Clean up how slurm_calibrate.sh is called

bin/slurm_calibrate.sh

@@ -7,24 +7,23 @@ ipcluster_profile=$3
 notebook=$4
 detector=$5
 caltype=$6
-final=$7
-finalize=$8
-cluster_cores=$9
-notebook_python_path=${10}
+finalize=$7
+cluster_cores=$8
+cal_python_path=$9
 
 echo "Running with the following parameters:"
 echo "Notebook path: $nb_path"
 echo "Python path: $python_path"
+echo "Calibration Python: $cal_python_path"
 echo "IP-Cluster profile: $ipcluster_profile"
 echo "notebook: $notebook"
 echo "detector: $detector"
 echo "caltype: $caltype"
-echo "final: $final"
 echo "finalize: $finalize"
 echo "cluster_cores: $cluster_cores"
 echo "job ID: $SLURM_JOB_ID"
 
-export CAL_NOTEBOOK_NAME=$notebook
+export CAL_NOTEBOOK_NAME="$notebook"
 
 # set-up enviroment
 source /etc/profile.d/modules.sh
@@ -44,8 +43,8 @@ fi
 
 
 echo "Running notebook"
-${notebook_python_path} -m princess ${nb_path} --save --on-error-resume-next
-${notebook_python_path} -m nbconvert --to rst --TemplateExporter.exclude_input=True ${nb_path}
+${python_path} -m princess ${nb_path} --save --on-error-resume-next
+${cal_python_path} -m nbconvert --to rst --TemplateExporter.exclude_input=True ${nb_path}
 
 # stop the cluster if requested
 if [ "${ipcluster_profile}" != "NO_CLUSTER" ]
@@ -56,7 +55,7 @@ then
     rm -rf $profile_path
 fi
 
-if [ "${final}" == "FINAL" ]
+if [ -n "${finalize}" ]
 then
-   ${python_path} ${finalize} $SLURM_JOB_ID
+   ${cal_python_path} ${finalize} $SLURM_JOB_ID
 fi

src/xfel_calibrate/calibrate.py

@@ -580,20 +580,21 @@ def set_figure_format(nb, enable_vector_format):
         cell.source += "\n%config InlineBackend.figure_formats = ['svg']\n"
 
 
-def create_finalize_script(fmt_args, temp_path, job_list):
+def create_finalize_script(fmt_args, temp_path, job_list) -> str:
     """
     Create a finalize script to produce output report
     :param fmt_args: Dictionary of fmt arguments
     :param temp_path: Path to temporary folder to run slurm job
     :param job_list: List of slurm jobs
+    :return: The path of the created script
     """
     tmpl = Template("""\
                     #!/usr/bin/env python3
-                    import sys
+                    import os
                     from xfel_calibrate.finalize import finalize
 
                     finalize(joblist={{joblist}},
-                             finaljob=sys.argv[1],
+                             finaljob=os.environ.get('SLURM_JOB_ID', ''),
                              run_path='{{run_path}}',
                              out_path='{{out_path}}',
                              project='{{project}}',
@@ -616,6 +617,7 @@ def create_finalize_script(fmt_args, temp_path, job_list):
     # executed and writable for user, readable for user, group and others
     all_stats = stat.S_IXUSR | stat.S_IWUSR | stat.S_IRUSR | stat.S_IRGRP | stat.S_IROTH
     os.chmod(f_name, all_stats)
+    return f_name
 
 
 def save_executed_command(run_tmp_path, version):
@@ -742,7 +744,9 @@ def concurrent_run(
 
     # add finalization to the last job
     if final_job:
-        create_finalize_script(fmt_args, temp_path, job_list)
+        finalize_script = create_finalize_script(fmt_args, temp_path, job_list)
+    else:
+        finalize_script = ''
 
     # then run an sbatch job
     srun_base = []
@@ -752,19 +756,21 @@ def concurrent_run(
 
     if user_venv:
         print(f"Running job in user venv at {user_venv}\n")
+        python = str(user_venv / 'bin' / 'python')
+    else:
+        python = python_path  # From settings.py, default is sys.executable
 
     srun_base += [
         os.path.join(PKG_DIR, "bin", "slurm_calibrate.sh"),  # path to helper sh
         os.path.abspath(nbpath),  # path to notebook
-        python_path,  # path to python
+        python,  # path to python to run notebook (& ipcluster)
         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)),
+        base_name.upper(),
+        args["detector"].upper(),
+        args["type"].upper(),
+        finalize_script,
         str(cluster_cores),
-        user_venv + "/bin/python" if user_venv else python_path  # used for nb execution
+        sys.executable,  # Python for calib machinery (nbconvert, finalize)
     ]
 
     output = check_output(srun_base).decode('utf8')

src/xfel_calibrate/finalize.py

@@ -403,7 +403,8 @@ def finalize(joblist, finaljob, run_path, out_path, project, calibration,
     prepare_plots(run_path)
 
     # Archiving files in slurm_tmp
-    joblist.append(str(finaljob))
+    if finaljob:
+        joblist.append(str(finaljob))
     metadata = cal_tools.tools.CalibrationMetadata(out_path)
     job_time_fmt = 'JobID,Start,End,Elapsed,Suspended,State'.split(',')
     job_time_summary = get_job_info(joblist, job_time_fmt)