Add pycodestyle rules

disdrodb/api/checks.py

@@ -129,7 +129,7 @@ def check_sensor_name(sensor_name: str, product: str = "L0A") -> None:
 
 
 def check_campaign_name(campaign_name):
-    """Check the campaign name is upper case !"""
+    """Check the campaign name is upper case !."""
     upper_campaign_name = campaign_name.upper()
     if campaign_name != upper_campaign_name:
         msg = f"The campaign directory name {campaign_name} must be defined uppercase: {upper_campaign_name}"
@@ -138,7 +138,7 @@ def check_campaign_name(campaign_name):
 
 
 def check_data_source(data_source):
-    """Check the data_source name is upper case !"""
+    """Check the data_source name is upper case !."""
     upper_data_source = data_source.upper()
     if data_source != upper_data_source:
         msg = f"The data source directory name {data_source} must be defined uppercase: {upper_data_source}"

disdrodb/api/create_directories.py

@@ -376,6 +376,7 @@ def create_station_directory(base_dir, product, data_source, campaign_name, stat
 
 
 def create_issue_directory(base_dir, data_source, campaign_name):
+    """Create issue directory."""
     issue_dir = define_issue_dir(
         base_dir=base_dir,
         data_source=data_source,

disdrodb/api/info.py

@@ -91,45 +91,45 @@ def _get_version_from_filepath(filepath):
 
 
 def get_version_from_filepaths(filepaths):
-    """Return the DISDROB product version of the specified files"""
+    """Return the DISDROB product version of the specified files."""
     if isinstance(filepaths, str):
         filepaths = [filepaths]
     list_version = [_get_version_from_filepath(filepath) for filepath in filepaths]
     return list_version
 
 
 def get_campaign_name_from_filepaths(filepaths):
-    """Return the DISDROB campaign name of the specified files"""
+    """Return the DISDROB campaign name of the specified files."""
     list_id = get_key_from_filepaths(filepaths, key="campaign_name")
     return list_id
 
 
 def get_station_name_from_filepaths(filepaths):
-    """Return the DISDROB station name of the specified files"""
+    """Return the DISDROB station name of the specified files."""
     list_id = get_key_from_filepaths(filepaths, key="station_name")
     return list_id
 
 
 def get_product_from_filepaths(filepaths):
-    """Return the DISDROB product name of the specified files"""
+    """Return the DISDROB product name of the specified files."""
     list_id = get_key_from_filepaths(filepaths, key="product")
     return list_id
 
 
 def get_start_time_from_filepaths(filepaths):
-    """Return the start time of the specified files"""
+    """Return the start time of the specified files."""
     list_start_time = get_key_from_filepaths(filepaths, key="start_time")
     return list_start_time
 
 
 def get_end_time_from_filepaths(filepaths):
-    """Return the end time of the specified files"""
+    """Return the end time of the specified files."""
     list_end_time = get_key_from_filepaths(filepaths, key="end_time")
     return list_end_time
 
 
 def get_start_end_time_from_filepaths(filepaths):
-    """Return the start and end time of the specified files"""
+    """Return the start and end time of the specified files."""
     list_start_time = get_key_from_filepaths(filepaths, key="start_time")
     list_end_time = get_key_from_filepaths(filepaths, key="end_time")
     return np.array(list_start_time), np.array(list_end_time)

disdrodb/api/io.py

@@ -281,7 +281,7 @@ def available_stations(
 ):
     """Return stations for which data are available on disk."""
     base_dir = get_base_dir(base_dir)
-    # Checks
+    # Checks arguments
     product = check_product(product)
     data_sources = _check_data_sources(
         base_dir=base_dir,
@@ -293,11 +293,6 @@ def available_stations(
         product=product,
         campaign_names=campaign_names,
     )
-    # Format arguments to list
-    if isinstance(data_sources, str):
-        data_sources = [data_sources]
-    if isinstance(campaign_names, str):
-        campaign_names = [campaign_names]
 
