral-sh/ruff-pre-commit: v0.4.8 → v0.4.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.8...v0.4.9) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8716b237..3f896cbb 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.28.4 + rev: 0.28.5 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.28.4 + rev: 0.28.5 hooks: - id: check-jsonschema files: "packages/.*/meta.yaml" @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.8 + rev: v0.4.9 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 9b429e291364c285d4f4f2128325abe08de2f458 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 25 Jun 2024 09:36:41 -0700 Subject: [PATCH 013/126] [pre-commit.ci] pre-commit autoupdate (#179) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/python-jsonschema/check-jsonschema: 0.28.5 → 0.28.6](https://github.com/python-jsonschema/check-jsonschema/compare/0.28.5...0.28.6) - [github.com/python-jsonschema/check-jsonschema: 0.28.5 → 0.28.6](https://github.com/python-jsonschema/check-jsonschema/compare/0.28.5...0.28.6) - [github.com/astral-sh/ruff-pre-commit: v0.4.9 → v0.4.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.9...v0.4.10) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3f896cbb..b69f3104 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.28.5 + rev: 0.28.6 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.28.5 + rev: 0.28.6 hooks: - id: check-jsonschema files: "packages/.*/meta.yaml" @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.9 + rev: v0.4.10 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From b128a83ff8b618fc080b1bfb47eeea17b13db793 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Mon, 1 Jul 2024 05:10:18 +0000 Subject: [PATCH 014/126] Updated template-repos.yml --- template-repos.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/template-repos.yml b/template-repos.yml index 9b648cc1..4d5e4c53 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -53,6 +53,7 @@ - url: https://github.com/scverse/spatialdata-plot - url: https://github.com/scverse/squidpy - url: https://github.com/smgoggin10/ESCHR +- url: https://github.com/tddough98/airgradient - url: https://github.com/theislab/ehrdata - url: https://github.com/theislab/geome - url: https://github.com/theislab/transcription_factor_activity From 314c8bb27510ab7921463c5d104785cffe5d6a77 Mon Sep 17 00:00:00 2001 From: bernheder <37223124+bernheder@users.noreply.github.com> Date: Tue, 2 Jul 2024 08:19:28 +0200 Subject: [PATCH 015/126] Added meta.yaml for the Rectangle package (#180) * Added meta.yaml for the Rectangle package * Added meta.yaml for the Rectangle package * added link to tutorial --- packages/Rectangle/meta.yaml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 packages/Rectangle/meta.yaml diff --git a/packages/Rectangle/meta.yaml b/packages/Rectangle/meta.yaml new file mode 100644 index 00000000..8890fa25 --- /dev/null +++ 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 From 2cbe3686379b7f305b38e007850ab66689565d8a Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 2 Jul 2024 08:19:45 +0200 Subject: [PATCH 016/126] [pre-commit.ci] pre-commit autoupdate (#181) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.10 → v0.5.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.10...v0.5.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b69f3104..deb9883e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.10 + rev: v0.5.0 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 5e8a4ff280a3bbf962e35852a50b7c50b7f387ae Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 11 Jul 2024 11:17:47 +0200 Subject: [PATCH 017/126] [pre-commit.ci] pre-commit autoupdate (#183) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index deb9883e..cc9bd85a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.0 + rev: v0.5.1 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From b91a7a07835c8cf107337010f3472298a18c1bf7 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Mon, 15 Jul 2024 05:10:13 +0000 Subject: [PATCH 018/126] Updated template-repos.yml --- template-repos.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/template-repos.yml b/template-repos.yml index 4d5e4c53..aa0af73e 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -36,6 +36,7 @@ - url: https://github.com/immunitastx/monkeybread - url: https://github.com/ivirshup/binsparse-python - url: https://github.com/jlause/scverse-tutorials +- url: https://github.com/karadavis-lab/anndata-utils - url: https://github.com/lhqing/scmallet - url: https://github.com/lucas-diedrich/sccoral - url: https://github.com/macwiatrak/scverse-hackathon-data-4-ai From 89acb3799272af03cabfef6c734c276a4c14ef5c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 18 Jul 2024 15:47:10 +0200 Subject: [PATCH 019/126] [pre-commit.ci] pre-commit autoupdate (#184) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/python-jsonschema/check-jsonschema: 0.28.6 → 0.29.0](https://github.com/python-jsonschema/check-jsonschema/compare/0.28.6...0.29.0) - [github.com/python-jsonschema/check-jsonschema: 0.28.6 → 0.29.0](https://github.com/python-jsonschema/check-jsonschema/compare/0.28.6...0.29.0) - [github.com/astral-sh/ruff-pre-commit: v0.5.1 → v0.5.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.5.1...v0.5.2) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index cc9bd85a..6b9905e9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.28.6 + rev: 0.29.0 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.28.6 + rev: 0.29.0 hooks: - id: check-jsonschema files: "packages/.*/meta.yaml" @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.1 + rev: v0.5.2 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 49eda997be3460ec53a1b46fc24be4fdec383621 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 23 Jul 2024 07:52:38 +0200 Subject: [PATCH 020/126] [pre-commit.ci] pre-commit autoupdate (#191) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.2 → v0.5.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.5.2...v0.5.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6b9905e9..58ec6dfa 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.2 + rev: v0.5.4 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From c9de2e17fe1b606283dbe17fa6b09e19428bbc2c Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Fri, 26 Jul 2024 17:51:40 +0200 Subject: [PATCH 021/126] Be explicit about test coverage and add footnotes (#190) * Be explicit about test coverage and add footnotes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README.md * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- README.md | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index c63f1c2e..cd85738d 100644 --- a/README.md +++ b/README.md @@ -40,8 +40,9 @@ How does the package use scverse data structures (please describe in a few sente - [ ] 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 +- [ ] 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 @@ -55,3 +56,9 @@ How does the package use scverse data structures (please describe in a few sente - 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). + +[^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) From 98cef2c44c8039401d3bd8dd0f3fd536fdaa7f15 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 30 Jul 2024 11:44:40 +0200 Subject: [PATCH 022/126] [pre-commit.ci] pre-commit autoupdate (#192) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 58ec6dfa..cd93674b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.0 + rev: 0.29.1 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.0 + rev: 0.29.1 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: v0.5.4 + rev: v0.5.5 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 137ce369ba507a3783b47bb4943d582d017ff590 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Thu, 1 Aug 2024 05:10:13 +0000 Subject: [PATCH 023/126] Updated template-repos.yml --- template-repos.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index aa0af73e..6a31f105 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -22,6 +22,7 @@ - url: https://github.com/aertslab/EnhancerAI - url: https://github.com/angelolab/Nimbus-Inference - url: https://github.com/angelolab/ark-spatial +- url: https://github.com/angelolab/tonic-vitessce - url: https://github.com/blengerich/auto_ehr - url: https://github.com/cameronraysmith/perturbvelo - url: https://github.com/cobioda/scispy @@ -29,6 +30,7 @@ - url: https://github.com/d-j-k/donorpy - url: https://github.com/dertrotl/geneGATer - url: https://github.com/ergonyc/lblator +- url: https://github.com/greenelab/single_translator_VAE - url: https://github.com/grst/spatialdata-plot - url: https://github.com/icbi-lab/atlas_protocol - url: https://github.com/icbi-lab/infercnvpy @@ -54,9 +56,11 @@ - url: https://github.com/scverse/spatialdata-plot - url: https://github.com/scverse/squidpy - url: https://github.com/smgoggin10/ESCHR +- url: https://github.com/tansey-lab/nf-rnaseq - url: https://github.com/tddough98/airgradient - url: https://github.com/theislab/ehrdata - url: https://github.com/theislab/geome +- url: https://github.com/theislab/multimil - url: https://github.com/theislab/transcription_factor_activity - url: https://github.com/timtreis/gefslim - url: https://github.com/vitkl/cell2module From c9b96a05ac7c91b2815b719093b3ba35d66fb768 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 6 Aug 2024 09:53:54 +0200 Subject: [PATCH 024/126] [pre-commit.ci] pre-commit autoupdate (#194) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index cd93674b..c177d7c2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.5 + rev: v0.5.6 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 7f1468026977b4506f38610e147ab115b175b692 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 13 Aug 2024 12:23:35 +0200 Subject: [PATCH 025/126] [pre-commit.ci] pre-commit autoupdate (#196) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c177d7c2..60391626 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.6 + rev: v0.5.7 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 45dac560f0b2ae16d9968fb909c099c0d6d23ecc Mon Sep 17 00:00:00 2001 From: Mehdi Joodaki <39383809+mehdijoodaki@users.noreply.github.com> Date: Tue, 13 Aug 2024 12:35:12 +0200 Subject: [PATCH 026/126] Add PILOT (#189) * Add PILOT * Update meta.yaml --- packages/PILOT/meta.yaml | 50 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 packages/PILOT/meta.yaml diff --git a/packages/PILOT/meta.yaml b/packages/PILOT/meta.yaml new file mode 100644 index 00000000..0fd32877 --- /dev/null +++ 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 From 6bb40901cfd86c24ab27cdc6d10ea547785e13d0 Mon Sep 17 00:00:00 2001 From: Shenghui Date: Tue, 13 Aug 2024 18:44:39 +0800 Subject: [PATCH 027/126] add GPTBioInsightor (#193) * add GPTBioInsightor * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- packages/GPTBioInsightor/meta.yaml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 packages/GPTBioInsightor/meta.yaml diff --git a/packages/GPTBioInsightor/meta.yaml b/packages/GPTBioInsightor/meta.yaml new file mode 100644 index 00000000..f65abb9b --- /dev/null +++ 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 From 0ccb52977c6e46aac0866c4d91f55ccb775037f2 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Thu, 15 Aug 2024 05:10:48 +0000 Subject: [PATCH 028/126] Updated template-repos.yml --- template-repos.