ran black

docs/create_metadata_tables.py

@@ -12,9 +12,7 @@
 from pathlib import Path
 import textwrap
 
-fn = Path(
-    r"c:\Users\peaco\Documents\GitHub\mth5\mth5\docs\mt_metadata_guide.tex"
-)
+fn = Path(r"c:\Users\peaco\Documents\GitHub\mth5\mth5\docs\mt_metadata_guide.tex")
 
 
 def wrap_description(description, column_width):
@@ -53,55 +51,43 @@ def write_lines(lines_list, c1, c2, c3):
 
     lines = [
         hline,
-        line.format(
-            "**Metadata Key**", c1, "**Description**", c2, "**Example**", c3
-        ),
+        line.format("**Metadata Key**", c1, "**Description**", c2, "**Example**", c3),
         mline,
     ]
 
     for entry in lines_list:
         d_lines = wrap_description(entry[5], c2)
         e_lines = wrap_description(entry[-1], c3)
         # line 1 is with the entry
-        lines.append(
-            line.format(f"**{entry[0]}**", c1, d_lines[0], c2, e_lines[0], c3)
-        )
+        lines.append(line.format(f"**{entry[0]}**", c1, d_lines[0], c2, e_lines[0], c3))
         # line 2 skip an entry in the
         lines.append(line.format("", c1, d_lines[1], c2, e_lines[1], c3))
         # line 3 required
         lines.append(
-            line.format(
-                f"Required: {entry[1]}", c1, d_lines[2], c2, e_lines[2], c3
-            )
+            line.format(f"Required: {entry[1]}", c1, d_lines[2], c2, e_lines[2], c3)
         )
         # line 4 blank
         lines.append(line.format("", c1, d_lines[3], c2, e_lines[3], c3))
 
         # line 5 units
         lines.append(
-            line.format(
-                f"Units: {entry[2]}", c1, d_lines[4], c2, e_lines[4], c3
-            )
+            line.format(f"Units: {entry[2]}", c1, d_lines[4], c2, e_lines[4], c3)
         )
 
         # line 6 blank
         lines.append(line.format("", c1, d_lines[5], c2, e_lines[5], c3))
 
         # line 7 type
         lines.append(
-            line.format(
-                f"Type: {entry[3]}", c1, d_lines[6], c2, e_lines[6], c3
-            )
+            line.format(f"Type: {entry[3]}", c1, d_lines[6], c2, e_lines[6], c3)
         )
 
         # line 8 blank
         lines.append(line.format("", c1, d_lines[7], c2, e_lines[7], c3))
 
         # line 9 type
         lines.append(
-            line.format(
-                f"Style: {entry[4]}", c1, d_lines[8], c2, e_lines[8], c3
-            )
+            line.format(f"Style: {entry[4]}", c1, d_lines[8], c2, e_lines[8], c3)
         )
 
         # line 10 blank
@@ -151,46 +137,36 @@ def write_block(entry, c1, c2, c3):
         f"       :widths: {c1} {c2} {c3}",
         "",
         hline,
-        line.format(
-            f"**{entry[0]}**", c1, "**Description**", c2, "**Example**", c3
-        ),
+        line.format(f"**{entry[0]}**", c1, "**Description**", c2, "**Example**", c3),
         mline,
     ]
 
     d_lines = wrap_description(entry[5], c2)
     e_lines = wrap_description(entry[-1], c3)
     # line 1 is with the entry
     lines.append(
-        line.format(
-            f"**Required**: {entry[1]}", c1, d_lines[0], c2, e_lines[0], c3
-        )
+        line.format(f"**Required**: {entry[1]}", c1, d_lines[0], c2, e_lines[0], c3)
     )
     # line 2 skip an entry in the
     lines.append(line.format("", c1, d_lines[1], c2, e_lines[1], c3))
     # line 3 required
     lines.append(
-        line.format(
-            f"**Units**: {entry[2]}", c1, d_lines[2], c2, e_lines[2], c3
-        )
+        line.format(f"**Units**: {entry[2]}", c1, d_lines[2], c2, e_lines[2], c3)
     )
     # line 4 blank
     lines.append(line.format("", c1, d_lines[3], c2, e_lines[3], c3))
 
     # line 5 units
     lines.append(
-        line.format(
-            f"**Type**: {entry[3]}", c1, d_lines[4], c2, e_lines[4], c3
-        )
+        line.format(f"**Type**: {entry[3]}", c1, d_lines[4], c2, e_lines[4], c3)
     )
 
     # line 6 blank
     lines.append(line.format("", c1, d_lines[5], c2, e_lines[5], c3))
 
     # line 7 type
     lines.append(
-        line.format(
-            f"**Style**: {entry[4]}", c1, d_lines[6], c2, e_lines[6], c3
-        )
+        line.format(f"**Style**: {entry[4]}", c1, d_lines[6], c2, e_lines[6], c3)
     )
 
