diff --git a/README.md b/README.md index 352b66f..4732e7c 100644 --- a/README.md +++ b/README.md @@ -2,32 +2,33 @@ GitHub Dashboard ================ ![](https://github.com/gadenbuie/status/workflows/Render%20Status/badge.svg) -2024-01-23 12:10:10 UTC +2024-01-24 12:10:08 UTC | Repo | Stars | Subscribers | Issues | Forks | Status | Commit | |:----------------------------------------------------------------------------------------------------|------:|------------:|-------:|------:|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | [theislab/single-cell-best-practices](https://github.com/theislab/single-cell-best-practices) | 568 | 15 | 48 | 123 | [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20book/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/7338718027) [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20environments/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/7338718025) [![](https://github.com/theislab/single-cell-best-practices/workflows/Labeler/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/7338718026) [![](https://github.com/theislab/single-cell-best-practices/workflows/pre-commit/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/7338718029) | 2e0a1f | | [theislab/single-cell-best-practices](https://github.com/theislab/single-cell-best-practices) | 568 | 15 | 48 | 123 | [![](https://github.com/theislab/single-cell-best-practices/workflows/Release%20Drafter/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/4784044952) | c06ca9 | -| [theislab/scvelo](https://github.com/theislab/scvelo) | 370 | 13 | 56 | 100 | [![](https://github.com/theislab/scvelo/workflows/Check%20Build/badge.svg)](https://github.com/theislab/scvelo/actions/runs/7076514631) [![](https://github.com/theislab/scvelo/workflows/CI/badge.svg)](https://github.com/theislab/scvelo/actions/runs/7076514630) [![](https://github.com/theislab/scvelo/workflows/Release/badge.svg)](https://github.com/theislab/scvelo/actions/runs/7076589652) | 809632 | -| [theislab/cellrank](https://github.com/theislab/cellrank) | 281 | 7 | 13 | 35 | [![](https://github.com/theislab/cellrank/workflows/Deployment/badge.svg)](https://github.com/theislab/cellrank/actions/runs/7005093203) | c11a86 | -| [theislab/cellrank](https://github.com/theislab/cellrank) | 281 | 7 | 13 | 35 | [![](https://github.com/theislab/cellrank/workflows/Test/badge.svg)](https://github.com/theislab/cellrank/actions/runs/7604769607) [![](https://github.com/theislab/cellrank/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank/actions/runs/7604824170) | cabbd3 | +| [theislab/scvelo](https://github.com/theislab/scvelo) | 372 | 13 | 56 | 100 | [![](https://github.com/theislab/scvelo/workflows/Check%20Build/badge.svg)](https://github.com/theislab/scvelo/actions/runs/7076514631) [![](https://github.com/theislab/scvelo/workflows/CI/badge.svg)](https://github.com/theislab/scvelo/actions/runs/7076514630) [![](https://github.com/theislab/scvelo/workflows/Release/badge.svg)](https://github.com/theislab/scvelo/actions/runs/7076589652) | 809632 | +| [theislab/cellrank](https://github.com/theislab/cellrank) | 282 | 7 | 13 | 35 | [![](https://github.com/theislab/cellrank/workflows/Deployment/badge.svg)](https://github.com/theislab/cellrank/actions/runs/7005093203) | c11a86 | +| [theislab/cellrank](https://github.com/theislab/cellrank) | 282 | 7 | 13 | 35 | [![](https://github.com/theislab/cellrank/workflows/Test/badge.svg)](https://github.com/theislab/cellrank/actions/runs/7604769607) [![](https://github.com/theislab/cellrank/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank/actions/runs/7604824170) | cabbd3 | | [theislab/scib](https://github.com/theislab/scib) | 252 | 16 | 34 | 57 | [![](https://github.com/theislab/scib/workflows/Deployment/badge.svg)](https://github.com/theislab/scib/actions/runs/7468185443) | d42f91 | -| [theislab/scgen](https://github.com/theislab/scgen) | 237 | 9 | 20 | 51 | [![](https://github.com/theislab/scgen/workflows/scgen-test/badge.svg)](https://github.com/theislab/scgen/actions/runs/6370224484) | d79e1f | -| [theislab/sfaira](https://github.com/theislab/sfaira) | 131 | 8 | 166 | 13 | [![](https://github.com/theislab/sfaira/workflows/Check%20URLs/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7619026594) | 55bcbb | +| [theislab/scgen](https://github.com/theislab/scgen) | 236 | 9 | 20 | 51 | [![](https://github.com/theislab/scgen/workflows/scgen-test/badge.svg)](https://github.com/theislab/scgen/actions/runs/6370224484) | d79e1f | +| [theislab/sfaira](https://github.com/theislab/sfaira) | 