From 0045132bc6618c67290bf438c81b773f542b16dc Mon Sep 17 00:00:00 2001 From: Franciszek Walkowiak Date: Thu, 20 Jun 2024 14:29:33 +0200 Subject: [PATCH] Add remaining Fedora-based rhub images --- .github/workflows/deploy.yaml | 9 +++++++-- .github/workflows/scheduled.yaml | 20 ++++++++++++++++++++ scripts/install_bioc_pkgs.R | 7 ++++++- scripts/install_cran_pkgs.R | 9 +++++++-- scripts/install_gh_pkgs.R | 7 ++++++- scripts/install_other_pkgs.R | 7 ++++++- scripts/install_pip_pkgs.py | 5 +++++ scripts/install_sysdeps.sh | 7 ++++++- 8 files changed, 63 insertions(+), 8 deletions(-) diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml index aea119c..d3703e9 100755 --- a/.github/workflows/deploy.yaml +++ b/.github/workflows/deploy.yaml @@ -30,6 +30,11 @@ on: - rstudio-local - gcc13 - gcc14 + - atlas + - valgrind + - intel + - nosuggests + - mkl r_version: description: | R version (also used as the tag to pull the origin image). @@ -206,8 +211,8 @@ jobs: run: | # Set Image name image_name="${{ needs.normalize-inputs.outputs.distribution }}_${{ needs.normalize-inputs.outputs.r_version }}_bioc_${{ needs.normalize-inputs.outputs.bioc_version }}" - # For Fedora (gcc13 and gcc14) rhub images. - if [[ "${{ needs.normalize-inputs.outputs.distribution }}" =~ ^gcc.* ]] + # For Fedora-based rhub images. + if [[ "${{ needs.normalize-inputs.outputs.distribution }}" =~ ^gcc.*|^atlas$|^valgrind$|^intel$|^nosuggests$|^mkl$ ]] then { image_name="${{ needs.normalize-inputs.outputs.distribution }}" } diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml index 20089b7..ad5f86c 100644 --- a/.github/workflows/scheduled.yaml +++ b/.github/workflows/scheduled.yaml @@ -52,6 +52,26 @@ jobs: bioc: 'devel' distro: gcc14 origin: rhub + - distro_tag: 'latest' + bioc: 'devel' + distro: atlas + origin: rhub + - distro_tag: 'latest' + bioc: 'devel' + distro: valgrind + origin: rhub + - distro_tag: 'latest' + bioc: 'devel' + distro: intel + origin: rhub + - distro_tag: 'latest' + bioc: 'devel' + distro: nosuggests + origin: rhub + - distro_tag: 'latest' + bioc: 'devel' + distro: mkl + origin: rhub # Trigger steps steps: diff --git a/scripts/install_bioc_pkgs.R b/scripts/install_bioc_pkgs.R index f53a7b5..07459d0 100755 --- a/scripts/install_bioc_pkgs.R +++ b/scripts/install_bioc_pkgs.R @@ -31,7 +31,12 @@ bioc_pkgs <- list( rstudio = shared_pkgs, `rstudio-local` = shared_pkgs, `gcc13` = shared_pkgs, - `gcc14` = shared_pkgs + `gcc14` = shared_pkgs, + `atlas` = shared_pkgs, + `valgrind` = shared_pkgs, + `intel` = shared_pkgs, + `nosuggests` = shared_pkgs, + `mkl` = shared_pkgs ) # Get diff of installed and uninstalled packages for diff --git a/scripts/install_cran_pkgs.R b/scripts/install_cran_pkgs.R index 20d6fb2..5f3bbc0 100755 --- a/scripts/install_cran_pkgs.R +++ b/scripts/install_cran_pkgs.R @@ -240,7 +240,12 @@ cran_pkgs <- list( local_dev_packages ), `gcc13` = shared_pkgs[!shared_pkgs %in% c("rjags")], - `gcc14` = shared_pkgs[!shared_pkgs %in% c("rjags")] + `gcc14` = shared_pkgs[!shared_pkgs %in% c("rjags")], + `atlas` = shared_pkgs[!shared_pkgs %in% c("rjags")], + `valgrind` = shared_pkgs[!shared_pkgs %in% c("rjags")], + `intel` = shared_pkgs[!shared_pkgs %in% c("rjags")], + `nosuggests` = shared_pkgs[!shared_pkgs %in% c("rjags")], + `mkl` = shared_pkgs[!shared_pkgs %in% c("rjags")] ) # Re-install packages with newer versions @@ -266,7 +271,7 @@ if (length(new_pkgs_from_src)) { } # Install rjags with special params for fedora distros -if (startsWith(distribution, "gcc")) { +if (startsWith(distribution, "gcc") || distribution == "atlas" || distribution == "valgrind" || distribution == "intel" || distribution == "nosuggests" || distribution == "mkl") { install.packages( "rjags", type = "source", diff --git a/scripts/install_gh_pkgs.R b/scripts/install_gh_pkgs.R index fa861b9..0328141 100755 --- a/scripts/install_gh_pkgs.R +++ b/scripts/install_gh_pkgs.R @@ -18,7 +18,12 @@ gh_pkgs <- list( rstudio = shared_pkgs, `rstudio-local` = shared_pkgs, `gcc13` = shared_pkgs, - `gcc14` = shared_pkgs + `gcc14` = shared_pkgs, + `atlas` = shared_pkgs, + `valgrind` = shared_pkgs, + `intel` = shared_pkgs, + `nosuggests` = shared_pkgs, + `mkl` = shared_pkgs ) # Get diff of installed and uninstalled packages for diff --git a/scripts/install_other_pkgs.R b/scripts/install_other_pkgs.R index ed2e0b6..a6026cf 100755 --- a/scripts/install_other_pkgs.R +++ b/scripts/install_other_pkgs.R @@ -33,7 +33,12 @@ other_pkgs <- list( stat_pkgs ), `gcc13` = c(stat_pkgs), - `gcc14` = c(stat_pkgs) + `gcc14` = c(stat_pkgs), + `atlas` = c(stat_pkgs), + `valgrind` = c(stat_pkgs), + `intel` = c(stat_pkgs), + `nosuggests` = c(stat_pkgs), + `mkl` = c(stat_pkgs) ) # Get diff of installed and uninstalled packages for diff --git a/scripts/install_pip_pkgs.py b/scripts/install_pip_pkgs.py index 6ee0cdf..a606a3b 100755 --- a/scripts/install_pip_pkgs.py +++ b/scripts/install_pip_pkgs.py @@ -33,6 +33,11 @@ def install(packages=[]): ], "gcc13": [], "gcc14": [], + "atlas": [], + "valgrind": [], + "intel": [], + "nosuggests": [], + "mkl": [], } # Install packages diff --git a/scripts/install_sysdeps.sh b/scripts/install_sysdeps.sh index c92aa8f..1b4291d 100755 --- a/scripts/install_sysdeps.sh +++ b/scripts/install_sysdeps.sh @@ -115,6 +115,11 @@ nano \ # Deps specific to the gcc rhub image. pkgs_to_install_fedora["gcc13"]="${shared_deps_fedora}" pkgs_to_install_fedora["gcc14"]="${shared_deps_fedora}" +pkgs_to_install_fedora["atlas"]="${shared_deps_fedora}" +pkgs_to_install_fedora["valgrind"]="${shared_deps_fedora}" +pkgs_to_install_fedora["intel"]="${shared_deps_fedora}" +pkgs_to_install_fedora["nosuggests"]="${shared_deps_fedora}" +pkgs_to_install_fedora["mkl"]="${shared_deps_fedora}" # Perform installations for debian distros if [[ "$distribution" =~ ^rstudio.* ]] @@ -168,7 +173,7 @@ then { } fi -if [[ "$distribution" =~ ^gcc.* ]] +if [[ "$distribution" =~ ^gcc.*|^atlas$|^valgrind$|^intel$|^nosuggests$|^mkl$ ]] then { # Update dnf update -y