diff --git a/README.md b/README.md index 5118694..3c648da 100644 --- a/README.md +++ b/README.md @@ -2,26 +2,26 @@ GitHub Dashboard ================ ![](https://github.com/gadenbuie/status/workflows/Render%20Status/badge.svg) -2024-06-25 12:10:47 UTC +2024-06-26 12:10:28 UTC | Repo | Stars | Subscribers | Issues | Forks | Status | Commit | |:----------------------------------------------------------------------------------------------------|------:|------------:|-------:|------:|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| [theislab/single-cell-best-practices](https://github.com/theislab/single-cell-best-practices) | 679 | 17 | 59 | 148 | [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20book/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/9363542512) [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20environments/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/9363542534) [![](https://github.com/theislab/single-cell-best-practices/workflows/Labeler/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/9363542513) [![](https://github.com/theislab/single-cell-best-practices/workflows/pre-commit/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/9363542526) | bcb43c | -| [theislab/single-cell-best-practices](https://github.com/theislab/single-cell-best-practices) | 679 | 17 | 59 | 148 | [![](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/single-cell-best-practices](https://github.com/theislab/single-cell-best-practices) | 680 | 17 | 59 | 148 | [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20book/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/9363542512) [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20environments/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/9363542534) [![](https://github.com/theislab/single-cell-best-practices/workflows/Labeler/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/9363542513) [![](https://github.com/theislab/single-cell-best-practices/workflows/pre-commit/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/9363542526) | bcb43c | +| [theislab/single-cell-best-practices](https://github.com/theislab/single-cell-best-practices) | 680 | 17 | 59 | 148 | [![](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) | 397 | 12 | 58 | 102 | [![](https://github.com/theislab/scvelo/workflows/Release/badge.svg)](https://github.com/theislab/scvelo/actions/runs/8317755189) | b2f31b | | [theislab/scvelo](https://github.com/theislab/scvelo) | 397 | 12 | 58 | 102 | [![](https://github.com/theislab/scvelo/workflows/Check%20Build/badge.svg)](https://github.com/theislab/scvelo/actions/runs/9561018598) [![](https://github.com/theislab/scvelo/workflows/CI/badge.svg)](https://github.com/theislab/scvelo/actions/runs/9561018597) | d3e81d | -| [theislab/cellrank](https://github.com/theislab/cellrank) | 323 | 8 | 20 | 40 | [![](https://github.com/theislab/cellrank/workflows/Deployment/badge.svg)](https://github.com/theislab/cellrank/actions/runs/8601715542) | 08f1c9 | -| [theislab/cellrank](https://github.com/theislab/cellrank) | 323 | 8 | 20 | 40 | [![](https://github.com/theislab/cellrank/workflows/Test/badge.svg)](https://github.com/theislab/cellrank/actions/runs/9637498214) [![](https://github.com/theislab/cellrank/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank/actions/runs/9637563994) | 607491 | +| [theislab/cellrank](https://github.com/theislab/cellrank) | 323 | 8 | 20 | 41 | [![](https://github.com/theislab/cellrank/workflows/Deployment/badge.svg)](https://github.com/theislab/cellrank/actions/runs/8601715542) | 08f1c9 | +| [theislab/cellrank](https://github.com/theislab/cellrank) | 323 | 8 | 20 | 41 | [![](https://github.com/theislab/cellrank/workflows/Test/badge.svg)](https://github.com/theislab/cellrank/actions/runs/9637498214) [![](https://github.com/theislab/cellrank/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank/actions/runs/9637563994) | 607491 | | [theislab/scib](https://github.com/theislab/scib) | 281 | 14 | 37 | 61 | [![](https://github.com/theislab/scib/workflows/Deployment/badge.svg)](https://github.com/theislab/scib/actions/runs/8788684911) | 9c5a93 | -| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 133 | 5 | 42 | 16 | [![](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) | 133 | 5 | 42 | 16 | [![](https://github.com/theislab/ehrapy/workflows/Release/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/9164725536) | 869cd3 | -| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 133 | 5 | 42 | 16 | [![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/9658448107) | a893f3 | +| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 133 | 5 | 43 | 16 | [![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/9669837788) | 7315c2 | +| [theislab/ehrapy](https://github.com/theislab/ehrapy) | 133 | 5 | 43 | 16 | [![](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) | 133 | 5 | 43 | 16 | [![](https://github.com/theislab/ehrapy/workflows/Release/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/9164725536) | 869cd3 | | [theislab/sfaira](https://github.com/theislab/sfaira) | 133 | 8 | 167 | 13 | [![](https://github.com/theislab/sfaira/workflows/Check%20URLs/badge.svg)](https://github.com/theislab/sfaira/actions/runs/9457340256) | 55bcbb | | [theislab/sfaira](https://github.com/theislab/sfaira) | 133 | 8 | 167 | 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) | 133 | 8 | 167 | 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) | 133 | 5 | 24 | 26 | [![](https://github.com/theislab/zellkonverter/workflows/.github/workflows/check-bioc.yml/badge.svg)](https://github.com/theislab/zellkonverter/actions/runs/9611012269) | 328e7e | | [theislab/anndata2ri](https://github.com/theislab/anndata2ri) | 115 | 7 | 15 | 16 | [![](https://github.com/theislab/anndata2ri/workflows/Unit%20Tests/badge.svg)](https://github.com/theislab/anndata2ri/actions/runs/9660231721) | 465a6a | -| [theislab/moscot](https://github.com/theislab/moscot) | 100 | 3 | 52 | 8 | [![](https://github.com/theislab/moscot/workflows/Deployment/badge.svg)](https://github.com/theislab/moscot/actions/runs/8263290173) | 6ea9a1 | +| [theislab/moscot](https://github.com/theislab/moscot) | 100 | 3 | 53 | 8 | [![](https://github.com/theislab/moscot/workflows/Deployment/badge.svg)](https://github.com/theislab/moscot/actions/runs/8263290173) | 6ea9a1 | | [theislab/ncem](https://github.com/theislab/ncem) | 100 | 6 | 26 | 13 | [![](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) | 100 | 6 | 26 | 13 | [![](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/destiny](https://github.com/theislab/destiny) | 69 | 5 | 32 | 12 | [![](https://github.com/theislab/destiny/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/theislab/destiny/actions/runs/7347769080) | 300eb2 | @@ -29,7 +29,7 @@ GitHub Dashboard | [theislab/hadge](https://github.com/theislab/hadge) | 23 | 3 | 10 | 6 | [![](https://github.com/theislab/hadge/workflows/sphinx-docs/badge.svg)](https://github.com/theislab/hadge/actions/runs/7569650236) | 1ed105 | | [theislab/hadge](https://github.com/theislab/hadge) | 23 | 3 | 10 | 6 | [![](https://github.com/theislab/hadge/workflows/pre-commit/badge.svg)](https://github.com/theislab/hadge/actions/runs/9366149796) [![](https://github.com/theislab/hadge/workflows/hadge%20test%20workflow/badge.svg)](https://github.com/theislab/hadge/actions/runs/9366149805) | 490a55 | | [theislab/spapros](https://github.com/theislab/spapros) | 23 | 3 | 12 | 5 | [![](https://github.com/theislab/spapros/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/spapros/actions/runs/9623196491) [![](https://github.com/theislab/spapros/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/spapros/actions/runs/9623196496) | 600d1b | -| [theislab/spapros](https://github.com/theislab/spapros) | 23 | 3 | 12 | 5 | [![](https://github.com/theislab/spapros/workflows/Labeler/badge.svg)](https://github.com/theislab/spapros/actions/runs/8661094687) [![](https://github.com/theislab/spapros/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/spapros/actions/runs/9654958144) | e8a37c | +| [theislab/spapros](https://github.com/theislab/spapros) | 23 | 3 | 12 | 5 | [![](https://github.com/theislab/spapros/workflows/Labeler/badge.svg)](https://github.com/theislab/spapros/actions/runs/8661094687) [![](https://github.com/theislab/spapros/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/spapros/actions/runs/9672088114) | e8a37c | | [theislab/mubind](https://github.com/theislab/mubind) | 20 | 3 | 30 | 0 | [![](https://github.com/theislab/mubind/workflows/Python%20package/badge.svg)](https://github.com/theislab/mubind/actions/runs/9496414877) | d438de | | [theislab/geome](https://github.com/theislab/geome) | 16 | 3 | 3 | 4 | [![](https://github.com/theislab/geome/workflows/Check%20Build/badge.svg)](https://github.com/theislab/geome/actions/runs/9339397729) [![](https://github.com/theislab/geome/workflows/Test/badge.svg)](https://github.com/theislab/geome/actions/runs/9525653701) | 22ce1f | | [theislab/geome](https://github.com/theislab/geome) | 16 | 3 | 3 | 4 | [![](https://github.com/theislab/geome/workflows/Sync%20Template/badge.svg)](https://github.com/theislab/geome/actions/runs/4904831582) | 5bf0cd | @@ -37,9 +37,9 @@ GitHub Dashboard | [theislab/scanpydoc](https://github.com/theislab/scanpydoc) | 12 | 6 | 3 | 6 | [![](https://github.com/theislab/scanpydoc/workflows/Python%20tests/badge.svg)](https://github.com/theislab/scanpydoc/actions/runs/9660230075) | 58ae2b | | [theislab/cellrank_notebooks](https://github.com/theislab/cellrank_notebooks) | 6 | 4 | 1 | 5 | [![](https://github.com/theislab/cellrank_notebooks/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank_notebooks/actions/runs/6686677756) | 677784 | | [theislab/moscot_notebooks](https://github.com/theislab/moscot_notebooks) | 6 | 1 | 4 | 3 | [![](https://github.com/theislab/moscot_notebooks/workflows/lint/badge.svg)](https://github.com/theislab/moscot_notebooks/actions/runs/9658033646) | 507f24 | +| [theislab/cellrank2_reproducibility](https://github.com/theislab/cellrank2_reproducibility) | 5 | 1 | 1 | 0 | [![](https://github.com/theislab/cellrank2_reproducibility/workflows/deploy-jupyter-book/badge.svg)](https://github.com/theislab/cellrank2_reproducibility/actions/runs/8315825726) [![](https://github.com/theislab/cellrank2_reproducibility/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank2_reproducibility/actions/runs/8315825728) | f5c767 | | [theislab/ehrapy-datasets](https://github.com/theislab/ehrapy-datasets) | 5 | 2 | 0 | 2 | [![](https://github.com/theislab/ehrapy-datasets/workflows/Run%20Notebooks/badge.svg)](https://github.com/theislab/ehrapy-datasets/actions/runs/8356857136) | e441a5 | -| [theislab/cellrank2_reproducibility](https://github.com/theislab/cellrank2_reproducibility) | 4 | 1 | 1 | 0 | [![](https://github.com/theislab/cellrank2_reproducibility/workflows/deploy-jupyter-book/badge.svg)](https://github.com/theislab/cellrank2_reproducibility/actions/runs/8315825726) [![](https://github.com/theislab/cellrank2_reproducibility/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank2_reproducibility/actions/runs/8315825728) | f5c767 | -| [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/9662015927) | b71822 | +| [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/9679231634) | e06fd3 | | [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/cookietemple%20sync/badge.svg)](https://github.com/theislab/idtrack/actions/runs/4836150850) | 63e94a | @@ -58,9 +58,9 @@ GitHub Dashboard | [theislab/kBET](https://github.com/theislab/kBET) | 147 | 8 | 8 | 23 | | [theislab/scCODA](https://github.com/theislab/scCODA) | 141 | 9 | 6 | 23 | | [theislab/sc-pert](https://github.com/theislab/sc-pert) | 134 | 6 | 6 | 10 | -| [theislab/single-cell-transformer-papers](https://github.com/theislab/single-cell-transformer-papers) | 119 | 7 | 0 | 11 | +| [theislab/single-cell-transformer-papers](https://github.com/theislab/single-cell-transformer-papers) | 