Skip to content

refactor: dependency installation for Quarto computing features #14

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 7 commits into from
Jan 30, 2025
Merged

refactor: dependency installation for Quarto computing features #14

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
42ed702
refactor: use fully defined "dependsOn" in feature
mcanouil Jan 30, 2025
8bb8760
fix: don't use "su" for Python
mcanouil Jan 30, 2025
77f064d
chore: don't set feature option
mcanouil Jan 30, 2025
e5081e3
fix: install all dependencies
mcanouil Jan 30, 2025
5bb35e0
revert: debug change
mcanouil Jan 30, 2025
1fc5163
feat: use options to set dependencies
mcanouil Jan 30, 2025
3c9246d
fix: options to variable
mcanouil Jan 30, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
41 changes: 9 additions & 32 deletions .github/.devcontainer/devcontainer.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,38 +10,15 @@
},
"remoteUser": "vscode",
"features": {
"ghcr.io/devcontainers/features/common-utils:2": {
"installZsh": "true",
"username": "vscode",
"userUid": "1000",
"userGid": "1000",
"upgradePackages": "true"
},
"ghcr.io/devcontainers/features/git:1": {
"version": "latest",
"ppa": "false"
},
"ghcr.io/rocker-org/devcontainer-features/r-rig:1": {
"version": "release",
"vscodeRSupport": "none",
"installDevTools": "false",
"installREnv": "true",
"installRMarkdown": "false"
},
"ghcr.io/devcontainers/features/python:1": {
"version": "latest",
"enableShared": "true"
},
"ghcr.io/julialang/devcontainer-features/julia:1": {
"channel": "release"
},
"./quarto-computing-dependencies": {
"dependencies": "all"
},
"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {
"version": "prerelease",
"installTinyTex": "true",
"installChromium": "false"
}
"rDeps": "rmarkdown,httpgd",
"pythonDeps": "jupyter,papermill",
"juliaDeps": "IJulia"
}//,
// "ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {
// "version": "prerelease",
// "installTinyTex": "true",
// "installChromium": "false"
// }
}
}
49 changes: 40 additions & 9 deletions .github/.devcontainer/quarto-computing-dependencies/devcontainer-feature.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,21 +4,52 @@
"name": "Install Computing Dependencies for Quarto",
"description": "Install R, Python, and Julia dependencies for Quarto.",
"options": {
"dependencies": {
"rDeps": {
"type": "string",
"enum": ["all", "r", "python", "julia"],
"default": "all",
"description": "Specify what dependencies to install."
}
"default": "rmarkdown",
"description": "Specify what R dependencies to install."
},
"pythonDeps": {
"type": "string",
"default": "jupyter,papermill",
"description": "Specify what Python dependencies to install."
},
"juliaDeps": {
"type": "string",
"default": "IJulia",
"description": "Specify what Julia dependencies to install."
}
},
"dependsOn": {
"ghcr.io/devcontainers/features/common-utils": {},
"ghcr.io/rocker-org/devcontainer-features/r-rig": {},
"ghcr.io/devcontainers/features/python": {},
"ghcr.io/julialang/devcontainer-features/julia": {}
"ghcr.io/devcontainers/features/common-utils:2": {
"installZsh": "true",
"username": "vscode",
"userUid": "1000",
"userGid": "1000",
"upgradePackages": "true"
},
"ghcr.io/devcontainers/features/git:1": {
"version": "latest",
"ppa": "false"
},
"ghcr.io/rocker-org/devcontainer-features/r-rig:1": {
"version": "release",
"vscodeRSupport": "none",
"installDevTools": "false",
"installREnv": "true",
"installRMarkdown": "false"
},
"ghcr.io/devcontainers/features/python:1": {
"version": "latest",
"enableShared": "true"
},
"ghcr.io/julialang/devcontainer-features/julia:1": {
"channel": "release"
}
},
"installsAfter": [
"ghcr.io/devcontainers/features/common-utils",
"ghcr.io/devcontainers/features/git",
"ghcr.io/rocker-org/devcontainer-features/r-rig",
"ghcr.io/devcontainers/features/python",
"ghcr.io/julialang/devcontainer-features/julia"
Expand Down
37 changes: 16 additions & 21 deletions .github/.devcontainer/quarto-computing-dependencies/install.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,12 @@ set -e

export DEBIAN_FRONTEND=noninteractive

DEPENDENCIES=${DEPENDENCIES:-"all"}

USERNAME=${USERNAME:-${_REMOTE_USER:-"automatic"}}

R_DEPS=${RDEPS:-"rmarkdown"}
PYTHON_DEPS=${PYTHONDEPS:-"jupyter,papermill"}
JULIA_DEPS=${JULIADEPS:-"IJulia"}

set -e

if [ "$(id -u)" -ne 0 ]; then
Expand All @@ -33,30 +35,23 @@ elif [ "${USERNAME}" = "none" ] || ! id -u "${USERNAME}" >/dev/null 2>&1; then
fi

quarto_r_deps() {
su "${USERNAME}" -c "Rscript -e 'pak::pkg_install(\"rmarkdown\")'"
local deps=$1
deps=$(echo "${deps}" | sed 's/,/","/g')
su "${USERNAME}" -c "Rscript -e 'pak::pkg_install(c(\"${deps}\"))'"
}

quarto_python_deps() {
su "${USERNAME}" -c "python3 -m pip install jupyter papermill"
local deps=$1
deps=$(echo "${deps}" | sed 's/,/ /g')
python3 -m pip install ${deps}
}

quarto_julia_deps() {
su "${USERNAME}" -c "~/.juliaup/bin/julia -e 'using Pkg; Pkg.add(\"IJulia\")'"
local deps=$1
deps=$(echo "${deps}" | sed 's/,/","/g')
su "${USERNAME}" -c "~/.juliaup/bin/julia -e 'using Pkg; Pkg.add.([\"${deps}\"])'"
}

case ${DEPENDENCIES} in
all)
quarto_r_deps
quarto_python_deps
quarto_julia_deps
;;
r)
quarto_r_deps
;;
python)
quarto_python_deps
;;
julia)
quarto_julia_deps
;;
esac
quarto_r_deps ${R_DEPS}
quarto_python_deps ${PYTHON_DEPS}
quarto_julia_deps ${JULIA_DEPS}