Fix various bugs and adds features to code (#60)

* renamed specfem station writing function, and added an ordering component

* bumping version in setup and changing url and author

* small mt typo change

* added an example config that gathers a small amount of data for testing/dev purposes

* added a new kwarg 'order_stations_list_by' which sets the order of the output stations list, related to #36

* bugfix typo parameter call

* bugfix rotating was not actually rotating streams in place for arbitrary components ->ENZ

* bugfix fixed rotation testing, which was not actually evaluating as expected. some confusion about editing streams and inventories in place which was not actually happening. Fixed and now rotate test works as expected

* added 12Z test data for rotating 12Z -> ENZ which works now, added test to cover this case

* moved 2012 central alaska IU gather script (which gathers 12Z component) into examples

* bugfix pysep was not setting log level properly from the config file. now in the load() function, config log level is allowed to override logger level

* changed config examples dir name to test, to be used as a test bed for checking specific data gathering features such as data gap removal

* bugfix #57, reading event origin time from sac header was shifting times unexpectedly

pysep/configs/README.md

@@ -6,3 +6,6 @@ The below information describes each of the category directories.
 	Quantification (MTUQ) workshop to demonstrate code capabilities.
 - denali_nodal: Events recorded by the PASSCAL Denali Fault nodal deployment
 - misc_events: One-off events with no overarching category 
+- test: test data collection that exhibits certain traits that are useful for
+	checking rejection criteria etc. Check comments at top of file to show
+	what the file is used for

pysep/configs/test/check_rotate_12Z.yaml

@@ -0,0 +1,46 @@
+# Testing IU Rotation Error - PySEP Issue #37
+# IU.COLA raw stream returns 12Z which gets rotated appropriately
+event_tag: null
+config_file: null
+client: IRIS
+client_debug: false
+timeout: 600
+taup_model: ak135
+event_selection: default
+origin_time: '2012-04-11T09:21:57.444'
+seconds_before_event: 20
+seconds_after_event: 20
+event_latitude: 64.9222
+event_longitude: -148.9461
+event_depth_km: 160.00
+event_magnitude: 3.8
+networks: 'IU'
+stations: 'COLA'
+channels: 'BH?,HH?'
+locations: '*'
+reference_time: null
+seconds_before_ref: 100
+seconds_after_ref: 600
+phase_list: null
+mindistance: 0
+maxdistance: 200.0
+minazimuth: 0
+maxazimuth: 360
+minlatitude: null
+maxlatitude: null
+minlongitude: null
+maxlongitude: null
+demean: true
+detrend: true
+taper_percentage: 0
+rotate:
+- ENZ
+- RTZ
+remove_response: true
+output_unit: VEL
+water_level: 60
+pre_filt: default
+scale_factor: 1.0
+resample_freq: 50
+remove_clipped: false
+log_level: DEBUG

pysep/configs/test/test_remove_data_gaps.yaml

@@ -0,0 +1,47 @@
+# Testing Data gap removal
+# FIB has data gaps, should be removed from final data retrieval
+event_tag: 2009-04-07T201255_SOUTHERN_ALASKA
+config_file: null
+client: IRIS
+client_debug: false
+timeout: 600
+taup_model: ak135
+event_selection: default
+origin_time: '2009-04-07T20:12:55.351000Z'
+seconds_before_event: 20
+seconds_after_event: 20
+event_latitude: 61.4542
+event_longitude: -149.7428
+event_depth_km: 33.033
+event_magnitude: 4.6
+networks: AK
+stations: 'FIB,SWD'
+channels: BH?
+locations: '*'
+reference_time: '2009-04-07T20:12:55.351000Z'
+seconds_before_ref: 100
+seconds_after_ref: 300
+phase_list: null
+mindistance: 0
+maxdistance: 300.0
+minazimuth: 0
+maxazimuth: 360
+minlatitude: null
+maxlatitude: null
+minlongitude: null
+maxlongitude: null
+demean: true
+detrend: true
+taper_percentage: 0
+rotate:
+- ENZ
+- RTZ
+remove_response: true
+output_unit: VEL
+water_level: 60
+pre_filt: default
+scale_factor: 1.0
+resample_freq: 50
+remove_clipped: false
+log_level: DEBUG
+

pysep/pysep.py

@@ -65,10 +65,6 @@ def __init__(self, config_file=None, event_selection="default",
         """
         Define a default set of parameters
 