120 | 8 | 0 | 11 | | [theislab/chemCPA](https://github.com/theislab/chemCPA) | 88 | 5 | 10 | 23 | -| [theislab/cpa](https://github.com/theislab/cpa) | 76 | 5 | 18 | 17 | +| [theislab/cpa](https://github.com/theislab/cpa) | 76 | 5 | 17 | 17 | | [theislab/scib-pipeline](https://github.com/theislab/scib-pipeline) | 61 | 7 | 17 | 28 | | [theislab/AutoGeneS](https://github.com/theislab/AutoGeneS) | 53 | 6 | 5 | 8 | | [theislab/trVAE](https://github.com/theislab/trVAE) | 53 | 7 | 2 | 11 | @@ -72,8 +72,8 @@ GitHub Dashboard | [theislab/scArches-reproducibility](https://github.com/theislab/scArches-reproducibility) | 32 | 5 | 5 | 0 | | [theislab/deepflow](https://github.com/theislab/deepflow) | 31 | 5 | 1 | 14 | | [theislab/scTab](https://github.com/theislab/scTab) | 29 | 3 | 0 | 3 | +| [theislab/scvelo_notebooks](https://github.com/theislab/scvelo_notebooks) | 28 | 2 | 4 | 13 | | [theislab/DeepRT](https://github.com/theislab/DeepRT) | 27 | 2 | 11 | 10 | -| [theislab/scvelo_notebooks](https://github.com/theislab/scvelo_notebooks) | 27 | 2 | 4 | 13 | | [theislab/graph_abstraction](https://github.com/theislab/graph_abstraction) | 26 | 8 | 0 | 10 | | [theislab/Covid_meta_analysis](https://github.com/theislab/Covid_meta_analysis) | 24 | 8 | 2 | 11 | | [theislab/interactive_plotting](https://github.com/theislab/interactive_plotting) | 21 | 4 | 11 | 7 | @@ -110,6 +110,7 @@ GitHub Dashboard | [theislab/cpa-reproducibility](https://github.com/theislab/cpa-reproducibility) | 7 | 2 | 1 | 1 | | [theislab/mouse_cross-condition_pancreatic_islet_atlas](https://github.com/theislab/mouse_cross-condition_pancreatic_islet_atlas) | 7 | 2 | 0 | 3 | | [theislab/scachepy](https://github.com/theislab/scachepy) | 7 | 5 | 3 | 1 | +| [theislab/scatac_poisson_reproducibility](https://github.com/theislab/scatac_poisson_reproducibility) | 7 | 3 | 0 | 0 | | [theislab/scCODA_reproducibility](https://github.com/theislab/scCODA_reproducibility) | 7 | 5 | 0 | 1 | | [theislab/spapros-pipeline](https://github.com/theislab/spapros-pipeline) | 7 | 2 | 0 | 0 | | [theislab/theislab.github.io](https://github.com/theislab/theislab.github.io) | 7 | 2 | 9 | 0 | @@ -117,10 +118,10 @@ GitHub Dashboard | [theislab/2019_Strunz](https://github.com/theislab/2019_Strunz) | 6 | 5 | 1 | 11 | | [theislab/disent](https://github.com/theislab/disent) | 6 | 3 | 0 | 0 | | [theislab/intercode](https://github.com/theislab/intercode) | 6 | 3 | 1 | 1 | -| [theislab/scatac_poisson_reproducibility](https://github.com/theislab/scatac_poisson_reproducibility) | 6 | 3 | 0 | 0 | | [theislab/sfaira_tutorials](https://github.com/theislab/sfaira_tutorials) | 6 | 4 | 4 | 2 | | [theislab/trVAE_reproducibility](https://github.com/theislab/trVAE_reproducibility) | 6 | 3 | 2 | 5 | -| [theislab/ehrapy-tutorials](https://github.com/theislab/ehrapy-tutorials) | 5 | 3 | 1 | 2 | +| [theislab/atlas-feature-selection-benchmark](https://github.com/theislab/atlas-feature-selection-benchmark) | 5 | 2 | 0 | 0 | +| [theislab/ehrapy-tutorials](https://github.com/theislab/ehrapy-tutorials) | 5 | 3 | 0 | 2 | | [theislab/ehrdata](https://github.com/theislab/ehrdata) | 5 | 3 | 1 | 1 | | [theislab/flowVI](https://github.com/theislab/flowVI) | 5 | 3 | 0 | 0 | | [theislab/InterpretableAutoencoders](https://github.com/theislab/InterpretableAutoencoders) | 5 | 4 | 0 | 1 | @@ -130,7 +131,6 @@ GitHub Dashboard | [theislab/scanpy-demo-czbiohub](https://github.com/theislab/scanpy-demo-czbiohub) | 5 | 5 | 0 | 5 | | [theislab/singlecell_proteomics](https://github.com/theislab/singlecell_proteomics) | 5 | 5 | 6 | 3 | | [theislab/2022_Tritschler_pancreas_cross_species](https://github.com/theislab/2022_Tritschler_pancreas_cross_species) | 4 | 3 | 0 | 1 | -| [theislab/atlas-feature-selection-benchmark](https://github.com/theislab/atlas-feature-selection-benchmark) | 4 | 2 | 0 | 0 | | [theislab/cellrank_reproducibility_preprint](https://github.com/theislab/cellrank_reproducibility_preprint) | 4 | 2 | 0 | 0 | | [theislab/covid-perturbation](https://github.com/theislab/covid-perturbation) | 4 | 3 | 0 | 0 | | [theislab/extended-single-cell-best-practices-container](https://github.com/theislab/extended-single-cell-best-practices-container) | 4 | 4 | 2 | 1 | diff --git a/index.html b/index.html index 20788ca..6f53200 100644 --- a/index.html +++ b/index.html @@ -49,7 +49,7 @@

