feat: make images fully amalthea ready

The goal of this is to move maintain as much of the current bahaviour
with Amalthea-based sessions, while also keeping the images backwards
compatible for now.

docker/julia/post-init.sh

@@ -2,10 +2,21 @@
 
 # Slip in a replacement for the julia command that sets uses the project
 # environment rather than the root environment
+
+# Pre amalthea
 if [[ -v CI_PROJECT ]];
 then
     ln -sf /work/${CI_PROJECT} ~/work
     echo '#!/usr/bin/env bash' > ~/.local/bin/julia
     printf '/usr/local/bin/julia --project=/work/%s/ "$@"\n' ${CI_PROJECT} >> ~/.local/bin/julia
     chmod u+x ~/.local/bin/julia
 fi
+
+# With amalthea
+if [[ -v PROJECT_NAME && -v NOTEBOOK_DIR ]];
+then
+    echo '#!/usr/bin/env bash' > ~/.local/bin/julia
+    printf '/usr/local/bin/julia --project=%s/ "$@"\n' ${NOTEBOOK_DIR} >> ~/.local/bin/julia
+    chmod u+x ~/.local/bin/julia
+fi
+

docker/py/entrypoint.sh

@@ -1,37 +1,26 @@
 #!/bin/bash
 
-# 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
-
-# configure global git credentials
-if [[ -v CI_PROJECT ]];
+if [[ -v GIT_AUTHOR_NAME && -v EMAIL && -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
+    # 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
+
+    # configure global git credentials
+    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
 fi
 
-#
-# 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 ${GITLAB_URL}/${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
 

docker/py/git-config.bashrc

@@ -1,8 +1,8 @@
 
 # Setup git user
-if [ -z "$(git config --global --get user.name)" ]; then
+if [[ -z "$(git config --global --get user.name)" && -v GIT_AUTHOR_NAME ]]; then
     git config --global user.name "$GIT_AUTHOR_NAME"
 fi
-if [ -z "$(git config --global --get user.email)" ]; then
+if [[ -z "$(git config --global --get user.email)" && -v EMAIL ]]; then
     git config --global user.email "$EMAIL"
 fi

docker/r/post-init.sh

@@ -1,20 +1,32 @@
 #!/bin/bash
 
 # Copy the relevant system environment variables to the R-specific locations
+# Note: In the case of Amalthea-based sessions none of these env variables are
+#       defined and nothing will happen. This is ok as we can deal without global
+#       git config.
 VariableArray=("GIT_COMMITTER_NAME"  "GIT_AUTHOR_NAME"  "EMAIL")
 for var in ${VariableArray[*]}; do
     if [ -n "${!var}" ]; then
         echo $var=${!var} >> ${HOME}/.Renviron
     fi
 done
 
-# add a symlink to the project directory in /home/rstudio
-[ -n "$CI_PROJECT" ] && ln -s /work/${CI_PROJECT} /home/rstudio
+if [[ -v NOTEBOOK_DIR && -v PROJECT_NAME ]];
+then
+    RPROJ_FILE_PATH=${NOTEBOOK_DIR}/${PROJECT_NAME}.Rproj
+fi
 
+if [[ -v CI_PROJECT ]];
+then
+    # add a symlink to the project directory in /home/rstudio
+    [ -n "$CI_PROJECT" ] && ln -s /work/${CI_PROJECT} /home/rstudio
+    RPROJ_FILE_PATH=${HOME}/${CI_PROJECT}/${CI_PROJECT}.Rproj
+fi
 
 # configure rstudio to open the rpath project
-if [[ ! -f /home/rstudio/${CI_PROJECT}/${CI_PROJECT}.Rproj ]]; then
-cat > /home/rstudio/${CI_PROJECT}/${CI_PROJECT}.Rproj <<- EOM
+if [[ -v RPROJ_FILE_PATH && ( ! -f $RPROJ_FILE_PATH ) ]];
+then
+cat > $RPROJ_FILE_PATH <<- EOF
 Version: 1.0
 
 RestoreWorkspace: Default
@@ -28,8 +40,11 @@ Encoding: UTF-8
 
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
-EOM
+EOF
+fi
+
+mkdir -p ${HOME}/.rstudio/projects_settings
+if [[ -v RPROJ_FILE_PATH ]];
+then
+    echo $RPROJ_FILE_PATH >> ${HOME}/.rstudio/projects_settings/next-session-project
 fi
-mkdir -p /home/rstudio/.rstudio/projects_settings
-echo /home/rstudio/${CI_PROJECT}/${CI_PROJECT}.Rproj | tee /home/rstudio/.rstudio/projects_settings/next-session-project
-chown -R rstudio:root /home/rstudio/.rstudio/projects_settings

docker/vnc/post-init.sh

@@ -1,6 +1,13 @@
 #!/bin/bash
 
 # Make the default terminal folder the project folder in the vnc
-echo "cd /work/${CI_PROJECT}" >> ~/.bashrc
+if [[ -v CI_PROJECT ]]
+then
+    echo "cd /work/${CI_PROJECT}" >> ~/.bashrc
+fi
+if [[ -v NOTEBOOK_DIR ]]
+then
+    echo "cd ${NOTEBOOK_DIR}" >> ~/.bashrc
+fi
 # Turn the bell off
 echo "bind 'set bell-style none'" >> ~/.bashrc