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index 6a31f105..ce33bbfd 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -1,3 +1,4 @@ +- url: https://github.com/Bendemeurichy/flowSOM - url: https://github.com/BoevaLab/infercnvpy - url: https://github.com/CSOgroup/cellcharter - url: https://github.com/ChanghaoGong/STutils @@ -19,6 +20,7 @@ - url: https://github.com/YosefLab/visionpy - url: https://github.com/Zethson/fknni - url: https://github.com/adamgayoso/figmasvg +- url: https://github.com/aertslab/CREsted - url: https://github.com/aertslab/EnhancerAI - url: https://github.com/angelolab/Nimbus-Inference - url: https://github.com/angelolab/ark-spatial @@ -36,9 +38,11 @@ - url: https://github.com/icbi-lab/infercnvpy - url: https://github.com/ilia-kats/PolarbearPlus - url: https://github.com/immunitastx/monkeybread +- url: https://github.com/imsb-uke/nichepca - url: https://github.com/ivirshup/binsparse-python - url: https://github.com/jlause/scverse-tutorials - url: https://github.com/karadavis-lab/anndata-utils +- url: https://github.com/karadavis-lab/nbl - url: https://github.com/lhqing/scmallet - url: https://github.com/lucas-diedrich/sccoral - url: https://github.com/macwiatrak/scverse-hackathon-data-4-ai From 27dfd68bde15100a455bda9749d4c5eb84f2692a Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 22 Aug 2024 12:01:27 +0200 Subject: [PATCH 029/126] [pre-commit.ci] pre-commit autoupdate (#197) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 60391626..91e51052 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.7 + rev: v0.6.1 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 3e3befde1ae7f8bc0e8a7fc26a6218d1a8a23b59 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 27 Aug 2024 15:56:16 +0200 Subject: [PATCH 030/126] [pre-commit.ci] pre-commit autoupdate (#199) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 91e51052..3395915d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.1 + rev: 0.29.2 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.1 + rev: 0.29.2 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: v0.6.1 + rev: v0.6.2 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From f443ec2c16c200d3c9fdea5b050f0a34ad746458 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Sun, 1 Sep 2024 05:11:34 +0000 Subject: [PATCH 031/126] Updated template-repos.yml --- template-repos.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index ce33bbfd..369614c7 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -1,13 +1,17 @@ +- url: https://github.com/Bendemeurichy/FlowSOM_parallel - url: https://github.com/Bendemeurichy/flowSOM +- url: https://github.com/Boehringer-Ingelheim/dso - url: https://github.com/BoevaLab/infercnvpy - url: https://github.com/CSOgroup/cellcharter - url: https://github.com/ChanghaoGong/STutils - url: https://github.com/CompCy-lab/scHub - url: https://github.com/ComputationalBiomedicineGroup/Rectangle +- url: https://github.com/Gabriellvl/FlowSOM - url: https://github.com/NKI-CCB/sobolev_alignment - url: https://github.com/Teichlab/multi-view-atlas - url: https://github.com/YosefLab/PopV - url: https://github.com/YosefLab/embedding-scvi +- url: https://github.com/YosefLab/pycea - url: https://github.com/YosefLab/scib-metrics - url: https://github.com/YosefLab/scvi-criticism skip: true @@ -60,6 +64,7 @@ - url: https://github.com/scverse/spatialdata-plot - url: https://github.com/scverse/squidpy - url: https://github.com/smgoggin10/ESCHR +- url: https://github.com/srivarra/anatomize - url: https://github.com/tansey-lab/nf-rnaseq - url: https://github.com/tddough98/airgradient - url: https://github.com/theislab/ehrdata From 4db2d648fa9d7e762589b60c16403bbbf365e196 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 2 Sep 2024 20:26:23 +0200 Subject: [PATCH 032/126] [pre-commit.ci] pre-commit autoupdate (#200) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3395915d..4371fcdf 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.2 + rev: v0.6.3 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 8d68647f9691842411f48010cbd1a9193d4244e5 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 10 Sep 2024 10:57:09 +0200 Subject: [PATCH 033/126] [pre-commit.ci] pre-commit autoupdate (#201) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4371fcdf..4eb6d10c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.3 + rev: v0.6.4 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From d9fb2dd1a9a4faef600bb61499ce56c404868ee0 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Sun, 15 Sep 2024 05:10:53 +0000 Subject: [PATCH 034/126] Updated template-repos.yml --- template-repos.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/template-repos.yml b/template-repos.yml index 369614c7..522f4b4d 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -3,6 +3,7 @@ - url: https://github.com/Boehringer-Ingelheim/dso - url: https://github.com/BoevaLab/infercnvpy - url: https://github.com/CSOgroup/cellcharter +- url: https://github.com/CSOgroup/torchgmm - url: https://github.com/ChanghaoGong/STutils - url: https://github.com/CompCy-lab/scHub - url: https://github.com/ComputationalBiomedicineGroup/Rectangle From eadaabe3226d091fff044363694c6ad57a4bfd03 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 16 Sep 2024 20:21:54 +0200 Subject: [PATCH 035/126] [pre-commit.ci] pre-commit autoupdate (#202) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4eb6d10c..46b17352 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.4 + rev: v0.6.5 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From b20fe5dfc2d1ddaf035465dd7b548f40b3f35126 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 23 Sep 2024 20:00:52 +0200 Subject: [PATCH 036/126] [pre-commit.ci] pre-commit autoupdate (#203) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 46b17352..200de6a8 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.5 + rev: v0.6.7 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 627820c5310d8f739ac4bed330aeece087c95168 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Tue, 1 Oct 2024 05:11:13 +0000 Subject: [PATCH 037/126] Updated template-repos.yml --- template-repos.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/template-repos.yml b/template-repos.yml index 522f4b4d..5259d3f4 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -35,6 +35,7 @@ - url: https://github.com/cobioda/scispy - url: https://github.com/const-ae/pyLemur - url: https://github.com/d-j-k/donorpy +- url: https://github.com/data-intuitive/dummy-anndata - url: https://github.com/dertrotl/geneGATer - url: https://github.com/ergonyc/lblator - url: https://github.com/greenelab/single_translator_VAE From 3c7dc86890a5ff9ec2ea69ba0509bc2c985dbd3d Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 1 Oct 2024 09:48:17 +0200 Subject: [PATCH 038/126] [pre-commit.ci] pre-commit autoupdate (#204) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 200de6a8..df61fa79 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.2 + rev: 0.29.3 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.2 + rev: 0.29.3 hooks: - id: check-jsonschema files: "packages/.*/meta.yaml" @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.7 + rev: v0.6.8 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 1d1a1cddf0db1d11c82d98c2135c9769bdfc779d Mon Sep 17 00:00:00 2001 From: Marco Date: Wed, 2 Oct 2024 10:13:55 +0200 Subject: [PATCH 039/126] add CellCharter (#198) * add CellCharter * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix typo --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Lukas Heumos Co-authored-by: Gregor Sturm --- packages/CellCharter/meta.yaml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 packages/CellCharter/meta.yaml diff --git a/packages/CellCharter/meta.yaml b/packages/CellCharter/meta.yaml new file mode 100644 index 00000000..345ba462 --- /dev/null +++ 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 From 458febfd370050487ac8b6c9107b7f16371cb5db Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 8 Oct 2024 08:56:09 +0200 Subject: [PATCH 040/126] [pre-commit.ci] pre-commit autoupdate (#205) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Philipp A. --- .pre-commit-config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index df61fa79..537fadcd 100644 --- 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: v5.0.0 hooks: - id: detect-private-key - id: check-ast @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.8 + rev: v0.6.9 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 6683e8bf11bd19e2cf63ff026d8a1970668f8704 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Tue, 15 Oct 2024 05:11:55 +0000 Subject: [PATCH 041/126] Updated template-repos.yml --- template-repos.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index 5259d3f4..73ee9704 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -38,6 +38,7 @@ - url: https://github.com/data-intuitive/dummy-anndata - url: https://github.com/dertrotl/geneGATer - url: https://github.com/ergonyc/lblator +- url: https://github.com/eroell/mypackage-cruft-oct - url: https://github.com/greenelab/single_translator_VAE - url: https://github.com/grst/spatialdata-plot - url: https://github.com/icbi-lab/atlas_protocol @@ -52,6 +53,7 @@ - url: https://github.com/lhqing/scmallet - url: https://github.com/lucas-diedrich/sccoral - url: https://github.com/macwiatrak/scverse-hackathon-data-4-ai +- url: https://github.com/mengerj/mmcontext - url: https://github.com/nitzanlab/biolord - url: https://github.com/saeyslab/FlowSOM_Python - url: https://github.com/scverse/cookiecutter-scverse-instance @@ -72,6 +74,7 @@ - url: https://github.com/theislab/ehrdata - url: https://github.com/theislab/geome - url: https://github.com/theislab/multimil +- url: https://github.com/theislab/spatialdata-db - url: https://github.com/theislab/transcription_factor_activity - url: https://github.com/timtreis/gefslim - url: https://github.com/vitkl/cell2module From d1337b0af8e1951f1ae5887c786b43eee65e742f Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 15 Oct 2024 08:45:13 +0200 Subject: [PATCH 042/126] [pre-commit.ci] pre-commit autoupdate (#206) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 537fadcd..12129061 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.3 + rev: 0.29.4 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.3 + rev: 0.29.4 hooks: - id: check-jsonschema files: "packages/.*/meta.yaml" From 7ce6fb49261ad25de7442e1f5fdf43ab05b21d8f Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 22 Oct 2024 13:48:29 +0200 Subject: [PATCH 043/126] [pre-commit.ci] pre-commit autoupdate (#207) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 12129061..5886c26e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.9 + rev: v0.7.0 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 238d8e03fd1505429903cbb7aa99abcb156f96d8 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 28 Oct 2024 19:17:48 +0100 Subject: [PATCH 044/126] [pre-commit.ci] pre-commit autoupdate (#208) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5886c26e..3d0192fa 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.7.0 + rev: v0.7.1 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From e1588cfb0486ce109be268da9ddc676776f02def Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Fri, 1 Nov 2024 05:11:58 +0000 Subject: [PATCH 045/126] Updated template-repos.yml --- template-repos.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index 73ee9704..726d4694 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -30,6 +30,7 @@ - url: https://github.com/angelolab/Nimbus-Inference - url: https://github.com/angelolab/ark-spatial - url: https://github.com/angelolab/tonic-vitessce +- url: https://github.com/bartuschimschek/mmil-refactored - url: https://github.com/blengerich/auto_ehr - url: https://github.com/cameronraysmith/perturbvelo - url: https://github.com/cobioda/scispy @@ -52,6 +53,7 @@ - url: https://github.com/karadavis-lab/nbl - url: https://github.com/lhqing/scmallet - url: https://github.com/lucas-diedrich/sccoral +- url: https://github.com/lueckenlab/patpy - url: https://github.com/macwiatrak/scverse-hackathon-data-4-ai - url: https://github.com/mengerj/mmcontext - url: https://github.com/nitzanlab/biolord From e5b9171036d5fb848dde5d8e684518cf47317007 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 4 Nov 2024 19:19:39 +0100 Subject: [PATCH 046/126] [pre-commit.ci] pre-commit autoupdate (#209) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3d0192fa..013ff76e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.7.1 + rev: v0.7.2 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 8a8cd144078f6fdd3f460e8a009e9419352f6db2 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 11 Nov 2024 19:32:45 +0100 Subject: [PATCH 047/126] [pre-commit.ci] pre-commit autoupdate (#210) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 013ff76e..4cd6f12e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.7.2 + rev: v0.7.3 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From a4c6103dd8eaaf25c08039b9c65aad1c24dc4b0d Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Fri, 15 Nov 2024 05:11:44 +0000 Subject: [PATCH 048/126] Updated template-repos.yml --- template-repos.