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Repos without Github Actions

+ + + + + + + - + - + - + - + - + - + - - - - - - - @@ -953,82 +953,82 @@

Repos without Github Actions

+ + + + + + + - + - + - + - + - + - + - + - + - + - + - - - - - - - diff --git a/repos.csv b/repos.csv index 0b6ac13..27ae425 100644 --- a/repos.csv +++ b/repos.csv @@ -35,7 +35,7 @@ Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.gi theislab,archmap_admin,theislab/archmap_admin,0,2,0,0,FALSE,https://github.com/theislab/archmap_admin,0,NA,NA,NA theislab,archmap_doc,theislab/archmap_doc,0,3,0,0,FALSE,https://github.com/theislab/archmap_doc,0,NA,NA,NA theislab,astrocytes_reprogramming_analysis,theislab/astrocytes_reprogramming_analysis,1,5,0,0,FALSE,https://github.com/theislab/astrocytes_reprogramming_analysis,1,NA,NA,NA -theislab,atlas-feature-selection-benchmark,theislab/atlas-feature-selection-benchmark,4,2,0,0,FALSE,https://github.com/theislab/atlas-feature-selection-benchmark,4,NA,NA,NA +theislab,atlas-feature-selection-benchmark,theislab/atlas-feature-selection-benchmark,5,2,0,0,FALSE,https://github.com/theislab/atlas-feature-selection-benchmark,5,NA,NA,NA theislab,augurpy,theislab/augurpy,2,2,10,0,FALSE,https://github.com/theislab/augurpy,2,NA,NA,NA theislab,autoencoderPS,theislab/autoencoderPS,1,3,0,2,FALSE,https://github.com/theislab/autoencoderPS,1,NA,NA,NA theislab,bartSeq,theislab/bartSeq,1,5,1,5,FALSE,https://github.com/theislab/bartSeq,1,NA,NA,NA @@ -44,15 +44,15 @@ theislab,batchglm,theislab/batchglm,26,3,47,9,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,323,8,20,40,FALSE,https://github.com/theislab/cellrank,323,08f1c901cc4ba1f6500f6fced4df8f5c076755e9,"Fix/importError #1183 (#1184) +theislab,cellrank,theislab/cellrank,323,8,20,41,FALSE,https://github.com/theislab/cellrank,323,08f1c901cc4ba1f6500f6fced4df8f5c076755e9,"Fix/importError #1183 (#1184) * fixed importError, issue #1183 * Removed 'renamed_arg' * linting",[![](https://github.com/theislab/cellrank/workflows/Deployment/badge.svg)](https://github.com/theislab/cellrank/actions/runs/8601715542) -theislab,cellrank,theislab/cellrank,323,8,20,40,FALSE,https://github.com/theislab/cellrank,323,6074913214f087301dd49bd9ef581c20ec56e759,Fix failing test,[![](https://github.com/theislab/cellrank/workflows/Test/badge.svg)](https://github.com/theislab/cellrank/actions/runs/9637498214) [![](https://github.com/theislab/cellrank/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank/actions/runs/9637563994) -theislab,cellrank2_reproducibility,theislab/cellrank2_reproducibility,4,1,1,0,FALSE,https://github.com/theislab/cellrank2_reproducibility,4,f5c767a08bd0db4b58036afaffc91d0a649c90a5,"Add initial state identification (#59) +theislab,cellrank,theislab/cellrank,323,8,20,41,FALSE,https://github.com/theislab/cellrank,323,6074913214f087301dd49bd9ef581c20ec56e759,Fix failing test,[![](https://github.com/theislab/cellrank/workflows/Test/badge.svg)](https://github.com/theislab/cellrank/actions/runs/9637498214) [![](https://github.com/theislab/cellrank/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank/actions/runs/9637563994) +theislab,cellrank2_reproducibility,theislab/cellrank2_reproducibility,5,1,1,0,FALSE,https://github.com/theislab/cellrank2_reproducibility,5,f5c767a08bd0db4b58036afaffc91d0a649c90a5,"Add initial state identification (#59) * Add `embryoid_body/initial_state.ipynb` @@ -72,7 +72,7 @@ theislab,consensus-clustering-evaluation,theislab/consensus-clustering-evaluatio theislab,countae,theislab/countae,1,4,0,0,FALSE,https://github.com/theislab/countae,1,NA,NA,NA