From 404d5b9d5ae649b760256ce02f557dd4ce854bfd Mon Sep 17 00:00:00 2001 From: niklasmueboe Date: Wed, 19 Jun 2024 10:08:43 +0200 Subject: [PATCH 1/7] CI badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 911b99e..ff4ced2 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,7 @@ [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://niklasmueboe.github.io/Sainsc.jl/dev) [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle) [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl) +[![CI](https://github.com/niklasmueboe/Sainsc.jl/workflows/CI)](https://github.com/niklasmueboe/Sainsc.jl/actions?query=workflows/CI) /ˈsaiəns/ From 4909e3ae89eb906721410aa991b5722d9cb379c1 Mon Sep 17 00:00:00 2001 From: niklasmueboe Date: Wed, 19 Jun 2024 10:10:14 +0200 Subject: [PATCH 2/7] fix CI badge svg --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ff4ced2..fe7e5b0 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://niklasmueboe.github.io/Sainsc.jl/dev) [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle) [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl) -[![CI](https://github.com/niklasmueboe/Sainsc.jl/workflows/CI)](https://github.com/niklasmueboe/Sainsc.jl/actions?query=workflows/CI) +[![CI](https://github.com/niklasmueboe/Sainsc.jl/workflows/CI/badge.svg)](https://github.com/niklasmueboe/Sainsc.jl/actions?query=workflows/CI) /ˈsaiəns/ From c9ca5298ae4d1a73d62aadfff1afc39417aef74c Mon Sep 17 00:00:00 2001 From: niklasmueboe Date: Mon, 24 Jun 2024 10:22:38 +0200 Subject: [PATCH 3/7] fix SingleCellProjections extension --- ext/SingleCellProjectionsExt.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ext/SingleCellProjectionsExt.jl b/ext/SingleCellProjectionsExt.jl index a3aa034..07e0d87 100644 --- a/ext/SingleCellProjectionsExt.jl +++ b/ext/SingleCellProjectionsExt.jl @@ -5,11 +5,11 @@ using SingleCellProjections: DataMatrix using Sainsc function Sainsc.getlocalmaxima(::Type{DataMatrix}, counts, localmax, kernel; genes=nothing) - return DataMatrix(getlocalmaxima(counts, localmax, kernel; genes=genes)) + return DataMatrix(getlocalmaxima(counts, localmax, kernel; genes=genes)...) end function Sainsc.readstereoseqbinned(::Type{DataMatrix}, file, binsize::Integer) - return DataMatrix(readstereoseqbinned(file, binsize)) + return DataMatrix(readstereoseqbinned(file, binsize)...) end end # module SingleCellProjectionsExt From 3da8974eaeab02c10216719688e48f10c31ba660 Mon Sep 17 00:00:00 2001 From: niklasmueboe Date: Wed, 19 Jun 2024 10:08:43 +0200 Subject: [PATCH 4/7] CI badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 911b99e..ff4ced2 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,7 @@ [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://niklasmueboe.github.io/Sainsc.jl/dev) [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle) [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl) +[![CI](https://github.com/niklasmueboe/Sainsc.jl/workflows/CI)](https://github.com/niklasmueboe/Sainsc.jl/actions?query=workflows/CI) /ˈsaiəns/ From 17f6b5f457a9204df7ef239c3a9556fb77a67b0d Mon Sep 17 00:00:00 2001 From: niklasmueboe Date: Wed, 19 Jun 2024 10:10:14 +0200 Subject: [PATCH 5/7] fix CI badge svg --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ff4ced2..fe7e5b0 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://niklasmueboe.github.io/Sainsc.jl/dev) [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle) [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl) -[![CI](https://github.com/niklasmueboe/Sainsc.jl/workflows/CI)](https://github.com/niklasmueboe/Sainsc.jl/actions?query=workflows/CI) +[![CI](https://github.com/niklasmueboe/Sainsc.jl/workflows/CI/badge.svg)](https://github.com/niklasmueboe/Sainsc.jl/actions?query=workflows/CI) /ˈsaiəns/ From 3bfcc58cd5a4c870a4df92e400be929f3f948e77 Mon Sep 17 00:00:00 2001 From: niklasmueboe Date: Mon, 24 Jun 2024 10:22:38 +0200 Subject: [PATCH 6/7] fix SingleCellProjections extension --- ext/SingleCellProjectionsExt.