diff --git a/README.md b/README.md index d81cd2f..6f86406 100644 --- a/README.md +++ b/README.md @@ -2,17 +2,16 @@ GitHub Dashboard ================ ![](https://github.com/gadenbuie/status/workflows/Render%20Status/badge.svg) -2025-01-28 12:11:23 UTC +2025-01-29 12:13:34 UTC | Repo | Stars | Subscribers | Issues | Forks | Status | Commit | |:------------------------------------------------------------------------------------------------------|------:|------------:|-------:|------:|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| [theislab/single-cell-best-practices](https://github.com/theislab/single-cell-best-practices) | 826 | 19 | 73 | 198 | [![](https://github.com/theislab/single-cell-best-practices/workflows/Labeler/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/12954592920) | 3a7040 | -| [theislab/single-cell-best-practices](https://github.com/theislab/single-cell-best-practices) | 826 | 19 | 73 | 198 | [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20book/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13006809549) [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20environments/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13006809565) [![](https://github.com/theislab/single-cell-best-practices/workflows/pre-commit/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13006809554) | 7e30e7 | -| [theislab/scvelo](https://github.com/theislab/scvelo) | 422 | 13 | 60 | 104 | [![](https://github.com/theislab/scvelo/workflows/Check%20Build/badge.svg)](https://github.com/theislab/scvelo/actions/runs/11127835313) [![](https://github.com/theislab/scvelo/workflows/CI/badge.svg)](https://github.com/theislab/scvelo/actions/runs/11127835314) [![](https://github.com/theislab/scvelo/workflows/Release/badge.svg)](https://github.com/theislab/scvelo/actions/runs/12231133032) | 22b6e7 | +| [theislab/single-cell-best-practices](https://github.com/theislab/single-cell-best-practices) | 827 | 19 | 72 | 198 | [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20book/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13012838219) [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20environments/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13012838223) [![](https://github.com/theislab/single-cell-best-practices/workflows/Labeler/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13012838203) [![](https://github.com/theislab/single-cell-best-practices/workflows/pre-commit/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13012838225) | 0acea1 | +| [theislab/scvelo](https://github.com/theislab/scvelo) | 423 | 13 | 60 | 104 | [![](https://github.com/theislab/scvelo/workflows/Check%20Build/badge.svg)](https://github.com/theislab/scvelo/actions/runs/11127835313) [![](https://github.com/theislab/scvelo/workflows/CI/badge.svg)](https://github.com/theislab/scvelo/actions/runs/11127835314) [![](https://github.com/theislab/scvelo/workflows/Release/badge.svg)](https://github.com/theislab/scvelo/actions/runs/12231133032) | 22b6e7 | | [theislab/cellrank](https://github.com/theislab/cellrank) | 360 | 8 | 18 | 47 | [![](https://github.com/theislab/cellrank/workflows/Deployment/badge.svg)](https://github.com/theislab/cellrank/actions/runs/10872921434) | b5e993 | | [theislab/cellrank](https://github.com/theislab/cellrank) | 360 | 8 | 18 | 47 | [![](https://github.com/theislab/cellrank/workflows/Test/badge.svg)](https://github.com/theislab/cellrank/actions/runs/12979701009) [![](https://github.com/theislab/cellrank/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank/actions/runs/12979793908) | bf27c9 | | [theislab/scib](https://github.com/theislab/scib) | 325 | 13 | 40 | 64 | [![](https://github.com/theislab/scib/workflows/Deployment/badge.svg)](https://github.com/theislab/scib/actions/runs/12754078859) [![](https://github.com/theislab/scib/workflows/Test/badge.svg)](https://github.com/theislab/scib/actions/runs/12754078846) | 023c4e | -| [theislab/single-cell-transformer-papers](https://github.com/theislab/single-cell-transformer-papers) | 289 | 15 | 41 | 38 | [![](https://github.com/theislab/single-cell-transformer-papers/workflows/Document%20Generation/badge.svg)](https://github.com/theislab/single-cell-transformer-papers/actions/runs/13009900640) | 