Clean up repository

.gitattributes

@@ -1 +1,7 @@
 * text=auto
+
+# Files under a files/ directory are COPY'd into Docker images and
+# run/sourced as Unix scripts. Force LF line endings on checkout so a
+# fresh enlistment is always correct, regardless of the checkout
+# machine's core.autocrlf setting.
+**/files/** text eol=lf

.github/workflows/hadolint.yml

@@ -6,6 +6,9 @@ name: hadolint
     branches:
       - develop
 
+permissions:
+  contents: read
+
 jobs:
   hadolint:
     name: hadolint

.github/workflows/shellcheck.yml

@@ -0,0 +1,19 @@
+---
+name: 'Run Shellcheck'
+
+"on":
+  - pull_request
+
+permissions:
+  contents: read
+
+jobs:
+  shellcheck:
+    name: Shellcheck
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Run ShellCheck
+        uses: ludeeus/action-shellcheck@2.0.0

.github/workflows/validate_pr.yml

@@ -10,6 +10,9 @@ name: PR Validation
       - reopened
       - ready_for_review
 
+permissions:
+  contents: read
+
 jobs:
   validate_pr:
     if: github.event.pull_request.head.repo.owner.login == 'LabKey'

.github/workflows/yamllint.yml

@@ -4,6 +4,9 @@ name: 'Yamllint GitHub Actions'
 "on":
   - pull_request
 
+permissions:
+  contents: read
+
 jobs:
   yamllint:
     name: 'Yamllint'

images/labkey/Makefile

@@ -0,0 +1,31 @@
+# Build the LabKey R Docker images.
+#
+# Usage:
+#   make <target> [R_VERSION=<tag>]
+#
+# Targets:
+#   r             labkey/r            (from ubuntu; version is fixed in the Dockerfile)
+#   rsandbox      labkey/rsandbox     (from rocker/r-ver:$(R_VERSION))
+#   rstudio-base  labkey/rstudio-base (from rocker/rstudio:$(R_VERSION))
+#   rstudio       labkey/rstudio      (from labkey/rstudio-base:$(R_VERSION); builds rstudio-base first)
+#   all           build every image above
+#
+# Requires Docker 17.05.0 or greater.
+
+.PHONY: all r rsandbox rstudio-base rstudio
+
+R_VERSION ?= latest
+
+all: r rsandbox rstudio-base rstudio
+
+r:
+	docker build -t labkey/r:latest r
+
+rsandbox:
+	docker build --build-arg VERSION=$(R_VERSION) -t labkey/rsandbox:$(R_VERSION) rsandbox
+
+rstudio-base:
+	docker build --build-arg VERSION=$(R_VERSION) -t labkey/rstudio-base:$(R_VERSION) rstudio-base
+
+rstudio: rstudio-base
+	docker build --build-arg VERSION=$(R_VERSION) -t labkey/rstudio:$(R_VERSION) rstudio

images/labkey/r/Dockerfile

@@ -1,9 +1,9 @@
-ARG VERSION=18.04
+ARG VERSION=24.04
 FROM ubuntu:${VERSION}
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends apt-transport-https apt-utils software-properties-common && \
-    apt-get install -y --no-install-recommends build-essential dos2unix libopenblas-dev libssl-dev libxml2-dev nano pandoc procps xvfb x11-common && \
+    apt-get install -y --no-install-recommends build-essential libopenblas-dev libssl-dev libxml2-dev nano pandoc procps xvfb x11-common && \
     DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
     r-base \
     r-cran-bitops \
@@ -29,7 +29,7 @@ RUN apt-get update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-COPY install.R /tmp/
+COPY files/install.R /tmp/
 RUN R --vanilla -f /tmp/install.R
 
 RUN ln -fs /usr/share/zoneinfo/America/Los_Angeles /etc/localtime && \

images/labkey/rsandbox/Dockerfile

@@ -1,9 +1,9 @@
-ARG VERSION=3.6.3
+ARG VERSION=latest
 FROM rocker/r-ver:${VERSION}
 
 RUN apt-get update && \
 	apt-get install -y --no-install-recommends apt-transport-https apt-utils software-properties-common && \
-	apt-get install -y --no-install-recommends build-essential dos2unix libopenblas-dev libxml2-dev nano pandoc procps xvfb x11-common libuv1-dev && \
+	apt-get install -y --no-install-recommends build-essential libopenblas-dev libxml2-dev nano pandoc procps xvfb x11-common libuv1-dev && \
 	apt-get install -y --no-install-recommends sudo && \
 	apt-get install -y --no-install-recommends  \
 		curl libcurl4-openssl-dev \
@@ -28,9 +28,8 @@ RUN useradd docker || true \
 	&& chmod -R 775 /home/docker || true
 