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index 726d4694..d4bcc63a 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -1,6 +1,7 @@ - url: https://github.com/Bendemeurichy/FlowSOM_parallel - url: https://github.com/Bendemeurichy/flowSOM - url: https://github.com/Boehringer-Ingelheim/dso +- url: https://github.com/Boehringer-Ingelheim/dso-mgr - url: https://github.com/BoevaLab/infercnvpy - url: https://github.com/CSOgroup/cellcharter - url: https://github.com/CSOgroup/torchgmm @@ -33,6 +34,7 @@ - url: https://github.com/bartuschimschek/mmil-refactored - url: https://github.com/blengerich/auto_ehr - url: https://github.com/cameronraysmith/perturbvelo +- url: https://github.com/clinicalomx/napari-prism - url: https://github.com/cobioda/scispy - url: https://github.com/const-ae/pyLemur - url: https://github.com/d-j-k/donorpy @@ -56,6 +58,7 @@ - url: https://github.com/lueckenlab/patpy - url: https://github.com/macwiatrak/scverse-hackathon-data-4-ai - url: https://github.com/mengerj/mmcontext +- url: https://github.com/mostafavilabuw/drum - url: https://github.com/nitzanlab/biolord - url: https://github.com/saeyslab/FlowSOM_Python - url: https://github.com/scverse/cookiecutter-scverse-instance @@ -71,6 +74,7 @@ - url: https://github.com/scverse/squidpy - url: https://github.com/smgoggin10/ESCHR - url: https://github.com/srivarra/anatomize +- url: https://github.com/srivarra/annsel - url: https://github.com/tansey-lab/nf-rnaseq - url: https://github.com/tddough98/airgradient - url: https://github.com/theislab/ehrdata From 442463b3648fedb703e476227cbf23adbb40be6a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Mon, 18 Nov 2024 14:06:29 +0100 Subject: [PATCH 049/126] adding scPRINT and its suite of packages (#195) * Create meta.yaml * Create meta.yaml * Create meta.yaml * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Gregor Sturm --- packages/GRnnData/meta.yaml | 21 +++++++++++++++++++++ packages/benGRN/meta.yaml | 20 ++++++++++++++++++++ packages/scDataLoader/meta.yaml | 24 ++++++++++++++++++++++++ packages/scPRINT/meta.yaml | 26 ++++++++++++++++++++++++++ 4 files changed, 91 insertions(+) create mode 100644 packages/GRnnData/meta.yaml create mode 100644 packages/benGRN/meta.yaml create mode 100644 packages/scDataLoader/meta.yaml create mode 100644 packages/scPRINT/meta.yaml diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml new file mode 100644 index 00000000..d3983e8a --- /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://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/benGRN/meta.yaml b/packages/benGRN/meta.yaml new file mode 100644 index 00000000..43d716b3 --- /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://www.jkobject.com/benGRN +publications: + - 10.1101/2024.07.29.605556 +install: + pypi: bengrn +tags: + - single cell + - RNAseq + - gene network inference + - benchmark +license: MIT +version: v1.2.1 +authors: + - jkobject (jeremie kalfon) +test_command: pip install . && make test diff --git a/packages/scDataLoader/meta.yaml b/packages/scDataLoader/meta.yaml new file mode 100644 index 00000000..115553f7 --- /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://www.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: v1.2.2 +authors: + - jkobject (jeremie kalfon) +test_command: pip install . && make test diff --git a/packages/scPRINT/meta.yaml b/packages/scPRINT/meta.yaml new file mode 100644 index 00000000..5fbf626a --- /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://cantinilab.github.io/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: v1.6.2 +authors: + - jkobject (jeremie kalfon) +test_command: pip install . && make test From cd3bac46aef89ba89f6c7a04cc7b57d55fb8d47a Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 18 Nov 2024 21:00:10 +0100 Subject: [PATCH 050/126] [pre-commit.ci] pre-commit autoupdate (#211) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4cd6f12e..a085c86f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.7.3 + rev: v0.7.4 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From c1bf98dcb5f1332c8c2bb953bbdf54c1ece51309 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 29 Nov 2024 14:52:40 +0100 Subject: [PATCH 051/126] [pre-commit.ci] pre-commit autoupdate (#212) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a085c86f..c71dba97 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.7.4 + rev: v0.8.0 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From b90375a62809101ab588f4deba7a126a1f1447ec Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Sun, 1 Dec 2024 05:11:49 +0000 Subject: [PATCH 052/126] Updated template-repos.yml --- template-repos.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index d4bcc63a..97d716ae 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -8,6 +8,7 @@ - url: https://github.com/ChanghaoGong/STutils - url: https://github.com/CompCy-lab/scHub - url: https://github.com/ComputationalBiomedicineGroup/Rectangle +- url: https://github.com/FroeseLab/bulkpy - url: https://github.com/Gabriellvl/FlowSOM - url: https://github.com/NKI-CCB/sobolev_alignment - url: https://github.com/Teichlab/multi-view-atlas @@ -30,6 +31,7 @@ - url: https://github.com/aertslab/EnhancerAI - url: https://github.com/angelolab/Nimbus-Inference - url: https://github.com/angelolab/ark-spatial +- url: https://github.com/angelolab/pici-vitessce - url: https://github.com/angelolab/tonic-vitessce - url: https://github.com/bartuschimschek/mmil-refactored - url: https://github.com/blengerich/auto_ehr @@ -64,6 +66,7 @@ - url: https://github.com/scverse/cookiecutter-scverse-instance skip: true reason: Instance repo gets updated by the bot via the template +- url: https://github.com/scverse/formulaic-contrasts - url: https://github.com/scverse/genomic-features - url: https://github.com/scverse/multi-condition-comparisions - url: https://github.com/scverse/pytometry @@ -79,6 +82,7 @@ - url: https://github.com/tddough98/airgradient - url: https://github.com/theislab/ehrdata - url: https://github.com/theislab/geome +- url: https://github.com/theislab/multigrate - url: https://github.com/theislab/multimil - url: https://github.com/theislab/spatialdata-db - url: https://github.com/theislab/transcription_factor_activity From 2b3bec4c092d69797cbdd91910e12ecd434c8fda Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 2 Dec 2024 20:37:26 +0100 Subject: [PATCH 053/126] [pre-commit.ci] pre-commit autoupdate (#213) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c71dba97..43018300 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.4 + rev: 0.30.0 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.4 + rev: 0.30.0 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: v0.8.0 + rev: v0.8.1 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From a95c861eedbf6b866d495bfb28cff352ede95e08 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 10 Dec 2024 10:04:53 +0100 Subject: [PATCH 054/126] [pre-commit.ci] pre-commit autoupdate (#214) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 43018300..42e395d6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.8.1 + rev: v0.8.2 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From e1dc3cc1473e00b590ab9092a57282b849730561 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Sun, 15 Dec 2024 05:11:32 +0000 Subject: [PATCH 055/126] Updated template-repos.yml --- template-repos.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index 97d716ae..c52f202c 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -14,6 +14,7 @@ - url: https://github.com/Teichlab/multi-view-atlas - url: https://github.com/YosefLab/PopV - url: https://github.com/YosefLab/embedding-scvi +- url: https://github.com/YosefLab/popV - url: https://github.com/YosefLab/pycea - url: https://github.com/YosefLab/scib-metrics - url: https://github.com/YosefLab/scvi-criticism @@ -42,6 +43,7 @@ - url: https://github.com/d-j-k/donorpy - url: https://github.com/data-intuitive/dummy-anndata - url: https://github.com/dertrotl/geneGATer +- url: https://github.com/edbiomedai/scmorph - url: https://github.com/ergonyc/lblator - url: https://github.com/eroell/mypackage-cruft-oct - url: https://github.com/greenelab/single_translator_VAE @@ -52,6 +54,8 @@ - url: https://github.com/immunitastx/monkeybread - url: https://github.com/imsb-uke/nichepca - url: https://github.com/ivirshup/binsparse-python +- url: https://github.com/jkobject/hierarchical_classifier +- url: https://github.com/jkobject/simpler_flash - url: https://github.com/jlause/scverse-tutorials - url: https://github.com/karadavis-lab/anndata-utils - url: https://github.com/karadavis-lab/nbl @@ -86,6 +90,7 @@ - url: https://github.com/theislab/multimil - url: https://github.com/theislab/spatialdata-db - url: https://github.com/theislab/transcription_factor_activity +- url: https://github.com/theislab/troutpy - url: https://github.com/timtreis/gefslim - url: https://github.com/vitkl/cell2module - url: https://github.com/zunderlab/eschr From d29f88320258163d73994af8f4cfbc19756a1c51 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:58:04 +0100 Subject: [PATCH 056/126] [pre-commit.ci] pre-commit autoupdate (#216) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- README.md | 38 +++++++++++++++++++------------------- 2 files changed, 20 insertions(+), 20 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 42e395d6..abf07e38 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.8.2 + rev: v0.8.3 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] diff --git a/README.md b/README.md index cd85738d..7388625f 100644 --- a/README.md +++ b/README.md @@ -15,9 +15,9 @@ 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? @@ -37,25 +37,25 @@ 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 +- [ ] 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: + - 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). [^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 e8690577d62762d017b67466541225ea63b95e75 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 26 Dec 2024 21:41:37 +0100 Subject: [PATCH 057/126] [pre-commit.ci] pre-commit autoupdate (#217) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index abf07e38..0cdd2999 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.8.3 + rev: v0.8.4 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 4790749bab706152089504ebac5a9859132be10b Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Wed, 1 Jan 2025 05:11:08 +0000 Subject: [PATCH 058/126] Updated template-repos.yml --- template-repos.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index c52f202c..8823a7eb 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -7,6 +7,7 @@ - url: https://github.com/CSOgroup/torchgmm - url: https://github.com/ChanghaoGong/STutils - url: https://github.com/CompCy-lab/scHub +- url: https://github.com/Computational-Morphogenomics-Group/Ladder - url: https://github.com/ComputationalBiomedicineGroup/Rectangle - url: https://github.com/FroeseLab/bulkpy - url: https://github.com/Gabriellvl/FlowSOM @@ -42,6 +43,7 @@ - url: https://github.com/const-ae/pyLemur - url: https://github.com/d-j-k/donorpy - url: https://github.com/data-intuitive/dummy-anndata +- url: https://github.com/decomverse/scmetric - url: https://github.com/dertrotl/geneGATer - url: https://github.com/edbiomedai/scmorph - url: https://github.com/ergonyc/lblator From 5f719a947484ccf0224aac242fafffb85964d33d Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 7 Jan 2025 10:51:41 +0100 Subject: [PATCH 059/126] [pre-commit.ci] pre-commit autoupdate (#218) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0cdd2999..8dc891f5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.8.4 + rev: v0.8.6 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From ce318970f33b8bf189845e3afa2f428d6bf8b740 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 13 Jan 2025 19:19:29 +0100 Subject: [PATCH 060/126] [pre-commit.ci] pre-commit autoupdate (#219) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8dc891f5..1ac5eb49 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.30.0 + rev: 0.31.0 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.30.0 + rev: 0.31.0 hooks: - id: check-jsonschema files: "packages/.*/meta.yaml" @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.8.6 + rev: v0.9.1 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 4d6dac954d0b4b80df9f28e7411db01b53c4a671 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 20 Jan 2025 19:52:05 +0100 Subject: [PATCH 061/126] [pre-commit.ci] pre-commit autoupdate (#220) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1ac5eb49..ae03e62a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.9.1 + rev: v0.9.2 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From ed9fa6bb9fd6487e0c432771866c86278a8fe2aa Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 27 Jan 2025 23:00:46 +0100 Subject: [PATCH 062/126] [pre-commit.ci] pre-commit autoupdate (#221) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ae03e62a..334c7065 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.9.2 + rev: v0.9.3 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 0b4c74764b549aec05091fda7b64b380dbbdc58e Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Sat, 1 Feb 2025 05:10:17 +0000 Subject: [PATCH 063/126] Updated template-repos.yml --- template-repos.