Normalize line endings and clean up Docker build inputs - #10
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labkey-tchad wants to merge 15 commits into
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Normalize line endings and clean up Docker build inputs#10labkey-tchad wants to merge 15 commits into
labkey-tchad wants to merge 15 commits into
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Pin eol=lf for files COPY'd into images as Unix scripts (install.R, conf, Rprofile.site, cleanupSessionFiles.sh, rstudio-singleuser) so a fresh checkout is always correct, then remove the now-redundant dos2unix steps (and unused packages) from the affected Dockerfiles.
Separate files a Dockerfile COPYs into the image from host-side build tooling (make, README) by moving the former into a files/ subdirectory per image and updating COPY paths. Build context is unchanged.
Neither file has ever been referenced by any Dockerfile.
Also drop the now-dead rstudio-singleuser eol=lf rule from .gitattributes.
Now that Dockerfile build inputs consistently live under a files/ subdirectory per image, one path pattern covers them instead of an enumerated filename list, so new files added there are covered automatically.
Add images/labkey/Makefile with a target per R image (r, rsandbox, rstudio-base, rstudio). rsandbox, rstudio-base, and rstudio share a single R_VERSION variable (the R/RStudio version); r's Dockerfile pins its own Ubuntu base version, so it takes no version argument. rstudio depends on rstudio-base like the old scripts' pushd/popd did. Remove the now-redundant make and make.bat scripts and update rsandbox/README.md's build instructions accordingly.
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Leftover from the pre-Makefile build scripts; superseded by images/labkey/Makefile.
The single 'dockerfile: Dockerfile' step only linted a root-level Dockerfile that doesn't exist in this repo. Add recursive: true so it finds every file named Dockerfile anywhere in the tree (recursive mode globs on the literal filename, so it won't catch Dockerfile.echo), and add a second explicit step for python/nbconvert/Dockerfile.echo.
r/Dockerfile: - Consolidate the three apt-get RUN instructions into one (DL3059) and clean up /var/lib/apt/lists afterward (DL3009). - Add --no-install-recommends to the r-cran-* install (DL3015). - Fix 'ln -fs .../America/Los_Angeles/etc/localtime' — a missing space glued the source and destination into one argument, so ln was silently linking into the wrong place (SC2226). rstudio-base/Dockerfile: - Set SHELL with -o pipefail so the piped 'R --version | grep' RUN fails loudly on error instead of masking it (DL4006).
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Rationale
Several Dockerfiles ran
dos2unixat build time to repair CRLF line endings, and the files those Dockerfiles consumed were mixed in flat alongside host-side build tooling (make,README.md), making it hard to tell which files were build inputs. This PR fixes line endings at the source via.gitattributes(removing the need fordos2unix), reorganizes build inputs into a consistentfiles/subdirectory per image, and removes dead/unused files and images found along the way.Related Pull Requests
Changes
.gitattributeseol=lfrule (generalized to**/files/**) so build-input files always check out with LF, regardless of the checkout machine'score.autocrlf.dos2unixRUN steps (and unused packages) fromrsandbox,rsandbox-ver,rstudio,rstudio-base, andrstudio-singleuserDockerfiles.install.R,conf,Rprofile.site,cleanupSessionFiles.sh,entrypoint, etc.) into afiles/subdirectory, separate frommake/Makefile/README.md, updatingCOPYpaths accordingly.rstudio-base/initandrstudio-base/rstudio-singleuser— dead files never referenced by any Dockerfile.rstudio-singleuserandrsandbox-verimages.latestand addhadolint/shellcheck/yamllintvalidation workflows.