From 46a1748b1cbe0317202077b018781c0f19355740 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 24 Oct 2023 11:24:01 -0400 Subject: [PATCH 1/5] bump x.y.z version to even y prior to creation of RELEASE_3_18 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9c13ddb..8ab393b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: SpatialExperiment -Version: 1.11.2 +Version: 1.12.0 Title: S4 Class for Spatially Resolved -omics Data Description: Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to From ce59e345fb7bc7059d2cfa43f930a94f130b212e Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 24 Oct 2023 11:24:01 -0400 Subject: [PATCH 2/5] bump x.y.z version to odd y following creation of RELEASE_3_18 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8ab393b..7a6654d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: SpatialExperiment -Version: 1.12.0 +Version: 1.13.0 Title: S4 Class for Spatially Resolved -omics Data Description: Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to From 5fcc22c0869ce364dc0e44b26d9e1e60402db89d Mon Sep 17 00:00:00 2001 From: Lukas Weber Date: Thu, 14 Mar 2024 13:35:04 -0400 Subject: [PATCH 3/5] update github actions --- .github/workflows/check-bioc.yml | 52 ++++++++++++++++---------------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 8d1071a..2c6427f 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -52,9 +52,9 @@ jobs: fail-fast: false matrix: config: - - { os: ubuntu-latest, r: '4.3', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } - - { os: macOS-latest, r: '4.3', bioc: '3.17'} - - { os: windows-latest, r: '4.3', bioc: '3.17'} + - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } + - { os: macOS-latest, r: '4.3', bioc: '3.18'} + - { os: windows-latest, r: '4.3', bioc: '3.18'} ## Check https://github.com/r-lib/actions/tree/master/examples ## for examples using the http-user-agent env: @@ -105,23 +105,23 @@ jobs: uses: actions/cache@v3 with: path: ${{ env.R_LIBS_USER }} - key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3- + key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3- - name: Cache R packages on Linux if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " uses: actions/cache@v3 with: path: /home/runner/work/_temp/Library - key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3- + key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3- - - name: Install Linux system dependencies - if: runner.os == 'Linux' - run: | - sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))') - echo $sysreqs - sudo -s eval "$sysreqs" + # - name: Install Linux system dependencies + # if: runner.os == 'Linux' + # run: | + # sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))') + # echo $sysreqs + # sudo -s eval "$sysreqs" - name: Install macOS system dependencies if: matrix.config.os == 'macOS-latest' @@ -237,22 +237,22 @@ jobs: BiocGenerics:::testPackage() shell: Rscript {0} -# - name: Run BiocCheck -# env: -# DISPLAY: 99.0 -# run: | -# BiocCheck::BiocCheck( -# dir('check', 'tar.gz$', full.names = TRUE), -# `quit-with-status` = TRUE, -# `no-check-R-ver` = TRUE, -# `no-check-bioc-help` = TRUE -# ) -# shell: Rscript {0} + - name: Run BiocCheck + env: + DISPLAY: 99.0 + run: | + BiocCheck::BiocCheck( + dir('check', 'tar.gz$', full.names = TRUE), + `quit-with-status` = TRUE, + `no-check-R-ver` = TRUE, + `no-check-bioc-help` = TRUE + ) + shell: Rscript {0} - name: Test coverage if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' run: | - covr::codecov() + covr::codecov(coverage = covr::package_coverage(type = "all")) shell: Rscript {0} - name: Install package @@ -285,7 +285,7 @@ jobs: if: failure() uses: actions/upload-artifact@master with: - name: ${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-results + name: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-results path: check From c1cbf117d0ec3d76802942545fabdabe3e11cbad Mon Sep 17 00:00:00 2001 From: Lukas Weber Date: Thu, 14 Mar 2024 13:37:46 -0400 Subject: [PATCH 4/5] version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7a6654d..a208ac1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: SpatialExperiment -Version: 1.13.0 +Version: 1.13.1 Title: S4 Class for Spatially Resolved -omics Data Description: Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to From e8c88833ca2f9b25da1f6f95474a2fdb452116af Mon Sep 17 00:00:00 2001 From: Lukas Weber Date: Thu, 14 Mar 2024 15:23:03 -0400 Subject: [PATCH 5/5] skip BiocCheck in github actions --- .github/workflows/check-bioc.yml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 2c6427f..7f97c9a 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -237,17 +237,17 @@ jobs: BiocGenerics:::testPackage() shell: Rscript {0} - - name: Run BiocCheck - env: - DISPLAY: 99.0 - run: | - BiocCheck::BiocCheck( - dir('check', 'tar.gz$', full.names = TRUE), - `quit-with-status` = TRUE, - `no-check-R-ver` = TRUE, - `no-check-bioc-help` = TRUE - ) - shell: Rscript {0} + # - name: Run BiocCheck + # env: + # DISPLAY: 99.0 + # run: | + # BiocCheck::BiocCheck( + # dir('check', 'tar.gz$', full.names = TRUE), + # `quit-with-status` = TRUE, + # `no-check-R-ver` = TRUE, + # `no-check-bioc-help` = TRUE + # ) + # shell: Rscript {0} - name: Test coverage if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'