Add flake8-commas rules

disdrodb/api/checks.py

@@ -207,7 +207,11 @@ def check_station_has_data(product, data_source, campaign_name, station_name, ba
 def check_metadata_dir(product, data_source, campaign_name, base_dir=None):
     """Check existence of the metadata directory. If does not exists, raise an error."""
     metadata_dir = define_metadata_dir(
-        product=product, base_dir=base_dir, data_source=data_source, campaign_name=campaign_name, check_exists=False
+        product=product,
+        base_dir=base_dir,
+        data_source=data_source,
+        campaign_name=campaign_name,
+        check_exists=False,
     )
     if not os.path.exists(metadata_dir) and os.path.isdir(metadata_dir):
         msg = f"The metadata directory does not exist at {metadata_dir}."
@@ -253,7 +257,10 @@ def check_metadata_file(product, data_source, campaign_name, station_name, base_
 def check_issue_dir(data_source, campaign_name, base_dir=None):
     """Check existence of the issue directory. If does not exists, raise an error."""
     issue_dir = define_issue_dir(
-        base_dir=base_dir, data_source=data_source, campaign_name=campaign_name, check_exists=False
+        base_dir=base_dir,
+        data_source=data_source,
+        campaign_name=campaign_name,
+        check_exists=False,
     )
     if not os.path.exists(issue_dir) and os.path.isdir(issue_dir):
         msg = "The issue directory does not exist at {issue_dir}."

disdrodb/api/create_directories.py

@@ -117,7 +117,11 @@ def _check_campaign_name_consistency(raw_dir: str, processed_dir: str) -> str:
 
 
 def _copy_station_metadata(
-    data_source: str, campaign_name: str, station_name: str, base_dir: str = None, check_validity: bool = False
+    data_source: str,
+    campaign_name: str,
+    station_name: str,
+    base_dir: str = None,
+    check_validity: bool = False,
 ) -> None:
     """Copy the station YAML file from the ``raw_dir/metadata`` into ``processed_dir/metadata``.
 
@@ -159,7 +163,12 @@ def _copy_station_metadata(
 
 
 def _check_pre_existing_station_data(
-    data_source: str, campaign_name: str, station_name: str, product: str, base_dir=None, force=False
+    data_source: str,
+    campaign_name: str,
+    station_name: str,
+    product: str,
+    base_dir=None,
+    force=False,
 ):
     """Check for pre-existing station data.
 
@@ -328,7 +337,10 @@ def _create_station_directories(
         station_name=station_name,
     )
     _ = create_metadata_directory(
-        base_dir=base_dir, product=product, data_source=data_source, campaign_name=campaign_name
+        base_dir=base_dir,
+        product=product,
+        data_source=data_source,
+        campaign_name=campaign_name,
     )
 
     if product.upper() == "RAW":
@@ -400,7 +412,7 @@ def create_initial_station_structure(
         raise ValueError(
             f"A metadata file already exists at {metadata_filepath}. "
             "The station is already part of the DISDRODB Archive or "
-            "or you already initialized the directory structure for the station !"
+            "or you already initialized the directory structure for the station !",
         )
 
     # Create directory structure (/metadata, /issue and /data/<station_name>)
@@ -429,7 +441,10 @@ def create_initial_station_structure(
 
     # Report location of the campaign directory
     campaign_dir = define_campaign_dir(
-        base_dir=base_dir, data_source=data_source, campaign_name=campaign_name, product="RAW"
+        base_dir=base_dir,
+        data_source=data_source,
+        campaign_name=campaign_name,
+        product="RAW",
     )
     print(f"Initial station directory structure created at: {campaign_dir}")
 
@@ -479,7 +494,10 @@ def create_test_archive(test_base_dir, data_source, campaign_name, station_name,
         base_dir=base_dir,
     )
     dst_issue_fpath = define_issue_filepath(
-        data_source=data_source, campaign_name=campaign_name, station_name=station_name, base_dir=test_base_dir
+        data_source=data_source,
+        campaign_name=campaign_name,
+        station_name=station_name,
+        base_dir=test_base_dir,
     )
     copy_file(src_issue_fpath, dst_issue_fpath)
     copy_file(src_metadata_fpath, dst_metadata_fpath)

disdrodb/data_transfer/download_data.py

@@ -315,7 +315,7 @@ def _download_file_from_url(url: str, dst_dir: str, force: bool = False) -> str:
         else:
             raise ValueError(
                 f"There are already raw files within {dst_dir}. Download is suspended. "
-                "Use force=True to force the download and overwrite existing raw files."
+                "Use force=True to force the download and overwrite existing raw files.",
             )
 
     os.makedirs(dst_dir, exist_ok=True)

disdrodb/data_transfer/zenodo.py

@@ -195,7 +195,7 @@ def _define_zenodo_metadata(metadata):
             "upload_type": "dataset",
             "description": description,
             "creators": _define_creators_list(metadata),
-        }
+        },
     }
     return zenodo_metadata
 