     # line 8 blank

examples/make_mth5_from_nims.py

@@ -22,6 +22,7 @@
 #
 # =============================================================================
 
+
 def test_make_mth5_from_nims():
     print(f"Data Directory: {DATA_DIR}")
     # set to true if you want to interact with the mth5 object in the console
@@ -98,6 +99,5 @@ def test_make_mth5_from_nims():
         m.close_mth5()
 
 
-
 if __name__ == "__main__":
     test_make_mth5_from_nims()

examples/make_mth5_from_xml.py

@@ -25,13 +25,15 @@
 # functions
 # =============================================================================
 
-#<XML HELPERS>
+# <XML HELPERS>
 def is_a_station_xml(fn):
     return fn.count(".") == 1
 
+
 def is_a_run_xml(fn):
     return fn.count(".") == 2
 
+
 def is_a_channel_xml(fn):
     return fn.count(".") > 2
 
@@ -92,7 +94,10 @@ def collect_xml_fn(station, directory):
             continue
 
     return station_dict
-#</XML HELPERS>
+
+
+# </XML HELPERS>
+
 
 def add_station(station, directory, h5_obj):
     """
@@ -108,9 +113,7 @@ def add_station(station, directory, h5_obj):
 
     # add station
     new_station = h5_obj.stations_group.add_station(station)
-    new_station.metadata.from_xml(
-        read_xml(directory.joinpath(station_dict["station"]))
-    )
+    new_station.metadata.from_xml(read_xml(directory.joinpath(station_dict["station"])))
     new_station.write_metadata()
 
     # loop over runs
@@ -126,9 +129,7 @@ def add_station(station, directory, h5_obj):
         # loop over channels
         for channel, channel_fn in run_dict["channels"].items():
             _, _, channel_type, component, _ = channel_fn.split(".")
-            channel = run.add_channel(
-                component, channel_type, np.random.rand(4096)
-            )
+            channel = run.add_channel(component, channel_type, np.random.rand(4096))
             channel.metadata.from_xml(read_xml(directory.joinpath(channel_fn)))
             channel.metadata.time_period.start = run.metadata.time_period.start
             channel.metadata.time_period.end = run.metadata.time_period.end

examples/make_mth5_from_z3d.py

@@ -59,8 +59,7 @@ def test_make_mth5_from_z3d():
         mtts_obj = read_file(zen_dir.joinpath(fn.filename))
 
         station_group = m.add_station(
-            mtts_obj.station_metadata.id,
-            station_metadata=mtts_obj.station_metadata,
+            mtts_obj.station_metadata.id, station_metadata=mtts_obj.station_metadata,
         )
 
         run_id = station_group.locate_run(mtts_obj.sample_rate, mtts_obj.start)
@@ -78,7 +77,6 @@ def test_make_mth5_from_z3d():
         )
         station_group.validate_station_metadata()
 
-
     end = MTime()
     end.now()
 
@@ -87,6 +85,6 @@ def test_make_mth5_from_z3d():
     if not interact:
         m.close_mth5()
 
+
 if __name__ == "__main__":
     test_make_mth5_from_z3d()
-

examples/make_stationxml_from_mt.py

@@ -201,8 +201,5 @@ def test_make_stationxml_from_mt():
     to_stationxml.to_stationxml("Test_station.xml")
 
 
-
-
 if __name__ == "__main__":
     test_make_stationxml_from_mt()
-

examples/metadata/make_example_files.py

@@ -19,17 +19,13 @@
         s = getattr(metadata, c)()
         if style == "xml":
             x = s.to_xml(required=False)
-            with open(
-                p.joinpath("{0}_example.xml".format(c.lower())), "w"
-            ) as fid:
+            with open(p.joinpath("{0}_example.xml".format(c.lower())), "w") as fid:
                 fid.write(
                     minidom.parseString(et.tostring(x).decode()).toprettyxml(
                         indent="    "
                     )
                 )
         elif style == "json":
             jstr = s.to_json(nested=True, required=False)
-            with open(
-                p.joinpath("{0}_example.json".format(c.lower())), "w"
-            ) as fid:
+            with open(p.joinpath("{0}_example.json".format(c.lower())), "w") as fid:
                 fid.write(jstr)

examples/test_examples.py

@@ -13,6 +13,7 @@
 
 """
 
+
 def run_the_tests():
     """
     """
@@ -22,6 +23,5 @@ def run_the_tests():
     test_make_stationxml_from_mt()
 
