fix: global git credentials and some other stuff

README.md

@@ -29,6 +29,21 @@ If you would like to add the ability to launch RenkuLab interactive environments
 to your own pre-existing images, see the **Adding renku to your own images** section
 below.
 
+
+## Container initialization
+
+Sometimes certain actions need to be performed on container start-up to prepare
+the environment. Some of these are carried out already in the `entrypoint.sh`
+script in the base image, but if you extend the image you may want to add your
+own. This can be done by adding a `post-init.sh` script to the root directory of
+the container. It must be executable by a non-privileged user because it will
+run with the user restrictions of the container.
+
+Projects using the base images may additionally place a `post-init.sh` script in
+the root directory of the _project_. This script will also run upon initialization
+of the container, but _after_ the `/entrypoint.sh` and `/post-init.sh` scripts.
+
+
 ## Naming Conventions
 
 You can find these base images on
@@ -148,10 +163,6 @@ docker build -t <image-tag> \
   https://github.com/SwissDataScienceCenter/renkulab-docker.git#docker/r
 ```
 
-
-
-
-
 ## Contributing
 
 If you have any suggestions for different languages or base images you would like

docker/py/entrypoint.sh

@@ -24,11 +24,25 @@ find /tmp/renku-env -not -path '*.git*' -type f -print0 | xargs --null -I{} sh -
 
 if [[ -v CI_PROJECT ]];
 then
+    # set the global git credentials
+    git config --global credential.helper "store --file=/work/${CI_PROJECT}/.git/credentials"
+
+    # link to the home work directory
     ln -sf /work/${CI_PROJECT} ~/work
 fi
 
 # install git hooks
 ~/.local/bin/renku githooks install || true
 
+# run the post-init script in the root directory (i.e. coming from the image)
+if [ -f "/post-init.sh" ]; then
+    /post-init.sh
+fi
+
+# run the post-init script in the project directory
+if [ -f "./post-init.sh" ]; then
+    ./post-init.sh
+fi
+
 # run the command
 $@

docker/r/Dockerfile

@@ -67,6 +67,7 @@ RUN apt-get update --fix-missing && \
 COPY --from=renku_base /opt/conda /opt/conda
 COPY --from=renku_base --chown=rstudio:rstudio \
     /home/jovyan/ /home/rstudio/
+COPY --from=renku_base /entrypoint.sh /entrypoint.sh
 
 # set permissions of the R library directory to be editable by NB_USER
 ADD fix-permissions.sh /usr/local/bin
@@ -90,7 +91,7 @@ RUN R --quiet -e "install.packages('IRkernel')" && \
 
 RUN  echo "source ~/.bashrc" >> ~/.bash_profile
 
-COPY entrypoint.sh /entrypoint.sh
+COPY post-init.sh /post-init.sh
 ENTRYPOINT [ "/tini", "--", "/entrypoint.sh" ]
 CMD [ "jupyterhub-singleuser" ]
 

docker/r/entrypoint.sh → docker/r/post-init.sh

@@ -8,14 +8,6 @@ for var in ${VariableArray[*]}; do
     fi
 done
 
-# Setup git user
-if [ -z "$(git config --global --get user.name)" ]; then
-    git config --global user.name "$GIT_AUTHOR_NAME"
-fi
-if [ -z "$(git config --global --get user.email)" ]; then
-    git config --global user.email "$EMAIL"
-fi
-
 # add a symlink to the project directory in /home/rstudio
 [ -n "$CI_PROJECT" ] && ln -s /work/${CI_PROJECT} /home/rstudio
 
@@ -41,23 +33,3 @@ fi
 mkdir -p /home/rstudio/.rstudio/projects_settings
 echo /home/rstudio/${CI_PROJECT}/${CI_PROJECT}.Rproj | tee /home/rstudio/.rstudio/projects_settings/next-session-project
 chown -R rstudio:root /home/rstudio/.rstudio/projects_settings
-
-#
-# copy the environment from renku-env repo
-#
-
-# clone the repo
-proto=$(echo $GITLAB_URL | sed -e's,^\(.*://\).*,\1,g')
-url=$(echo ${GITLAB_URL/$proto/})
-user=$(echo ${CI_REPOSITORY_URL/$proto/} | grep @ | cut -d@ -f1)
-
-git clone --depth 1 ${proto}${user}@${url}/${JUPYTERHUB_USER}/renku-env.git /tmp/renku-env || true
-
-# append the contents of all the files to same files in ${HOME}
-find /tmp/renku-env -not -path '*.git*' -type f -print0 | xargs --null -I{} sh -c 'cat {} >> ${HOME}/$(basename "{}")' || true
-
-# install git hooks
-~/.local/bin/renku githooks install || true
-
-# run the command
-$@