131 | 8 | 166 | 13 | [![](https://github.com/theislab/sfaira/workflows/Check%20URLs/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7633455153) | 55bcbb | | [theislab/sfaira](https://github.com/theislab/sfaira) | 131 | 8 | 166 | 13 | [![](https://github.com/theislab/sfaira/workflows/Build%20sfaira%20Package/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672388) [![](https://github.com/theislab/sfaira/workflows/Create%20sfaira%20data-loader%20templates/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672382) [![](https://github.com/theislab/sfaira/workflows/Run%20bandit/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672385) [![](https://github.com/theislab/sfaira/workflows/Run%20flake8%20linting/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672384) | 5fcf93 | | [theislab/sfaira](https://github.com/theislab/sfaira) | 131 | 8 | 166 | 13 | [![](https://github.com/theislab/sfaira/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/sfaira/actions/runs/6812817430) | ceb14c | | [theislab/zellkonverter](https://github.com/theislab/zellkonverter) | 113 | 6 | 18 | 22 | [![](https://github.com/theislab/zellkonverter/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/theislab/zellkonverter/actions/runs/7558891230) | 9d557f | | [theislab/anndata2ri](https://github.com/theislab/anndata2ri) | 104 | 6 | 15 | 15 | [![](https://github.com/theislab/anndata2ri/workflows/Unit%20Tests/badge.svg)](https://github.com/theislab/anndata2ri/actions/runs/7622968900) | a84a45 | | [theislab/ncem](https://github.com/theislab/ncem) | 95 | 6 | 24 | 12 | [![](https://github.com/theislab/ncem/workflows/Labeler/badge.svg)](https://github.com/theislab/ncem/actions/runs/5392074704) | 216fd5 | | [theislab/ncem](https://github.com/theislab/ncem) | 95 | 6 | 24 | 12 | [![](https://github.com/theislab/ncem/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/ncem/actions/runs/6666317399) [![](https://github.com/theislab/ncem/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/ncem/actions/runs/6666317397) | d03a07 | -| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 93 | 7 | 33 | 11 | [![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457160) [![](https://github.com/theislab/ehrapy/workflows/Run%20Notebooks/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457159) [![](https://github.com/theislab/ehrapy/workflows/Test/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457157) [![](https://github.com/theislab/ehrapy/workflows/Release%20Drafter/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457163) [![](https://github.com/theislab/ehrapy/workflows/Check%20Build/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457156) | 2c70a2 | -| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 93 | 7 | 33 | 11 | [![](https://github.com/theislab/ehrapy/workflows/Test%20windows%20stuff/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/5577003787) | 84d33c | -| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 93 | 7 | 33 | 11 | [![](https://github.com/theislab/ehrapy/workflows/Release/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7260760638) | ea6b44 | -| [theislab/moscot](https://github.com/theislab/moscot) | 81 | 3 | 38 | 6 | [![](https://github.com/theislab/moscot/workflows/Deployment/badge.svg)](https://github.com/theislab/moscot/actions/runs/6456571831) | b23360 | +| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 94 | 7 | 33 | 11 | [![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457160) [![](https://github.com/theislab/ehrapy/workflows/Run%20Notebooks/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457159) [![](https://github.com/theislab/ehrapy/workflows/Test/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457157) [![](https://github.com/theislab/ehrapy/workflows/Release%20Drafter/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457163) [![](https://github.com/theislab/ehrapy/workflows/Check%20Build/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457156) | 2c70a2 | +| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 94 | 7 | 33 | 11 | [![](https://github.com/theislab/ehrapy/workflows/Test%20windows%20stuff/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/5577003787) | 84d33c | +| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 94 | 7 | 33 | 11 | [![](https://github.com/theislab/ehrapy/workflows/Release/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7260760638) | ea6b44 | +| [theislab/moscot](https://github.com/theislab/moscot) | 81 | 3 | 36 | 6 | [![](https://github.com/theislab/moscot/workflows/Deployment/badge.svg)](https://github.com/theislab/moscot/actions/runs/6456571831) | b23360 | +| [theislab/moscot](https://github.com/theislab/moscot) | 81 | 3 | 36 | 6 | [![](https://github.com/theislab/moscot/workflows/Lint/badge.svg)](https://github.com/theislab/moscot/actions/runs/7639479837) [![](https://github.com/theislab/moscot/workflows/Test/badge.svg)](https://github.com/theislab/moscot/actions/runs/7639479845) | ca1357 | | [theislab/pertpy](https://github.com/theislab/pertpy) | 69 | 4 | 33 | 15 | [![](https://github.com/theislab/pertpy/workflows/Run%20Notebooks/badge.svg)](https://github.com/theislab/pertpy/actions/runs/4629618853) | \” title=“Revert”Deleted JaxscgenPlot”“\>404835 | | [theislab/pertpy](https://github.com/theislab/pertpy) | 69 | 4 | 33 | 15 | [![](https://github.com/theislab/pertpy/workflows/Labeler/badge.svg)](https://github.com/theislab/pertpy/actions/runs/7611051244) | aecbf8 | | [theislab/pertpy](https://github.com/theislab/pertpy) | 69 | 4 | 33 | 15 | [![](https://github.com/theislab/pertpy/workflows/Release/badge.svg)](https://github.com/theislab/pertpy/actions/runs/6737423407) | d00c5f | -| [theislab/destiny](https://github.com/theislab/destiny) | 67 | 5 | 30 | 11 | [![](https://github.com/theislab/destiny/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/theislab/destiny/actions/runs/7347769080) | 300eb2 | +| [theislab/destiny](https://github.com/theislab/destiny) | 67 | 5 | 30 | 12 | [![](https://github.com/theislab/destiny/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/theislab/destiny/actions/runs/7347769080) | 300eb2 | | [theislab/scib-pipeline](https://github.com/theislab/scib-pipeline) | 49 | 7 | 16 | 27 | [![](https://github.com/theislab/scib-pipeline/workflows/Manual%20workflow/badge.svg)](https://github.com/theislab/scib-pipeline/actions/runs/4118363146) | 1180bc | | [theislab/batchglm](https://github.com/theislab/batchglm) | 26 | 3 | 46 | 9 | [![](https://github.com/theislab/batchglm/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/batchglm/actions/runs/4348825767) [![](https://github.com/theislab/batchglm/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/batchglm/actions/runs/4348825761) | 11ffbb | | [theislab/batchglm](https://github.com/theislab/batchglm) | 26 | 3 | 46 | 9 | [![](https://github.com/theislab/batchglm/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/batchglm/actions/runs/4898948664) | b893fd | @@ -40,7 +41,7 @@ GitHub Dashboard | [theislab/cellrank_notebooks](https://github.com/theislab/cellrank_notebooks) | 6 | 4 | 1 | 6 | [![](https://github.com/theislab/cellrank_notebooks/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank_notebooks/actions/runs/6686677756) | 677784 | | [theislab/ehrapy-datasets](https://github.com/theislab/ehrapy-datasets) | 4 | 2 | 0 | 2 | [![](https://github.com/theislab/ehrapy-datasets/workflows/Run%20Notebooks/badge.svg)](https://github.com/theislab/ehrapy-datasets/actions/runs/4510904353) | cb7707 | | [theislab/cellrank2_reproducibility](https://github.com/theislab/cellrank2_reproducibility) | 3 | 1 | 0 | 0 | [![](https://github.com/theislab/cellrank2_reproducibility/workflows/deploy-jupyter-book/badge.svg)](https://github.com/theislab/cellrank2_reproducibility/actions/runs/7102882080) [![](https://github.com/theislab/cellrank2_reproducibility/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank2_reproducibility/actions/runs/7102882073) | 9ab01c | -| [theislab/gh-dashboard](https://github.com/theislab/gh-dashboard) | 1 | 2 | 0 | 0 | [![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/7625382571) | eea9e4 | +| [theislab/gh-dashboard](https://github.com/theislab/gh-dashboard) | 1 | 2 | 0 | 0 | [![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/7639847737) | f3770b | | [theislab/transcription_factor_activity](https://github.com/theislab/transcription_factor_activity) | 1 | 1 | 5 | 1 | [![](https://github.com/theislab/transcription_factor_activity/workflows/Check%20Build/badge.svg)](https://github.com/theislab/transcription_factor_activity/actions/runs/5133287206) [![](https://github.com/theislab/transcription_factor_activity/workflows/Test/badge.svg)](https://github.com/theislab/transcription_factor_activity/actions/runs/5133287208) | ced39f | | [theislab/idtrack](https://github.com/theislab/idtrack) | 0 | 1 | 6 | 0 | [![](https://github.com/theislab/idtrack/workflows/Labeler/badge.svg)](https://github.com/theislab/idtrack/actions/runs/5369045662) | 12aa73 | | [theislab/idtrack](https://github.com/theislab/idtrack) | 