Docker: install aiida in conda environment, fix .bashrc (#3745)

fixes #3739 

In the latest update of the aiida-prerequisites image, python is provided
within conda environment. Respectively, this PR adapts aiida-core image
to use python from conda. Also, it fixes autocompletion enabling in user's
.bashrc file

.docker/opt/configure-aiida.sh

@@ -6,11 +6,26 @@
 set -x
 
 # Environment.
-reentry scan
 export SHELL=/bin/bash
 
+# Activate conda.
+__conda_setup="$('/opt/conda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
+if [ $? -eq 0 ]; then
+    eval "$__conda_setup"
+else
+    if [ -f "/opt/conda/etc/profile.d/conda.sh" ]; then
+        . "/opt/conda/etc/profile.d/conda.sh"
+    else
+        export PATH="/opt/conda/bin:$PATH"
+    fi
+fi
+unset __conda_setup
+
+# Very important to run after conda activation, otherwise AiiDA won't work.
+reentry scan
+
 # Setup AiiDA autocompletion.
-grep _VERDI_COMPLETE .bash_profile &> /dev/null || echo 'eval "$(_VERDI_COMPLETE=source verdi)"' >> /home/$SYSTEM_USER/.bashrc
+grep _VERDI_COMPLETE /home/$SYSTEM_USER/.bashrc &> /dev/null || echo 'eval "$(_VERDI_COMPLETE=source verdi)"' >> /home/$SYSTEM_USER/.bashrc
 
 # Check if user requested to set up AiiDA profile (and if it exists already)
 if [[ $SETUP_DEFAULT_PROFILE == true ]] && ! verdi profile show $PROFILE_NAME &> /dev/null; then
@@ -57,4 +72,4 @@ verdi profile show || echo "The default profile is not set."
 verdi database migrate --force || echo "Database migration failed."
 
 # Daemon will start only if the database exists and is migrated to the latest version.
-verdi daemon start || echo "AiiDA daemon is not running."
+verdi daemon start || echo "AiiDA daemon is not running."

.github/workflows/ci.yml

@@ -176,14 +176,14 @@ jobs:
         sudo apt-get update
         sudo apt-get install docker-ce
 
-    - name: Build the aiida-core image and run it
-      run: |
+    - name: Build the aiida-core image
+      run:
         docker build -t aiida-core .
-        docker run -d aiida-core
 
-    - name: Check that default AiiDA profile was set up
+    - name: Run aiida-core image and test the default aiida profile and localhost computer.
       run: |
-        export DOCKERID=`docker ps -qf 'ancestor=aiida-core'`
+        export DOCKERID=`docker run -d aiida-core`
         docker exec --tty $DOCKERID wait-for-services
+        docker logs $DOCKERID
         docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'verdi profile show default'
         docker exec --tty --user aiida $DOCKERID /bin/bash -l -c 'verdi computer show localhost'

Dockerfile

@@ -21,5 +21,3 @@ COPY .docker/my_init.d/configure-aiida.sh /etc/my_init.d/40_configure-aiida.sh
 
 # Use phusion baseimage docker init system.
 CMD ["/sbin/my_init"]
-
-#EOF