 
-COPY install.R /
-RUN dos2unix install.R && \
-    R --no-site-file -f install.R &&  \
+COPY files/install.R /
+RUN R --no-site-file -f install.R &&  \
     chmod -R 755 /usr/local/lib/R/site-library
 
 CMD ["su", "docker", "-c", "/bin/bash"]

images/labkey/rsandbox/README.md

@@ -3,11 +3,11 @@ labkey/rsandbox:latest
 
 Dockerfile for building Dockerized LabKey R image using with the latest R release version. 
 
-Run `./make` to generate R image `labkey/rsandbox:latest`. 
+Run `make rsandbox` from `images/labkey/` to generate R image `labkey/rsandbox:latest`.
 
-Note that actual R version might differ based on latest R version at the time the image is built. 
+Note that actual R version might differ based on latest R version at the time the image is built.
 
-To tag the image with the actual R version at the time of build, change `latest` in `make` file to the latest R version, for example: `3.5.1`.
+To tag the image with the actual R version at the time of build, pass `R_VERSION`, for example: `make rsandbox R_VERSION=4.6.1`.
 
 For more information, see:
 

images/labkey/rstudio-base/Dockerfile

@@ -1,28 +1,25 @@
-ARG VERSION=4.0.5
+ARG VERSION=latest
 FROM rocker/rstudio:${VERSION}
 
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends apt-utils && \
-    apt-get install -y --no-install-recommends dos2unix nano procps libxml2-dev xvfb zlib1g-dev libuv1-dev && \
+    apt-get install -y --no-install-recommends nano procps libxml2-dev xvfb zlib1g-dev libuv1-dev && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-COPY conf /etc/cont-init.d/
-RUN dos2unix /etc/cont-init.d/conf
+COPY files/conf /etc/cont-init.d/
 
-COPY install.R /
+COPY files/install.R /
 RUN R --no-site-file -f install.R &&  \
     chmod -R 755 /usr/local/lib/R/library && \
     chmod -R 755 /usr/local/lib/R/site-library
 
-COPY Rprofile.site /Rprofile.site.tmp
-RUN dos2unix /Rprofile.site.tmp && \
-    cat /Rprofile.site.tmp >> /usr/local/lib/R/etc/Rprofile.site && \
+COPY files/Rprofile.site /Rprofile.site.tmp
+RUN cat /Rprofile.site.tmp >> /usr/local/lib/R/etc/Rprofile.site && \
     rm /Rprofile.site.tmp
 RUN echo "R_LIBS_USER=~/R/$(R --version | grep -Eo '[0-9]+[.]+[0-9]+')/library" >> /usr/local/lib/R/etc/Renviron
 
-COPY cleanupSessionFiles.sh /
-RUN dos2unix /cleanupSessionFiles.sh && \
-    chmod 755 /cleanupSessionFiles.sh
+COPY files/cleanupSessionFiles.sh /
+RUN chmod 755 /cleanupSessionFiles.sh

images/labkey/rstudio/Dockerfile

@@ -9,7 +9,6 @@ RUN apt-get update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-COPY install.R /
-RUN dos2unix install.R && \
-    R --no-site-file -f install.R &&  \
+COPY files/install.R /
+RUN R --no-site-file -f install.R &&  \
     chmod -R 755 /usr/local/lib/R/site-library

python/nbconvert/Dockerfile

@@ -6,12 +6,12 @@ RUN apt-get install -y jq
 
 RUN python3 -m pip install --upgrade pip
 RUN pip install jupyterlab
-COPY requirements.txt /requirements.txt
+COPY files/requirements.txt /requirements.txt
 RUN pip install -r /requirements.txt
 
 RUN ln -fs /usr/share/zoneinfo/America/Los_Angeles/etc/localtime && dpkg-reconfigure --frontend noninteractive tzdata
 
-COPY ReportConfig.py /
-COPY entrypoint exec_runreport_tar execute /
+COPY files/ReportConfig.py /
+COPY files/entrypoint files/exec_runreport_tar files/execute /
 RUN chmod 777 /entrypoint /exec_runreport_tar /execute
 ENTRYPOINT /entrypoint