0 | 1 | 6 | 0 | [![](https://github.com/theislab/idtrack/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/idtrack/actions/runs/6140914377) [![](https://github.com/theislab/idtrack/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/idtrack/actions/runs/6140914379) | 1f47f4 | @@ -50,12 +51,12 @@ GitHub Dashboard | Repo | Stars | Subscribers | Issues | Forks | |:------------------------------------------------------------------------------------------------------------------------------------|------:|------------:|-------:|------:| -| [theislab/single-cell-tutorial](https://github.com/theislab/single-cell-tutorial) | 1238 | 30 | 20 | 431 | +| [theislab/single-cell-tutorial](https://github.com/theislab/single-cell-tutorial) | 1236 | 30 | 20 | 431 | | [theislab/scarches](https://github.com/theislab/scarches) | 294 | 14 | 34 | 48 | -| [theislab/dca](https://github.com/theislab/dca) | 227 | 11 | 31 | 67 | -| [theislab/paga](https://github.com/theislab/paga) | 175 | 10 | 21 | 30 | +| [theislab/dca](https://github.com/theislab/dca) | 226 | 11 | 31 | 67 | +| [theislab/paga](https://github.com/theislab/paga) | 174 | 10 | 21 | 30 | | [theislab/diffxpy](https://github.com/theislab/diffxpy) | 168 | 6 | 106 | 22 | -| [theislab/kBET](https://github.com/theislab/kBET) | 137 | 9 | 7 | 23 | +| [theislab/kBET](https://github.com/theislab/kBET) | 136 | 9 | 7 | 23 | | [theislab/scCODA](https://github.com/theislab/scCODA) | 123 | 9 | 12 | 22 | | [theislab/sc-pert](https://github.com/theislab/sc-pert) | 118 | 6 | 6 | 10 | | [theislab/chemCPA](https://github.com/theislab/chemCPA) | 81 | 4 | 7 | 22 | @@ -64,9 +65,9 @@ GitHub Dashboard | [theislab/trVAE](https://github.com/theislab/trVAE) | 52 | 7 | 2 | 10 | | [theislab/scib-reproducibility](https://github.com/theislab/scib-reproducibility) | 47 | 6 | 3 | 13 | | [theislab/spatial_scog_workshop_2022](https://github.com/theislab/spatial_scog_workshop_2022) | 42 | 9 | 0 | 24 | -| [theislab/pseudodynamics](https://github.com/theislab/pseudodynamics) | 40 | 7 | 0 | 6 | +| [theislab/pseudodynamics](https://github.com/theislab/pseudodynamics) | 39 | 7 | 0 | 6 | | [theislab/tcellmatch](https://github.com/theislab/tcellmatch) | 37 | 9 | 3 | 7 | -| [theislab/single-cell-transformer-papers](https://github.com/theislab/single-cell-transformer-papers) | 31 | 2 | 0 | 2 | +| [theislab/single-cell-transformer-papers](https://github.com/theislab/single-cell-transformer-papers) | 32 | 2 | 0 | 2 | | [theislab/deepflow](https://github.com/theislab/deepflow) | 30 | 5 | 1 | 14 | | [theislab/scArches-reproducibility](https://github.com/theislab/scArches-reproducibility) | 30 | 5 | 5 | 1 | | [theislab/DeepRT](https://github.com/theislab/DeepRT) | 26 | 2 | 11 | 10 | @@ -76,7 +77,7 @@ GitHub Dashboard | [theislab/scTab](https://github.com/theislab/scTab) | 22 | 2 | 2 | 3 | | [theislab/interactive_plotting](https://github.com/theislab/interactive_plotting) | 20 | 4 | 10 | 7 | | [theislab/mubind](https://github.com/theislab/mubind) | 19 | 3 | 30 | 0 | -| [theislab/scgen-reproducibility](https://github.com/theislab/scgen-reproducibility) | 18 | 4 | 5 | 8 | +| [theislab/scgen-reproducibility](https://github.com/theislab/scgen-reproducibility) | 17 | 4 | 5 | 8 | | [theislab/cellrank_reproducibility](https://github.com/theislab/cellrank_reproducibility) | 14 | 2 | 0 | 8 | | [theislab/campa](https://github.com/theislab/campa) | 13 | 4 | 5 | 4 | | [theislab/DeepCollisionalCrossSection](https://github.com/theislab/DeepCollisionalCrossSection) | 13 | 5 | 1 | 6 | @@ -88,16 +89,16 @@ GitHub Dashboard | [theislab/diffxpy_tutorials](https://github.com/theislab/diffxpy_tutorials) | 10 | 8 | 4 | 2 | | [theislab/GWAS-scRNAseq-Integration](https://github.com/theislab/GWAS-scRNAseq-Integration) | 10 | 5 | 0 | 12 | | [theislab/ncem_tutorials](https://github.com/theislab/ncem_tutorials) | 10 | 4 | 5 | 0 | -| [theislab/scAnalysisTutorial](https://github.com/theislab/scAnalysisTutorial) | 10 | 3 | 0 | 3 | | [theislab/cross_system_integration](https://github.com/theislab/cross_system_integration) | 9 | 2 | 10 | 0 | | [theislab/enrichment_analysis_celltype](https://github.com/theislab/enrichment_analysis_celltype) | 9 | 5 | 0 | 4 | +| [theislab/inVAE](https://github.com/theislab/inVAE) | 9 | 3 | 0 | 1 | | [theislab/moslin](https://github.com/theislab/moslin) | 9 | 1 | 0 | 1 | +| [theislab/scAnalysisTutorial](https://github.com/theislab/scAnalysisTutorial) | 9 | 3 | 0 | 3 | | [theislab/superexacttestpy](https://github.com/theislab/superexacttestpy) | 9 | 2 | 3 | 0 | | [theislab/trvaep](https://github.com/theislab/trvaep) | 9 | 3 | 0 | 4 | | [theislab/expiMap_reproducibility](https://github.com/theislab/expiMap_reproducibility) | 8 | 5 | 3 | 4 | | [theislab/gastrulation_analysis](https://github.com/theislab/gastrulation_analysis) | 8 | 4 | 0 | 1 | | [theislab/greatpy](https://github.com/theislab/greatpy) | 8 | 3 | 4 | 0 | -| [theislab/inVAE](https://github.com/theislab/inVAE) | 8 | 3 | 0 | 1 | | [theislab/ncem_benchmarks](https://github.com/theislab/ncem_benchmarks) | 8 | 4 | 4 | 2 | | 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GitHub Dashboard