@@ -235,7 +235,9 @@ def upload_station_to_zenodo(metadata_filepath: str, sandbox: bool = True) -> st
     print(" - Uploading station data")
     try:
         disdrodb_data_url = _upload_file_to_zenodo(
-            filepath=station_zip_filepath, metadata_filepath=metadata_filepath, sandbox=sandbox
+            filepath=station_zip_filepath,
+            metadata_filepath=metadata_filepath,
+            sandbox=sandbox,
         )
         os.remove(station_zip_filepath)
     except Exception as e:

disdrodb/l0/check_configs.py

@@ -294,10 +294,16 @@ def _check_bin_consistency(sensor_name: str) -> None:
     if all(arr.size > 1 for arr in [velocity_bin_center, velocity_bin_lower, velocity_bin_upper, velocity_bin_width]):
         np.testing.assert_allclose(velocity_bin_upper - velocity_bin_lower, velocity_bin_width, atol=1e-3, rtol=1e-4)
         np.testing.assert_allclose(
-            velocity_bin_lower + velocity_bin_width / 2, velocity_bin_center, atol=1e-3, rtol=1e-4
+            velocity_bin_lower + velocity_bin_width / 2,
+            velocity_bin_center,
+            atol=1e-3,
+            rtol=1e-4,
         )
         np.testing.assert_allclose(
-            velocity_bin_upper - velocity_bin_width / 2, velocity_bin_center, atol=1e-3, rtol=1e-4
+            velocity_bin_upper - velocity_bin_width / 2,
+            velocity_bin_center,
+            atol=1e-3,
+            rtol=1e-4,
         )
 
 

disdrodb/l0/l0_processing.py

@@ -480,7 +480,7 @@ def run_l0a(
                 force=force,
                 verbose=verbose,
                 parallel=parallel,
-            )
+            ),
         )
     if parallel:
         list_logs = dask.compute(*list_tasks)
@@ -611,7 +611,7 @@ def run_l0b(
                     verbose=verbose,
                     debugging_mode=debugging_mode,
                     parallel=parallel,
-                )
+                ),
             )
     else:
         bag = db.from_sequence(filepaths, npartitions=len(filepaths))
@@ -770,7 +770,7 @@ def run_l0b_from_nc(
                     force=force,
                     verbose=verbose,
                     parallel=parallel,
-                )
+                ),
             )
     else:
         bag = db.from_sequence(filepaths, npartitions=len(filepaths))

disdrodb/l0/l0_reader.py

@@ -281,7 +281,7 @@ def _check_metadata_reader(metadata):
     if "/" not in reader_reference:
         raise ValueError(
             f"The reader '{reader_reference}' reported in the metadata is not valid. Must have"
-            " '<DATA_SOURCE>/<READER_NAME>' pattern."
+            " '<DATA_SOURCE>/<READER_NAME>' pattern.",
         )
     # - Get the reader_reference component list
     reader_components = reader_reference.split("/")
@@ -335,7 +335,7 @@ def get_station_reader_function(data_source, campaign_name, station_name, base_d
     if "reader" not in metadata:
         raise ValueError(
             "The `reader` key is not available in the metadata of the"
-            f" {data_source} {campaign_name} {station_name} station."
+            f" {data_source} {campaign_name} {station_name} station.",
         )
 
     # ------------------------------------------------------------------------.

disdrodb/l0/standards.py

@@ -716,7 +716,7 @@ def _check_contiguous_chunksize_agrees(encoding_dict, var):
     contiguous = encoding_dict[var].get("contiguous", False)
     if isinstance(chunksizes, list) and len(chunksizes) >= 1 and contiguous:
         raise ValueError(
-            f"Invalid encodings for variable {var}. 'chunksizes' are specified but 'contiguous' is set to True !"
+            f"Invalid encodings for variable {var}. 'chunksizes' are specified but 'contiguous' is set to True !",
         )
 