 
-
 if __name__ == "__main__":
     run_the_tests()

examples/translate_mt_metadata_to_station_xml.py

@@ -43,9 +43,7 @@
 # Inputs: xml file names for each level
 # =============================================================================
 # directory where xml files reside
-print(
-    "WARNING THIS TEST IS NOT YET READY TO BE PART OF THE REGULAR TESTING SUITE"
-)
+print("WARNING THIS TEST IS NOT YET READY TO BE PART OF THE REGULAR TESTING SUITE")
 xml_path = Path(r"c:\Users\peaco\Documents\MT\mth5")
 
 # filenames for each level

mth5/filters/filters.py

@@ -159,10 +159,7 @@ def to_lookup_table(self, frequencies=None):
         """
 
         pz = signal.ZerosPolesGain(
-            self.zeros,
-            self.poles,
-            self.normalization_factor,
-            dt=self.sample_rate,
+            self.zeros, self.poles, self.normalization_factor, dt=self.sample_rate,
         )
 
         f, amp = signal.dfreqresp(pz, frequencies)
@@ -217,16 +214,10 @@ class LookupTable:
 
     def __init__(self, frequency, real, imaginary, amplitude_phase=False):
 
-        self.logger = logging.getLogger(
-            f"{__name__}.{self.__class__.__name__}"
-        )
+        self.logger = logging.getLogger(f"{__name__}.{self.__class__.__name__}")
         self.lookup_table = None
 
-        if (
-            frequency is not None
-            and real is not None
-            and imaginary is not None
-        ):
+        if frequency is not None and real is not None and imaginary is not None:
             if not isinstance(frequency, np.ndarray):
                 frequency = np.array(frequency)
             if not isinstance(real, np.ndarray):
@@ -274,10 +265,7 @@ def __str__(self):
                 + [
                     f"{ff:<14.5e}{vv.real:<14.5e}{vv.imag:<14.5e}{aa:<14.5e}{pp:<14.5e}"
                     for ff, vv, aa, pp in zip(
-                        self.frequency,
-                        self.filter_values,
-                        self.amplitude,
-                        self.phase,
+                        self.frequency, self.filter_values, self.amplitude, self.phase,
                     )
                 ]
             )
@@ -331,9 +319,7 @@ def filter_values(self, values):
     @property
     def amplitude(self):
         try:
-            return np.sqrt(
-                self.filter_values.real ** 2 + self.filter_values.imag ** 2
-            )
+            return np.sqrt(self.filter_values.real ** 2 + self.filter_values.imag ** 2)
         except AttributeError:
             return None
 
@@ -437,9 +423,7 @@ def __init__(
         instrument_gain=None,
     ):
 
-        self.logger = logging.getLogger(
-            f"{__name__}.{self.__class__.__name__}"
-        )
+        self.logger = logging.getLogger(f"{__name__}.{self.__class__.__name__}")
         self.metadata = metadata.Filter()
         if zeros is None:
             zeros = []
@@ -475,20 +459,14 @@ def __str__(self):
         info = self.metadata.__str__()
         if self.conversion_factor is not None:
             info += "\n".join(
-                [
-                    "",
-                    "Conversion Factor:",
-                    f"\t{self.conversion_factor:<12.5e}",
-                ]
+                ["", "Conversion Factor:", f"\t{self.conversion_factor:<12.5e}",]
             )
         if self.instrument_gain is not None:
             info += "\n".join(
                 ["", "Instrument Gain:", f"\t{self.instrument_gain:<12.5e}"]
             )
         if self.time_delay is not None:
-            info += "\n".join(
-                ["", "Time Delay:", f"\t{self.time_delay:<12.5e}"]
-            )
+            info += "\n".join(["", "Time Delay:", f"\t{self.time_delay:<12.5e}"])
 
         if len(self.zpk.poles) > 0 or len(self.zpk.zeros) > 0:
             pz = [""]

mth5/groups/base.py

@@ -264,9 +264,7 @@ def initialize_summary_table(self):
         )
         self.logger.debug(
             "used options: "
-            + "; ".join(
-                [f"{k} = {v}" for k, v in self.dataset_options.items()]
-            )
+            + "; ".join([f"{k} = {v}" for k, v in self.dataset_options.items()])
         )
 
     def initialize_group(self):

mth5/groups/filter_dataset.py

@@ -262,9 +262,7 @@ def write_metadata(self):
 
         for key, value in self.metadata.to_dict(single=True):
             value = to_numpy_type(value)
-            self.logger.debug(
-                f"wrote metadata {key} = {value}".format(key, value)
-            )
+            self.logger.debug(f"wrote metadata {key} = {value}".format(key, value))
             self.hdf5_dataset.attrs.create(key, value)
 
     def to_filter_object(self):