Merge branch 'slurm-fixes' into 'master'

Some cleanup in calibrate.py

See merge request detectors/pycalibration!331

xfel_calibrate/finalize.py

@@ -263,15 +263,18 @@ def make_report(run_path, tmp_path, out_path, project, author, version,
     lead_rstfiles = ['InputParameters.rst', 'timing_summary.rst']
 
     # Order rst files based on the known order(lead_rstfiles).
-    for f in direntries:
+    # TODO: fix order somewhere else instead of munging filenames
+    def sort_key(f):
         if f in lead_rstfiles:
-            direntries.insert(lead_rstfiles.index(f),
-                              direntries.pop(direntries.index(f)))
-        # Move summary to the top, if it is exists,
-        # after the known leading rst files.
-        if "summary" in f.lower() and f not in lead_rstfiles:
-            direntries.insert(len(lead_rstfiles),
-                              direntries.pop(direntries.index(f)))
+            return lead_rstfiles.index(f), f
+        elif "summary" in f.lower():
+            return len(lead_rstfiles), f
+        elif "precorrection" in f.lower():
+            return len(lead_rstfiles) + 1, f
+        else:
+            return len(lead_rstfiles) + 2, f
+    direntries.sort(key=sort_key)
+
     files_to_handle = []
     for entry in direntries:
         if isfile("{}/{}".format(run_path, entry)):

xfel_calibrate/settings.py

 import os
 
 # path into which temporary files from each run are placed
-temp_path = "{}/temp/".format(os.getcwd())
+temp_path = os.path.abspath("temp/")
 
 # Path to use for calling Python. If the environment is correctly set, simply the command
 python_path = "python"