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index 8823a7eb..e9ceb2de 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -62,12 +62,14 @@ - url: https://github.com/karadavis-lab/anndata-utils - url: https://github.com/karadavis-lab/nbl - url: https://github.com/lhqing/scmallet +- url: https://github.com/lucas-diedrich/dvp-io - url: https://github.com/lucas-diedrich/sccoral - url: https://github.com/lueckenlab/patpy - url: https://github.com/macwiatrak/scverse-hackathon-data-4-ai - url: https://github.com/mengerj/mmcontext - url: https://github.com/mostafavilabuw/drum - url: https://github.com/nitzanlab/biolord +- url: https://github.com/quadbio/cell-annotator - url: https://github.com/saeyslab/FlowSOM_Python - url: https://github.com/scverse/cookiecutter-scverse-instance skip: true From d9118b139dadf8ccd1d02f199ee3751838cd4864 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 5 Feb 2025 10:17:31 +0100 Subject: [PATCH 064/126] [pre-commit.ci] pre-commit autoupdate (#222) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/python-jsonschema/check-jsonschema: 0.31.0 → 0.31.1](https://github.com/python-jsonschema/check-jsonschema/compare/0.31.0...0.31.1) - [github.com/python-jsonschema/check-jsonschema: 0.31.0 → 0.31.1](https://github.com/python-jsonschema/check-jsonschema/compare/0.31.0...0.31.1) - [github.com/astral-sh/ruff-pre-commit: v0.9.3 → v0.9.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.3...v0.9.4) * update action versions --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Phil Schaf --- .github/workflows/make-json.yml | 6 +++--- .github/workflows/register-template-repos.yml | 4 ++-- .pre-commit-config.yaml | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/make-json.yml b/.github/workflows/make-json.yml index 10bc0f95..3499b0ee 100644 --- 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 index 1426af7d..40cf2f86 100644 --- 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: ${{ secrets.BOT_GH_TOKEN }} - name: Set up Python 3.11 - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: "3.11" cache: "pip" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 334c7065..fb229a0b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.31.0 + rev: 0.31.1 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.31.0 + rev: 0.31.1 hooks: - id: check-jsonschema files: "packages/.*/meta.yaml" @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.9.3 + rev: v0.9.4 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From d583a6efcc342660e559223f1a1dae90d91d1bf8 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Mon, 10 Feb 2025 16:30:16 +0100 Subject: [PATCH 065/126] Update README.md --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 7388625f..e29155f3 100644 --- a/README.md +++ b/README.md @@ -50,10 +50,11 @@ How does the package use scverse data structures (please describe in a few sente - [ ] 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: + - 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). From b56dbaab915b3ac63177ab3dfb1323fdeb7a6e8c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 11 Feb 2025 16:14:44 +0100 Subject: [PATCH 066/126] [pre-commit.ci] pre-commit autoupdate (#225) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.9.4 → v0.9.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.4...v0.9.6) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fb229a0b..5ca7995c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.9.4 + rev: v0.9.6 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From ead719605e3f4bbd29f550f2f812dc2db7931054 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Sat, 15 Feb 2025 05:11:17 +0000 Subject: [PATCH 067/126] Updated template-repos.yml --- template-repos.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/template-repos.yml b/template-repos.yml index e9ceb2de..d712ccb1 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -66,6 +66,7 @@ - url: https://github.com/lucas-diedrich/sccoral - url: https://github.com/lueckenlab/patpy - url: https://github.com/macwiatrak/scverse-hackathon-data-4-ai +- url: https://github.com/mengerj/adata_hf_datasets - url: https://github.com/mengerj/mmcontext - url: https://github.com/mostafavilabuw/drum - url: https://github.com/nitzanlab/biolord From 48515a2bba18a3c80ed0ea17c2b896918cc2bb6a Mon Sep 17 00:00:00 2001 From: Sricharan Reddy Varra Date: Tue, 18 Feb 2025 02:21:00 -0800 Subject: [PATCH 068/126] Add annsel (#227) * added annsel * removed extra whitespace * just uv instead of uv pip --- packages/annsel/meta.yaml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 packages/annsel/meta.yaml diff --git a/packages/annsel/meta.yaml b/packages/annsel/meta.yaml new file mode 100644 index 00000000..e3eb527d --- /dev/null +++ b/packages/annsel/meta.yaml @@ -0,0 +1,20 @@ +name: annsel +description: | + Annsel is a user-friendly library that brings familiar dataframe-style operations to AnnData objects such as + selection, filtering and group by's. +project_home: https://github.com/srivarra/annsel +documentation_home: https://annsel.readthedocs.io/en/latest/ +tutorials_home: https://annsel.readthedocs.io/en/latest/notebooks/all_of_annsel.html +install: + pypi: annsel +license: MIT +version: v0.0.8 +authors: + - srivarra +tags: + - narwhals + - dataframe + - accessor + - utilities +test_command: | + pip install ".[test]" && pytest From 3a12ac95c837546a425bb128076899c3e71ab700 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 24 Feb 2025 19:06:44 +0100 Subject: [PATCH 069/126] [pre-commit.ci] pre-commit autoupdate (#228) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5ca7995c..a6142e06 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.31.1 + rev: 0.31.2 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.31.1 + rev: 0.31.2 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: v0.9.6 + rev: v0.9.7 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 73d5f412793e01c2ea304bdd12d6db1cfe5816f1 Mon Sep 17 00:00:00 2001 From: Wouter-Michiel Vierdag Date: Fri, 28 Feb 2025 15:31:33 +0100 Subject: [PATCH 070/126] Update README.md --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e29155f3..f75966d8 100644 --- 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. From 7414334a1747bf9827fb83aeca0bde2954fb6fe2 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Sat, 1 Mar 2025 05:11:08 +0000 Subject: [PATCH 071/126] Updated template-repos.yml --- template-repos.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index d712ccb1..3b48c8c3 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -52,6 +52,7 @@ - url: https://github.com/grst/spatialdata-plot - url: https://github.com/icbi-lab/atlas_protocol - url: https://github.com/icbi-lab/infercnvpy +- url: https://github.com/icbi-lab/shears - url: https://github.com/ilia-kats/PolarbearPlus - url: https://github.com/immunitastx/monkeybread - url: https://github.com/imsb-uke/nichepca @@ -89,6 +90,7 @@ - url: https://github.com/srivarra/annsel - url: https://github.com/tansey-lab/nf-rnaseq - url: https://github.com/tddough98/airgradient +- url: https://github.com/theislab/cell_flow_perturbation - url: https://github.com/theislab/ehrdata - url: https://github.com/theislab/geome - url: https://github.com/theislab/multigrate From 9325ae103bce453973e8dcbe45183dc00d158c60 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 3 Mar 2025 19:18:53 +0100 Subject: [PATCH 072/126] [pre-commit.ci] pre-commit autoupdate (#230) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.9.7 → v0.9.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.7...v0.9.9) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a6142e06..b231b7ae 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.9.7 + rev: v0.9.9 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] diff --git a/README.md b/README.md index f75966d8..306e5ae4 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # Scverse Ecosystem Packages -This repository contains the list of scverse ecosystem packages that are displayed on scverse.org and are part of +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. From 83b138be494998dcaefb68bfb66be9e1e25f4038 Mon Sep 17 00:00:00 2001 From: Nils Gehlenborg Date: Wed, 5 Mar 2025 07:28:37 -0500 Subject: [PATCH 073/126] Updated description, publications, and version information for Vitessce (#231) Updated description, publications, and version information. --- packages/vitessce/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/packages/vitessce/meta.yaml b/packages/vitessce/meta.yaml index 071d0259..875a9a81 100644 --- a/packages/vitessce/meta.yaml +++ b/packages/vitessce/meta.yaml @@ -1,19 +1,18 @@ name: vitessce description: | - Vitessce consists of reusable interactive views including a scatterplot, - spatial+imaging plot, genome browser tracks, statistical plots, and control - views, built on web technologies such as WebGL. + Vitessce is an integrative visualization framework for multimodal and 2D/3D spatially resolved single-cell data. It consists of reusable, interactive linked views including scatterplot embedding views, + 2D/3D spatial image views, genome browser tracks, statistical plots, and control views, built on web technologies such as WebGL and WebXR. project_home: https://github.com/vitessce/vitessce documentation_home: https://vitessce.github.io/vitessce-python/ tutorials_home: https://github.com/vitessce/vitessce/tree/main/examples publications: - - 10.31219/osf.io/y8thv + - 10.1038/s41592-024-02436-x install: pypi: vitessce tags: - imaging license: MIT -version: v1.1.20 +version: v3.5.7 authors: - keller-mark - mccalluc From e4a72dec1c4d8d61b0ae4bd0d8838893c1d41b7a Mon Sep 17 00:00:00 2001 From: Can Ergen Date: Wed, 5 Mar 2025 13:30:53 +0100 Subject: [PATCH 074/126] Add popV (#229) * Create meta.yml * Merge popV * Rename meta.yml to meta.yaml * Update meta.yaml --- packages/popV/meta.yaml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 packages/popV/meta.yaml diff --git a/packages/popV/meta.yaml b/packages/popV/meta.yaml new file mode 100644 index 00000000..03bc000d --- /dev/null +++ b/packages/popV/meta.yaml @@ -0,0 +1,16 @@ +name: popV +description: | + p(opular)V(oting) is a consensus tool for transfering labels from an annotated reference dataset to an unannotated query dataset. Consensus calling allows interpretable scores that quantify certainty. +project_home: https://github.com/YosefLab/popV +documentation_home: https://popv.readthedocs.io/en/latest/ +install: + pypi: popv +tags: + - cell type labels + - batch integration + - automatic annotation +license: MIT +version: v0.5.2 +authors: + - canergen +test_command: pip install -e '.[test]' && pytest From a79226be18c9a26c1e7f0bdf2d22a8947ae1e801 Mon Sep 17 00:00:00 2001 From: Quentin Blampey <33903498+quentinblampey@users.noreply.github.com> Date: Thu, 6 Mar 2025 15:54:45 +0100 Subject: [PATCH 075/126] Add Novae (#215) * added novae yaml file * update sopa article DOI * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gregor Sturm --- README.md | 2 ++ packages/novae/meta.yaml | 20 ++++++++++++++++++++ packages/sopa/meta.yaml | 2 +- 3 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 packages/novae/meta.yaml diff --git a/README.md b/README.md index 306e5ae4..daafa74f 100644 --- a/README.md +++ b/README.md @@ -51,11 +51,13 @@ How does the package use scverse data structures (please describe in a few sente - [ ] 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). diff --git a/packages/novae/meta.yaml b/packages/novae/meta.yaml new file mode 100644 index 00000000..e32704b7 --- /dev/null +++ b/packages/novae/meta.yaml @@ -0,0 +1,20 @@ +name: novae +description: | + Graph-based foundation model for spatial transcriptomics data. + Zero-shot spatial domain inference, batch-effect correction, and many other features. +project_home: https://github.com/MICS-Lab/novae +documentation_home: https://mics-lab.github.io/novae/ +publications: + - 10.1101/2024.09.09.612009 +install: + pypi: novae +tags: + - spatial-omics + - spatial-transcriptomics + - spatialdata + - deep learning +license: BSD-3-Clause +version: v0.2.1 +authors: + - quentinblampey +test_command: pip install ".