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Add remaining Fedora-based rhub images
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walkowif committed Jun 20, 2024
1 parent 7f58323 commit 0045132
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Showing 8 changed files with 63 additions and 8 deletions.
9 changes: 7 additions & 2 deletions .github/workflows/deploy.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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).
Expand Down Expand Up @@ -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 }}"
}
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20 changes: 20 additions & 0 deletions .github/workflows/scheduled.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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:
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7 changes: 6 additions & 1 deletion scripts/install_bioc_pkgs.R
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
9 changes: 7 additions & 2 deletions scripts/install_cran_pkgs.R
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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",
Expand Down
7 changes: 6 additions & 1 deletion scripts/install_gh_pkgs.R
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
7 changes: 6 additions & 1 deletion scripts/install_other_pkgs.R
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
5 changes: 5 additions & 0 deletions scripts/install_pip_pkgs.py
Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,11 @@ def install(packages=[]):
],
"gcc13": [],
"gcc14": [],
"atlas": [],
"valgrind": [],
"intel": [],
"nosuggests": [],
"mkl": [],
}

# Install packages
Expand Down
7 changes: 6 additions & 1 deletion scripts/install_sysdeps.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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.* ]]
Expand Down Expand Up @@ -168,7 +173,7 @@ then {
}
fi

if [[ "$distribution" =~ ^gcc.* ]]
if [[ "$distribution" =~ ^gcc.*|^atlas$|^valgrind$|^intel$|^nosuggests$|^mkl$ ]]
then {
# Update
dnf update -y
Expand Down

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