     # If data_source is None, first retrieve all stations
     if data_sources is None:
@@ -309,14 +304,17 @@ def available_stations(
             data_sources=data_sources,
             product=product,
         )
-
     # Then, if campaign_name is not None, subset by campaign_name
     if campaign_names is not None:
         list_info = [info for info in list_info if info[1] in campaign_names]
 
     if return_tuple:
         return list_info
 
+    # TODO:
+    # - Filter by station names !
+    # - Add check_station_names
+
     # TODO: ENSURE THAT NO DUPLICATED STATION NAMES ?
     list_stations = [info[2] for info in list_info]
     return list_stations

disdrodb/api/scripts/disdrodb_initialize_station.py

@@ -14,6 +14,7 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 # -----------------------------------------------------------------------------.
+"""Script to initialize the DISDRODB station directory structure."""
 import sys
 from typing import Optional
 
@@ -38,7 +39,7 @@ def disdrodb_initialize_station(
     # Processing options
     base_dir: Optional[str] = None,
 ):
-    """Initialize the DISDRODB directory structure for a station.
+    r"""Initialize the DISDRODB directory structure for a station.
 
     It adds the relevant directories and the default issue and metadata YAML files..
 

disdrodb/configs.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Created on Thu Nov  2 15:39:01 2023
+Created on Thu Nov  2 15:39:01 2023.
 
 @author: ghiggi
 """

disdrodb/data_transfer/download_data.py

@@ -83,7 +83,6 @@ def click_download_options(function: object):
     function : object
         Function.
     """
-
     function = click.option(
         "-f",
         "--force",
@@ -103,8 +102,7 @@ def download_archive(
     force: bool = False,
     base_dir: Optional[str] = None,
 ):
-    """Get all YAML files that contain the ``disdrodb_data_url`` key
-    and download the data locally.
+    """Download DISDRODB stations with the ``disdrodb_data_url`` in the metadata.
 
     Parameters
     ----------

disdrodb/data_transfer/scripts/disdrodb_download_archive.py

@@ -38,6 +38,29 @@ def disdrodb_download_archive(
     base_dir: Optional[str] = None,
     force: bool = False,
 ):
+    """Download DISDRODB stations with the ``disdrodb_data_url`` in the metadata.
+
+    Parameters
+    ----------
+    data_sources : str or list of str, optional
+        Data source name (eg : EPFL).
+        If not provided (``None``), all data sources will be downloaded.
+        The default is ``data_source=None``.
+    campaign_names : str or list of str, optional
+        Campaign name (eg :  EPFL_ROOF_2012).
+        If not provided (``None``), all campaigns will be downloaded.
+        The default is ``campaign_name=None``.
+    station_names : str or list of str, optional
+        Station name.
+        If not provided (``None``), all stations will be downloaded.
+        The default is ``station_name=None``.
+    force : bool, optional
+        If ``True``, overwrite the already existing raw data file.
+        The default is ``False``.
+    base_dir : str (optional)
+        Base directory of DISDRODB. Format: ``<...>/DISDRODB``.
+        If ``None`` (the default), the disdrodb config variable ``base_dir`` is used.
+    """
     from disdrodb.data_transfer.download_data import download_archive
 
     base_dir = parse_base_dir(base_dir)

disdrodb/data_transfer/scripts/disdrodb_download_station.py

@@ -40,6 +40,29 @@ def disdrodb_download_station(
     base_dir: Optional[str] = None,
     force: bool = False,
 ):
+    """
+    Download data of a single DISDRODB station from the DISDRODB remote repository.
+
+    Parameters
+    ----------
+    data_source : str
+        The name of the institution (for campaigns spanning multiple countries) or
+        the name of the country (for campaigns or sensor networks within a single country).
+        Must be provided in UPPER CASE.
+    campaign_name : str
+        The name of the campaign. Must be provided in UPPER CASE.
+    station_name : str
+        The name of the station.
+    base_dir : str, optional
+        The base directory of DISDRODB, expected in the format ``<...>/DISDRODB``.
+        If not specified, the path specified in the DISDRODB active configuration will be used.
+    force: bool, optional
+        If ``True``, overwrite the already existing raw data file.
+        The default is ``False``.
+    base_dir : str (optional)
+        Base directory of DISDRODB. Format: ``<...>/DISDRODB``.
+        If ``None`` (the default), the disdrodb config variable ``base_dir`` is used.
+    """
     from disdrodb.data_transfer.download_data import download_station
 
