add an option to save all important files to path_out

studyprocessor.py

@@ -1,6 +1,9 @@
 # coding: utf-8
 
+
 import os
+from distutils.file_util import copy_file
+
 import glob
 import numpy as np
 from functools import partial
@@ -82,6 +85,20 @@ class StudyProcessor(Aggregator, HDF5Container):
         run0 = self.runs[0]
         self.info = selector.info[run0][self.nums[run0][0]]
         self.namelist = selector.namelist
+
+        # Save namelist and logs
+        if self.params.out.copy_info:
+            for run in self.runs:
+                nml_src = f"{self.path}/{run}/{self.params.input.nml_filename}"
+                nml_dest = f"{self.path_out}/{run}/{self.params.input.nml_filename}"
+                copy_file(nml_src, nml_dest, update=1)
+
+                logs = self.get_logs(run)
+                os.makedirs(f"{self.path_out}/{run}/logs", exist_ok=True)
+                for log in logs:
+                    dest = f"{self.path_out}/{run}/logs/{os.path.basename(log)}"
+                    copy_file(log, dest, update=1)
+
         # log info
         self.log_id = "[study {}] ".format(self.params.out.tag)
 
@@ -334,6 +351,14 @@ class StudyProcessor(Aggregator, HDF5Container):
                 series["turb_energy"][run].append(np.nan)
         return series
 
+    def get_logs(self, run):
+        glob_str = f"{self.path}/{run}/{self.params.input.log_prefix}*"
+        logs = glob.glob(glob_str)
+        if len(logs) == 0:
+            glob_str = f"{self.path}/{run}/logs/{self.params.input.log_prefix}*"
+            logs = glob.glob(glob_str)
+        return logs
+
     def _from_log(self, keys, extractor):
 
         # Initialize series
@@ -346,14 +371,11 @@ class StudyProcessor(Aggregator, HDF5Container):
             for key in keys:
                 series[key][run] = []
 
-            # get one preprocessor
-            path_run = self.path + "/" + run
-
-            # Get list of run files
-            log_files = path_run + "/" + self.params.input.log_prefix + "*"
+            # Get list of log files
+            log_files = self.get_logs(run)
 
             # Parse files
-            for log_filename in glob.glob(log_files):
+            for log_filename in log_files:
                 series = extractor(series, log_filename, run)
 
             # Numpify the lists