Add Docker-based CI environment image on GHCR to eliminate repeated dependency installation - #267
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ShixiangWang with Copilot wants to merge 3 commits into
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Add Docker-based CI environment image on GHCR to eliminate repeated dependency installation#267ShixiangWang with Copilot wants to merge 3 commits into
ShixiangWang with Copilot wants to merge 3 commits into
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- Add Dockerfile with pre-installed R, Python, Julia, and Quarto dependencies - Add .dockerignore to optimize Docker build context - Add build-env-image.yml workflow to build/push image to GHCR weekly - Update quarto-publish.yml to use the container image - Update quarto-publish-update-cache.yml to use the container image This eliminates 30-40 min of dependency installation per CI run by pulling a pre-built image with all 180+ R packages, Python, Julia, and Quarto already installed. Agent-Logs-Url: https://github.com/openbiox/Bizard/sessions/01dddaf6-2291-43d5-8b63-d55977dd7136 Co-authored-by: ShixiangWang <25057508+ShixiangWang@users.noreply.github.com>
…ing, add comments Agent-Logs-Url: https://github.com/openbiox/Bizard/sessions/01dddaf6-2291-43d5-8b63-d55977dd7136 Co-authored-by: ShixiangWang <25057508+ShixiangWang@users.noreply.github.com>
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Add Docker-based CI environment image on GHCR to eliminate repeated dependency installation
Apr 3, 2026
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CI runs take 1+ hours, with 30-40 min spent reinstalling 180+ R packages, Python, Julia, and Quarto from scratch every time. This adds a pre-built Docker image on GHCR so CI pulls it and only does differential dependency updates.
New files
Dockerfile— Based onrocker/r-ver:4. Installs all system libs, R packages viapak(CRAN/Bioconductor/GitHub Remotes), Python venv with pip deps, Julia 1.10.7 + CairoMakie/DataFrames/Statistics/QuartoNotebookRunner, Quarto latest + TinyTeX..github/workflows/build-env-image.yml— Builds and pushesghcr.io/openbiox/bizard-env:latest. Triggers: weekly (Sunday), on dependency file changes (DESCRIPTION,requirements.txt,Julia/Project.toml,Dockerfile), manual dispatch. Uses GHA cache for Docker layers..dockerignore— Excludes_site/,_freeze/,.git/, etc.Modified workflows
quarto-publish.yml/quarto-publish-update-cache.yml— Replace all setup actions (setup-r,setup-python,setup-julia,setup-r-dependencies,quarto-actions/setup) with:Differential dep steps (
pak::local_install_deps(),pip install,Pkg.instantiate()) are kept as fast no-ops when the image is current.First-time setup
After merge, manually trigger the "Build CI Environment Image" workflow once to create the initial image. Subsequent rebuilds are automatic.