 

disdrodb/l0/template_tools.py

@@ -522,7 +522,7 @@ def infer_column_names(df: pd.DataFrame, sensor_name: str, row_idx: int = 1):
         if not _has_constant_characters(arr):
             print(
                 f"ATTENTION: Column {i} values have non-unique number of characters. "
-                f"Selecting row {row_idx} to infer possible columns."
+                f"Selecting row {row_idx} to infer possible columns.",
             )
 
         # Subset a single string

disdrodb/metadata/checks.py

@@ -90,7 +90,7 @@ def _check_metadata_campaign_name(metadata, expected_name):
         raise ValueError("The 'campaign_name' key in the metadata is empty.")
     if campaign_name != expected_name:
         raise ValueError(
-            f"The campaign_name in the metadata is '{campaign_name}' but the campaign directory is '{expected_name}'"
+            f"The campaign_name in the metadata is '{campaign_name}' but the campaign directory is '{expected_name}'",
         )
     return None
 
@@ -104,7 +104,7 @@ def _check_metadata_data_source(metadata, expected_name):
         raise ValueError("The 'data_source' key in the metadata is empty.")
     if data_source != expected_name:
         raise ValueError(
-            f"The data_source in the metadata is '{data_source}' but the data_source directory is '{expected_name}'"
+            f"The data_source in the metadata is '{data_source}' but the data_source directory is '{expected_name}'",
         )
     return None
 
@@ -123,7 +123,8 @@ def _check_metadata_station_name(metadata, expected_name):
         raise ValueError("The 'station_name' key in the metadata is empty.")
     if station_name != expected_name:
         raise ValueError(
-            f"The station_name in the metadata is '{station_name}' but the metadata file is named '{expected_name}.yml'"
+            f"The station_name in the metadata is '{station_name}' but the metadata file is named"
+            f" '{expected_name}.yml'",
         )
     return None
 
