First stable version

- PATH bug fixed (injected in userconfig.sh)
- PYTHONPATH being unset
- internal ipykernel installed

swan-cern/Dockerfile

@@ -6,7 +6,6 @@ LABEL maintainer="[email protected]"
 ARG NB_UID="1000"
 ARG BUILD_TAG=daily
 ENV VERSION_DOCKER_IMAGE=$BUILD_TAG
-ENV PATH="/srv/singleuser/bin:${PATH}"
 
 RUN echo "Building swan-cern image with tag ${VERSION_DOCKER_IMAGE} from parent tag ${VERSION_PARENT}."
 
@@ -42,9 +41,9 @@ USER root
 
 # Crate a new bin path for allowing the user to run it with an alias
 # Add script for virtual environment creation
-RUN mkdir /srv/singleuser/bin
-RUN mv /srv/singleuser/makenv.sh /srv/singleuser/bin/makenv
-RUN chmod u+x /srv/singleuser/bin/makenv
+RUN mkdir /srv/singleuser/bin && \
+    mv /srv/singleuser/makenv.sh /srv/singleuser/bin/makenv && \
+    chmod +x /srv/singleuser/bin/makenv
 
 # HTCondor requirements
 RUN dnf install -y \

swan-cern/scripts/others/makenv.sh

@@ -16,7 +16,7 @@ _log () {
 NAME_ENV=$1
 REQ_PATH=$2
 
-# Help page
+# Help page (passing -h as first argument)
 if [ "$NAME_ENV" = "-h" ]; then
     _log "This script builds a virtual environment."
     _log "Usage: makenv <virtualenv_name> <requirements_file>"
@@ -28,44 +28,50 @@ fi
 # Checks if a name for the environment is given
 if [ -z "$NAME_ENV" ]; then
     _log "ERROR: No virtual environment name provided."
-    exit 0
+    exit 1
 fi
 
 # Checks if a requirements file is given
 if [ -z "$REQ_PATH" ]; then
     _log "ERROR: No requirements file provided."
-    exit 0
+    exit 1
 fi
 
 # Checks if the requirements file is found
 if [ ! -f "$REQ_PATH" ]; then
     _log "ERROR: Requirements file not found."
-    exit 0
+    exit 1
 fi
 
 # Checks if an environment with the same name was already created
 if [ -d "/home/$USER/${NAME_ENV}" ]; then
-    _log "ERROR: Virtual environment already exists. Skipping..."
-    exit 0
+    _log "ERROR: Virtual environment already exists."
+    exit 1
 fi
 
 # Create virtual environment using Python venv
-_log "WARNING: Creating ${NAME_ENV} virtual environment..."
-
-python3 -m venv /home/$USER/${NAME_ENV}
+_log "Creating ${NAME_ENV} virtual environment..."
+python3 -m venv /home/$USER/${NAME_ENV} --copies
 
 # Activate the created virtual environment
-_log "WARNING: Activating virtual environment..."
-
+_log "Activating virtual environment..."
 source /home/$USER/${NAME_ENV}/bin/activate
 
-# Install kernel (within the environment), so it can be ran in Jupyter 
-/home/$USER/${NAME_ENV}/bin/python3 -m ipykernel install --name ${NAME_ENV} --display-name "Python (${NAME_ENV})" --prefix /home/$USER/.local
+# Unset PYTHONPATH to avoid that the virtual environment uses the system packages
+unset PYTHONPATH
+
+# Ensure pip is installed on venv so ipykernel and requirements can be installed
+python3 -m ensurepip --upgrade
 
-# Configure venv kernel so Jupyter can recognise it as a proper Python language
-/home/$USER/${NAME_ENV}/bin/python3 -I /srv/singleuser/configure_kernels_and_terminal.py
+# Install ipykernel so the kernel can be used in Jupyter
+pip3 install ipykernel -q 
+
+# Install kernel (within the environment), so it can be ran in Jupyter 
+python3 -m ipykernel install --name ${NAME_ENV} --display-name "Python (${NAME_ENV})" --prefix /home/$USER/.local
 
 # Install the given requirements
-_log "WARNING: Installing packages from ${REQ_PATH}..."
+_log "Installing packages from ${REQ_PATH}..."
+pip3 install -q -r ${REQ_PATH}
 
-/home/$USER/${NAME_ENV}/bin/python3 -m pip install -r ${REQ_PATH}
+_log "Virtual environment ${NAME_ENV} created successfully."
+_log "WARNING: You may need to refresh the page"

swan/scripts/others/userconfig.sh

@@ -32,6 +32,9 @@ ln -s $LOCAL_NB_NBEXTENSIONS $NBCONFIG/notebook.json
 START_TIME_SETUP_LCG=$( date +%s.%N )
 export JUPYTER_DATA_DIR=$LCG_VIEW/share/jupyter 
 
+# Path for scripts to build custom user environments (e.g. makenv.sh)
+export PATH="${PATH}:/srv/singleuser/bin"
+
 # Setup LCG
 source $LCG_VIEW/setup.sh