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Merged
lmweber merged 5 commits into from
Mar 18, 2024
Merged

Merging version bumps from last Bioc release and updating GHA #148

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46a1748
bump x.y.z version to even y prior to creation of RELEASE_3_18 branch
jwokaty Oct 24, 2023
ce59e34
bump x.y.z version to odd y following creation of RELEASE_3_18 branch
jwokaty Oct 24, 2023
5fcc22c
update github actions
lmweber Mar 14, 2024
c1cbf11
version
lmweber Mar 14, 2024
e8c8883
skip BiocCheck in github actions
lmweber Mar 14, 2024
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52 changes: 26 additions & 26 deletions .github/workflows/check-bioc.yml
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Expand Up@@ -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:
Expand DownExpand Up@@ -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'
Expand DownExpand Up@@ -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
Expand DownExpand Up@@ -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


Expand Down
2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,5 +1,5 @@
Package: SpatialExperiment
Version: 1.11.2
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
Expand Down