Oops, re-implement multiple pythonpath

slurm_calibrate.sh options

bin/slurm_calibrate.sh

@@ -10,6 +10,7 @@ caltype=$6
 final=$7
 finalize=$8
 cluster_cores=$9
+notebook_python_path=$10
 
 echo "Running with the following parameters:"
 echo "Notebook path: $nb_path"
@@ -43,8 +44,8 @@ fi
 
 
 echo "Running notebook"
-${python_path} -m princess ${nb_path} --save --on-error-resume-next
-${python_path} -m nbconvert --to rst --TemplateExporter.exclude_input=True ${nb_path}
+${notebook_python_path} -m princess ${nb_path} --save --on-error-resume-next
+${notebook_python_path} -m nbconvert --to rst --TemplateExporter.exclude_input=True ${nb_path}
 
 # stop the cluster if requested
 if [ "${ipcluster_profile}" != "NO_CLUSTER" ]

src/xfel_calibrate/calibrate.py

@@ -757,14 +757,15 @@ def concurrent_run(
     srun_base += [
         os.path.join(PKG_DIR, "bin", "slurm_calibrate.sh"),  # path to helper sh
         os.path.abspath(nbpath),  # path to notebook
-        user_venv + "/bin/python" if user_venv else python_path,  # path to python
+        python_path,  # path to python
         cluster_profile,
         '"{}"'.format(base_name.upper()),
         '"{}"'.format(args["detector"].upper()),
         '"{}"'.format(args["type"].upper()),
         "FINAL" if final_job else "NONFINAL",
         "{}/finalize.py".format(os.path.abspath(temp_path)),
-        str(cluster_cores)
+        str(cluster_cores),
+        user_venv + "/bin/python" if user_venv else python_path  # used for nb execution
     ]
 
     output = check_output(srun_base).decode('utf8')