From 3273b681b6de709f183d0dca17c1dc02c74bfc08 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Tue, 3 Mar 2026 23:52:04 -0800 Subject: [PATCH 1/2] ci_fix --- .github/workflows/pkgdown.yml | 2 - pixi.toml | 84 ----------------------------------- 2 files changed, 86 deletions(-) delete mode 100644 pixi.toml diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 2af0f100..e0ca771d 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -32,8 +32,6 @@ jobs: - name: Setup pixi uses: prefix-dev/setup-pixi@v0.9.4 - with: - manifest-path: /tmp/pixi/pixi.toml - name: Build pkgdown site run: pixi run --environment r44 pkgdown_build diff --git a/pixi.toml b/pixi.toml deleted file mode 100644 index 05903967..00000000 --- a/pixi.toml +++ /dev/null @@ -1,84 +0,0 @@ -[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" = "*" From eee9acc4287bcd875a4226c9e3d8e0a382d58960 Mon Sep 17 00:00:00 2001 From: danielnachun Date: Wed, 4 Mar 2026 07:53:36 +0000 Subject: [PATCH 2/2] Update documentation --- pixi.toml | 84 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 84 insertions(+) create mode 100644 pixi.toml 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" = "*"