theislab,covid-perturbation,theislab/covid-perturbation,4,3,0,0,FALSE,https://github.com/theislab/covid-perturbation,4,NA,NA,NA theislab,covid_macrophages_integration,theislab/covid_macrophages_integration,2,5,0,5,FALSE,https://github.com/theislab/covid_macrophages_integration,2,NA,NA,NA -theislab,cpa,theislab/cpa,76,5,18,17,FALSE,https://github.com/theislab/cpa,76,NA,NA,NA +theislab,cpa,theislab/cpa,76,5,17,17,FALSE,https://github.com/theislab/cpa,76,NA,NA,NA theislab,cpa-reproducibility,theislab/cpa-reproducibility,7,2,1,1,FALSE,https://github.com/theislab/cpa-reproducibility,7,NA,NA,NA theislab,cross_system_integration,theislab/cross_system_integration,10,2,10,1,FALSE,https://github.com/theislab/cross_system_integration,10,NA,NA,NA theislab,dali,theislab/dali,0,7,0,1,FALSE,https://github.com/theislab/dali,0,NA,NA,NA @@ -83,25 +83,81 @@ theislab,diffxpy,theislab/diffxpy,179,6,107,23,FALSE,https://github.com/theislab theislab,diffxpy_tutorials,theislab/diffxpy_tutorials,10,8,4,2,FALSE,https://github.com/theislab/diffxpy_tutorials,10,NA,NA,NA theislab,disent,theislab/disent,6,3,0,0,FALSE,https://github.com/theislab/disent,6,NA,NA,NA theislab,edgepy,theislab/edgepy,0,3,0,0,FALSE,https://github.com/theislab/edgepy,0,NA,NA,NA -theislab,ehrapy,theislab/ehrapy,133,5,42,16,FALSE,https://github.com/theislab/ehrapy,133,84d33c8988ea560aa557fbe6a99b926befa84457,"Add test windows +theislab,ehrapy,theislab/ehrapy,133,5,43,16,FALSE,https://github.com/theislab/ehrapy,133,7315c2163a55b94176c0bfd92b8b177121063a0b,"Enhancement/normalization dask (#763) + +* store + +* save progress + +* updates + +* more cleaning up, modify pyroject.toml + +* [pre-commit.ci] auto fixes from pre-commit.com hooks + +for more information, see https://pre-commit.ci + +* cleanup + +* fix return type & update docs + +* restrict scipy for lifelines + +* Update ehrapy/__init__.py + +Co-authored-by: Lukas Heumos + +* move test things to conftest.py + +* add dask to doc dependencies + +* check if this helps readthedocs? + +* move constants back to _normalization.py + +* test changed .readthedocs.yml + +* check other config + +* no uv + +* restrict scanpy <=1.10.1 + +* remove uv from ehrapy install in notebooks to trigger restriction? + +* remove uv from ehrapy install in notebooks to trigger restriction? + +* pip-ify notebook yml + +* run on pull_request + +* use uv again in notebooks + +* fix --system + +* update doc + +* fix link + +* fix name + +--------- + +Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> +Co-authored-by: Lukas Heumos ",[![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/9669837788) +theislab,ehrapy,theislab/ehrapy,133,5,43,16,FALSE,https://github.com/theislab/ehrapy,133,84d33c8988ea560aa557fbe6a99b926befa84457,"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,133,5,42,16,FALSE,https://github.com/theislab/ehrapy,133,869cd3fdada67d26c0a45650ac0ddd346ef7bedc,"Version 0.8.0 +theislab,ehrapy,theislab/ehrapy,133,5,43,16,FALSE,https://github.com/theislab/ehrapy,133,869cd3fdada67d26c0a45650ac0ddd346ef7bedc,"Version 0.8.0 Signed-off-by: zethson ",[![](https://github.com/theislab/ehrapy/workflows/Release/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/9164725536) -theislab,ehrapy,theislab/ehrapy,133,5,42,16,FALSE,https://github.com/theislab/ehrapy,133,a893f390b624bbd84008ba39217fcec65c601c5b,"[pre-commit.ci] pre-commit autoupdate (#761) - -updates: -- [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>",[![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/9658448107) theislab,ehrapy-cli,theislab/ehrapy-cli,1,3,0,0,FALSE,https://github.com/theislab/ehrapy-cli,1,NA,NA,NA theislab,ehrapy-datasets,theislab/ehrapy-datasets,5,2,0,2,FALSE,https://github.com/theislab/ehrapy-datasets,5,e441a5d0912396064360799f10de973b377ba6a5,"Merge pull request #23 from theislab/diabetes-update change diabetes dataset doc",[![](https://github.com/theislab/ehrapy-datasets/workflows/Run%20Notebooks/badge.svg)](https://github.com/theislab/ehrapy-datasets/actions/runs/8356857136) theislab,ehrapy-reproducibility,theislab/ehrapy-reproducibility,0,1,1,0,FALSE,https://github.com/theislab/ehrapy-reproducibility,0,NA,NA,NA