-        TODO
-            * removed resample_TF, was this used?
-            * load config FIRST and then set defaults, make all defaults None?
-
         :type client: str
         :param client: ObsPy FDSN client to query data from, e.g., IRIS, LLNL,
             NCEDC or any FDSN clients accepted by ObsPy
@@ -269,6 +265,10 @@ def __init__(self, config_file=None, event_selection="default",
         else:
             logger.disabled = True
 
+        # Allow User to throw in general kwargs. This allows things to be
+        # more general, but also may obscure some parameters.
+        self.kwargs = kwargs
+
     def check(self):
         """
         Check input parameter validity against expected Pysep behavior
@@ -448,6 +448,13 @@ def load(self, config_file=None, overwrite_event=True):
                         logger.debug(f"{key}: {old_val} -> {val}")
                         setattr(self, key, val)
 
+        # Reset log level based on the config file
+        if self.log_level is not None:
+            logger.debug(f"`log_level` set to {self.log_level}")
+            logger.setLevel(self.log_level)
+        else:
+            logger.disabled = True
+
     def get_event(self):
         """
         Exposed API for grabbing event metadata depending on the
@@ -890,8 +897,8 @@ def rotate_streams(self):
                 # important as some IRIS data will be in ZNE but not be aligned
                 # https://github.com/obspy/obspy/issues/2056
                 _st.rotate(method="->ZNE", inventory=self.inv, 
-                           components=["ZNE"])
-            st_out += st_zne
+                           components=["ZNE", "Z12", "123"])
+                st_out += _st
         if "UVW" in self.rotate:
             logger.info("rotating to components UVW")
             st_uvw = rotate_to_uvw(st_out)
@@ -908,9 +915,12 @@ def rotate_streams(self):
                 _st.rotate(method="NE->RT")  # in place rot.
                 if hasattr(_st[0].stats, "back_azimuth"):
                     logger.debug(f"{sta}: BAz={_st[0].stats.back_azimuth}")
-            st_out += st_rtz
-
-        st_out = format_sac_headers_post_rotation(st_out)
+                st_out += _st
+
+        try:
+            st_out = format_sac_headers_post_rotation(st_out)
+        except AttributeError as e:
+            logger.warning(f"cannot format SAC headers after rotating {e}")
 
         return st_out
 
@@ -957,6 +967,9 @@ def write(self, write_files=None, _return_filenames=False,
         :type stream_fid: optional name for saved ObsPy Stream miniseed object,
             defaults to 'stream.ms'
         """
+        # Collect kwargs for writing
+        order_stations_list_by = kwargs.get("order_stations_list_by", None)
+
         # This is defined here so that all these filenames are in one place,
         # but really this set is just required by check(), not by write()
         _acceptable_files = {"weights_az", "weights_dist", "weights_code",
@@ -995,7 +1008,10 @@ def write(self, write_files=None, _return_filenames=False,
                                stations_fid or "stations_list.txt")
             logger.info("writing stations file")
             logger.debug(fid)
-            write_pysep_stations_file(self.inv, self.event, fid)
+            write_pysep_stations_file(
+                    self.inv, self.event, fid, 
+                    order_stations_list_by=order_stations_list_by
+                    )
 
         if "inv" in write_files or "all" in write_files:
             fid = os.path.join(self.output_dir, inv_fid or f"inv.xml")
@@ -1199,7 +1215,7 @@ def run(self, event=None, inv=None, st=None, **kwargs):
         self.st = quality_check_waveforms_after_processing(self.st)
 
         # Generate outputs for user consumption
-        self.write(**kwargs)
+        self.write(**{**kwargs, **self.kwargs})
         self.plot()
 
 
@@ -1239,7 +1255,7 @@ def parse_args():
                              "filled in by the User")
     parser.add_argument("-l", "--list", default=False, action="store_true",
                         help="list out avaialable `preset` config options")
-    parser.add_argument("-L", "--log_level", default="INFO", type=str,
+    parser.add_argument("-L", "--log_level", default="DEBUG", type=str,
                         nargs="?", help="verbosity of logging: 'WARNING', "
                                         "'INFO', 'DEBUG'")
     parser.add_argument("--legacy_naming", default=False, action="store_true",