Remove runconfig.yaml.log (#828)

* yamlargparse tweaks and updates

removed runconfig.yaml.log generated before yaml is read for log path
fixed reading of nonsensical file in persistence
add more details to docstrings in parser arguments

* fixed logging bug

force restart when no log path found in runconfig yaml
updated where persistence restart arg
added documentation and whitespace cleanup

Author: Liang Yu

python/packages/pybind_nisar/workflows/insar.py

@@ -68,7 +68,7 @@ def run(cfg: dict, out_paths: dict, run_steps: dict):
     insar_runcfg = InsarRunConfig(args)
 
     # determine what steps if any need to be rerun
-    persist = Persistence(args.restart)
+    persist = Persistence(insar_runcfg.args.restart)
 
     # run InSAR workflow
     if persist.run:

python/packages/pybind_nisar/workflows/runconfig.py

@@ -86,7 +86,9 @@ def load_geocode_yaml_to_dict(self):
         self.cfg = self.cfg['runconfig']['groups']
         self.user = self.user['runconfig']['groups']
 
-        # update logging destination
+        # attempt updating logging destination only if:
+        # CLI arg for log is True AND valid path provided in yaml
+        # otherwise indicate restart
         if self.args.log_file and 'logging' in self.cfg:
             log_path = self.cfg['logging']['path']
             helpers.check_log_dir_writable(log_path)
@@ -95,7 +97,10 @@ def load_geocode_yaml_to_dict(self):
                 write_mode = self.cfg['logging']['write_mode']
             else:
                 write_mode = 'a'
+            journal.debug.journal.device = "journal.file"
             journal.debug.journal.device.log = open(log_path, write_mode)
+        else:
+            self.args.restart = True
 
         # remove default frequency(s) if not chosen by user
         default_freqs = self.cfg['processing']['input_subset']['list_of_frequencies']
@@ -231,7 +236,7 @@ def prep_cubes_geocode_cfg(self):
 
         # check for user provided EPSG and grab geocode group EPSG if not provided
 
-        if self.cfg['processing']['radar_grid_cubes']['outputEPSG'] is None: 
+        if self.cfg['processing']['radar_grid_cubes']['outputEPSG'] is None:
             cubes_epsg = geocode_dict['outputEPSG']
         else:
             cubes_epsg = self.cfg['processing']['radar_grid_cubes']['outputEPSG']
@@ -258,7 +263,7 @@ def prep_cubes_geocode_cfg(self):
         frequency_ref = 'A'
         frequency_group = None
         cubes_geogrid = geogrid.create(
-            self.cfg, frequency_group = frequency_group, 
+            self.cfg, frequency_group = frequency_group,
             frequency = frequency_ref,
             geocode_dict = radar_grid_cubes_dict,
             default_spacing_x = default_cube_geogrid_spacing_x,

python/packages/pybind_nisar/workflows/yaml_argparse.py

@@ -46,9 +46,9 @@ def __init__(self, resample_type = False):
         self.parser.add_argument('run_config_path', type=str, nargs='?',
                                  default=None, help='Path to run config file')
         self.parser.add_argument('--no-log-file', dest='log_file', action='store_false',
-                                 default=True, help='Disable logging to file. Log to file on by default.')
+                                 default=True, help='Disable logging to file. Log to file on/True by default. If off/False, log file in runconfig yaml will not be read nor altered, log messasges will be sent to stdout, and all submodules will run i.e. no persistence checking.')
         self.parser.add_argument('--restart', action='store_true', default=False,
-                                 help='Restart the InSAR workflow from the beginning and ignore the previous run. False by default.')
+                                 help='Restart the InSAR workflow from the beginning and, if applicable, ignore the persistence state of previous run. Off/False by default.')
         if resample_type:
             self.parser.add_argument('--resample-type', dest='resample_type', default='coarse',
                                      help='Type of offsets (coregistered slc) to use in resample_slc (crossmul).\n'
@@ -62,6 +62,10 @@ def parse(self):
         '''
         self.args = self.parser.parse_args()
         self.check_run_config_path()
+        # Force restart if no log file provided
+        # Otherwise persistence will attempt reading nonexistent file
+        if not self.args.log_file:
+            self.args.restart = True
         return self.args
 
     def check_run_config_path(self):
@@ -76,13 +80,6 @@ def check_run_config_path(self):
             error_channel.log(err_str)
             raise FileNotFoundError(err_str)
 
-        if self.args.log_file:
-            helpers.check_log_dir_writable(self.args.run_config_path)
-
-            # make a journal device that is attached to a file
-            journal.debug.journal.device = "journal.file"
-            journal.debug.journal.device.log = open(self.args.run_config_path + ".log", 'a')
-
 
 # only used for unit tests
 if __name__ == "__main__":