[dev]" && pytest diff --git a/packages/sopa/meta.yaml b/packages/sopa/meta.yaml index a7037f8a..c686735e 100644 --- a/packages/sopa/meta.yaml +++ b/packages/sopa/meta.yaml @@ -6,7 +6,7 @@ description: | project_home: https://github.com/gustaveroussy/sopa documentation_home: https://gustaveroussy.github.io/sopa/ publications: - - 10.1101/2023.12.22.571863 + - 10.1038/s41467-024-48981-z install: pypi: sopa tags: From 6b8e90ef2d5bc809b76b028b83510e928eb651da Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 10 Mar 2025 21:16:40 +0100 Subject: [PATCH 076/126] [pre-commit.ci] pre-commit autoupdate (#232) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/python-jsonschema/check-jsonschema: 0.31.2 → 0.31.3](https://github.com/python-jsonschema/check-jsonschema/compare/0.31.2...0.31.3) - [github.com/python-jsonschema/check-jsonschema: 0.31.2 → 0.31.3](https://github.com/python-jsonschema/check-jsonschema/compare/0.31.2...0.31.3) - [github.com/astral-sh/ruff-pre-commit: v0.9.9 → v0.9.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.9...v0.9.10) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b231b7ae..5bf7d922 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.31.2 + rev: 0.31.3 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.31.2 + rev: 0.31.3 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: v0.9.9 + rev: v0.9.10 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 50c7badfd14680ca3ce0e2d227b72cfdaa80b913 Mon Sep 17 00:00:00 2001 From: Yimin Zheng Date: Tue, 11 Mar 2025 14:33:38 +0100 Subject: [PATCH 077/126] Add entries for wsidata and LazySlide (#223) Add entry for wsidata and LazySlide --- packages/LazySlide/meta.yaml | 18 ++++++++++++++++++ packages/wsidata/meta.yaml | 17 +++++++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 packages/LazySlide/meta.yaml create mode 100644 packages/wsidata/meta.yaml diff --git a/packages/LazySlide/meta.yaml b/packages/LazySlide/meta.yaml new file mode 100644 index 00000000..ae8c9d5d --- /dev/null +++ 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/wsidata/meta.yaml b/packages/wsidata/meta.yaml new file mode 100644 index 00000000..9f1acfa4 --- /dev/null +++ b/packages/wsidata/meta.yaml @@ -0,0 +1,17 @@ +name: wsidata +description: | + wsidata is a data-structure for efficient IO of Whole Slide Images based on spatialdata. +project_home: https://github.com/rendeirolab/wsidata +documentation_home: https://wsidata.readthedocs.io/en/latest/ +install: + pypi: wsidata +tags: + - Pathology + - Whole Slide Imaging +license: MIT +version: v0.3.0 +authors: + - Mr-Milk + - eabila + - afrendeiro +test_command: uv run task test From a1bbde1b253cf946cfc280574615e7ec73475af0 Mon Sep 17 00:00:00 2001 From: Marius Lange Date: Tue, 11 Mar 2025 16:29:09 +0100 Subject: [PATCH 078/126] Add CellAnnotator (#224) * Add a meta.yaml for CellAnnotator * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- packages/CellAnnotator/meta.yaml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 packages/CellAnnotator/meta.yaml diff --git a/packages/CellAnnotator/meta.yaml b/packages/CellAnnotator/meta.yaml new file mode 100644 index 00000000..366e5cb4 --- /dev/null +++ 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 From 8f5828bd180a7a3dd0185a1d09426ab5bc9eaa17 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 18 Mar 2025 14:45:57 +0100 Subject: [PATCH 079/126] [pre-commit.ci] pre-commit autoupdate (#233) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.9.10 → v0.11.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.10...v0.11.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5bf7d922..77116eaa 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.9.10 + rev: v0.11.0 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From f9a325e9238b91b771302a96d25e7db47bee6929 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 24 Mar 2025 18:55:58 +0100 Subject: [PATCH 080/126] [pre-commit.ci] pre-commit autoupdate (#234) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.0 → v0.11.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.0...v0.11.2) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 77116eaa..e61dc896 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.0 + rev: v0.11.2 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 2f4593626081ca8adccf833d6b8324d68133e5fe Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Tue, 1 Apr 2025 05:12:53 +0000 Subject: [PATCH 081/126] Updated template-repos.yml --- template-repos.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index 3b48c8c3..7de1a861 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -9,6 +9,8 @@ - url: https://github.com/CompCy-lab/scHub - url: https://github.com/Computational-Morphogenomics-Group/Ladder - url: https://github.com/ComputationalBiomedicineGroup/Rectangle +- url: https://github.com/David-M-P/insight +- url: https://github.com/Floto-Lab/BactGraph - url: https://github.com/FroeseLab/bulkpy - url: https://github.com/Gabriellvl/FlowSOM - url: https://github.com/NKI-CCB/sobolev_alignment @@ -36,6 +38,7 @@ - url: https://github.com/angelolab/pici-vitessce - url: https://github.com/angelolab/tonic-vitessce - url: https://github.com/bartuschimschek/mmil-refactored +- url: https://github.com/bioFAM/prismo - url: https://github.com/blengerich/auto_ehr - url: https://github.com/cameronraysmith/perturbvelo - url: https://github.com/clinicalomx/napari-prism @@ -60,6 +63,7 @@ - url: https://github.com/jkobject/hierarchical_classifier - url: https://github.com/jkobject/simpler_flash - url: https://github.com/jlause/scverse-tutorials +- url: https://github.com/joechanlab/scDeBussy - url: https://github.com/karadavis-lab/anndata-utils - url: https://github.com/karadavis-lab/nbl - url: https://github.com/lhqing/scmallet @@ -73,9 +77,11 @@ - url: https://github.com/nitzanlab/biolord - url: https://github.com/quadbio/cell-annotator - url: https://github.com/saeyslab/FlowSOM_Python +- url: https://github.com/scverse/anndata-plot - url: https://github.com/scverse/cookiecutter-scverse-instance skip: true reason: Instance repo gets updated by the bot via the template +- url: https://github.com/scverse/deres - url: https://github.com/scverse/formulaic-contrasts - url: https://github.com/scverse/genomic-features - url: https://github.com/scverse/multi-condition-comparisions @@ -83,6 +89,7 @@ - url: https://github.com/scverse/scirpy - url: https://github.com/scverse/scverse-tutorials - url: https://github.com/scverse/simple-scvi +- url: https://github.com/scverse/spatial-sample-aggregation - url: https://github.com/scverse/spatialdata-plot - url: https://github.com/scverse/squidpy - url: https://github.com/smgoggin10/ESCHR @@ -90,9 +97,12 @@ - url: https://github.com/srivarra/annsel - url: https://github.com/tansey-lab/nf-rnaseq - url: https://github.com/tddough98/airgradient +- url: https://github.com/theislab/CellFlow - url: https://github.com/theislab/cell_flow_perturbation +- url: https://github.com/theislab/devVI - url: https://github.com/theislab/ehrdata - url: https://github.com/theislab/geome +- url: https://github.com/theislab/mapqc - url: https://github.com/theislab/multigrate - url: https://github.com/theislab/multimil - url: https://github.com/theislab/spatialdata-db From eb8016ddd149b4396ab15607b71159058194e78c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 1 Apr 2025 12:19:54 +0200 Subject: [PATCH 082/126] [pre-commit.ci] pre-commit autoupdate (#235) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/python-jsonschema/check-jsonschema: 0.31.3 → 0.32.1](https://github.com/python-jsonschema/check-jsonschema/compare/0.31.3...0.32.1) - [github.com/python-jsonschema/check-jsonschema: 0.31.3 → 0.32.1](https://github.com/python-jsonschema/check-jsonschema/compare/0.31.3...0.32.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e61dc896..7d232d08 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.31.3 + rev: 0.32.1 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.31.3 + rev: 0.32.1 hooks: - id: check-jsonschema files: "packages/.*/meta.yaml" From 14207330e7014cc71524039d72025f91e22e14c8 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 10:52:22 +0200 Subject: [PATCH 083/126] [pre-commit.ci] pre-commit autoupdate (#236) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.2 → v0.11.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.2...v0.11.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7d232d08..2019f487 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.2 + rev: v0.11.4 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 7c24d7a4bf611ca764cd46bdcc72e6816c2e1368 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 14 Apr 2025 20:32:09 +0200 Subject: [PATCH 084/126] [pre-commit.ci] pre-commit autoupdate (#239) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2019f487..a44f8705 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.32.1 + rev: 0.33.0 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.32.1 + rev: 0.33.0 hooks: - id: check-jsonschema files: "packages/.*/meta.yaml" @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.4 + rev: v0.11.5 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From d642793b63b596d2d3384613e60d6a9a634dee68 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Tue, 15 Apr 2025 05:12:56 +0000 Subject: [PATCH 085/126] Updated template-repos.yml --- template-repos.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index 7de1a861..2858eb15 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -38,7 +38,9 @@ - url: https://github.com/angelolab/pici-vitessce - url: https://github.com/angelolab/tonic-vitessce - url: https://github.com/bartuschimschek/mmil-refactored +- url: https://github.com/bioFAM/mofaflex - url: https://github.com/bioFAM/prismo +- url: https://github.com/bioFAM/scDoRI - url: https://github.com/blengerich/auto_ehr - url: https://github.com/cameronraysmith/perturbvelo - url: https://github.com/clinicalomx/napari-prism @@ -48,6 +50,7 @@ - url: https://github.com/data-intuitive/dummy-anndata - url: https://github.com/decomverse/scmetric - url: https://github.com/dertrotl/geneGATer +- url: https://github.com/devsystemslab/HNOCA-tools - url: https://github.com/edbiomedai/scmorph - url: https://github.com/ergonyc/lblator - url: https://github.com/eroell/mypackage-cruft-oct @@ -76,6 +79,7 @@ - url: https://github.com/mostafavilabuw/drum - url: https://github.com/nitzanlab/biolord - url: https://github.com/quadbio/cell-annotator +- url: https://github.com/quadbio/slurm_sweep - url: https://github.com/saeyslab/FlowSOM_Python - url: https://github.com/scverse/anndata-plot - url: https://github.com/scverse/cookiecutter-scverse-instance @@ -99,6 +103,7 @@ - url: https://github.com/tddough98/airgradient - url: https://github.com/theislab/CellFlow - url: https://github.com/theislab/cell_flow_perturbation +- url: https://github.com/theislab/cellflow_reproducibility - url: https://github.com/theislab/devVI - url: https://github.com/theislab/ehrdata - url: https://github.com/theislab/geome From 1c84792819d4ceca1ccb507e2ec3192b315c7f3e Mon Sep 17 00:00:00 2001 From: Sarah Goggin <35312830+smgoggin10@users.noreply.github.com> Date: Tue, 22 Apr 2025 02:34:13 -0400 Subject: [PATCH 086/126] Add eschr (#226) * Add eschr * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gregor Sturm --- packages/eschr/meta.yaml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 packages/eschr/meta.yaml diff --git a/packages/eschr/meta.yaml b/packages/eschr/meta.yaml new file mode 100644 index 00000000..de9c36f4 --- /dev/null +++ b/packages/eschr/meta.yaml @@ -0,0 +1,20 @@ +name: eschr +description: | + ESCHR is an ensemble clustering method that provides hard clustering along with + uncertainty scores and soft clustering outputs for enhanced interpretability. +project_home: https://github.com/zunderlab/eschr +documentation_home: https://eschr.readthedocs.io/en/latest/ +tutorials_home: https://eschr.readthedocs.io/en/latest/notebooks/paul15_mouse_hematopoiesis.html +publications: + - 10.1186/s13059-024-03386-5 +install: + pypi: eschr +tags: + - clustering + - uncertainty + - ensemble +license: "MIT" +version: v1.0.1 +authors: + - smgoggin10 +test_command: pip install ".