3af87c | +| [theislab/single-cell-transformer-papers](https://github.com/theislab/single-cell-transformer-papers) | 289 | 15 | 38 | 38 | [![](https://github.com/theislab/single-cell-transformer-papers/workflows/Document%20Generation/badge.svg)](https://github.com/theislab/single-cell-transformer-papers/actions/runs/13009900640) | 3af87c | | [theislab/ehrapy](https://github.com/theislab/ehrapy) | 259 | 5 | 43 | 22 | [![](https://github.com/theislab/ehrapy/workflows/Labeler/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/12998549905) [![](https://github.com/theislab/ehrapy/workflows/Test/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/12998549908) [![](https://github.com/theislab/ehrapy/workflows/Release%20Drafter/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/12998549906) [![](https://github.com/theislab/ehrapy/workflows/Check%20Build/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/12998549900) | 3dab24 | | [theislab/ehrapy](https://github.com/theislab/ehrapy) | 259 | 5 | 43 | 22 | [![](https://github.com/theislab/ehrapy/workflows/Release/badge.svg)](https://github.com/theislab/ehrapy/actions/runs/12636007214) | 61bd7b | | [theislab/zellkonverter](https://github.com/theislab/zellkonverter) | 157 | 5 | 13 | 28 | [![](https://github.com/theislab/zellkonverter/workflows/.github/workflows/check-bioc.yml/badge.svg)](https://github.com/theislab/zellkonverter/actions/runs/12250677013) | 8358a4 | @@ -21,16 +20,16 @@ GitHub Dashboard | [theislab/sfaira](https://github.com/theislab/sfaira) | 135 | 8 | 167 | 11 | [![](https://github.com/theislab/sfaira/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/sfaira/actions/runs/6812817430) | ceb14c | | [theislab/anndata2ri](https://github.com/theislab/anndata2ri) | 130 | 7 | 13 | 16 | [![](https://github.com/theislab/anndata2ri/workflows/Unit%20Tests/badge.svg)](https://github.com/theislab/anndata2ri/actions/runs/12999122465) | 6839d2 | | [theislab/moscot](https://github.com/theislab/moscot) | 127 | 4 | 41 | 9 | [![](https://github.com/theislab/moscot/workflows/Deployment/badge.svg)](https://github.com/theislab/moscot/actions/runs/12301003048) | 29764d | -| [theislab/moscot](https://github.com/theislab/moscot) | 127 | 4 | 41 | 9 | [![](https://github.com/theislab/moscot/workflows/Lint/badge.svg)](https://github.com/theislab/moscot/actions/runs/13005839513) [![](https://github.com/theislab/moscot/workflows/Test%20examples/badge.svg)](https://github.com/theislab/moscot/actions/runs/13005839510) [![](https://github.com/theislab/moscot/workflows/Test/badge.svg)](https://github.com/theislab/moscot/actions/runs/13005839512) | d90db3 | -| [theislab/scib-pipeline](https://github.com/theislab/scib-pipeline) | 68 | 7 | 16 | 27 | [![](https://github.com/theislab/scib-pipeline/workflows/Manual%20workflow/badge.svg)](https://github.com/theislab/scib-pipeline/actions/runs/12927788428) | e97631 | +| [theislab/moscot](https://github.com/theislab/moscot) | 127 | 4 | 41 | 9 | [![](https://github.com/theislab/moscot/workflows/Lint/badge.svg)](https://github.com/theislab/moscot/actions/runs/13013444477) [![](https://github.com/theislab/moscot/workflows/Test%20examples/badge.svg)](https://github.com/theislab/moscot/actions/runs/13013444475) [![](https://github.com/theislab/moscot/workflows/Test/badge.svg)](https://github.com/theislab/moscot/actions/runs/13013444469) | 81a75c | +| [theislab/scib-pipeline](https://github.com/theislab/scib-pipeline) | 68 | 6 | 16 | 27 | [![](https://github.com/theislab/scib-pipeline/workflows/Manual%20workflow/badge.svg)](https://github.com/theislab/scib-pipeline/actions/runs/12927788428) | e97631 | | [theislab/graphcompass](https://github.com/theislab/graphcompass) | 34 | 2 | 1 | 0 | [![](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) | 7c4551 | -| [theislab/spapros](https://github.com/theislab/spapros) | 33 | 3 | 12 | 7 | [![](https://github.com/theislab/spapros/workflows/Labeler/badge.svg)](https://github.com/theislab/spapros/actions/runs/11988703697) [![](https://github.com/theislab/spapros/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/spapros/actions/runs/13001828092) | 1ec08e | +| [theislab/spapros](https://github.com/theislab/spapros) | 33 | 3 | 12 | 7 | [![](https://github.com/theislab/spapros/workflows/Labeler/badge.svg)](https://github.com/theislab/spapros/actions/runs/11988703697) [![](https://github.com/theislab/spapros/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/spapros/actions/runs/13022891021) | 1ec08e | | [theislab/spapros](https://github.com/theislab/spapros) | 33 | 3 | 12 | 7 | [![](https://github.com/theislab/spapros/workflows/Build%20spapros%20Package/badge.svg)](https://github.com/theislab/spapros/actions/runs/12087589767) [![](https://github.com/theislab/spapros/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/spapros/actions/runs/12087589776) [![](https://github.com/theislab/spapros/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/spapros/actions/runs/12087589778) [![](https://github.com/theislab/spapros/workflows/Run%20spapros%20Tests/badge.svg)](https://github.com/theislab/spapros/actions/runs/12087589764) | 2f6c1a | | [theislab/mubind](https://github.com/theislab/mubind) | 28 | 3 | 29 | 0 | [![](https://github.com/theislab/mubind/workflows/Python%20package/badge.svg)](https://github.com/theislab/mubind/actions/runs/10632591185) | 3f62f8 | | [theislab/regvelo](https://github.com/theislab/regvelo) | 27 | 2 | 1 | 1 | [![](https://github.com/theislab/regvelo/workflows/regvelo/badge.svg)](https://github.com/theislab/regvelo/actions/runs/11323656087) | 619e02 | | [theislab/regvelo](https://github.com/theislab/regvelo) | 27 | 2 | 1 | 1 | [![](https://github.com/theislab/regvelo/workflows/Release/badge.svg)](https://github.com/theislab/regvelo/actions/runs/11307228307) | a98518 | | [theislab/hadge](https://github.com/theislab/hadge) | 24 | 3 | 15 | 7 | [![](https://github.com/theislab/hadge/workflows/sphinx-docs/badge.svg)](https://github.com/theislab/hadge/actions/runs/7569650236) | 1ed105 | -| [theislab/multimil](https://github.com/theislab/multimil) | 21 | 5 | 6 | 3 | [![](https://github.com/theislab/multimil/workflows/Check%20Build/badge.svg)](https://github.com/theislab/multimil/actions/runs/11870932723) [![](https://github.com/theislab/multimil/workflows/Test/badge.svg)](https://github.com/theislab/multimil/actions/runs/12781855051) | c721ba | +| [theislab/multimil](https://github.com/theislab/multimil) | 22 | 5 | 6 | 3 | [![](https://github.com/theislab/multimil/workflows/Check%20Build/badge.svg)](https://github.com/theislab/multimil/actions/runs/11870932723) [![](https://github.com/theislab/multimil/workflows/Test/badge.svg)](https://github.com/theislab/multimil/actions/runs/12781855051) | c721ba | | [theislab/geome](https://github.com/theislab/geome) | 16 | 3 | 3 | 4 | [![](https://github.com/theislab/geome/workflows/Test/badge.svg)](https://github.com/theislab/geome/actions/runs/10868284169) | 402a0a | | [theislab/scanpydoc](https://github.com/theislab/scanpydoc) | 12 | 6 | 2 | 6 | [![](https://github.com/theislab/scanpydoc/workflows/Python%20tests/badge.svg)](https://github.com/theislab/scanpydoc/actions/runs/12999105464) | 765ad9 | | [theislab/cellrank2_reproducibility](https://github.com/theislab/cellrank2_reproducibility) | 9 | 1 | 2 | 2 | [![](https://github.com/theislab/cellrank2_reproducibility/workflows/deploy-jupyter-book/badge.svg)](https://github.com/theislab/cellrank2_reproducibility/actions/runs/10706963288) [![](https://github.com/theislab/cellrank2_reproducibility/workflows/Lint/badge.svg)](https://github.com/theislab/cellrank2_reproducibility/actions/runs/10706963242) | 8020e7 | @@ -39,7 +38,7 @@ GitHub Dashboard | [theislab/spapros-pipeline](https://github.com/theislab/spapros-pipeline) | 7 | 2 | 0 | 0 | [![](https://github.com/theislab/spapros-pipeline/workflows/Run%20Example/badge.svg)](https://github.com/theislab/spapros-pipeline/actions/runs/11988359512) | fe84cf | | [theislab/ehrdata](https://github.com/theislab/ehrdata) | 5 | 2 | 21 | 1 | [![](https://github.com/theislab/ehrdata/workflows/Check%20Build/badge.svg)](https://github.com/theislab/ehrdata/actions/runs/12998561060) [![](https://github.com/theislab/ehrdata/workflows/Test/badge.svg)](https://github.com/theislab/ehrdata/actions/runs/12998561036) | 6139d9 | | [theislab/regvelo_reproducibility](https://github.com/theislab/regvelo_reproducibility) | 4 | 0 | 0 | 0 | [![](https://github.com/theislab/regvelo_reproducibility/workflows/deploy-jupyter-book/badge.svg)](https://github.com/theislab/regvelo_reproducibility/actions/runs/12651733568) [![](https://github.com/theislab/regvelo_reproducibility/workflows/Lint/badge.svg)](https://github.com/theislab/regvelo_reproducibility/actions/runs/12651733570) | 56512e | -| [theislab/gh-dashboard](https://github.com/theislab/gh-dashboard) | 3 | 2 | 0 | 0 | [![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/13009971939) | 5e5735 | +| [theislab/gh-dashboard](https://github.com/theislab/gh-dashboard) | 3 | 2 | 0 | 0 | [![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/13030859164) | 18d7cc | | [theislab/spatialdata-db](https://github.com/theislab/spatialdata-db) | 1 | 1 | 25 | 0 | [![](https://github.com/theislab/spatialdata-db/workflows/Check%20Build/badge.svg)](https://github.com/theislab/spatialdata-db/actions/runs/12905974532) [![](https://github.com/theislab/spatialdata-db/workflows/Test/badge.svg)](https://github.com/theislab/spatialdata-db/actions/runs/12905974535) | 21d022 | | [theislab/idtrack](https://github.com/theislab/idtrack) | 0 | 1 | 6 | 0 | [![](https://github.com/theislab/idtrack/workflows/Build%20idtrack%20Package/badge.svg)](https://github.com/theislab/idtrack/actions/runs/8296702245) [![](https://github.com/theislab/idtrack/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/idtrack/actions/runs/8296702249) [![](https://github.com/theislab/idtrack/workflows/Release%20Drafter/badge.svg)](https://github.com/theislab/idtrack/actions/runs/8296702241) [![](https://github.com/theislab/idtrack/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/idtrack/actions/runs/8296702236) [![](https://github.com/theislab/idtrack/workflows/Run%20idtrack%20Tests/badge.svg)](https://github.com/theislab/idtrack/actions/runs/8296702246) | ec9e9f | @@ -47,8 +46,8 @@ GitHub Dashboard | Repo | Stars | Subscribers | Issues | Forks | |:------------------------------------------------------------------------------------------------------------------------------------|------:|------------:|-------:|------:| -| [theislab/single-cell-tutorial](https://github.com/theislab/single-cell-tutorial) | 1434 | 30 | 21 | 469 | -| [theislab/scarches](https://github.com/theislab/scarches) | 348 | 12 | 55 | 52 | +| [theislab/single-cell-tutorial](https://github.com/theislab/single-cell-tutorial) | 1435 | 30 | 21 | 469 | +| [theislab/scarches](https://github.com/theislab/scarches) | 348 | 12 | 56 | 52 | | [theislab/scgen](https://github.com/theislab/scgen) | 278 | 9 | 28 | 56 | | [theislab/dca](https://github.com/theislab/dca) | 252 | 11 | 32 | 71 | | [theislab/paga](https://github.com/theislab/paga) | 211 | 10 | 24 | 33 | @@ -56,7 +55,7 @@ GitHub Dashboard | [theislab/kBET](https://github.com/theislab/kBET) | 157 | 8 | 9 | 23 | | [theislab/scCODA](https://github.com/theislab/scCODA) | 155 | 9 | 5 | 24 | | [theislab/sc-pert](https://github.com/theislab/sc-pert) | 149 | 5 | 6 | 14 | -| [theislab/chemCPA](https://github.com/theislab/chemCPA) | 105 | 5 | 13 | 24 | +| [theislab/chemCPA](https://github.com/theislab/chemCPA) | 105 | 5 | 14 | 24 | | [theislab/ncem](https://github.com/theislab/ncem) | 105 | 6 | 28 | 13 | | [theislab/cpa](https://github.com/theislab/cpa) | 93 | 5 | 21 | 16 | | [theislab/destiny](https://github.com/theislab/destiny) | 81 | 5 | 31 | 11 | @@ -80,7 +79,7 @@ GitHub Dashboard | [theislab/Covid_meta_analysis](https://github.com/theislab/Covid_meta_analysis) | 24 | 8 | 2 | 11 | | [theislab/scgen-reproducibility](https://github.com/theislab/scgen-reproducibility) | 24 | 4 | 7 | 9 | | [theislab/interactive_plotting](https://github.com/theislab/interactive_plotting) | 21 | 4 | 11 | 7 | -| [theislab/multigrate](https://github.com/theislab/multigrate) | 17 | 2 | 6 | 6 | +| [theislab/multigrate](https://github.com/theislab/multigrate) | 18 | 2 | 6 | 6 | | [theislab/campa](https://github.com/theislab/campa) | 14 | 4 | 6 | 5 | | [theislab/cellrank_reproducibility](https://github.com/theislab/cellrank_reproducibility) | 14 | 2 | 1 | 8 | | [theislab/DeepCollisionalCrossSection](https://github.com/theislab/DeepCollisionalCrossSection) | 14 | 5 | 1 | 6 | diff --git a/index.html b/index.html 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Repos without Github Actions