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GitHub Dashboard

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GitHub Dashboard

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GitHub Dashboard

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Repos without Github Actions

+ + + + + + + - + - + - + - + - - - - - - - diff --git a/repos.csv b/repos.csv index 8e3b878..7953436 100644 --- a/repos.csv +++ b/repos.csv @@ -57,12 +57,12 @@ theislab,batchglm,theislab/batchglm,26,3,46,9,FALSE,https://github.com/theislab/ theislab,bindome,theislab/bindome,1,3,5,1,FALSE,https://github.com/theislab/bindome,1,NA,NA,NA theislab,campa,theislab/campa,13,4,5,4,FALSE,https://github.com/theislab/campa,13,NA,NA,NA theislab,campa_ana,theislab/campa_ana,2,4,0,0,FALSE,https://github.com/theislab/campa_ana,2,NA,NA,NA -theislab,cellrank,theislab/cellrank,281,7,13,35,FALSE,https://github.com/theislab/cellrank,281,c11a86bbf3dd34f5c2b72f87c52ed6da4920f5a8,"Use new PyPI trusted publisher management (#1138) +theislab,cellrank,theislab/cellrank,282,7,13,35,FALSE,https://github.com/theislab/cellrank,282,c11a86bbf3dd34f5c2b72f87c52ed6da4920f5a8,"Use new PyPI trusted publisher management (#1138) * Use new PyPI trusted publisher management * Add forgotten on",[![](https://github.com/theislab/cellrank/workflows/Deployment/badge.svg)](https://github.com/theislab/cellrank/actions/runs/7005093203) -theislab,cellrank,theislab/cellrank,281,7,13,35,FALSE,https://github.com/theislab/cellrank,281,cabbd348b97661251a7dfa37186b178ff489e746,"Remove matplotlib upper pin from (#1143) +theislab,cellrank,theislab/cellrank,282,7,13,35,FALSE,https://github.com/theislab/cellrank,282,cabbd348b97661251a7dfa37186b178ff489e746,"Remove matplotlib upper pin from (#1143) * Remove upper pin from #1099 @@ -86,23 +86,23 @@ theislab,cpa,theislab/cpa,66,4,13,13,FALSE,https://github.com/theislab/cpa,66,NA theislab,cpa-reproducibility,theislab/cpa-reproducibility,7,3,0,1,FALSE,https://github.com/theislab/cpa-reproducibility,7,NA,NA,NA theislab,cross_system_integration,theislab/cross_system_integration,9,2,10,0,FALSE,https://github.com/theislab/cross_system_integration,9,NA,NA,NA theislab,dali,theislab/dali,0,7,0,1,FALSE,https://github.com/theislab/dali,0,NA,NA,NA -theislab,dca,theislab/dca,227,11,31,67,FALSE,https://github.com/theislab/dca,227,NA,NA,NA +theislab,dca,theislab/dca,226,11,31,67,FALSE,https://github.com/theislab/dca,226,NA,NA,NA theislab,deepflow,theislab/deepflow,30,5,1,14,FALSE,https://github.com/theislab/deepflow,30,NA,NA,NA -theislab,destiny,theislab/destiny,67,5,30,11,FALSE,https://github.com/theislab/destiny,67,300eb293fb773fb3d667818b946fdd3c62b0aa05,Fix sparse matrix cast and ggplot aes_string deprecations (#65),[![](https://github.com/theislab/destiny/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/theislab/destiny/actions/runs/7347769080) +theislab,destiny,theislab/destiny,67,5,30,12,FALSE,https://github.com/theislab/destiny,67,300eb293fb773fb3d667818b946fdd3c62b0aa05,Fix sparse matrix cast and ggplot aes_string deprecations (#65),[![](https://github.com/theislab/destiny/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/theislab/destiny/actions/runs/7347769080) 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<66853113+pre-commit-ci[bot]@users.noreply.github.com>",[![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457160) [![](https://github.com/theislab/ehrapy/workflows/Run%20Notebooks/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457159) [![](https://github.com/theislab/ehrapy/workflows/Test/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457157) [![](https://github.com/theislab/ehrapy/workflows/Release%20Drafter/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457163) [![](https://github.com/theislab/ehrapy/workflows/Check%20Build/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7624457156) -theislab,ehrapy,theislab/ehrapy,93,7,33,11,FALSE,https://github.com/theislab/ehrapy,93,84d33c8988ea560aa557fbe6a99b926befa84457,"Add