fetching package name from description file (#16)

* fetching package name from description file

* ignoring .RData and history

* fetching package name with R

* escaping $ for R

.github/workflows/create-publish-docker.yml

@@ -7,8 +7,9 @@ on:
 
 env:
   DOCKER_REGISTRY: ghcr.io             # where to register the image
-  PACKAGE: abn
   REPO_PATH: github.com:furrer-lab/devel-abn.git
+  # Set the path to the DESCRIPTION file in the R package you want to target
+  DESCRIPTION_FILE: ${{ vars.DESCRIPTION_FILE || './DESCRIPTION' }}
   JAGS: JAGS-4.3.2
   R_VERSION: R-devel
 
@@ -22,7 +23,7 @@ jobs:
 
     strategy:
       matrix:
-        target-os: ['fedora', 'debian']
+        target-os: ['fedora', ]  # 'debian']
         compiler: ['clang', ]  # , 'gcc']
         r-version: ['R-devel', ]
 
@@ -63,7 +64,7 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
           build-args: |
             FLAVOUR=${{ matrix.r-version }}
-            PACKAGE=${{ env.PACKAGE }}
+            DESCRIPTION_FILE=${{ env.DESCRIPTION_FILE }}
             REPO_PATH=${{ env.REPO_PATH }}
             JAGS=${{ env.JAGS}}
           secret-files: |

.gitignore

@@ -1,5 +1,7 @@
 # vim temp. files
 *.swp
+# R files
+.R*
 # renv files
 .Rprofile
 renv.lock

README.md

@@ -2,6 +2,8 @@
 
 This is a selection of Docker container that provide r-environments for testing purposes.
 
+## Configuration
+
 ### Releasing new versions
 New registry entries are triggered by tagging the specific commit.
 For the image to be built the tag needs to be a valid [semver](https://semver.org/), i.e. of the form `[MAJOR].[MINOR].[PATCH]` (e.g. `1.3.0`).

containers/debian/clang/R-devel/Dockerfile

@@ -2,6 +2,8 @@ FROM rhub/debian-clang-devel
 
 # defines the flavour (e.g. FLAVOUR=)
 ARG FLAVOUR
+# ARG PACKAGE
+ARG DESCRIPTION_FILE
 ARG REPO_PATH
 ARG SSH_PRIV_KEY 
 # # sets the date for the CRAN snapshot (e.g. BUILD_DATE=2023-12-20)
@@ -59,12 +61,16 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 RUN R -e "install.packages('INLA',repos=c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'), dep=TRUE)"
 
 ###
-# install all abn dependencies
+# install all package dependencies
 ###
+RUN dnf -y install \
+      git \
+      openssh-clients
 WORKDIR /root/
 # get a shallow copy of the target repository
+# Note: If the repository is private you must use a deploy token here (ssh key) 
 RUN --mount=type=secret,id=key,dst=/root/.ssh/key GIT_SSH_COMMAND="ssh -i /root/.ssh/key -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no" git clone --depth=1 git@$REPO_PATH target
 WORKDIR target/
 # get a list of all dependencies; install remaining packages
-# NOTE: abn is hardcoded here
-RUN R -e 'pckgs<-unique(renv::dependencies("abn")$Package);pres_pckgs<-installed.packages()[,"Package"];install.packages(pckgs[!(pckgs %in% pres_pckgs)])'
+# escape=\
+RUN R -e "package<-desc::desc(file='$DESCRIPTION_FILE')\$get_field('Package');pckgs<-unique(renv::dependencies(package)[,'Package']);pres_pckgs<-installed.packages()[,'Package'];install.packages(pckgs[!(pckgs %in% pres_pckgs)])"

containers/fedora/clang/R-devel/Dockerfile

@@ -2,8 +2,8 @@ FROM rhub/fedora-clang-devel
 
 # defines the flavour (e.g. FLAVOUR=)
 ARG FLAVOUR
-# Folder name in the root directory that contains the package (package name)
-ARG PACKAGE
+# ARG PACKAGE
+ARG DESCRIPTION_FILE
 ARG REPO_PATH
 ARG SSH_PRIV_KEY
 ARG JAGS
@@ -87,4 +87,5 @@ WORKDIR /root/
 RUN --mount=type=secret,id=key,dst=/root/.ssh/key GIT_SSH_COMMAND="ssh -i /root/.ssh/key -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no" git clone --depth=1 git@$REPO_PATH target
 WORKDIR target/
 # get a list of all dependencies; install remaining packages
-RUN R -e "pckgs<-unique(renv::dependencies('$PACKAGE')[,'Package']);pres_pckgs<-installed.packages()[,'Package'];install.packages(pckgs[!(pckgs %in% pres_pckgs)])"
+# escape=\
+RUN R -e "package<-desc::desc(file='$DESCRIPTION_FILE')\$get_field('Package');pckgs<-unique(renv::dependencies(package)[,'Package']);pres_pckgs<-installed.packages()[,'Package'];install.packages(pckgs[!(pckgs %in% pres_pckgs)])"