theislab,ehrapy-site,theislab/ehrapy-site,1,2,0,0,FALSE,https://github.com/theislab/ehrapy-site,1,NA,NA,NA -theislab,ehrapy-tutorials,theislab/ehrapy-tutorials,5,3,1,2,FALSE,https://github.com/theislab/ehrapy-tutorials,5,NA,NA,NA +theislab,ehrapy-tutorials,theislab/ehrapy-tutorials,5,3,0,2,FALSE,https://github.com/theislab/ehrapy-tutorials,5,NA,NA,NA theislab,ehrdata,theislab/ehrdata,5,3,1,1,FALSE,https://github.com/theislab/ehrdata,5,NA,NA,NA theislab,enrichment_analysis_celltype,theislab/enrichment_analysis_celltype,9,5,0,4,FALSE,https://github.com/theislab/enrichment_analysis_celltype,9,NA,NA,NA theislab,epicardiods_analysis,theislab/epicardiods_analysis,2,2,1,0,FALSE,https://github.com/theislab/epicardiods_analysis,2,NA,NA,NA @@ -117,7 +173,7 @@ obs_names and var_names added to fields",[![](https://github.com/theislab/geome/ theislab,geome,theislab/geome,16,3,3,4,FALSE,https://github.com/theislab/geome,16,5bf0cd07b2ea7fa224a37f69232542a9e686c5bf,"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,b71822ce9cc6710cf537b63efe4bb24f6e878d25,[status] 2024-06-24 12:12:05 UTC,[![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/9662015927) +theislab,gh-dashboard,theislab/gh-dashboard,1,2,0,0,FALSE,https://github.com/theislab/gh-dashboard,1,e06fd3d82ed8168ed015cdd24de4e39782900b3e,[status] 2024-06-25 12:12:28 UTC,[![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/9679231634) theislab,graph_abstraction,theislab/graph_abstraction,26,8,0,10,FALSE,https://github.com/theislab/graph_abstraction,26,NA,NA,NA theislab,graphcompass,theislab/graphcompass,15,2,0,0,FALSE,https://github.com/theislab/graphcompass,15,7c455146402592d7ba73173a72d2abc4d5f7737b,initial commit,[![](https://github.com/theislab/graphcompass/workflows/Labeler/badge.svg)](https://github.com/theislab/graphcompass/actions/runs/7630989244) [![](https://github.com/theislab/graphcompass/workflows/Release/badge.svg)](https://github.com/theislab/graphcompass/actions/runs/7630989237) theislab,greatpy,theislab/greatpy,8,3,4,0,FALSE,https://github.com/theislab/greatpy,8,NA,NA,NA @@ -146,7 +202,7 @@ theislab,jump-cpg0016-segmentation,theislab/jump-cpg0016-segmentation,5,1,2,0,FA theislab,kBET,theislab/kBET,147,8,8,23,FALSE,https://github.com/theislab/kBET,147,NA,NA,NA theislab,kbranches,theislab/kbranches,5,7,0,0,FALSE,https://github.com/theislab/kbranches,5,NA,NA,NA theislab,masterpraktikum_ssl_segmentation,theislab/masterpraktikum_ssl_segmentation,1,3,1,1,FALSE,https://github.com/theislab/masterpraktikum_ssl_segmentation,1,NA,NA,NA -theislab,moscot,theislab/moscot,100,3,52,8,FALSE,https://github.com/theislab/moscot,100,6ea9a1612b829aaa4a1c192210e340a9c08d4ac6,"fix bug in quad problem marginals (#666) +theislab,moscot,theislab/moscot,100,3,53,8,FALSE,https://github.com/theislab/moscot,100,6ea9a1612b829aaa4a1c192210e340a9c08d4ac6,"fix bug in quad problem marginals (#666) Co-authored-by: Dominik Klein ",[![](https://github.com/theislab/moscot/workflows/Deployment/badge.svg)](https://github.com/theislab/moscot/actions/runs/8263290173) theislab,moscot-framework_reproducibility,theislab/moscot-framework_reproducibility,1,2,1,0,FALSE,https://github.com/theislab/moscot-framework_reproducibility,1,NA,NA,NA @@ -212,7 +268,7 @@ theislab,scanpydoc,theislab/scanpydoc,12,6,3,6,FALSE,https://github.com/theislab Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",[![](https://github.com/theislab/scanpydoc/workflows/Python%20tests/badge.svg)](https://github.com/theislab/scanpydoc/actions/runs/9660230075) theislab,scarches,theislab/scarches,319,13,43,50,FALSE,https://github.com/theislab/scarches,319,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,scatac_poisson_reproducibility,theislab/scatac_poisson_reproducibility,7,3,0,0,FALSE,https://github.com/theislab/scatac_poisson_reproducibility,7,NA,NA,NA