test windows +theislab,ehrapy,theislab/ehrapy,94,7,33,11,FALSE,https://github.com/theislab/ehrapy,94,84d33c8988ea560aa557fbe6a99b926befa84457,"Add test windows Signed-off-by: zethson ",[![](https://github.com/theislab/ehrapy/workflows/Test%20windows%20stuff/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/5577003787) -theislab,ehrapy,theislab/ehrapy,93,7,33,11,FALSE,https://github.com/theislab/ehrapy,93,ea6b4430d58d4ff8660eb15bd5db4d248f1c74ea,"Submodule +theislab,ehrapy,theislab/ehrapy,94,7,33,11,FALSE,https://github.com/theislab/ehrapy,94,ea6b4430d58d4ff8660eb15bd5db4d248f1c74ea,"Submodule Signed-off-by: zethson ",[![](https://github.com/theislab/ehrapy/workflows/Release/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/7260760638) theislab,ehrapy-cli,theislab/ehrapy-cli,1,3,0,0,FALSE,https://github.com/theislab/ehrapy-cli,1,NA,NA,NA @@ -125,7 +125,7 @@ API Update, Transform and ToIterable classes.",[![](https://github.com/theislab/ theislab,geome,theislab/geome,13,3,4,4,FALSE,https://github.com/theislab/geome,13,5bf0cd07b2ea7fa224a37f69232542a9e686c5bf,"Merge pull request #31 from theislab/template-update Automated template update from cookiecutter-scverse",[![](https://github.com/theislab/geome/workflows/Sync%20Template/badge.svg)](https://github.com/theislab/geome/actions/runs/4904831582) -theislab,gh-dashboard,theislab/gh-dashboard,1,2,0,0,FALSE,https://github.com/theislab/gh-dashboard,1,eea9e44f7f1a237fbb6044afa0b46545736a5815,[status] 2024-01-22 12:12:54 UTC,[![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/7625382571) +theislab,gh-dashboard,theislab/gh-dashboard,1,2,0,0,FALSE,https://github.com/theislab/gh-dashboard,1,f3770b33220ccf457fce4698f47266e75d14bbaa,[status] 2024-01-23 12:12:00 UTC,[![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/7639847737) theislab,graph_abstraction,theislab/graph_abstraction,26,8,0,10,FALSE,https://github.com/theislab/graph_abstraction,26,NA,NA,NA theislab,greatpy,theislab/greatpy,8,3,4,0,FALSE,https://github.com/theislab/greatpy,8,NA,NA,NA theislab,gut_lineage,theislab/gut_lineage,2,3,0,3,FALSE,https://github.com/theislab/gut_lineage,2,NA,NA,NA @@ -154,21 +154,24 @@ theislab,idtrack,theislab/idtrack,0,1,6,0,FALSE,https://github.com/theislab/idtr Release",[![](https://github.com/theislab/idtrack/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/idtrack/actions/runs/4836150850) theislab,ifcseq,theislab/ifcseq,1,3,0,1,FALSE,https://github.com/theislab/ifcseq,1,NA,NA,NA -theislab,inVAE,theislab/inVAE,8,3,0,1,FALSE,https://github.com/theislab/inVAE,8,NA,NA,NA 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theislab,masterpraktikum_ssl_segmentation,theislab/masterpraktikum_ssl_segmentation,0,2,0,0,FALSE,https://github.com/theislab/masterpraktikum_ssl_segmentation,0,NA,NA,NA -theislab,moscot,theislab/moscot,81,3,38,6,FALSE,https://github.com/theislab/moscot,81,b233601b6aecd7259aaa1a5dba107f2963420614,"Update/lrgw2 (#613) +theislab,moscot,theislab/moscot,81,3,36,6,FALSE,https://github.com/theislab/moscot,81,b233601b6aecd7259aaa1a5dba107f2963420614,"Update/lrgw2 (#613) Co-authored-by: Arina Danilina Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",[![](https://github.com/theislab/moscot/workflows/Deployment/badge.svg)](https://github.com/theislab/moscot/actions/runs/6456571831) +theislab,moscot,theislab/moscot,81,3,36,6,FALSE,https://github.com/theislab/moscot,81,ca135725193b70541f054d8cd853b0dee76f3bb0,"Merge pull request #648 from theislab/pre-commit-ci-update-config + +[pre-commit.ci] pre-commit autoupdate",[![](https://github.com/theislab/moscot/workflows/Lint/badge.svg)](https://github.com/theislab/moscot/actions/runs/7639479837) [![](https://github.com/theislab/moscot/workflows/Test/badge.svg)](https://github.com/theislab/moscot/actions/runs/7639479845) theislab,moscot-framework_reproducibility,theislab/moscot-framework_reproducibility,1,2,1,0,FALSE,https://github.com/theislab/moscot-framework_reproducibility,1,NA,NA,NA theislab,moscot_benchmarks,theislab/moscot_benchmarks,1,2,1,0,FALSE,https://github.com/theislab/moscot_benchmarks,1,NA,NA,NA theislab,moscot_not,theislab/moscot_not,2,2,8,0,FALSE,https://github.com/theislab/moscot_not,2,NA,NA,NA @@ -190,7 +193,7 @@ theislab,ncem_benchmarks,theislab/ncem_benchmarks,8,4,4,2,FALSE,https://github.c theislab,ncem_tutorials,theislab/ncem_tutorials,10,4,5,0,FALSE,https://github.com/theislab/ncem_tutorials,10,NA,NA,NA