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Initial .devcontainer config for codespaces (#6)
* Initial .devcontainer config for codespaces * Change features install order * Add installAfter setting renv cache. * Remove version from installAfter. * Use overrideFeatureInstallOrder as installsAfter is for feature.json * Handling CA certificates for devcontainer * Fix for arm64 devcontainer build. * Update 4.2 and 4.1 * Add codespaces config for multi repository access. * Clean postAttachCommand command. * Fix typo
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,95 @@ | ||
| { | ||
| // https://containers.dev/implementors/json_reference/ | ||
| "name": "sdtm.oak (RStudio) container", | ||
| "image": "ghcr.io/pharmaverse/sdtm.oak-4.1:latest", | ||
| // Install Dev Container Features. More info: https://containers.dev/features | ||
| "containerEnv": { | ||
| "ROOT": "true", | ||
| "PASSWORD": "rstudio", | ||
| "DISABLE_AUTH": "true", | ||
| "RENV_AUTOLOADER_ENABLED": "false" | ||
| }, | ||
| "features": { | ||
| "./ca-cert": {}, | ||
| "ghcr.io/rocker-org/devcontainer-features/r-rig:1": { | ||
| "version": "none", | ||
| "vscodeRSupport": "full", | ||
| "installRadian": true, | ||
| "installVscDebugger": true | ||
| }, | ||
| "ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {}, | ||
| "ghcr.io/devcontainers/features/common-utils:2": { | ||
| "installZsh": true, | ||
| "configureZshAsDefaultShell": false, | ||
| "installOhMyZsh": true, | ||
| "username": "rstudio", | ||
| "upgradePackages": false | ||
| }, | ||
| "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {} | ||
| }, | ||
| "overrideFeatureInstallOrder": [ | ||
| "./ca-cert", | ||
| "./arm64-repos", | ||
| "ghcr.io/devcontainers/features/common-utils", | ||
| "ghcr.io/rocker-org/devcontainer-features/renv-cache", | ||
| "ghcr.io/rocker-org/devcontainer-features/r-rig", | ||
| "ghcr.io/mikaello/devcontainer-features/modern-shell-utils" | ||
| ], | ||
| "init": true, | ||
| "overrideCommand": false, | ||
|
|
||
| "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", | ||
|
|
||
| "postAttachCommand": "rstudio || true", | ||
|
|
||
| "customizations": { | ||
| "codespaces": { | ||
| "repositories": { | ||
| "pharmaverse/mint": { | ||
| "permissions": "write-all" | ||
| }, | ||
| "pharmaverse/raw.synthetic.data": { | ||
| "permissions": "write-all" | ||
| } | ||
| } | ||
| }, | ||
| "vscode": { | ||
| "settings": { | ||
| "r.rterm.linux": "/usr/local/bin/radian", | ||
| "r.bracketedPaste": true, | ||
| "editor.bracketPairColorization.enabled": true, | ||
| "editor.guides.bracketPairs": "active" | ||
| }, | ||
| "extensions": [ | ||
| "vsls-contrib.codetour", | ||
| "GitHub.copilot", | ||
| "GitHub.copilot-chat", | ||
| // R extensions | ||
| "ikuyadeu.r", | ||
| "REditorSupport.r-lsp", | ||
| // Extra extension | ||
| "streetsidesoftware.code-spell-checker", | ||
| "eamodio.gitlens", | ||
| "cweijan.vscode-office", | ||
| "donjayamanne.githistory", | ||
| "GitHub.vscode-github-actions", | ||
| "GitHub.vscode-pull-request-github", | ||
| "GitHub.remotehub", | ||
| "alefragnani.Bookmarks", | ||
| "vscode-icons-team.vscode-icons" | ||
| ] | ||
| } | ||
| }, | ||
|
|
||
| // RStudio ports | ||
| "forwardPorts": [8787], | ||
| "portsAttributes": { | ||
| "8787": { | ||
| "label": "Rstudio", | ||
| "requireLocalPort": true, | ||
| "onAutoForward": "openBrowser" | ||
| } | ||
| }, | ||
| // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root | ||
| "remoteUser": "rstudio" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,95 @@ | ||
| { | ||
| // https://containers.dev/implementors/json_reference/ | ||
| "name": "sdtm.oak R-4.2 (RStudio) container", | ||
| "image": "ghcr.io/pharmaverse/sdtm.oak-4.2:latest", | ||
| // Install Dev Container Features. More info: https://containers.dev/features | ||
| "containerEnv": { | ||
| "ROOT": "true", | ||
| "PASSWORD": "rstudio", | ||
| "DISABLE_AUTH": "true", | ||
| "RENV_AUTOLOADER_ENABLED": "false" | ||
| }, | ||
| "features": { | ||
