removed parameters 'log_level' and 'legacy_naming' from the default c…

…onfig writing function, remade the template config, added new test to check the example config files are still in order and removed some unncessary parameters from example configs

pysep/configs/alvizuri_tape_2018/2006-10-09T013528_NORTH_KOREA.yaml

@@ -47,4 +47,3 @@ remove_insufficient_length: true
 remove_masked_data: true
 fill_data_gaps: false
 gap_fraction: 1.0
-log_level: DEBUG

pysep/configs/misc_events/1988-02-15T181000_KERNVILLE_EXPLOSION.yaml

@@ -46,4 +46,3 @@ remove_insufficient_length: true
 remove_masked_data: true
 fill_data_gaps: false
 gap_fraction: 1.0
-log_level: DEBUG

pysep/configs/misc_events/2015-10-18T051831_TAAN_FJORD_LANDSLIDE.yaml

@@ -50,4 +50,3 @@ remove_insufficient_length: true
 remove_masked_data: true
 fill_data_gaps: false
 gap_fraction: 1.0
-log_level: DEBUG

pysep/configs/misc_events/2016-01-24T103037_INISKIN.yaml

@@ -47,4 +47,3 @@ remove_insufficient_length: true
 remove_masked_data: true
 fill_data_gaps: false
 gap_fraction: 1.0
-log_level: DEBUG

pysep/configs/template_config.yaml

@@ -1,48 +1,48 @@
-# PYSEP Config file - Template v0.1.0
+# PySEP Template config v0.5.0
+event_tag: null
 config_file: null
 client: IRIS
 client_debug: false
 timeout: 600
+taup_model: ak135
+use_mass_download: false
 event_selection: default
-origin_time: 2009-04-07T20:12:55.351
+origin_time: null
 seconds_before_event: 20
 seconds_after_event: 20
-event_latitude: 61.45420
-event_longitude: -149.7428
-event_depth_km: 33.033
-event_magnitude: 4.6
-networks: 'AK,YV,AV,AT,XZ,PN'
+event_latitude: null
+event_longitude: null
+event_depth_km: null
+event_magnitude: null
+networks: '*'
 stations: '*'
-channels: 'BH?'
+channels: '*'
 locations: '*'
 reference_time: null
 seconds_before_ref: 100
 seconds_after_ref: 300
-phase_list: null
-llnl_db_path: /store/raw/LLNL/UCRL-MI-222502/westernus.wfdisc
-min_dist: 0
-max_dist: 300.0
-min_az: 0
-max_az: 360
-min_lat: null
-max_lat: null
-min_lon: null
-max_lon: null
+phase_list:
+- ttall
+mindistance_km: 0
+maxdistance_km: 20000.0
+minazimuth: 0
+maxazimuth: 360
+minlatitude: null
+maxlatitude: null
+minlongitude: null
+maxlongitude: null
 demean: true
 detrend: true
-taper_percentage: 0
+taper_percentage: 0.0
 rotate: null
 remove_response: true
 output_unit: VEL
 water_level: 60
 pre_filt: default
-scale_factor: 100.0
-resample_freq: 50
-remove_clipped: false
-output_dir: ./
-write_files: !!set
-  all: null
-plot_files: !!set
-  all: null
-log_level: DEBUG
-event_tag: null
+scale_factor: 1
+resample_freq: null
+remove_clipped: true
+remove_insufficient_length: true
+remove_masked_data: true
+fill_data_gaps: false
+gap_fraction: 1.0

pysep/pysep.py

@@ -762,7 +762,6 @@ def load(self, config_file=None, overwrite_event=True):
                         logger.debug(f"{key}: {old_val} -> {val}")
                         setattr(self, key, val)
                 else:
-                    import pdb;pdb.set_trace()
                     logger.warning(f"config parameter '{key}' not explicitely "
                                    f"used by PySEP. adding to kwargs")
                     self.kwargs[key] = val
@@ -1681,10 +1680,9 @@ def write_config(self, fid=None, overwrite=False):
                     if not key.startswith("_")}
         # Internal attributes that don't need to go into the written config
         attr_remove_list = ["st", "st_raw", "event", "inv", "c", "write_files",
-                            "plot_files", "output_dir", "station_ids", "kwargs"]
+                            "plot_files", "output_dir", "station_ids", "kwargs",
+                            "llnl_db_path", "log_level", "legacy_naming"]
 
-        if self.client.upper() != "LLNL":
-            attr_remove_list.append("llnl_db_path")  # not important unless LLNL
         for key in attr_remove_list:
             del(dict_out[key])
         # Write times in as strings not UTCDateTime

pysep/tests/test_pysep.py

@@ -1,7 +1,11 @@
 """
 Test the general functionality of Pysep
 """
+from re import L
 import pytest
+import os
+import yaml
+from glob import glob
 from pysep import Pysep, logger
 
 
@@ -75,3 +79,28 @@ def test_curtail_stations(test_pysep):
 
     assert(nsta_pre_curtail - nsta_post_curtail == 6)
 
+
+def test_config_files_have_correct_parameters(tmpdir, test_pysep):
+    """
+    Check that all the config files have the correct parameters based on what
+    PySEP writes to ensure that the config files are up to date with codebase
+    """
+    # Write a config file from the Pysep instance and read in the yaml file
+    fid = os.path.join(tmpdir, "test_config.yaml")
+    test_pysep.write_config(fid=fid)
+    config = set(yaml.safe_load(open(fid)).keys())
+
+    # Get the directory containing the example config files
+    config_dir = "../configs/"
+
+    # Iterate over all the yaml files in the directory
+    for dir_ in glob(os.path.join(config_dir, "*")):
+        if not os.path.isdir(dir_):
+            continue
+        for fid in glob(os.path.join(dir_, "*")):
+            if not fid.endswith(".yaml"):
+                continue
+            with open(fid, "r") as f:
+                config_check = set(yaml.safe_load(f).keys())
+                assert(config.issubset(config_check)), \
+                    f"Config file {fid} does not have the correct parameters"