[test]" && pytest From d7b7a3c26556ac7c3192f61af91341cc8b36f57a Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 22 Apr 2025 08:35:02 +0200 Subject: [PATCH 087/126] [pre-commit.ci] pre-commit autoupdate (#240) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.5 → v0.11.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.5...v0.11.6) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a44f8705..529bf047 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.5 + rev: v0.11.6 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From e12d3e614e2f6b13fa93307acdbf72da74801948 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 29 Apr 2025 08:44:10 +0200 Subject: [PATCH 088/126] [pre-commit.ci] pre-commit autoupdate (#243) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 529bf047..6975e260 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.6 + rev: v0.11.7 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 571119d5e6ceaf30fd5093b42b829727cb52e5b4 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Thu, 1 May 2025 05:13:08 +0000 Subject: [PATCH 089/126] Updated template-repos.yml --- template-repos.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index 2858eb15..a8981f4f 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -79,6 +79,7 @@ - url: https://github.com/mostafavilabuw/drum - url: https://github.com/nitzanlab/biolord - url: https://github.com/quadbio/cell-annotator +- url: https://github.com/quadbio/cellmapper - url: https://github.com/quadbio/slurm_sweep - url: https://github.com/saeyslab/FlowSOM_Python - url: https://github.com/scverse/anndata-plot @@ -99,6 +100,8 @@ - url: https://github.com/smgoggin10/ESCHR - url: https://github.com/srivarra/anatomize - url: https://github.com/srivarra/annsel +- url: https://github.com/srivarra/mbt +- url: https://github.com/srivarra/spatial-collection - url: https://github.com/tansey-lab/nf-rnaseq - url: https://github.com/tddough98/airgradient - url: https://github.com/theislab/CellFlow From 12353d460187e8ecbd6c3853cc3fe61aae732979 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 6 May 2025 09:43:56 +0200 Subject: [PATCH 090/126] [pre-commit.ci] pre-commit autoupdate (#245) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6975e260..ea29e537 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.7 + rev: v0.11.8 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 56cfaa0127f7813a963c00070e4de869c8846c88 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 12 May 2025 19:34:22 +0200 Subject: [PATCH 091/126] [pre-commit.ci] pre-commit autoupdate (#247) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ea29e537..26b35f13 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.8 + rev: v0.11.9 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 978ecdf9874ff500b238394676dd53a4fd19a51c Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Thu, 15 May 2025 05:13:31 +0000 Subject: [PATCH 092/126] Updated template-repos.yml --- template-repos.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index a8981f4f..c7692ff1 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -3,6 +3,7 @@ - url: https://github.com/Boehringer-Ingelheim/dso - url: https://github.com/Boehringer-Ingelheim/dso-mgr - url: https://github.com/BoevaLab/infercnvpy +- url: https://github.com/COMBINE-lab/QCatch - url: https://github.com/CSOgroup/cellcharter - url: https://github.com/CSOgroup/torchgmm - url: https://github.com/ChanghaoGong/STutils @@ -67,6 +68,7 @@ - url: https://github.com/jkobject/simpler_flash - url: https://github.com/jlause/scverse-tutorials - url: https://github.com/joechanlab/scDeBussy +- url: https://github.com/jskerman/chronai - url: https://github.com/karadavis-lab/anndata-utils - url: https://github.com/karadavis-lab/nbl - url: https://github.com/lhqing/scmallet From 4aec741052d321384d8c5894414dd4296f453c99 Mon Sep 17 00:00:00 2001 From: Matthias Meyer-Bender <62450528+MeyerBender@users.noreply.github.com> Date: Thu, 15 May 2025 07:31:47 +0200 Subject: [PATCH 093/126] Added spatialproteomics (#242) * Added spatialproteomics * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- packages/spatialproteomics/meta.yaml | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 packages/spatialproteomics/meta.yaml diff --git a/packages/spatialproteomics/meta.yaml b/packages/spatialproteomics/meta.yaml new file mode 100644 index 00000000..ab21ec6d --- /dev/null +++ b/packages/spatialproteomics/meta.yaml @@ -0,0 +1,22 @@ +name: spatialproteomics +description: | + Spatialproteomics is an interoperable toolbox for analyzing highly multiplexed fluorescence image data. + This analysis involves a sequence of steps, including segmentation, image processing, + marker quantification, cell type classification, and neighborhood analysis. +project_home: https://github.com/sagar87/spatialproteomics +documentation_home: https://sagar87.github.io/spatialproteomics +tutorials_home: https://sagar87.github.io/spatialproteomics/notebooks/ExampleWorkflow.html +install: + pypi: spatialproteomics +tags: + - spatial-omics + - spatial-proteomics + - multiplex imaging + - spatialdata + - pipeline +license: MIT +version: v0.7.0 +authors: + - MeyerBender + - sagar87 +test_command: pip install ".[all,dev]" && pytest From cbcfcba6ad37739e40f738cd25e5066b4f4af8ed Mon Sep 17 00:00:00 2001 From: Jan Detleffsen <59668170+jan1034@users.noreply.github.com> Date: Tue, 20 May 2025 15:30:37 +0200 Subject: [PATCH 094/126] Add PEAKQC (#241) Added PEAKQC/meta.yaml Co-authored-by: Mikkel Niklas Rasmussen <77323950+mikkelnrasmussen@users.noreply.github.com> --- packages/PEAKQC/meta.yaml | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 packages/PEAKQC/meta.yaml diff --git a/packages/PEAKQC/meta.yaml b/packages/PEAKQC/meta.yaml new file mode 100644 index 00000000..7ba4957a --- /dev/null +++ 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 From 507d9d276be9c7f377909b9cfd6217fd5894bf41 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 22 May 2025 16:35:50 +0200 Subject: [PATCH 095/126] [pre-commit.ci] pre-commit autoupdate (#249) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.9 → v0.11.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.9...v0.11.10) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 26b35f13..7e64ee38 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.9 + rev: v0.11.10 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 00af0d7fc2163444b42c3d9ab8f95a30d96af5ff Mon Sep 17 00:00:00 2001 From: Marius Lange Date: Fri, 23 May 2025 09:23:13 +0200 Subject: [PATCH 096/126] Add CellMapper (#244) * Add meta.yaml for cellmapper * Fix meta.yaml * Update the meta.yaml --- packages/CellMapper/meta.yaml | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 packages/CellMapper/meta.yaml diff --git a/packages/CellMapper/meta.yaml b/packages/CellMapper/meta.yaml new file mode 100644 index 00000000..ee06b7b3 --- /dev/null +++ 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 From 0fde6900c78be7e3c79b1cfe707970bb7220a6e2 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 27 May 2025 11:19:48 +0200 Subject: [PATCH 097/126] [pre-commit.ci] pre-commit autoupdate (#250) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7e64ee38..fbd2fbb6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.10 + rev: v0.11.11 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From c0dbfaee5ad29b3a610b9fe73343a331bf98f538 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Sun, 1 Jun 2025 05:13:10 +0000 Subject: [PATCH 098/126] Updated template-repos.yml --- template-repos.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index c7692ff1..b993a4a2 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -34,6 +34,7 @@ - url: https://github.com/adamgayoso/figmasvg - url: https://github.com/aertslab/CREsted - url: https://github.com/aertslab/EnhancerAI +- url: https://github.com/agerardy/myeditdistance - url: https://github.com/angelolab/Nimbus-Inference - url: https://github.com/angelolab/ark-spatial - url: https://github.com/angelolab/pici-vitessce @@ -56,6 +57,7 @@ - url: https://github.com/ergonyc/lblator - url: https://github.com/eroell/mypackage-cruft-oct - url: https://github.com/greenelab/single_translator_VAE +- url: https://github.com/grst/kartapullautin2tiles - url: https://github.com/grst/spatialdata-plot - url: https://github.com/icbi-lab/atlas_protocol - url: https://github.com/icbi-lab/infercnvpy @@ -75,6 +77,9 @@ - url: https://github.com/lucas-diedrich/dvp-io - url: https://github.com/lucas-diedrich/sccoral - url: https://github.com/lueckenlab/patpy +- url: https://github.com/lzj1769/LR2net +- url: https://github.com/macwiatrak/BacBench +- url: https://github.com/macwiatrak/Bacformer - url: https://github.com/macwiatrak/scverse-hackathon-data-4-ai - url: https://github.com/mengerj/adata_hf_datasets - url: https://github.com/mengerj/mmcontext @@ -84,6 +89,7 @@ - url: https://github.com/quadbio/cellmapper - url: https://github.com/quadbio/slurm_sweep - url: https://github.com/saeyslab/FlowSOM_Python +- url: https://github.com/saezlab/decoupler-py - url: https://github.com/scverse/anndata-plot - url: https://github.com/scverse/cookiecutter-scverse-instance skip: true @@ -104,6 +110,7 @@ - url: https://github.com/srivarra/annsel - url: https://github.com/srivarra/mbt - url: https://github.com/srivarra/spatial-collection +- url: https://github.com/srivarra/xrdantic - url: https://github.com/tansey-lab/nf-rnaseq - url: https://github.com/tddough98/airgradient - url: https://github.com/theislab/CellFlow From 364a074745d0f30e20985332555e0802b3feb6ef Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 3 Jun 2025 10:56:00 +0200 Subject: [PATCH 099/126] [pre-commit.ci] pre-commit autoupdate (#251) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fbd2fbb6..1f942695 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.11 + rev: v0.11.12 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From f6681ad6d4a49a28cdf3bb15898e95df7b247e97 Mon Sep 17 00:00:00 2001 From: Sergey Isaev Date: Wed, 4 Jun 2025 16:03:48 +0200 Subject: [PATCH 100/126] Add a new package: scLiTr (#246) Create meta.yaml --- packages/scLiTr/meta.yaml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 packages/scLiTr/meta.yaml diff --git a/packages/scLiTr/meta.yaml b/packages/scLiTr/meta.yaml new file mode 100644 index 00000000..62679cc1 --- /dev/null +++ b/packages/scLiTr/meta.yaml @@ -0,0 +1,19 @@ +name: scLiTr +description: | + scLiTr (single-cell Lineage Tracing) is a python package for exploratory analysis of + barcoding-based scRNA-Seq lineage tracing experiments +project_home: https://github.com/kharchenkolab/scLiTr +documentation_home: https://sclitr.readthedocs.io/ +tutorials_home: https://sclitr.readthedocs.io/ +install: + pypi: sclitr +tags: + - label-transfer +license: MIT +publications: + - 10.1101/2024.11.15.623687 +version: v1.0.1 +authors: + - serjisa +test_command: | + pip install . && pytest From f859f032f8885d12be1adb3f9a67e3748edd641d Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Wed, 4 Jun 2025 17:39:37 +0100 Subject: [PATCH 101/126] Add scCellFie (#248) * Added meta.yaml for scCellFie * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: Erick Armingol Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- packages/scCellFie/meta.yaml | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 packages/scCellFie/meta.yaml diff --git a/packages/scCellFie/meta.yaml b/packages/scCellFie/meta.yaml new file mode 100644 index 00000000..60f57423 --- /dev/null +++ b/packages/scCellFie/meta.yaml @@ -0,0 +1,23 @@ +name: scCellFie +description: | + scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses. +project_home: https://github.com/earmingol/scCellFie +documentation_home: https://sccellfie.readthedocs.io +tutorials_home: https://sccellfie.readthedocs.io +install: + pypi: sccellfie +tags: + - single-cell + - spatial + - metabolism + - metabolic activities + - cell-cell communication +license: MIT +version: v0.4.5 +authors: + - earmingol +test_command: | + python -m pip install --upgrade pip + python -m pip install -r requirements.txt + python -m pip install -e . + pytest -vv --cov --cov-report xml From 087d02f422f7d2e6d45162d97006908c2ce88d1b Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 9 Jun 2025 14:04:57 -0700 Subject: [PATCH 102/126] [pre-commit.ci] pre-commit autoupdate (#252) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.12 → v0.11.