| "./ca-cert": {}, | ||
| "ghcr.io/rocker-org/devcontainer-features/r-rig:1": { | ||
| "version": "none", | ||
| "vscodeRSupport": "full", | ||
| "installRadian": true, | ||
| "installVscDebugger": true | ||
| }, | ||
| "ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {}, | ||
| "ghcr.io/devcontainers/features/common-utils:2": { | ||
| "installZsh": true, | ||
| "configureZshAsDefaultShell": false, | ||
| "installOhMyZsh": true, | ||
| "username": "rstudio", | ||
| "upgradePackages": false | ||
| }, | ||
| "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {} | ||
| }, | ||
| "overrideFeatureInstallOrder": [ | ||
| "./ca-cert", | ||
| "./arm64-repos", | ||
| "ghcr.io/devcontainers/features/common-utils", | ||
| "ghcr.io/rocker-org/devcontainer-features/renv-cache", | ||
| "ghcr.io/rocker-org/devcontainer-features/r-rig", | ||
| "ghcr.io/mikaello/devcontainer-features/modern-shell-utils" | ||
| ], | ||
| "init": true, | ||
| "overrideCommand": false, | ||
|
|
||
| "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", | ||
|
|
||
| "postAttachCommand": "rstudio || true", | ||
|
|
||
| "customizations": { | ||
| "codespaces": { | ||
| "repositories": { | ||
| "pharmaverse/mint": { | ||
| "permissions": "write-all" | ||
| }, | ||
| "pharmaverse/raw.synthetic.data": { | ||
| "permissions": "write-all" | ||
| } | ||
| } | ||
| }, | ||
| "vscode": { | ||
| "settings": { | ||
| "r.rterm.linux": "/usr/local/bin/radian", | ||
| "r.bracketedPaste": true, | ||
| "editor.bracketPairColorization.enabled": true, | ||
| "editor.guides.bracketPairs": "active" | ||
| }, | ||
| "extensions": [ | ||
| "vsls-contrib.codetour", | ||
| "GitHub.copilot", | ||
| "GitHub.copilot-chat", | ||
| // R extensions | ||
| "ikuyadeu.r", | ||
| "REditorSupport.r-lsp", | ||
| // Extra extension | ||
| "streetsidesoftware.code-spell-checker", | ||
| "eamodio.gitlens", | ||
| "cweijan.vscode-office", | ||
| "donjayamanne.githistory", | ||
| "GitHub.vscode-github-actions", | ||
| "GitHub.vscode-pull-request-github", | ||
| "GitHub.remotehub", | ||
| "alefragnani.Bookmarks", | ||
| "vscode-icons-team.vscode-icons" | ||
| ] | ||
| } | ||
| }, | ||
|
|
||
| // RStudio ports | ||
| "forwardPorts": [8787], | ||
| "portsAttributes": { | ||
| "8787": { | ||
| "label": "Rstudio", | ||
| "requireLocalPort": true, | ||
| "onAutoForward": "openBrowser" | ||
| } | ||
| }, | ||
| // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root | ||
| "remoteUser": "rstudio" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "name": "arm64 repos", | ||
| "id": "arm64-repos", | ||
| "version": "0.1.0", | ||
| "description": "Fix repos for arm64.", | ||
| "options": {} | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| #!/bin/bash | ||
|
|
||
| set -e | ||
|
|
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| ARCH=$(uname -m) | ||
|
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| ## source install if using RSPM and arm64 image | ||
| if [ "$ARCH" = "aarch64" ]; then | ||
|
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| CRAN="https://cloud.r-project.org" | ||
|
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| ## Add a default CRAN mirror | ||
| echo "options(repos = c(CRAN = '${CRAN}'), download.file.method = 'libcurl')" >"${R_HOME}/etc/Rprofile.site" | ||
|
|
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| ## Set HTTPUserAgent for RSPM (https://github.com/rocker-org/rocker/issues/400) | ||
| cat <<EOF >>"${R_HOME}/etc/Rprofile.site" | ||
| # https://docs.rstudio.com/rspm/admin/serving-binaries/#binaries-r-configuration-linux | ||
| options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"]))) | ||
| EOF | ||
|
|
||
| fi | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| *.crt |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "name": "CA cert", | ||
| "id": "ca-cert", | ||
| "version": "0.1.0", | ||
| "description": "Copy CA cert into the container.", | ||
| "options": {} | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| #!/bin/sh | ||
|
|
||
| set -e | ||
