From 665e420aff7388c20ca8a46afc7de60d8a362daf Mon Sep 17 00:00:00 2001 From: David Collins Date: Tue, 4 Feb 2025 17:34:39 -0500 Subject: [PATCH 1/5] Replace deprecated triggers for Integration Checks Add main as trigger for Integration Checks Drop develop as trigger for Integration Checks Drop master as trigger for Integration Checks --- .github/workflows/integration_checks.yaml | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/.github/workflows/integration_checks.yaml b/.github/workflows/integration_checks.yaml index a8e6e3f86..721225fe0 100644 --- a/.github/workflows/integration_checks.yaml +++ b/.github/workflows/integration_checks.yaml @@ -1,16 +1,14 @@ name: Integration Checks -# Because `develop` is a protected branch this workflow is triggered when a PR +# Because `main` is a protected branch this workflow is triggered when a PR # is opened/updated and again when it is merged. on: push: - branches: - - develop - - master + branches: + - main pull_request: branches: - - develop - - master + - main jobs: check-package: From 40d6cede8133ccec48d0ada38a91d254f4e3683a Mon Sep 17 00:00:00 2001 From: David Collins Date: Tue, 4 Feb 2025 17:37:55 -0500 Subject: [PATCH 2/5] Drop appveyor.yml --- appveyor.yml | 62 ---------------------------------------------------- 1 file changed, 62 deletions(-) delete mode 100644 appveyor.yml diff --git a/appveyor.yml b/appveyor.yml deleted file mode 100644 index 7a987f45a..000000000 --- a/appveyor.yml +++ /dev/null @@ -1,62 +0,0 @@ -# DO NOT CHANGE the "init" and "install" sections below - -# Download script file from GitHub -init: - ps: | - $ErrorActionPreference = "Stop" - Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" - Import-Module '..\appveyor-tool.ps1' -install: - - "%PYTHON%\\python.exe -m pip install wheel" - - "%PYTHON%\\python.exe -m pip install phate" - - ps: Bootstrap - -# Adapt as necessary starting from here - -environment: - global: - R_ARCH: x64 - USE_RTOOLS: true - BIOC_USE_DEVEL: "FALSE" - _R_CHECK_FORCE_SUGGESTS_: false - PYTHON: "C:\\Python36-x64" - RETICULATE_PYTHON: "C:\\Python36-x64" - CRAN: "https://cloud.r-project.org" - R_LIBCURL_SSL_REVOKE_BEST_EFFORT: "TRUE" - CURL_SSL_BACKEND: "openssl" - -build_script: - - travis-tool.sh install_deps - - travis-tool.sh r_binary_install curl - - travis-tool.sh bioc_install GenomeInfoDbData - - travis-tool.sh bioc_install DESeq2 - - travis-tool.sh bioc_install MAST - - travis-tool.sh bioc_install S4Vectors - - travis-tool.sh bioc_install SummarizedExperiment - - travis-tool.sh bioc_install SingleCellExperiment - -test_script: - - travis-tool.sh run_tests - -on_failure: - - 7z a failure.zip *.Rcheck\* - - appveyor PushArtifact failure.zip - -artifacts: - - path: '*.Rcheck\**\*.log' - name: Logs - - - path: '*.Rcheck\**\*.out' - name: Logs - - - path: '*.Rcheck\**\*.fail' - name: Logs - - - path: '*.Rcheck\**\*.Rout' - name: Logs - - - path: '\*_*.tar.gz' - name: Bits - - - path: '\*_*.zip' - name: Bits From 33a3e8f062dfe7ce4a72afaffa8374811a7338cf Mon Sep 17 00:00:00 2001 From: David Collins Date: Tue, 4 Feb 2025 17:38:18 -0500 Subject: [PATCH 3/5] Drop appveyor.yml from .Rbuildignore --- .Rbuildignore | 1 - 1 file changed, 1 deletion(-) diff --git a/.Rbuildignore b/.Rbuildignore index d203ce14f..e2d47f235 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -4,7 +4,6 @@ ^\.Rproj\.user$ ^.*\.old$ .git -appveyor.yml cran-comments.md CODE_OF_CONDUCT.md ^_pkgdown\.yaml$ From 425072ee29553331a2c96418ddb9ffbcefbe9754 Mon Sep 17 00:00:00 2001 From: David Collins Date: Tue, 4 Feb 2025 17:38:51 -0500 Subject: [PATCH 4/5] Drop AppVeyor badge from README --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index 56a7e94b1..bda205197 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,3 @@ -[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/satijalab/seurat?branch=master&svg=true)](https://ci.appveyor.com/project/satijalab/seurat) [![CRAN Version](https://www.r-pkg.org/badges/version/Seurat)](https://cran.r-project.org/package=Seurat) [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/Seurat)](https://cran.r-project.org/package=Seurat) From 1d67e41017fa765b3d0a59f5212616b90a535440 Mon Sep 17 00:00:00 2001 From: David Collins Date: Tue, 4 Feb 2025 17:39:01 -0500 Subject: [PATCH 5/5] Bump version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index e30bbb3a8..99acc584b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: Seurat -Version: 5.2.1 +Version: 5.2.99.9000 Title: Tools for Single Cell Genomics Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. Authors@R: c(