theislab,neural_organoid_atlas,theislab/neural_organoid_atlas,6,3,1,1,FALSE,https://github.com/theislab/neural_organoid_atlas,6,NA,NA,NA theislab,organoid_dexamethason_stimulation,theislab/organoid_dexamethason_stimulation,0,3,0,1,FALSE,https://github.com/theislab/organoid_dexamethason_stimulation,0,NA,NA,NA -theislab,paga,theislab/paga,175,10,21,30,FALSE,https://github.com/theislab/paga,175,NA,NA,NA +theislab,paga,theislab/paga,174,10,21,30,FALSE,https://github.com/theislab/paga,174,NA,NA,NA theislab,pancreas-targeted_pharmacology,theislab/pancreas-targeted_pharmacology,0,7,0,2,FALSE,https://github.com/theislab/pancreas-targeted_pharmacology,0,NA,NA,NA theislab,pancreatic-endocrinogenesis,theislab/pancreatic-endocrinogenesis,4,3,0,5,FALSE,https://github.com/theislab/pancreatic-endocrinogenesis,4,NA,NA,NA theislab,pertpy,theislab/pertpy,69,4,33,15,FALSE,https://github.com/theislab/pertpy,69,404835c82f9a3d943b85973c10130303d090839d,"Revert ""Deleted JaxscgenPlot"" @@ -201,12 +204,12 @@ theislab,pertpy,theislab/pertpy,69,4,33,15,FALSE,https://github.com/theislab/per theislab,pertpy-datasets,theislab/pertpy-datasets,1,3,0,1,FALSE,https://github.com/theislab/pertpy-datasets,1,NA,NA,NA theislab,pertpy-tutorials,theislab/pertpy-tutorials,4,4,2,6,FALSE,https://github.com/theislab/pertpy-tutorials,4,NA,NA,NA theislab,perturbation-metrics,theislab/perturbation-metrics,4,2,1,0,FALSE,https://github.com/theislab/perturbation-metrics,4,NA,NA,NA -theislab,pseudodynamics,theislab/pseudodynamics,40,7,0,6,FALSE,https://github.com/theislab/pseudodynamics,40,NA,NA,NA +theislab,pseudodynamics,theislab/pseudodynamics,39,7,0,6,FALSE,https://github.com/theislab/pseudodynamics,39,NA,NA,NA theislab,reproducability_AutoGeneS,theislab/reproducability_AutoGeneS,0,3,0,0,FALSE,https://github.com/theislab/reproducability_AutoGeneS,0,NA,NA,NA theislab,reproducibility_AutoGeneS,theislab/reproducibility_AutoGeneS,0,3,0,0,FALSE,https://github.com/theislab/reproducibility_AutoGeneS,0,NA,NA,NA theislab,sc-best-practices-ce,theislab/sc-best-practices-ce,8,8,2,3,FALSE,https://github.com/theislab/sc-best-practices-ce,8,NA,NA,NA theislab,sc-pert,theislab/sc-pert,118,6,6,10,FALSE,https://github.com/theislab/sc-pert,118,NA,NA,NA -theislab,scAnalysisTutorial,theislab/scAnalysisTutorial,10,3,0,3,FALSE,https://github.com/theislab/scAnalysisTutorial,10,NA,NA,NA +theislab,scAnalysisTutorial,theislab/scAnalysisTutorial,9,3,0,3,FALSE,https://github.com/theislab/scAnalysisTutorial,9,NA,NA,NA theislab,scArches-reproducibility,theislab/scArches-reproducibility,30,5,5,1,FALSE,https://github.com/theislab/scArches-reproducibility,30,NA,NA,NA theislab,scCODA,theislab/scCODA,123,9,12,22,FALSE,https://github.com/theislab/scCODA,123,NA,NA,NA theislab,scCODA_reproducibility,theislab/scCODA_reproducibility,7,5,0,1,FALSE,https://github.com/theislab/scCODA_reproducibility,7,NA,NA,NA @@ -227,8 +230,8 @@ Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.gi theislab,scarches,theislab/scarches,294,14,34,48,FALSE,https://github.com/theislab/scarches,294,NA,NA,NA theislab,scarches_notebooks,theislab/scarches_notebooks,0,3,0,0,FALSE,https://github.com/theislab/scarches_notebooks,0,NA,NA,NA theislab,scatac_poisson_reproducibility,theislab/scatac_poisson_reproducibility,6,3,0,0,FALSE,https://github.com/theislab/scatac_poisson_reproducibility,6,NA,NA,NA -theislab,scgen,theislab/scgen,237,9,20,51,FALSE,https://github.com/theislab/scgen,237,d79e1f04233c30f9a4eb5b8d57718127909807d7,Merge pull request #87 from theislab/batch_corr_labels,[![](https://github.com/theislab/scgen/workflows/scgen-test/badge.svg)](https://github.com/theislab/scgen/actions/runs/6370224484) -theislab,scgen-reproducibility,theislab/scgen-reproducibility,18,4,5,8,FALSE,https://github.com/theislab/scgen-reproducibility,18,NA,NA,NA +theislab,scgen,theislab/scgen,236,9,20,51,FALSE,https://github.com/theislab/scgen,236,d79e1f04233c30f9a4eb5b8d57718127909807d7,Merge pull request #87 from theislab/batch_corr_labels,[![](https://github.com/theislab/scgen/workflows/scgen-test/badge.svg)](https://github.com/theislab/scgen/actions/runs/6370224484) +theislab,scgen-reproducibility,theislab/scgen-reproducibility,17,4,5,8,FALSE,https://github.com/theislab/scgen-reproducibility,17,NA,NA,NA theislab,scib,theislab/scib,252,16,34,57,FALSE,https://github.com/theislab/scib,NA,d42f919b5b0aac86f19937d4d4d02bf2e4d8bdbd,"Update dependencies (#396) * pin pandas 2 and adapt breaking code @@ -238,11 +241,11 @@ theislab,scib,theislab/scib,252,16,34,57,FALSE,https://github.com/theislab/scib, * set minimum python