theislab,scgen,theislab/scgen,250,9,21,51,FALSE,https://github.com/theislab/scgen,250,NA,NA,NA theislab,scgen-reproducibility,theislab/scgen-reproducibility,18,4,5,8,FALSE,https://github.com/theislab/scgen-reproducibility,18,NA,NA,NA theislab,scib,theislab/scib,281,14,37,61,FALSE,https://github.com/theislab/scib,NA,9c5a936b0ecf21ba09b1bc803712a42c2a942fbc,"Use precomputed clustering (#406) @@ -254,7 +310,7 @@ Update `UFuncTypeError` to be compatible with `numpy>=2.0`. * Pin numpy from above Pin numpy until third party libraries have fixed related issues.",[![](https://github.com/theislab/scvelo/workflows/Check%20Build/badge.svg)](https://github.com/theislab/scvelo/actions/runs/9561018598) [![](https://github.com/theislab/scvelo/workflows/CI/badge.svg)](https://github.com/theislab/scvelo/actions/runs/9561018597) -theislab,scvelo_notebooks,theislab/scvelo_notebooks,27,2,4,13,FALSE,https://github.com/theislab/scvelo_notebooks,27,NA,NA,NA +theislab,scvelo_notebooks,theislab/scvelo_notebooks,28,2,4,13,FALSE,https://github.com/theislab/scvelo_notebooks,28,NA,NA,NA theislab,sfaira,theislab/sfaira,133,8,167,13,FALSE,https://github.com/theislab/sfaira,133,55bcbbf2588a08e4a98b1e65324119407ec6e75c,Merge pull request #741 from theislab/release,[![](https://github.com/theislab/sfaira/workflows/Check%20URLs/badge.svg)](https://github.com/theislab/sfaira/actions/runs/9457340256) theislab,sfaira,theislab/sfaira,133,8,167,13,FALSE,https://github.com/theislab/sfaira,133,5fcf932c44613e6bf4063ef3075ad6062bf5d9a1,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,133,8,167,13,FALSE,https://github.com/theislab/sfaira,133,ceb14c946f699c38d18a32192b76d4639caf845e,fix download links,[![](https://github.com/theislab/sfaira/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/sfaira/actions/runs/6812817430) @@ -263,7 +319,7 @@ theislab,sfaira-site,theislab/sfaira-site,0,4,0,0,FALSE,https://github.com/theis theislab,sfaira_benchmarks,theislab/sfaira_benchmarks,0,3,0,0,FALSE,https://github.com/theislab/sfaira_benchmarks,0,NA,NA,NA theislab,sfaira_extension,theislab/sfaira_extension,0,3,1,0,FALSE,https://github.com/theislab/sfaira_extension,0,NA,NA,NA theislab,sfaira_tutorials,theislab/sfaira_tutorials,6,4,4,2,FALSE,https://github.com/theislab/sfaira_tutorials,6,NA,NA,NA -theislab,single-cell-best-practices,theislab/single-cell-best-practices,679,17,59,148,FALSE,https://github.com/theislab/single-cell-best-practices,679,bcb43c7a11be0f012fe67df202ce78abf443a8cf,"Mostly minor text changes plus mentioning 5' kits (#279) +theislab,single-cell-best-practices,theislab/single-cell-best-practices,680,17,59,148,FALSE,https://github.com/theislab/single-cell-best-practices,680,bcb43c7a11be0f012fe67df202ce78abf443a8cf,"Mostly minor text changes plus mentioning 5' kits (#279) * Improve clarity (hopefully) @@ -295,7 +351,7 @@ Signed-off-by: zethson Signed-off-by: zethson Co-authored-by: zethson ",[![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20book/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/9363542512) [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20environments/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/9363542534) [![](https://github.com/theislab/single-cell-best-practices/workflows/Labeler/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/9363542513) [![](https://github.com/theislab/single-cell-best-practices/workflows/pre-commit/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/9363542526) -theislab,single-cell-best-practices,theislab/single-cell-best-practices,679,17,59,148,FALSE,https://github.com/theislab/single-cell-best-practices,679,c06ca90930bd6c34220a7df594ed477aec1d6a19,"scATAC part (#162) +theislab,single-cell-best-practices,theislab/single-cell-best-practices,680,17,59,148,FALSE,https://github.com/theislab/single-cell-best-practices,680,c06ca90930bd6c34220a7df594ed477aec1d6a19,"scATAC part (#162) * scATAC_pp @@ -409,13 +465,13 @@ 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) 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