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.12...v0.11.13) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1f942695..9aa1f130 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.12 + rev: v0.11.13 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From d0cca3d35b0ef26fff39f48eab2c437ca36ef8c8 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Sun, 15 Jun 2025 05:12:32 +0000 Subject: [PATCH 103/126] Updated template-repos.yml --- template-repos.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index b993a4a2..6a327931 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -70,6 +70,7 @@ - url: https://github.com/jkobject/simpler_flash - url: https://github.com/jlause/scverse-tutorials - url: https://github.com/joechanlab/scDeBussy +- url: https://github.com/joschif/delnx - url: https://github.com/jskerman/chronai - url: https://github.com/karadavis-lab/anndata-utils - url: https://github.com/karadavis-lab/nbl @@ -84,7 +85,9 @@ - url: https://github.com/mengerj/adata_hf_datasets - url: https://github.com/mengerj/mmcontext - url: https://github.com/mostafavilabuw/drum +- url: https://github.com/mumichae/scAtlasTb-utils - url: https://github.com/nitzanlab/biolord +- url: https://github.com/quadbio/atac_mapper - url: https://github.com/quadbio/cell-annotator - url: https://github.com/quadbio/cellmapper - url: https://github.com/quadbio/slurm_sweep @@ -94,6 +97,7 @@ - url: https://github.com/scverse/cookiecutter-scverse-instance skip: true reason: Instance repo gets updated by the bot via the template +- url: https://github.com/scverse/decoupler - url: https://github.com/scverse/deres - url: https://github.com/scverse/formulaic-contrasts - url: https://github.com/scverse/genomic-features @@ -111,6 +115,7 @@ - url: https://github.com/srivarra/mbt - url: https://github.com/srivarra/spatial-collection - url: https://github.com/srivarra/xrdantic +- url: https://github.com/sueoglu/myeditdistance - url: https://github.com/tansey-lab/nf-rnaseq - url: https://github.com/tddough98/airgradient - url: https://github.com/theislab/CellFlow From 0ca6fb65f9a6f87c57af2765a9aa835b34007642 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Tue, 1 Jul 2025 05:17:44 +0000 Subject: [PATCH 104/126] Updated template-repos.yml --- template-repos.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index 6a327931..f62b2c64 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -14,6 +14,7 @@ - url: https://github.com/Floto-Lab/BactGraph - url: https://github.com/FroeseLab/bulkpy - url: https://github.com/Gabriellvl/FlowSOM +- url: https://github.com/Lotfollahi-lab/mintflow - url: https://github.com/NKI-CCB/sobolev_alignment - url: https://github.com/Teichlab/multi-view-atlas - url: https://github.com/YosefLab/PopV @@ -58,6 +59,7 @@ - url: https://github.com/eroell/mypackage-cruft-oct - url: https://github.com/greenelab/single_translator_VAE - url: https://github.com/grst/kartapullautin2tiles +- url: https://github.com/grst/karttapullautin2tiles - url: https://github.com/grst/spatialdata-plot - url: https://github.com/icbi-lab/atlas_protocol - url: https://github.com/icbi-lab/infercnvpy From bb7dd3cbfca49c511ec886fc0d21f5b46e0ed1ff Mon Sep 17 00:00:00 2001 From: Shenghui Date: Tue, 1 Jul 2025 15:14:00 +0800 Subject: [PATCH 105/126] add scmcp (#238) * add scanpy-mcp * Rename meta.yml to meta.yaml * Update meta.yaml * rename to scmcp * Delete packages/scanpy-mcp directory * Create meta.yaml * Update meta.yaml --------- Co-authored-by: Gregor Sturm Co-authored-by: Mikkel Niklas Rasmussen <77323950+mikkelnrasmussen@users.noreply.github.com> --- packages/scmcp/meta.yaml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 packages/scmcp/meta.yaml diff --git a/packages/scmcp/meta.yaml b/packages/scmcp/meta.yaml new file mode 100644 index 00000000..fec5cc21 --- /dev/null +++ b/packages/scmcp/meta.yaml @@ -0,0 +1,16 @@ +name: scmcp +description: A MCP server hub for scRNA-Seq analysis software. +project_home: https://github.com/scmcphub +documentation_home: https://docs.scmcphub.org +install: + pypi: scmcp +tags: + - scRNA-seq + - bioinformatics + - LLM + - AI +license: BSD-3-Clause +version: v0.2.2 +authors: + - huangsh +test_command: uv run --no-sync pytest From 715b6a441ed832660a49a50c49bebbd0fea16301 Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Wed, 2 Jul 2025 03:00:23 -0700 Subject: [PATCH 106/126] Remove core packages (#257) Signed-off-by: Lukas Heumos --- packages/SnapATAC2 /meta.yaml | 21 -------------------- packages/decoupler/meta.yaml | 20 ------------------- packages/pertpy/meta.yaml | 29 ---------------------------- packages/rapids-singlecell/meta.yaml | 17 ---------------- 4 files changed, 87 deletions(-) delete mode 100644 packages/SnapATAC2 /meta.yaml delete mode 100644 packages/decoupler/meta.yaml delete mode 100644 packages/pertpy/meta.yaml delete mode 100644 packages/rapids-singlecell/meta.yaml diff --git a/packages/SnapATAC2 /meta.yaml b/packages/SnapATAC2 /meta.yaml deleted file mode 100644 index 28828280..00000000 --- a/packages/SnapATAC2 /meta.yaml +++ /dev/null @@ -1,21 +0,0 @@ -name: SnapATAC2 -description: | - SnapATAC2 is the successor of the SnapATAC R package, featuring: - - Faster and less memory usage, scale to >1M cells. - - Improved dimension reduction and sampling algorithm. -project_home: https://github.com/kaizhang/SnapATAC2 -documentation_home: https://kzhang.org/SnapATAC2/ -tutorials_home: https://kzhang.org/SnapATAC2/ -publications: - - 10.1038/s41467-021-21583-9 - - 10.1016/j.cell.2021.10.024 -install: - pypi: snapatac2 -tags: - - SnapATAC -license: MIT -version: v2.1.2 -authors: - - kaizhang - - yingyuan830 -test_command: null diff --git a/packages/decoupler/meta.yaml b/packages/decoupler/meta.yaml deleted file mode 100644 index ff1afad1..00000000 --- a/packages/decoupler/meta.yaml +++ /dev/null @@ -1,20 +0,0 @@ -name: decoupler -description: | - Python package to infer biological activities from omics data using a collection of methods. -project_home: https://github.com/saezlab/decoupler-py -documentation_home: https://decoupler-py.readthedocs.io/en/latest/ -tutorials_home: https://decoupler-py.readthedocs.io/en/latest/ -install: - pypi: decoupler -tags: - - TF - - GSEA - - Pathway -license: GPL-3.0-only -version: v1.2.0 -authors: - - PauBadiaM -test_command: | - pip install wheel && \ - pip install pytest-cov flake8 sklearn skranger omnipath scanpy adjustText . && \ - pytest --cov --disable-warnings decoupler diff --git a/packages/pertpy/meta.yaml b/packages/pertpy/meta.yaml deleted file mode 100644 index cc7689e1..00000000 --- a/packages/pertpy/meta.yaml +++ /dev/null @@ -1,29 +0,0 @@ -name: pertpy -description: | - pertpy is a framework for the analysis of multi-condition omics data. -project_home: https://github.com/scverse/pertpy -documentation_home: https://pertpy.readthedocs.io/en/stable/ -tutorials_home: https://pertpy.readthedocs.io/en/stable/tutorials/index.html -install: - pypi: pertpy -tags: - - single-cell - - perturbation - - condition -license: Apache-2.0 -version: v0.7.0 -authors: - - lukas heumos - - Lilly May - - Yuge Ji - - Alejandro Tejada - - Johannes Köster - - Emma Dann - - Xinyue Zhang - - Xichen Wu - - Tessa Green - - Stefan Peidli - - Antonia Schumacher - - Gregor Sturm -test_command: | - pip install ".[dev,test]" && pytest diff --git a/packages/rapids-singlecell/meta.yaml b/packages/rapids-singlecell/meta.yaml deleted file mode 100644 index 4c105c89..00000000 --- a/packages/rapids-singlecell/meta.yaml +++ /dev/null @@ -1,17 +0,0 @@ -name: rapids-singlecell -description: | - A GPU acclerated python package for singlecell data analysis -project_home: https://github.com/scverse/rapids_singlecell -documentation_home: https://rapids-singlecell.readthedocs.io/en/latest/ -tutorials_home: https://rapids-singlecell.readthedocs.io/en/latest/notebooks.html -install: - pypi: rapids-singlecell -tags: - - Singlecell Analysis - - GPU acceleration - - CUDA -license: MIT -version: v0.7.5 -authors: - - Severin Dicks -test_command: pytest From 08fc058366380335de6fc9deaed603a38e3bf309 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 10 Jul 2025 19:09:23 +0200 Subject: [PATCH 107/126] [pre-commit.ci] pre-commit autoupdate (#255) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Phil Schaf --- .gitignore | 2 +- .pre-commit-config.yaml | 6 +++--- scripts/src/ecosystem_scripts/template_repo_registry.py | 7 +++---- 3 files changed, 7 insertions(+), 8 deletions(-) diff --git a/.gitignore b/.gitignore index cb38f9b0..636e042e 100644 --- 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 index 9aa1f130..6cc681b7 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.33.0 + rev: 0.33.2 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.33.0 + rev: 0.33.2 hooks: - id: check-jsonschema files: "packages/.*/meta.yaml" @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.11.13 + rev: v0.12.2 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] diff --git a/scripts/src/ecosystem_scripts/template_repo_registry.py b/scripts/src/ecosystem_scripts/template_repo_registry.py index 1b7761fd..d329939f 100644 --- a/scripts/src/ecosystem_scripts/template_repo_registry.py +++ b/scripts/src/ecosystem_scripts/template_repo_registry.py @@ -18,6 +18,8 @@ from typing import NotRequired, TypedDict from github import Github +from rich.logging import RichHandler +from rich.traceback import install from yaml import safe_dump, safe_load log = getLogger(__name__) @@ -56,10 +58,7 @@ def merge_repos(known: Iterable[Repo], new: Iterable[str]) -> list[Repo]: return repos -def setup(): - from rich.logging import RichHandler - from rich.traceback import install - +def setup() -> None: basicConfig(level="INFO", handlers=[RichHandler()]) install(show_locals=True) From 5b229e88229ed8776a47c9011cc1ffe1e94576b8 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 14 Jul 2025 21:22:53 +0200 Subject: [PATCH 108/126] [pre-commit.ci] pre-commit autoupdate (#260) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- README.md | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6cc681b7..4a6f877e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.2 + rev: v0.12.3 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] diff --git a/README.md b/README.md index daafa74f..541f54fb 100644 --- a/README.md +++ b/README.md @@ -51,7 +51,6 @@ How does the package use scverse data structures (please describe in a few sente - [ ] 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: From 7233fb5870599e1621a18b287ba0c66f24b99eab Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 22 Jul 2025 10:35:56 +0200 Subject: [PATCH 109/126] [pre-commit.ci] pre-commit autoupdate (#261) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4a6f877e..65872c6b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.3 + rev: v0.12.4 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From e4be05a0aa7e3a4c24e9e842c3072a0f10bef697 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 29 Jul 2025 09:18:51 +0200 Subject: [PATCH 110/126] [pre-commit.ci] pre-commit autoupdate (#264) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 65872c6b..d8b4a4eb 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.4 + rev: v0.12.5 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From 32bb4c39edc44c833b27dcee0cd10a2d58f6556e Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Fri, 1 Aug 2025 05:26:25 +0000 Subject: [PATCH 111/126] Updated template-repos.yml --- template-repos.