version to 3.8",[![](https://github.com/theislab/scib/workflows/Deployment/badge.svg)](https://github.com/theislab/scib/actions/runs/7468185443) theislab,scib-pipeline,theislab/scib-pipeline,49,7,16,27,FALSE,https://github.com/theislab/scib-pipeline,49,1180bcb35829d6d2984202268b4d1d11c511e20c,Merge branch 'fix/igraph_dependency' into rpy2_unpin,[![](https://github.com/theislab/scib-pipeline/workflows/Manual%20workflow/badge.svg)](https://github.com/theislab/scib-pipeline/actions/runs/4118363146) theislab,scib-reproducibility,theislab/scib-reproducibility,47,6,3,13,FALSE,https://github.com/theislab/scib-reproducibility,47,NA,NA,NA -theislab,scvelo,theislab/scvelo,370,13,56,100,FALSE,https://github.com/theislab/scvelo,370,809632e03acc958a5f13d9321981af9c1cd95460,"Update `pyproject.toml` (#1166) +theislab,scvelo,theislab/scvelo,372,13,56,100,FALSE,https://github.com/theislab/scvelo,372,809632e03acc958a5f13d9321981af9c1cd95460,"Update `pyproject.toml` (#1166) Update version number.",[![](https://github.com/theislab/scvelo/workflows/Check%20Build/badge.svg)](https://github.com/theislab/scvelo/actions/runs/7076514631) [![](https://github.com/theislab/scvelo/workflows/CI/badge.svg)](https://github.com/theislab/scvelo/actions/runs/7076514630) [![](https://github.com/theislab/scvelo/workflows/Release/badge.svg)](https://github.com/theislab/scvelo/actions/runs/7076589652) theislab,scvelo_notebooks,theislab/scvelo_notebooks,25,2,2,12,FALSE,https://github.com/theislab/scvelo_notebooks,25,NA,NA,NA -theislab,sfaira,theislab/sfaira,131,8,166,13,FALSE,https://github.com/theislab/sfaira,131,55bcbbf2588a08e4a98b1e65324119407ec6e75c,Merge pull request #741 from theislab/release,[![](https://github.com/theislab/sfaira/workflows/Check%20URLs/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7619026594) +theislab,sfaira,theislab/sfaira,131,8,166,13,FALSE,https://github.com/theislab/sfaira,131,55bcbbf2588a08e4a98b1e65324119407ec6e75c,Merge pull request #741 from theislab/release,[![](https://github.com/theislab/sfaira/workflows/Check%20URLs/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7633455153) theislab,sfaira,theislab/sfaira,131,8,166,13,FALSE,https://github.com/theislab/sfaira,131,5fcf932c44613e6bf4063ef3075ad6062bf5d9a1,round restored counts in some affected datasets,[![](https://github.com/theislab/sfaira/workflows/Build%20sfaira%20Package/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672388) [![](https://github.com/theislab/sfaira/workflows/Create%20sfaira%20data-loader%20templates/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672382) [![](https://github.com/theislab/sfaira/workflows/Run%20bandit/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672385) [![](https://github.com/theislab/sfaira/workflows/Run%20flake8%20linting/badge.svg)](https://github.com/theislab/sfaira/actions/runs/7285672384) theislab,sfaira,theislab/sfaira,131,8,166,13,FALSE,https://github.com/theislab/sfaira,131,ceb14c946f699c38d18a32192b76d4639caf845e,fix download links,[![](https://github.com/theislab/sfaira/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/sfaira/actions/runs/6812817430) theislab,sfaira-portal,theislab/sfaira-portal,0,4,2,0,FALSE,https://github.com/theislab/sfaira-portal,0,NA,NA,NA @@ -367,8 +370,8 @@ Signed-off-by: zethson Co-authored-by: xlancelottx Co-authored-by: zethson Co-authored-by: Anna Schaar ",[![](https://github.com/theislab/single-cell-best-practices/workflows/Release%20Drafter/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/4784044952) -theislab,single-cell-transformer-papers,theislab/single-cell-transformer-papers,31,2,0,2,FALSE,https://github.com/theislab/single-cell-transformer-papers,31,NA,NA,NA -theislab,single-cell-tutorial,theislab/single-cell-tutorial,1238,30,20,431,FALSE,https://github.com/theislab/single-cell-tutorial,1238,NA,NA,NA +theislab,single-cell-transformer-papers,theislab/single-cell-transformer-papers,32,2,0,2,FALSE,https://github.com/theislab/single-cell-transformer-papers,32,NA,NA,NA +theislab,single-cell-tutorial,theislab/single-cell-tutorial,1236,30,20,431,FALSE,https://github.com/theislab/single-cell-tutorial,1236,NA,NA,NA theislab,singlecell_proteomics,theislab/singlecell_proteomics,3,5,5,3,FALSE,https://github.com/theislab/singlecell_proteomics,3,NA,NA,NA theislab,spapros,theislab/spapros,20,3,15,5,FALSE,https://github.com/theislab/spapros,20,642fb34d2ccbb1bb8730b239840bf1bfe06701f8,"[DEPENDABOT]: Bump importlib-resources from 5.12.0 to 6.1.1 in /docs
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