- + diff --git a/repos.csv b/repos.csv index e2399bf..a609819 100644 --- a/repos.csv +++ b/repos.csv @@ -140,7 +140,7 @@ Update references to published paper.",[![](https://github.com/theislab/cellrank theislab,cellrank_notebooks,theislab/cellrank_notebooks,6,4,1,5,FALSE,https://github.com/theislab/cellrank_notebooks,6,NA,NA,NA theislab,cellrank_reproducibility,theislab/cellrank_reproducibility,14,2,1,8,FALSE,https://github.com/theislab/cellrank_reproducibility,14,NA,NA,NA theislab,cellrank_reproducibility_preprint,theislab/cellrank_reproducibility_preprint,3,2,0,0,FALSE,https://github.com/theislab/cellrank_reproducibility_preprint,3,NA,NA,NA -theislab,chemCPA,theislab/chemCPA,105,5,13,24,FALSE,https://github.com/theislab/chemCPA,105,NA,NA,NA +theislab,chemCPA,theislab/chemCPA,105,5,14,24,FALSE,https://github.com/theislab/chemCPA,105,NA,NA,NA theislab,collideseq_reproducibility,theislab/collideseq_reproducibility,0,2,0,0,FALSE,https://github.com/theislab/collideseq_reproducibility,0,NA,NA,NA theislab,consensus-clustering-evaluation,theislab/consensus-clustering-evaluation,0,4,0,0,FALSE,https://github.com/theislab/consensus-clustering-evaluation,0,NA,NA,NA theislab,countae,theislab/countae,1,4,0,0,FALSE,https://github.com/theislab/countae,1,NA,NA,NA @@ -190,7 +190,7 @@ theislab,gastrulation_analysis,theislab/gastrulation_analysis,10,4,0,1,FALSE,htt theislab,geome,theislab/geome,16,3,3,4,FALSE,https://github.com/theislab/geome,16,402a0a8cdb442fee8666416e5f163c4098fa0c07,"Merge pull request #55 from theislab/fix/toarray Fix Sparse "".A"" Not Found",[![](https://github.com/theislab/geome/workflows/Test/badge.svg)](https://github.com/theislab/geome/actions/runs/10868284169) -theislab,gh-dashboard,theislab/gh-dashboard,3,2,0,0,FALSE,https://github.com/theislab/gh-dashboard,3,5e5735f349da585b5fd894110259bfb3a90b4d4d,[status] 2025-01-27 12:15:38 UTC,[![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/13009971939) +theislab,gh-dashboard,theislab/gh-dashboard,3,2,0,0,FALSE,https://github.com/theislab/gh-dashboard,3,18d7cc0b458f92622e7b80270b0241310e9bb4bc,[status] 2025-01-28 12:13:04 UTC,[![](https://github.com/theislab/gh-dashboard/workflows/Render%20Status/badge.svg)](https://github.com/theislab/gh-dashboard/actions/runs/13030859164) 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,34,2,1,0,FALSE,https://github.com/theislab/graphcompass,34,7c455146402592d7ba73173a72d2abc4d5f7737b,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,10,3,4,0,FALSE,https://github.com/theislab/greatpy,10,NA,NA,NA @@ -214,24 +214,9 @@ theislab,masterpraktikum_ssl_segmentation,theislab/masterpraktikum_ssl_segmentat theislab,moscot,theislab/moscot,127,4,41,9,FALSE,https://github.com/theislab/moscot,127,29764d40f7f0ce3d160ae901caf6bbaeada89043,"Merge pull request #748 from theislab/refactor/handle-solve-args Refactor/handle solve args",[![](https://github.com/theislab/moscot/workflows/Deployment/badge.svg)](https://github.com/theislab/moscot/actions/runs/12301003048) -theislab,moscot,theislab/moscot,127,4,41,9,FALSE,https://github.com/theislab/moscot,127,d90db30132554995a065aed266e57b0d84ec1bb5,"update readme (#791) +theislab,moscot,theislab/moscot,127,4,41,9,FALSE,https://github.com/theislab/moscot,127,81a75c8c0297e09be0c22b999b3ea52ee702feee,"Merge pull request #793 from theislab/adapt/readme -* update readme - -* formatting - -* link, version in contributing - -* [pre-commit.ci] auto fixes from pre-commit.com hooks - -for more information, see https://pre-commit.ci - -* precommit fix - ---------- - -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/Lint/badge.svg)](https://github.com/theislab/moscot/actions/runs/13005839513) [![](https://github.com/theislab/moscot/workflows/Test%20examples/badge.svg)](https://github.com/theislab/moscot/actions/runs/13005839510) [![](https://github.com/theislab/moscot/workflows/Test/badge.svg)](https://github.com/theislab/moscot/actions/runs/13005839512) +fix