Add summary job option

cal_tools/cal_tools/tools.py

@@ -31,9 +31,14 @@ def combine_report(run_path, calibration):
                     group, name_param, conc_param = "_".join(comps[:-2]), comps[-2], comps[-1]
                 else:
                     group, name_param,  conc_param = comps[0], "None", "None"
-                    
+
                 with open("{}/{}.rst".format(sphinx_path, group), "a") as gfile:
-                    if conc_param != "None":
+                    if conc_param == "summary":
+                        title = "{}. {}".format(calibration, "Summary.")
+                        gfile.write(title + "\n")
+                        gfile.write( "=" *len (title) + "\n")
+                        gfile.write("\n")
+                    elif conc_param != "None":
                         title = "{}. {} = {}".format(calibration, name_param, conc_param)
                         gfile.write(title + "\n")
                         gfile.write( "=" *len (title) + "\n")

xfel_calibrate/calibrate.py

@@ -358,9 +358,19 @@ def flatten_list(l):
     return "_".join([str(flatten_list(v)) for v in l]) if isinstance(l, list) else l
 
 
+def clean_nonfinal_cells(nb):
+    first_cell = False
+    for cell in nb.cells:
+        if not first_cell and cell.cell_type == 'code':
+            first_cell = True
+            continue
+        if '!!!FINAL!!!' not in cell.source:
+            cell.source = ''
+
+
 def concurrent_run(temp_path, nb, nbname, args, cparm=None, cval=None,
                    final_job=False, job_list=[], fmtcmd="", cluster_cores=8,
-                   sequential=False, priority=2):
+                   sequential=False, priority=2, dependent=False):
     """ Launch a concurrent job on the cluster via SLURM
     """
 
@@ -376,6 +386,10 @@ def concurrent_run(temp_path, nb, nbname, args, cparm=None, cval=None,
     parms = extract_parameters(nb)
     params = parameter_values(parms, **args)
     new_nb = replace_definitions(nb, params, execute=False)
+    if dependent:
+        suffix = "summary"
+        clean_nonfinal_cells(new_nb)
+
     base_name = nbname.replace(".ipynb", "")
     new_name = "{}__{}__{}.ipynb".format(
         os.path.basename(base_name), cparm, suffix)
@@ -416,6 +430,12 @@ def concurrent_run(temp_path, nb, nbname, args, cparm=None, cval=None,
     else:
         srun_base = []
 
+    if dependent:
+        srun_dep = "--dependency=afterok"
+        for jobid in job_list:
+            srun_dep += ":{}".format(jobid)
+        srun_base += [srun_dep]
+
     srun_base += [os.path.abspath("{}/bin/slurm_calibrate.sh".format(os.path.dirname(__file__))),  # path to helper sh
                   os.path.abspath(nbpath),  # path to notebook
                   python_path,  # path to python
@@ -634,15 +654,33 @@ def run():
                     cvtype = p.type
                     break
 
+            run_overall = False
+            for p in parms:
+                if p.name == 'run_overall':
+                    run_overall = p.value
+                    break
+
             for cnum, cval in enumerate(cvals):
                 jobid = concurrent_run(run_tmp_path, nb, notebook, args,
                                        cvar, [cval, ] if not isinstance(
                                            cval, list) and cvtype is list else cval,
                                        cnum == len(list(cvals)) -
-                                       1, joblist, fmtcmd,
+                                       1 and not run_overall,
+                                       joblist, fmtcmd,
                                        cluster_cores=cluster_cores, sequential=sequential, priority=priority)
                 joblist.append(jobid)
 
+
+            # Run summary job here if needed
+            if run_overall:
+                jobid = concurrent_run(run_tmp_path, nb, os.path.basename(notebook),
+                                   args,
+                                   final_job=True, job_list=joblist, fmtcmd=fmtcmd,
+                                   cluster_cores=cluster_cores,
+                                   sequential=sequential, priority=priority,
+                                   dependent=True)
+                joblist.append(jobid)
+
         if not all([j is None for j in joblist]):
             print("Submitted the following SLURM jobs: {}".format(",".join(joblist)))