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index f62b2c64..de14587d 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -15,6 +15,7 @@ - url: https://github.com/FroeseLab/bulkpy - url: https://github.com/Gabriellvl/FlowSOM - url: https://github.com/Lotfollahi-lab/mintflow +- url: https://github.com/MannLabs/dvp-io - url: https://github.com/NKI-CCB/sobolev_alignment - url: https://github.com/Teichlab/multi-view-atlas - url: https://github.com/YosefLab/PopV @@ -35,9 +36,11 @@ - url: https://github.com/adamgayoso/figmasvg - url: https://github.com/aertslab/CREsted - url: https://github.com/aertslab/EnhancerAI +- url: https://github.com/aertslab/TF-MInDi - url: https://github.com/agerardy/myeditdistance - url: https://github.com/angelolab/Nimbus-Inference - url: https://github.com/angelolab/ark-spatial +- url: https://github.com/angelolab/mbt - url: https://github.com/angelolab/pici-vitessce - url: https://github.com/angelolab/tonic-vitessce - url: https://github.com/bartuschimschek/mmil-refactored From 773142ce59432077f87a6445b9184b044d04ce66 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 5 Aug 2025 20:33:47 +0200 Subject: [PATCH 112/126] [pre-commit.ci] pre-commit autoupdate (#266) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d8b4a4eb..67b3abbf 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.5 + rev: v0.12.7 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From b2363d289490300c21365376a1fde43b27c3cdcb Mon Sep 17 00:00:00 2001 From: annmoel <131354170+annmoel@users.noreply.github.com> Date: Thu, 7 Aug 2025 09:30:16 +0200 Subject: [PATCH 113/126] add scxmatch (#256) * add scxmatch * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Corrected DOI format * Update meta.yaml --------- Co-authored-by: Anna Moeller Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Mikkel Niklas Rasmussen <77323950+mikkelnrasmussen@users.noreply.github.com> --- packages/scxmatch/meta.yaml | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 packages/scxmatch/meta.yaml diff --git a/packages/scxmatch/meta.yaml b/packages/scxmatch/meta.yaml new file mode 100644 index 00000000..42569afd --- /dev/null +++ b/packages/scxmatch/meta.yaml @@ -0,0 +1,26 @@ +name: scxmatch +description: | + Single-cell Cross Match (scxmatch) is a is a Python package that implements Rosenbaum's cross-match test using distance-based matching to assess distribution shifts between two groups of high-dimensional data. + This is particularly useful in analyzing multivariate distributions in structured data, such as single-cell RNA-seq or ATAC-seq. +project_home: https://github.com/bionetslab/scxmatch +documentation_home: https://github.com/bionetslab/scxmatch +tutorials_home: https://github.com/bionetslab/scxmatch +publications: + - 10.1101/2025.06.25.661473 +install: + conda: bioconda::scxmatch +tags: + - scRNA-seq + - single-cell + - python + - statistical testing + - distance-based matching + - perturbation + - condition +license: MIT +version: v0.1.0 +authors: + - annmoel + - dbblumenthal +test_command: | + conda install scxmatch -c conda-forge -c bioconda && git clone https://github.com/bionetslab/scxmatch.git && cd scxmatch/tests/ && python test_mwe.py From c6480db00259019c14b1721f0a19b6ba9f642c0e Mon Sep 17 00:00:00 2001 From: jonas Date: Thu, 7 Aug 2025 11:45:43 +0200 Subject: [PATCH 114/126] Add delnx (#259) add meta Co-authored-by: Mikkel Niklas Rasmussen <77323950+mikkelnrasmussen@users.noreply.github.com> --- packages/delnx/meta.yaml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 packages/delnx/meta.yaml diff --git a/packages/delnx/meta.yaml b/packages/delnx/meta.yaml new file mode 100644 index 00000000..350d7801 --- /dev/null +++ b/packages/delnx/meta.yaml @@ -0,0 +1,20 @@ +name: delnx +description: | + delnx is a python package for differential expression analysis of (single-cell) genomics data. It enables scalable analyses of atlas-level datasets through GPU-accelerated regression models and statistical tests implemented in JAX and provides a consistent interface to perform DE analysis with other methods, such as statsmodels and PyDESeq2. +project_home: https://github.com/joschif/delnx +documentation_home: https://delnx.readthedocs.io/en/latest/ +tutorials_home: https://delnx.readthedocs.io/en/latest/ +install: + pypi: delnx +tags: + - differential expression + - regression models + - dispersion estimation + - JAX +license: MIT +version: v0.2.3 +authors: + - joschif + - adaml9 +test_command: | + pip install ".[test]" && pytest From 737908c3b0292b6c381f1357ea37c03f8c214b44 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Philipp=20S=2E=20L=2E=20Sch=C3=A4fer?= <62442385+psl-schaefer@users.noreply.github.com> Date: Thu, 7 Aug 2025 16:07:07 +0200 Subject: [PATCH 115/126] adding partipy (#265) * adding partipy * fix typo --------- Co-authored-by: Mikkel Niklas Rasmussen <77323950+mikkelnrasmussen@users.noreply.github.com> --- packages/ParTIpy/meta.yaml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 packages/ParTIpy/meta.yaml diff --git a/packages/ParTIpy/meta.yaml b/packages/ParTIpy/meta.yaml new file mode 100644 index 00000000..75438ffa --- /dev/null +++ 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 From cfe613ca5947255225487e1f78d7a3f11eaed046 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 12 Aug 2025 10:36:53 +0200 Subject: [PATCH 116/126] [pre-commit.ci] pre-commit autoupdate (#267) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 67b3abbf..e29fc26b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -8,7 +8,7 @@ minimum_pre_commit_version: 2.16.0 repos: # all files - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v5.0.0 + rev: v6.0.0 hooks: - id: detect-private-key - id: check-ast @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.7 + rev: v0.12.8 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From cc18e5499d5bc10f6c7f472368593122b5a5e7b5 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Fri, 15 Aug 2025 05:14:21 +0000 Subject: [PATCH 117/126] Updated template-repos.yml --- template-repos.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/template-repos.yml b/template-repos.yml index de14587d..aff9706d 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -92,6 +92,7 @@ - url: https://github.com/mostafavilabuw/drum - url: https://github.com/mumichae/scAtlasTb-utils - url: https://github.com/nitzanlab/biolord +- url: https://github.com/peng-lab/hescape - url: https://github.com/quadbio/atac_mapper - url: https://github.com/quadbio/cell-annotator - url: https://github.com/quadbio/cellmapper From 2b89c92a216fbf36a8040e5efdc92b5ea48402c4 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 18 Aug 2025 20:02:28 +0200 Subject: [PATCH 118/126] [pre-commit.ci] pre-commit autoupdate (#268) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e29fc26b..4f268f4f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,13 +23,13 @@ repos: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.33.2 + rev: 0.33.3 hooks: - id: check-jsonschema files: "schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.33.2 + 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: v0.12.8 + rev: v0.12.9 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From da4521d333c1ac838e9c21352d1e7b646505d3e5 Mon Sep 17 00:00:00 2001 From: Malte Kuehl Date: Tue, 19 Aug 2025 08:44:09 +0200 Subject: [PATCH 119/126] Add spatiomic (#263) Co-authored-by: Mikkel Niklas Rasmussen <77323950+mikkelnrasmussen@users.noreply.github.com> --- packages/spatiomic/meta.yaml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 packages/spatiomic/meta.yaml diff --git a/packages/spatiomic/meta.yaml b/packages/spatiomic/meta.yaml new file mode 100644 index 00000000..80239330 --- /dev/null +++ b/packages/spatiomic/meta.yaml @@ -0,0 +1,20 @@ +name: spatiomic +description: | + spatiomic is a computational library for the analysis of spatial proteomics, mainly via pixel-based clustering, differential cluster abundance analysis and spatial statistics. +project_home: https://github.com/complextissue/spatiomic +documentation_home: https://spatiomic.org +tutorials_home: https://spatiomic.org/latest/tutorials/full_example.html +install: + pypi: spatiomic +tags: + - spatial biology + - spatial proteomics + - spatial omics + - multiplexed protein imaging + - PathoPlex + - subcellular analysis +license: GPL-3.0-only +version: v0.5.0 +authors: + - maltekuehl +test_command: uv run pytest -m "not gpu" From 12b46a08379bfbc2c2611217948d1c5061d4a43b Mon Sep 17 00:00:00 2001 From: Peisen Sun Date: Tue, 19 Aug 2025 07:52:19 +0100 Subject: [PATCH 120/126] add STMiner (#254) * add STMiner Name of the tool: STMiner Short description: Gene-centric spatial transcriptomics for deciphering complex spatial omics data How does the package use scverse data structures (please describe in a few sentences): STMiner uses AnnData as standardized input and output, and all operations are based on AnnData. STMiner also supports reading data in multiple formats (CSV, gem, etc.) and converting them into AnnData for unified operations. - [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 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Mikkel Niklas Rasmussen <77323950+mikkelnrasmussen@users.noreply.github.com> --- packages/STMiner/meta.yaml | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 packages/STMiner/meta.yaml diff --git a/packages/STMiner/meta.yaml b/packages/STMiner/meta.yaml new file mode 100644 index 00000000..336028af --- /dev/null +++ b/packages/STMiner/meta.yaml @@ -0,0 +1,17 @@ +name: STMiner +description: | + Gene-centric spatial transcriptomics for deciphering complex spatial omics data +project_home: https://github.com/xjtu-omics/STMiner +documentation_home: https://stminerdoc.readthedocs.io/en/latest +install: + pypi: stminer +tags: + - spatial variable genes + - spatial patterns + - optimal transport + - mechine learning +license: GPL-3.0-or-later +version: v1.1.0 +authors: + - Peisen Sun +test_command: pip install "." && pytest From 3f1dcf2c5b6a163cca340786c5e73dfd23a8d94c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 26 Aug 2025 08:46:08 +0200 Subject: [PATCH 121/126] [pre-commit.ci] pre-commit autoupdate (#269) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4f268f4f..9a278d01 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.9 + rev: v0.12.10 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From dcad1e2ed8dc432d87ce0c78a310a0bd724068ba Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Mon, 1 Sep 2025 05:13:19 +0000 Subject: [PATCH 122/126] Updated template-repos.yml --- template-repos.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/template-repos.yml b/template-repos.yml index aff9706d..fc781c01 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -96,6 +96,7 @@ - url: https://github.com/quadbio/atac_mapper - url: https://github.com/quadbio/cell-annotator - url: https://github.com/quadbio/cellmapper +- url: https://github.com/quadbio/scembed - url: https://github.com/quadbio/slurm_sweep - url: https://github.com/saeyslab/FlowSOM_Python - url: https://github.com/saezlab/decoupler-py From 76d605bdd924615cac0d204698b0b1cebcddfbc6 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 1 Sep 2025 20:41:17 +0200 Subject: [PATCH 123/126] [pre-commit.ci] pre-commit autoupdate (#270) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9a278d01..865f3267 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.10 + rev: v0.12.11 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From e3daf0abf514444bbdc76c8754e787f5b088b600 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 9 Sep 2025 08:54:39 +0200 Subject: [PATCH 124/126] [pre-commit.ci] pre-commit autoupdate (#273) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 865f3267..9f5df2cb 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.11 + rev: v0.12.12 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] From c4398e1005b2191384f83996a73a9300b7183392 Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Mon, 15 Sep 2025 05:12:45 +0000 Subject: [PATCH 125/126] Updated template-repos.yml --- template-repos.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/template-repos.yml b/template-repos.yml index fc781c01..9e0a0f47 100644 --- a/template-repos.yml +++ b/template-repos.yml @@ -19,6 +19,7 @@ - url: https://github.com/NKI-CCB/sobolev_alignment - url: https://github.com/Teichlab/multi-view-atlas - url: https://github.com/YosefLab/PopV +- url: https://github.com/YosefLab/cytovi-reference-implementation - url: https://github.com/YosefLab/embedding-scvi - url: https://github.com/YosefLab/popV - url: https://github.com/YosefLab/pycea @@ -79,6 +80,7 @@ - url: https://github.com/jskerman/chronai - url: https://github.com/karadavis-lab/anndata-utils - url: https://github.com/karadavis-lab/nbl +- url: https://github.com/laminlabs/arrayloaders - url: https://github.com/lhqing/scmallet - url: https://github.com/lucas-diedrich/dvp-io - url: https://github.com/lucas-diedrich/sccoral From e4e7357b145913585687860643c3f98bb103cd39 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 16 Sep 2025 11:34:14 +0200 Subject: [PATCH 126/126] [pre-commit.ci] pre-commit autoupdate (#275) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9f5df2cb..3f9e75a8 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -45,7 +45,7 @@ repos: exclude: "^packages/.*/meta.yaml$" # template repo registry - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.12 + rev: v0.13.0 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix]