ruff reformat metagen

pbp/meta_gen/gen_iclisten.py

@@ -13,7 +13,12 @@
 import pandas as pd
 from pathlib import Path
 from progressbar import progressbar
-from pbp.meta_gen.utils import InstrumentType, parse_s3_or_gcp_url, get_datetime, plot_daily_coverage
+from pbp.meta_gen.utils import (
+    InstrumentType,
+    parse_s3_or_gcp_url,
+    get_datetime,
+    plot_daily_coverage,
+)
 from pbp.meta_gen.json_generator import JsonGenerator
 from pbp.meta_gen.meta_reader import GenericWavFile
 from pbp.meta_gen.gen_abstract import MetadataGeneratorAbstract
@@ -94,7 +99,7 @@ def run(self):
                             wav_files.append(GenericWavFile(self.log, filename, wav_dt))
 
                 if scheme == "s3":
-                    client = boto3.client('s3', config=Config(signature_version=UNSIGNED))
+                    client = boto3.client("s3", config=Config(signature_version=UNSIGNED))
                     for day_hour in pd.date_range(start=start_dt, end=end_dt, freq="h"):
                         bucket = f"{bucket_name}-{day_hour.year:04d}"
 
@@ -176,9 +181,12 @@ def run(self):
             except Exception as ex:
                 self.log.exception(str(ex))
 
-        plot_file = plot_daily_coverage(InstrumentType.ICLISTEN, self.df, self.json_base_dir, self.start, self.end)
+        plot_file = plot_daily_coverage(
+            InstrumentType.ICLISTEN, self.df, self.json_base_dir, self.start, self.end
+        )
         self.log.info(f"Plot file: {plot_file}")
 
+
 if __name__ == "__main__":
     from pbp.logging_helper import create_logger
 

pbp/meta_gen/gen_nrs.py

@@ -107,7 +107,9 @@ def run(self):
                         sound_files.append(WavFile(self.log, f_path, f_dt))
                 # delay to avoid 400 error
                 if i % 100 == 0:
-                    self.log.info(f"{i} files searched...found {len(sound_files)} files that match the search pattern")
+                    self.log.info(
+                        f"{i} files searched...found {len(sound_files)} files that match the search pattern"
+                    )
                     time.sleep(1)
                 if f_dt > end_dt:
                     break
@@ -152,9 +154,12 @@ def run(self):
                 self.log.exception(str(ex))
 
         # plot the daily coverage
-        plot_file = plot_daily_coverage(InstrumentType.NRS, self.df, self.json_base_dir, self.start, self.end)
+        plot_file = plot_daily_coverage(
+            InstrumentType.NRS, self.df, self.json_base_dir, self.start, self.end
+        )
         self.log.info(f"Coverage plot saved to {plot_file}")
 
+
 if __name__ == "__main__":
     from pbp.logging_helper import create_logger
 

pbp/meta_gen/gen_soundtrap.py

@@ -18,7 +18,12 @@
 from pbp.meta_gen.gen_abstract import MetadataGeneratorAbstract
 from pbp.meta_gen.meta_reader import SoundTrapWavFile
 from pbp.meta_gen.json_generator import JsonGenerator
-from pbp.meta_gen.utils import parse_s3_or_gcp_url, InstrumentType, get_datetime, plot_daily_coverage
+from pbp.meta_gen.utils import (
+    parse_s3_or_gcp_url,
+    InstrumentType,
+    get_datetime,
+    plot_daily_coverage,
+)
 
 
 class SoundTrapMetadataGenerator(MetadataGeneratorAbstract):
@@ -92,7 +97,7 @@ def run(self):
                 # dates
                 self.log.info(f"Searching between {start_dt} and {end_dt}")
 
-                client = boto3.client('s3', config=Config(signature_version=UNSIGNED))
+                client = boto3.client("s3", config=Config(signature_version=UNSIGNED))
                 paginator = client.get_paginator("list_objects")
 
                 operation_parameters = {"Bucket": bucket}
@@ -121,7 +126,9 @@ def run(self):
                                 client.download_file(bucket, key_xml, xml_path)
                                 wav_files.append(SoundTrapWavFile(uri, xml_path, key_dt))
                             except Exception as ex:
-                                self.log.error(f"Could not download {key_xml} - {str(ex)}")
+                                self.log.error(
+                                    f"Could not download {key_xml} - {str(ex)}"
+                                )
                                 continue
 
             self.log.info(
@@ -171,7 +178,13 @@ def run(self):
                 json_gen.run()
 