typo",[![](https://github.com/theislab/moscot/workflows/Lint/badge.svg)](https://github.com/theislab/moscot/actions/runs/13013444477) [![](https://github.com/theislab/moscot/workflows/Test%20examples/badge.svg)](https://github.com/theislab/moscot/actions/runs/13013444475) [![](https://github.com/theislab/moscot/workflows/Test/badge.svg)](https://github.com/theislab/moscot/actions/runs/13013444469) theislab,moscot-framework_reproducibility,theislab/moscot-framework_reproducibility,6,2,1,0,FALSE,https://github.com/theislab/moscot-framework_reproducibility,6,NA,NA,NA theislab,moscot_benchmarks,theislab/moscot_benchmarks,2,2,1,0,FALSE,https://github.com/theislab/moscot_benchmarks,2,NA,NA,NA theislab,moscot_not,theislab/moscot_not,3,2,8,1,FALSE,https://github.com/theislab/moscot_not,3,NA,NA,NA @@ -244,9 +229,9 @@ theislab,mubind,theislab/mubind,28,3,29,0,FALSE,https://github.com/theislab/mubi theislab,mubind-benchmark,theislab/mubind-benchmark,0,2,19,0,FALSE,https://github.com/theislab/mubind-benchmark,0,NA,NA,NA theislab,multicpa,theislab/multicpa,13,2,1,2,FALSE,https://github.com/theislab/multicpa,13,NA,NA,NA theislab,multicpa-reproducibility,theislab/multicpa-reproducibility,0,2,0,0,FALSE,https://github.com/theislab/multicpa-reproducibility,0,NA,NA,NA -theislab,multigrate,theislab/multigrate,17,2,6,6,FALSE,https://github.com/theislab/multigrate,17,NA,NA,NA +theislab,multigrate,theislab/multigrate,18,2,6,6,FALSE,https://github.com/theislab/multigrate,18,NA,NA,NA theislab,multigrate_reproducibility,theislab/multigrate_reproducibility,3,1,0,0,FALSE,https://github.com/theislab/multigrate_reproducibility,3,NA,NA,NA -theislab,multimil,theislab/multimil,21,5,6,3,FALSE,https://github.com/theislab/multimil,21,c721babcaef2f9367cf0bea5e6ed07ef422afb6b,"Merge pull request #73 from theislab/mmq2r_benchmark +theislab,multimil,theislab/multimil,22,5,6,3,FALSE,https://github.com/theislab/multimil,22,c721babcaef2f9367cf0bea5e6ed07ef422afb6b,"Merge pull request #73 from theislab/mmq2r_benchmark Multimodal q2r",[![](https://github.com/theislab/multimil/workflows/Check%20Build/badge.svg)](https://github.com/theislab/multimil/actions/runs/11870932723) [![](https://github.com/theislab/multimil/workflows/Test/badge.svg)](https://github.com/theislab/multimil/actions/runs/12781855051) theislab,multimil_reproducibility,theislab/multimil_reproducibility,6,3,4,1,FALSE,https://github.com/theislab/multimil_reproducibility,6,NA,NA,NA @@ -301,15 +286,15 @@ updates: - [github.com/astral-sh/ruff-pre-commit: v0.9.2 → v0.9.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.2...v0.9.3) 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/12999105464) -theislab,scarches,theislab/scarches,348,12,55,52,FALSE,https://github.com/theislab/scarches,348,NA,NA,NA +theislab,scarches,theislab/scarches,348,12,56,52,FALSE,https://github.com/theislab/scarches,348,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,9,3,0,0,FALSE,https://github.com/theislab/scatac_poisson_reproducibility,9,NA,NA,NA theislab,scgen,theislab/scgen,278,9,28,56,FALSE,https://github.com/theislab/scgen,278,NA,NA,NA theislab,scgen-reproducibility,theislab/scgen-reproducibility,24,4,7,9,FALSE,https://github.com/theislab/scgen-reproducibility,24,NA,NA,NA theislab,scib,theislab/scib,325,13,40,64,FALSE,https://github.com/theislab/scib,NA,023c4e81f49156503e7e85ecc1d2d8405401eb1c,Bump version: 1.1.6 → 1.1.7 (#422),[![](https://github.com/theislab/scib/workflows/Deployment/badge.svg)](https://github.com/theislab/scib/actions/runs/12754078859) [![](https://github.com/theislab/scib/workflows/Test/badge.svg)](https://github.com/theislab/scib/actions/runs/12754078846) -theislab,scib-pipeline,theislab/scib-pipeline,68,7,16,27,FALSE,https://github.com/theislab/scib-pipeline,68,e97631a478e063883cee5db0dcebbf42d8268ab0,Add links to updated projects,[![](https://github.com/theislab/scib-pipeline/workflows/Manual%20workflow/badge.svg)](https://github.com/theislab/scib-pipeline/actions/runs/12927788428) +theislab,scib-pipeline,theislab/scib-pipeline,68,6,16,27,FALSE,https://github.com/theislab/scib-pipeline,68,e97631a478e063883cee5db0dcebbf42d8268ab0,Add links to updated projects,[![](https://github.com/theislab/scib-pipeline/workflows/Manual%20workflow/badge.svg)](https://github.com/theislab/scib-pipeline/actions/runs/12927788428) theislab,scib-reproducibility,theislab/scib-reproducibility,56,6,4,14,FALSE,https://github.com/theislab/scib-reproducibility,56,NA,NA,NA -theislab,scvelo,theislab/scvelo,422,13,60,104,FALSE,https://github.com/theislab/scvelo,422,22b6e7e6cdb3c321c5a1be4ab2f29486ba01ab4f,"Update logging (#1281) +theislab,scvelo,theislab/scvelo,423,13,60,104,FALSE,https://github.com/theislab/scvelo,423,22b6e7e6cdb3c321c5a1be4ab2f29486ba01ab4f,"Update logging (#1281) * Move logging to dedicated module @@ -342,24 +327,81 @@ 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,826,19,73,198,FALSE,https://github.com/theislab/single-cell-best-practices,826,3a70409729eb7fe0978fe98aed018a02d1d3f4f2,"support the latest ubuntu (#320) +theislab,single-cell-best-practices,theislab/single-cell-best-practices,827,19,72,198,FALSE,https://github.com/theislab/single-cell-best-practices,827,0acea127b5a53eb018a449507a44babb158fa05d,"preamble, prior art updates (#321) + +* restructure the preamble sentences. + +* Improve wording, insert missing spaces and symbols (, and .) and add a note field until third generation sequencing (inclusive). + +* Audience paragraph and small fixes + +* clean prior art chapter * change upload artifact to v4 in build_book.yml -* update to ubuntu-latest in build-book.yml +* Revert ""Improve wording, insert missing spaces and symbols (, and .) and add a note field until third generation sequencing (inclusive)."" + +This reverts commit 9ec1800cef0bfdc08919b28347fd35fff5ca2b45. + +* test + +* test pre-commit + +* small fixes + +* Revert ""change upload artifact to v4 in build_book.yml"" + +This reverts commit 91bfd40b391c963e0a43e4c06d9795e0c57d76d6. + +* Update jupyter-book/introduction/prior_art.md + +Co-authored-by: Lukas Heumos + +* Update jupyter-book/introduction/prior_art.md + +Co-authored-by: Lukas Heumos + +* Update jupyter-book/introduction/prior_art.md + +Co-authored-by: Lukas Heumos + +* Update jupyter-book/introduction/prior_art.md + +Co-authored-by: Lukas Heumos + +* Update jupyter-book/introduction/prior_art.md + +Co-authored-by: Lukas Heumos + +* Update jupyter-book/introduction/prior_art.md + +Co-authored-by: Lukas Heumos + +* Update jupyter-book/introduction/prior_art.md + +Co-authored-by: Lukas Heumos + +* Update jupyter-book/preamble.md + +Co-authored-by: Lukas Heumos + +* Update jupyter-book/preamble.md + +Co-authored-by: Lukas Heumos -* change package names, and remove some +* newlines, citation, add details for contributing --------- -Co-authored-by: Seo Kim ",[![](https://github.com/theislab/single-cell-best-practices/workflows/Labeler/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/12954592920) -theislab,single-cell-best-practices,theislab/single-cell-best-practices,826,19,73,198,FALSE,https://github.com/theislab/single-cell-best-practices,826,7e30e74c1aeb6644201f7c9e210fb5ccfab65459,proofreading of two paragraphs,[![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20book/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13006809549) [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20environments/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13006809565) [![](https://github.com/theislab/single-cell-best-practices/workflows/pre-commit/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13006809554) -theislab,single-cell-transformer-papers,theislab/single-cell-transformer-papers,289,15,41,38,FALSE,https://github.com/theislab/single-cell-transformer-papers,289,3af87c73c51ab63c44c3d080456faf3ad4362871,Added PertEval-scFM (#78),[![](https://github.com/theislab/single-cell-transformer-papers/workflows/Document%20Generation/badge.svg)](https://github.com/theislab/single-cell-transformer-papers/actions/runs/13009900640) -theislab,single-cell-tutorial,theislab/single-cell-tutorial,1434,30,21,469,FALSE,https://github.com/theislab/single-cell-tutorial,1434,NA,NA,NA +Co-authored-by: Seo Kim +Co-authored-by: Luis +Co-authored-by: Lukas Heumos ",[![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20book/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13012838219) [![](https://github.com/theislab/single-cell-best-practices/workflows/Build%20environments/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13012838223) [![](https://github.com/theislab/single-cell-best-practices/workflows/Labeler/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13012838203) [![](https://github.com/theislab/single-cell-best-practices/workflows/pre-commit/badge.svg)](https://github.com/theislab/single-cell-best-practices/actions/runs/13012838225) +theislab,single-cell-transformer-papers,theislab/single-cell-transformer-papers,289,15,38,38,FALSE,https://github.com/theislab/single-cell-transformer-papers,289,3af87c73c51ab63c44c3d080456faf3ad4362871,Added