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ext/SingleCellProjectionsExt.jl b/ext/SingleCellProjectionsExt.jl index a3aa034..07e0d87 100644 --- a/ext/SingleCellProjectionsExt.jl +++ b/ext/SingleCellProjectionsExt.jl @@ -5,11 +5,11 @@ using SingleCellProjections: DataMatrix using Sainsc function Sainsc.getlocalmaxima(::Type{DataMatrix}, counts, localmax, kernel; genes=nothing) - return DataMatrix(getlocalmaxima(counts, localmax, kernel; genes=genes)) + return DataMatrix(getlocalmaxima(counts, localmax, kernel; genes=genes)...) end function Sainsc.readstereoseqbinned(::Type{DataMatrix}, file, binsize::Integer) - return DataMatrix(readstereoseqbinned(file, binsize)) + return DataMatrix(readstereoseqbinned(file, binsize)...) end end # module SingleCellProjectionsExt From e52a155cecdc4d9949d8a8a0951293e784f3e3b4 Mon Sep 17 00:00:00 2001 From: niklasmueboe Date: Mon, 24 Jun 2024 11:18:18 +0200 Subject: [PATCH 7/7] fix format --- docs/src/examples/ExampleAnalysis.jl | 2 +- src/GridCount.jl | 2 +- src/IO.jl | 2 +- src/KDE.jl | 2 +- src/LocalMax.jl | 2 +- src/Utils.jl | 2 +- test/kde.jl | 2 +- test/utils.jl | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/src/examples/ExampleAnalysis.jl b/docs/src/examples/ExampleAnalysis.jl index f211b4c..7247545 100644 --- a/docs/src/examples/ExampleAnalysis.jl +++ b/docs/src/examples/ExampleAnalysis.jl @@ -187,4 +187,4 @@ highly variable genes that can be used for analysis. We again here demonstrate i `Muon.AnnData`. =# -adata = readstereoseqbinned(AnnData, stereoseq_file, 50) \ No newline at end of file +adata = readstereoseqbinned(AnnData, stereoseq_file, 50) diff --git a/src/GridCount.jl b/src/GridCount.jl index 2230307..e7bfc03 100644 --- a/src/GridCount.jl +++ b/src/GridCount.jl @@ -160,4 +160,4 @@ function totalrna(counts) return sparse((reduce(vcat, i) for i in (x, y, v))..., gridsize(counts)...) end -end # module GridCount \ No newline at end of file +end # module GridCount diff --git a/src/IO.jl b/src/IO.jl index f4c4b7d..fa356e8 100644 --- a/src/IO.jl +++ b/src/IO.jl @@ -70,4 +70,4 @@ function readstereoseqbinned(file, binsize::Integer) ) end -end # module IO \ No newline at end of file +end # module IO diff --git a/src/KDE.jl b/src/KDE.jl index 3732330..43a2874 100644 --- a/src/KDE.jl +++ b/src/KDE.jl @@ -231,4 +231,4 @@ function assigncelltype(counts, signatures, kernel; celltypes=nothing, log=false return celltypemap, cosine end -end # module KDE \ No newline at end of file +end # module KDE diff --git a/src/LocalMax.jl b/src/LocalMax.jl index b249cc4..6aff740 100644 --- a/src/LocalMax.jl +++ b/src/LocalMax.jl @@ -85,4 +85,4 @@ function getlocalmaxima(counts, localmax, kernel; genes=nothing) ) end -end # module LocalMax \ No newline at end of file +end # module LocalMax diff --git a/src/Utils.jl b/src/Utils.jl index 4696954..0c1234b 100644 --- a/src/Utils.jl +++ b/src/Utils.jl @@ -12,4 +12,4 @@ end stringcoordinates(x, y) = @. string(x) * "_" * string(y) stringcoordinates(x...) = [join((string(j) for j in i), "_") for i in zip(x...)] -end # module Utils \ No newline at end of file +end # module Utils diff --git a/test/kde.jl b/test/kde.jl index 64f6d77..c459451 100644 --- a/test/kde.jl +++ b/test/kde.jl @@ -58,4 +58,4 @@ end coords = map(CartesianIndex, [(1, 1), (2, 3), (2, 4)]) Sainsc.LocalMax.getkdeforcoordinates(counts, coords, kernel) == kdeatcoord -end \ No newline at end of file +end diff --git a/test/utils.jl b/test/utils.jl index df00326..ed8e3c4 100644 --- a/test/utils.jl +++ b/test/utils.jl @@ -13,4 +13,4 @@ end x, y = Int[0, 0, 1, 0, 1], Int[0, 1, 0, 0, 1] @test Sainsc.Utils.categoricalcoordinates(x, y) == ([1, 2, 3, 1, 4], ([0, 0, 1, 1], [0, 1, 0, 1])) -end \ No newline at end of file +end