             # plot the daily coverage
-            plot_file = plot_daily_coverage(InstrumentType.SOUNDTRAP, self.df, self.json_base_dir, self.start, self.end)
+            plot_file = plot_daily_coverage(
+                InstrumentType.SOUNDTRAP,
+                self.df,
+                self.json_base_dir,
+                self.start,
+                self.end,
+            )
             self.log.info(f"Coverage plot saved to {plot_file}")
 
 

pbp/meta_gen/json_generator.py

@@ -172,7 +172,9 @@ def no_jitter(self, day_df: pd.DataFrame) -> pd.DataFrame:
         :return:
             The corrected dataframe
         """
-        self.log.info(f"Using file start times as is, setting jitter to 0 and calculating end times.")
+        self.log.info(
+            f"Using file start times as is, setting jitter to 0 and calculating end times."
+        )
         # calculate the difference between each row start time and save as diff in a copy of the dataframe
         day_df = day_df.copy()
         day_df["diff"] = day_df["start"].diff()

pbp/meta_gen/utils.py

@@ -92,7 +92,13 @@ def get_datetime(time_str: str, prefixes: List[str]):
     return None
 
 
-def plot_daily_coverage(instrument_type: InstrumentType, df: pd.DataFrame, base_dir: str, start: datetime, end: datetime) -> str:
+def plot_daily_coverage(
+    instrument_type: InstrumentType,
+    df: pd.DataFrame,
+    base_dir: str,
+    start: datetime,
+    end: datetime,
+) -> str:
     """
     Plot the daily coverage of the recordings
     :param instrument_type: The type of instrument, e.g. NRS, ICLISTEN, SOUNDTRAP
@@ -104,20 +110,22 @@ def plot_daily_coverage(instrument_type: InstrumentType, df: pd.DataFrame, base_
     """
     # Create a plot of the dataframe with the x-axis as the month, and the y-axis as the daily recording coverage,
     # which is percent of the day covered by recordings
-    plt.rcParams['text.usetex'] = False
+    plt.rcParams["text.usetex"] = False
     df["duration"] = (df["end"] - df["start"]).dt.total_seconds()
     ts_df = df[["start", "duration"]].copy()
-    ts_df.set_index('start', inplace=True)
-    daily_sum_df = ts_df.resample('D').sum()
+    ts_df.set_index("start", inplace=True)
+    daily_sum_df = ts_df.resample("D").sum()
     daily_sum_df["coverage"] = 100 * daily_sum_df["duration"] / 86400
-    daily_sum_df["coverage"] = daily_sum_df["coverage"].round()  # round to nearest integer
+    daily_sum_df["coverage"] = daily_sum_df[
+        "coverage"
+    ].round()  # round to nearest integer
     plot = daily_sum_df["coverage"].plot()
     plot.set_ylabel("Daily Coverage (%)")
     plot.set_xlabel("Date")
     plot.set_xticks(daily_sum_df.index.values)
     # Angle the x-axis labels for better readability and force them to be in the format YYYY-MM-DD
-    plot.set_xticklabels([x.strftime('%Y-%m-%d') for x in daily_sum_df.index])
-    plot.set_xticklabels(plot.get_xticklabels(), rotation=45, horizontalalignment='right')
+    plot.set_xticklabels([x.strftime("%Y-%m-%d") for x in daily_sum_df.index])
+    plot.set_xticklabels(plot.get_xticklabels(), rotation=45, horizontalalignment="right")
     # Adjust the title based on the instrument type
     if instrument_type == InstrumentType.NRS:
         plot.set_title("Daily Coverage of NRS Recordings")
@@ -131,4 +139,4 @@ def plot_daily_coverage(instrument_type: InstrumentType, df: pd.DataFrame, base_
     fig.set_size_inches(10, 5)
     fig.set_dpi(dpi)
     fig.savefig(plot_file.as_posix(), bbox_inches="tight")
-    return plot_file.as_posix()
+    return plot_file.as_posix()

tests/test_meta_generator.py

@@ -83,6 +83,7 @@ def test_soundtrap_generator():
     coverage_plot = json_dir / "soundtrap_coverage_20230715_20230716.jpg"
     assert coverage_plot.exists()
 
+
 def test_iclisten_generator():
     """
     Test fixture for IcListenMetadataGenerator.