PertEval-scFM (#78),[![](https://github.com/theislab/single-cell-transformer-papers/workflows/Document%20Generation/badge.svg)](https://github.com/theislab/single-cell-transformer-papers/actions/runs/13009900640) +theislab,single-cell-tutorial,theislab/single-cell-tutorial,1435,30,21,469,FALSE,https://github.com/theislab/single-cell-tutorial,1435,NA,NA,NA theislab,singlecell_proteomics,theislab/singlecell_proteomics,5,5,6,3,FALSE,https://github.com/theislab/singlecell_proteomics,5,NA,NA,NA theislab,spapros,theislab/spapros,33,3,12,7,FALSE,https://github.com/theislab/spapros,33,1ec08e6809978021e7ad0d7b7ce4f5412f391f79,"Merge pull request #357 from theislab/scrinshot_probe_designer -adapter tutorials to new framework",[![](https://github.com/theislab/spapros/workflows/Labeler/badge.svg)](https://github.com/theislab/spapros/actions/runs/11988703697) [![](https://github.com/theislab/spapros/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/spapros/actions/runs/13001828092) +adapter tutorials to new framework",[![](https://github.com/theislab/spapros/workflows/Labeler/badge.svg)](https://github.com/theislab/spapros/actions/runs/11988703697) [![](https://github.com/theislab/spapros/workflows/cookietemple%20sync/badge.svg)](https://github.com/theislab/spapros/actions/runs/13022891021) theislab,spapros,theislab/spapros,33,3,12,7,FALSE,https://github.com/theislab/spapros,33,2f6c1ad9fdab44d29017e268ef215d18278f56b9,prints for identifying mem issues,[![](https://github.com/theislab/spapros/workflows/Build%20spapros%20Package/badge.svg)](https://github.com/theislab/spapros/actions/runs/12087589767) [![](https://github.com/theislab/spapros/workflows/Build%20Documentation/badge.svg)](https://github.com/theislab/spapros/actions/runs/12087589776) [![](https://github.com/theislab/spapros/workflows/cookietemple%20lint/badge.svg)](https://github.com/theislab/spapros/actions/runs/12087589778) [![](https://github.com/theislab/spapros/workflows/Run%20spapros%20Tests/badge.svg)](https://github.com/theislab/spapros/actions/runs/12087589764) theislab,spapros-pipeline,theislab/spapros-pipeline,7,2,0,0,FALSE,https://github.com/theislab/spapros-pipeline,7,fe84cf66cf6cf9b8fb441c74d4c004c20d1003cf,Update readme to refer to spapros smk repo,[![](https://github.com/theislab/spapros-pipeline/workflows/Run%20Example/badge.svg)](https://github.com/theislab/spapros-pipeline/actions/runs/11988359512) theislab,spapros-smk,theislab/spapros-smk,0,2,0,1,FALSE,https://github.com/theislab/spapros-smk,0,NA,NA,NA
theislab/single-cell-best-practices826827 197372 1983a7040 + + +0acea1
theislab/single-cell-best-practices8261973198 - -7e30e7
theislab/scvelo422423 13 60 104 22b6e7
theislab/cellrank 360 8 b5e993
theislab/cellrank 360 8 bf27c9
theislab/scib 325 13 023c4e
theislab/single-cell-transformer-papers 289 154138 38 3af87c
theislab/ehrapy 259 5 3dab24
theislab/ehrapy 259 5 61bd7b
theislab/zellkonverter 157 5 8358a4
theislab/sfaira 135 8 55bcbb
theislab/sfaira 135 8 5fcf93
theislab/sfaira 135 8 ceb14c
theislab/anndata2ri 130 7 6839d2
theislab/moscot 127 4 29764d
theislab/moscot 127 4 41 9 - -d90db3 + +81a75c
theislab/scib-pipeline 6876 16 27 e97631
theislab/graphcompass 34 2 7c4551
theislab/spapros 33 3 12 7 - 1ec08e
theislab/spapros 33 3 2f6c1a
theislab/mubind 28 3 3f62f8
theislab/regvelo 27 2 619e02
theislab/regvelo 27 2 a98518
theislab/hadge 24 3 1ed105
theislab/multimil2122 5 6 3 c721ba
theislab/geome 16 3 402a0a
theislab/scanpydoc 12 6 765ad9
theislab/cellrank2_reproducibility 9 1 8020e7
theislab/moscot_notebooks 8 1 de5900
theislab/ehrapy-datasets 7 2 e441a5
theislab/spapros-pipeline 7 2 fe84cf
theislab/ehrdata 5 2 6139d9
theislab/regvelo_reproducibility 4 0 56512e
theislab/gh-dashboard 3 2 0 05e573518d7cc
theislab/spatialdata-db 1 1 21d022
theislab/idtrack 0 1
theislab/single-cell-tutorial14341435 30 21 469 theislab/scarches 348 125556 52
theislab/chemCPA 105 51314 24
theislab/multigrate1718 2 6 6