@@ -265,7 +266,11 @@ def check_archive_metadata_keys(base_dir: str = None) -> bool:
     is_valid = True
     base_dir = get_base_dir(base_dir)
     list_metadata_paths = get_list_metadata(
-        base_dir=base_dir, data_sources=None, campaign_names=None, station_names=None, with_stations_data=False
+        base_dir=base_dir,
+        data_sources=None,
+        campaign_names=None,
+        station_names=None,
+        with_stations_data=False,
     )
     for filepath in list_metadata_paths:
         data_source = infer_data_source_from_path(filepath)
@@ -306,7 +311,11 @@ def check_archive_metadata_campaign_name(base_dir: str = None) -> bool:
     is_valid = True
     base_dir = get_base_dir(base_dir)
     list_metadata_paths = get_list_metadata(
-        base_dir=base_dir, data_sources=None, campaign_names=None, station_names=None, with_stations_data=False
+        base_dir=base_dir,
+        data_sources=None,
+        campaign_names=None,
+        station_names=None,
+        with_stations_data=False,
     )
     for filepath in list_metadata_paths:
         data_source = infer_data_source_from_path(filepath)
@@ -346,7 +355,11 @@ def check_archive_metadata_data_source(base_dir: str = None) -> bool:
     is_valid = True
     base_dir = get_base_dir(base_dir)
     list_metadata_paths = get_list_metadata(
-        base_dir=base_dir, data_sources=None, campaign_names=None, station_names=None, with_stations_data=False
+        base_dir=base_dir,
+        data_sources=None,
+        campaign_names=None,
+        station_names=None,
+        with_stations_data=False,
     )
     for filepath in list_metadata_paths:
         data_source = infer_data_source_from_path(filepath)
@@ -386,7 +399,11 @@ def check_archive_metadata_sensor_name(base_dir: str = None) -> bool:
     is_valid = True
     base_dir = get_base_dir(base_dir)
     list_metadata_paths = get_list_metadata(
-        base_dir=base_dir, data_sources=None, campaign_names=None, station_names=None, with_stations_data=False
+        base_dir=base_dir,
+        data_sources=None,
+        campaign_names=None,
+        station_names=None,
+        with_stations_data=False,
     )
     for filepath in list_metadata_paths:
         data_source = infer_data_source_from_path(filepath)
@@ -426,7 +443,11 @@ def check_archive_metadata_station_name(base_dir: str = None) -> bool:
     is_valid = True
     base_dir = get_base_dir(base_dir)
     list_metadata_paths = get_list_metadata(
-        base_dir=base_dir, data_sources=None, campaign_names=None, station_names=None, with_stations_data=False
+        base_dir=base_dir,
+        data_sources=None,
+        campaign_names=None,
+        station_names=None,
+        with_stations_data=False,
     )
     for filepath in list_metadata_paths:
         data_source = infer_data_source_from_path(filepath)
@@ -468,7 +489,11 @@ def check_archive_metadata_reader(base_dir: str = None) -> bool:
     is_valid = True
     base_dir = get_base_dir(base_dir)
     list_metadata_paths = get_list_metadata(
-        base_dir=base_dir, data_sources=None, campaign_names=None, station_names=None, with_stations_data=False
+        base_dir=base_dir,
+        data_sources=None,
+        campaign_names=None,
+        station_names=None,
+        with_stations_data=False,
     )
     for filepath in list_metadata_paths:
         data_source = infer_data_source_from_path(filepath)
@@ -511,7 +536,11 @@ def check_archive_metadata_compliance(base_dir: str = None, raise_error=False):
     is_valid = True
     base_dir = get_base_dir(base_dir)
     list_metadata_paths = get_list_metadata(
-        base_dir=base_dir, data_sources=None, campaign_names=None, station_names=None, with_stations_data=False
+        base_dir=base_dir,
+        data_sources=None,
+        campaign_names=None,
+        station_names=None,
+        with_stations_data=False,
     )
     for filepath in list_metadata_paths:
         data_source = infer_data_source_from_path(filepath)
@@ -554,7 +583,11 @@ def check_archive_metadata_geolocation(base_dir: str = None):
     is_valid = True
     base_dir = get_base_dir(base_dir)
     list_metadata_paths = get_list_metadata(
-        base_dir=base_dir, data_sources=None, campaign_names=None, station_names=None, with_stations_data=False
+        base_dir=base_dir,
+        data_sources=None,
+        campaign_names=None,
+        station_names=None,
+        with_stations_data=False,
     )
     for filepath in list_metadata_paths:
         data_source = infer_data_source_from_path(filepath)

disdrodb/metadata/info.py

@@ -52,7 +52,11 @@ def get_archive_metadata_key_value(key: str, return_tuple: bool = True, base_dir
     """
     base_dir = get_base_dir(base_dir)
     list_metadata_paths = get_list_metadata(
-        base_dir=base_dir, data_sources=None, campaign_names=None, station_names=None, with_stations_data=False
+        base_dir=base_dir,
+        data_sources=None,
+        campaign_names=None,
+        station_names=None,
+        with_stations_data=False,
     )
     list_info = []
     for filepath in list_metadata_paths:

disdrodb/metadata/scripts/disdrodb_check_metadata_archive.py

@@ -27,7 +27,11 @@
 @click.command()
 @click_base_dir_option
 @click.option(
-    "--raise_error", type=bool, show_default=True, default=True, help="Whether to raise error of finish the check"
+    "--raise_error",
+    type=bool,
+    show_default=True,
+    default=True,
+    help="Whether to raise error of finish the check",
 )
 def disdrodb_check_metadata_archive(base_dir=None, raise_error=True):
     from disdrodb.metadata.checks import check_archive_metadata_compliance

disdrodb/tests/conftest.py

@@ -17,12 +17,19 @@ def create_fake_metadata_directory(base_dir, product, data_source="DATA_SOURCE",
     from disdrodb.api.create_directories import create_metadata_directory
 
     return create_metadata_directory(
-        base_dir=base_dir, product=product, data_source=data_source, campaign_name=campaign_name
+        base_dir=base_dir,
+        product=product,
+        data_source=data_source,
+        campaign_name=campaign_name,
     )
 
 
 def create_fake_station_dir(
-    base_dir, product, data_source="DATA_SOURCE", campaign_name="CAMPAIGN_NAME", station_name="station_name"
+    base_dir,
+    product,
+    data_source="DATA_SOURCE",
+    campaign_name="CAMPAIGN_NAME",
+    station_name="station_name",
 ):
     from disdrodb.api.create_directories import create_station_directory