build: use GitHub PAT to install R packages on GitHub

.github/workflows/build-test-publish.yml

@@ -109,6 +109,7 @@ jobs:
           context: ${{ inputs.image }}
           platforms: linux/amd64
           build-args: ${{ inputs.build-args }}
+          secrets: "github_token=${{ secrets.GITHUB_TOKEN }}"
           tags: localhost:5000/${{ github.repository_owner }}/${{ inputs.image }}:amd64
           cache-from: type=registry,ref=ghcr.io/${{ github.repository_owner }}/${{ inputs.image }}
           cache-to: type=registry,ref=localhost:5000/${{ github.repository_owner }}/${{ inputs.image }}:buildcache-amd64,mode=max

CONTRIBUTING.md

@@ -0,0 +1,17 @@
+# Contributing to this project
+
+## Prerequisites
+
+These are required system dependencies for this project:
+
+- [Git](https://git-scm.com/)
+- [GitHub CLI](https://cli.github.com/)
+- [Docker](https://docs.docker.com/get-docker/)
+- [GNU Make](https://www.gnu.org/software/make/)
+
+## Setup
+
+1. Fork/Clone this repository
+2. Sign into GitHub CLI: `gh auth login`
+3. Ensure `buildx` is enabled: `docker buildx ls`
+4. Use `make` to get a list of available commands

Makefile

@@ -14,6 +14,8 @@ DS_RUN_ARGS?=
 export DOCKER_BUILDKIT:=1
 # Activate experimental mode
 export DOCKER_CLI_EXPERIMENTAL=enabled
+# Load the GitHub Personal Access Token from the environment
+export github_token:=$(shell gh auth token)
 
 # Check if the local registry is running
 LOCAL_REGISTRY_UP := $(shell docker ps --filter name=registry --format "{{.Names}}" | grep -q registry && echo true || echo false)
@@ -44,6 +46,7 @@ define build_image
 	@echo
 	docker buildx build $(COMMON_BUILD_ARGS) $(BUILD_ARGS) \
 		--platform $(1) \
+		--secret id=github_token \
 		--tag "$(LOCAL_REGISTRY)/$(DS_OWNER)/$(notdir $(2))" \
 		--push \
 		"./$(notdir $(2))"

essentials-notebook/Dockerfile

@@ -52,7 +52,8 @@ RUN --mount=type=cache,target="${CONDA_DIR}/pkgs",uid=${NB_UID},sharing=locked \
 # install all other R packages
 ARG R_REQUIREMENTS
 RUN --mount=type=bind,source="${R_REQUIREMENTS}",target=/tmp/requirements.r \
-  Rscript /tmp/requirements.r
+  --mount=type=secret,id=github_token,uid=${NB_UID} \
+  GITHUB_PAT=$(cat /run/secrets/github_token) Rscript /tmp/requirements.r
 
 
 # pre-shared-libs

r-notebook/Dockerfile

@@ -88,9 +88,10 @@ RUN --mount=type=cache,target=${CONDA_DIR}/pkgs,uid=${NB_UID},sharing=locked \
 
 # install all other R packages
 ARG R_REQUIREMENTS
+ENV CARGO_NET_GIT_FETCH_WITH_CLI=true
 RUN --mount=type=bind,source="${R_REQUIREMENTS}",target=/tmp/requirements.r \
-  export CARGO_NET_GIT_FETCH_WITH_CLI=true \
-  && Rscript /tmp/requirements.r
+  --mount=type=secret,id=github_token,uid=${NB_UID} \
+  GITHUB_PAT=$(cat /run/secrets/github_token) Rscript /tmp/requirements.r
 
 
 # pre-shared-libs