|
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| # Copy CA certificate to `/etc/ssl/cert` | ||
| if ls *.crt 1> /dev/null 2>&1; then | ||
| sudo cp *.crt /usr/local/share/ca-certificates | ||
| sudo update-ca-certificates | ||
| fi | ||
|
|
||
| echo "Done!" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| { | ||
| // https://containers.dev/implementors/json_reference/ | ||
| "name": "sdtm.oak R-4.3 (RStudio) container", | ||
| "image": "ghcr.io/pharmaverse/sdtm.oak-4.3:latest", | ||
| // Install Dev Container Features. More info: https://containers.dev/features | ||
| "containerEnv": { | ||
| "ROOT": "true", | ||
| "PASSWORD": "rstudio", | ||
| "DISABLE_AUTH": "true", | ||
| "RENV_AUTOLOADER_ENABLED": "false" | ||
| }, | ||
| "features": { | ||
| "./ca-cert": {}, | ||
| "./arm64-repos": {}, | ||
| "ghcr.io/rocker-org/devcontainer-features/r-rig:1": { | ||
| "version": "none", | ||
| "vscodeRSupport": "full", | ||
| "installRadian": true, | ||
| "installVscDebugger": true | ||
| }, | ||
| "ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {}, | ||
| "ghcr.io/devcontainers/features/common-utils:2": { | ||
| "installZsh": true, | ||
| "configureZshAsDefaultShell": false, | ||
| "installOhMyZsh": true, | ||
| "username": "rstudio", | ||
| "upgradePackages": false | ||
| }, | ||
| "ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {} | ||
| }, | ||
| "overrideFeatureInstallOrder": [ | ||
| "./ca-cert", | ||
| "./arm64-repos", | ||
| "ghcr.io/devcontainers/features/common-utils", | ||
| "ghcr.io/rocker-org/devcontainer-features/renv-cache", | ||
| "ghcr.io/rocker-org/devcontainer-features/r-rig", | ||
| "ghcr.io/mikaello/devcontainer-features/modern-shell-utils" | ||
| ], | ||
| "init": true, | ||
| "overrideCommand": false, | ||
|
|
||
| "postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh", | ||
|
|
||
| "postAttachCommand": "rstudio || true", | ||
|
|
||
| "customizations": { | ||
| "codespaces": { | ||
| "repositories": { | ||
| "pharmaverse/mint": { | ||
| "permissions": "read-all" | ||
| }, | ||
| "pharmaverse/raw.synthetic.data": { | ||
| "permissions": "read-all" | ||
| } | ||
| } | ||
| }, | ||
| "vscode": { | ||
| "settings": { | ||
| "r.rterm.linux": "/usr/local/bin/radian", | ||
| "r.bracketedPaste": true, | ||
| "editor.bracketPairColorization.enabled": true, | ||
| "editor.guides.bracketPairs": "active" | ||
| }, | ||
| "extensions": [ | ||
| "vsls-contrib.codetour", | ||
| "GitHub.copilot", | ||
| "GitHub.copilot-chat", | ||
| // R extensions | ||
| "ikuyadeu.r", | ||
| "REditorSupport.r-lsp", | ||
| // Extra extension | ||
| "streetsidesoftware.code-spell-checker", | ||
| "eamodio.gitlens", | ||
| "cweijan.vscode-office", | ||
| "donjayamanne.githistory", | ||
| "GitHub.vscode-github-actions", | ||
| "GitHub.vscode-pull-request-github", | ||
| "GitHub.remotehub", | ||
| "alefragnani.Bookmarks", | ||
| "vscode-icons-team.vscode-icons" | ||
| ] | ||
| } | ||
| }, | ||
|
|
||
| // RStudio ports | ||
| "forwardPorts": [8787], | ||
| "portsAttributes": { | ||
| "8787": { | ||
| "label": "Rstudio", | ||
| "requireLocalPort": true, | ||
| "onAutoForward": "openBrowser" | ||
| } | ||
| }, | ||
| // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root | ||
| "remoteUser": "rstudio" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| #!/bin/bash | ||
|
|
||
| # move script rstudio into /usr/bin | ||
| sudo cp "$(pwd)/.devcontainer/rstudio.sh" /usr/bin/rstudio | ||
| sudo chmod +x /usr/bin/rstudio | ||
|
|
||
| # Restore renv and install staged dependencies | ||
| R -q -e 'renv::restore(lockfile = file.path("renv", "profiles", paste(R.version$major, substr(R.version$minor, 1, 1), sep = "."), "renv.lock")); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = ".", verbose = 1), verbose = 1);' | ||
|
|
||
| # Define rstudio default working directory | ||
| jq --arg folder "$(pwd)/" '. + { "initial_working_directory": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json |
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