diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml index 261f6c35..e95c9dce 100644 --- a/.github/workflows/conda_build.yml +++ b/.github/workflows/conda_build.yml @@ -16,7 +16,6 @@ jobs: build_package: name: Build conda package (${{ matrix.platform }} / ${{ matrix.environment }}) runs-on: ${{ matrix.runner }} - runs-on: ubuntu-latest strategy: fail-fast: false matrix: diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 29da1ec7..f814e10f 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -34,7 +34,7 @@ jobs: outputs: commit: ${{ steps.commit-changes.outputs.commit_long_sha }} runs-on: ubuntu-latest - if: ${{ github.event.inputs.commit }} == "auto" + if: ${{ github.event.inputs.commit == "auto" }} steps: - name: Checkout repository uses: actions/checkout@v6 diff --git a/pixi.toml b/pixi.toml new file mode 100644 index 00000000..05903967 --- /dev/null +++ b/pixi.toml @@ -0,0 +1,84 @@ +[project] +name = "r-pecotmr" +channels = ["dnachun", "conda-forge", "bioconda"] +platforms = ["linux-64", "osx-arm64"] + +[system-requirements] +libc = { family="glibc", version="2.17" } + +[tasks] +devtools_document = "cd $GITHUB_WORKSPACE; R -e 'devtools::document()'" +devtools_test = "cd $GITHUB_WORKSPACE; R -e 'devtools::test()'" +codecov = "cd $GITHUB_WORKSPACE; R -e 'covr::codecov(quiet = FALSE)'" +rcmdcheck = "cd $GITHUB_WORKSPACE; R -e 'rcmdcheck::rcmdcheck()'" +bioccheck_git_clone = "cd $GITHUB_WORKSPACE; R -e 'BiocCheck::BiocCheckGitClone()'" +bioccheck = "cd $GITHUB_WORKSPACE; R -e 'BiocCheck::BiocCheck()'" +use_major_version = "cd $GITHUB_WORKSPACE; R -e 'usethis::use_version(which = \"major\", push = FALSE)'" +use_minor_version = "cd $GITHUB_WORKSPACE; R -e 'usethis::use_version(which = \"minor\", push = FALSE)'" +use_patch_version = "cd $GITHUB_WORKSPACE; R -e 'usethis::use_version(which = \"patch\", push = FALSE)'" +pkgdown_build = "cd $GITHUB_WORKSPACE; R -e 'pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)'" + +[feature.r44] +dependencies = {"r-base" = "4.4.*"} + +[feature.r45] +dependencies = {"r-base" = "4.5.*"} + +[environments] +r44 = {features = ["r44"]} +r45 = {features = ["r45"]} + +[target.linux-64.dependencies] +"gcc" = "*" + +[dependencies] +# "bioconductor-bioccheck" = "*" +"r-covr" = "*" +"r-devtools" = "*" +"r-knitr" = "*" +"r-markdown" = "*" +"r-pkgdown" = "*" +"r-rcmdcheck" = "*" +"r-testthat" = "*" +"r-tidyverse" = "*" +"bioconductor-iranges" = "*" +"bioconductor-qvalue" = "*" +"bioconductor-s4vectors" = "*" +"bioconductor-snpstats" = "*" +"r-base" = "*" +"r-bigsnpr" = "*" +"r-bigstatsr" = "*" +"r-coda" = "*" +"r-coloc" = "*" +"r-colocboost" = "*" +"r-dofuture" = "*" +"r-dplyr" = "*" +"r-flashier" = "*" +"r-fsusier" = "*" +"r-furrr" = "*" +"r-future" = "*" +"r-gbj" = "*" +"r-glmnet" = "*" +"r-harmonicmeanp" = "*" +"r-magrittr" = "*" +"r-mashr" = "*" +"r-matrixstats" = "*" +"r-mr.mashr" = "*" +"r-mvsusier" = "*" +"r-pgenlibr" = "*" +"r-purrr" = "*" +"r-qgg" = "*" +"r-quadprog" = "*" +"r-quantreg" = "*" +"r-rcpp" = "*" +"r-rcpparmadillo" = "*" +"r-readr" = "*" +"r-rfast" = "*" +"r-rlang" = "*" +"r-stringr" = "*" +"r-susier" = "*" +"r-tibble" = "*" +"r-tidyr" = "*" +"r-vctrs" = "*" +"r-vroom" = "*" +"r-xicor" = "*"