     base_dir = parse_base_dir(base_dir)

disdrodb/data_transfer/scripts/disdrodb_upload_archive.py

@@ -41,6 +41,36 @@ def disdrodb_upload_archive(
     platform: Optional[str] = None,
     force: bool = False,
 ):
+    """Find all stations containing local data and upload them to a remote repository.
+
+    Parameters
+    ----------
+    platform: str, optional
+        Name of the remote platform.
+        The default platform is ``"sandbox.zenodo"`` (for testing purposes).
+        Switch to ``"zenodo"`` for final data dissemination.
+    force: bool, optional
+        If ``True``, upload even if data already exists on another remote location.
+        The default is ``force=False``.
+    base_dir : str (optional)
+        Base directory of DISDRODB. Format: ``<...>/DISDRODB``.
+        If ``None`` (the default), the ``base_dir`` path specified in the DISDRODB active configuration will be used.
+
+    Other Parameters
+    ----------------
+    data_sources: str or list of str, optional
+        Data source name (eg: EPFL).
+        If not provided (``None``), all data sources will be uploaded.
+        The default is ``data_source=None``.
+    campaign_names: str or list of str, optional
+        Campaign name (eg:  EPFL_ROOF_2012).
+        If not provided (``None``), all campaigns will be uploaded.
+        The default is ``campaign_name=None``.
+    station_names: str or list of str, optional
+        Station name.
+        If not provided (``None``), all stations will be uploaded.
+        The default is ``station_name=None``.
+    """
     from disdrodb.data_transfer.upload_data import upload_archive
 
     base_dir = parse_base_dir(base_dir)

disdrodb/data_transfer/scripts/disdrodb_upload_station.py

@@ -41,6 +41,33 @@ def disdrodb_upload_station(
     base_dir: Optional[str] = None,
     force: bool = False,
 ):
+    """
+    Upload data from a single DISDRODB station on a remote repository.
+
+    This function also automatically update the disdrodb_data url in the metadata file.
+
+    Parameters
+    ----------
+    data_source : str
+        The name of the institution (for campaigns spanning multiple countries) or
+        the name of the country (for campaigns or sensor networks within a single country).
+        Must be provided in UPPER CASE.
+    campaign_name : str
+        The name of the campaign. Must be provided in UPPER CASE.
+    station_name : str
+        The name of the station.
+    base_dir : str, optional
+        The base directory of DISDRODB, expected in the format ``<...>/DISDRODB``.
+        If ``None`` (the default), the ``base_dir`` path specified in the DISDRODB active configuration will be used.
+    platform: str, optional
+        Name of the remote data storage platform.
+        The default platform is ``"sandbox.zenodo"`` (for testing purposes).
+        Switch to ``"zenodo"`` for final data dissemination.
+    force: bool, optional
+        If ``True``, upload the data and overwrite the ``disdrodb_data_url``.
+        The default is ``force=False``.
+
+    """
     from disdrodb.data_transfer.upload_data import upload_station
 
     base_dir = parse_base_dir(base_dir)

disdrodb/data_transfer/upload_data.py

@@ -29,6 +29,7 @@
 
 
 def click_upload_options(function: object):
+    """Click command arguments for DISDRODB data upload."""
     function = click.option(
         "--platform",
         type=click.Choice(["zenodo", "sandbox.zenodo"], case_sensitive=False),
@@ -199,7 +200,6 @@ def upload_archive(
 
     Other Parameters
     ----------------
-
     data_sources: str or list of str, optional
         Data source name (eg: EPFL).
         If not provided (``None``), all data sources will be uploaded.

disdrodb/data_transfer/zenodo.py

@@ -34,7 +34,6 @@ def _check_http_response(
     task_description: str,
 ) -> None:
     """Check the Zenodo HTTP request response status code and raise an error if not the expected one."""
-
     if response.status_code == expected_status_code:
         return
 
@@ -95,7 +94,6 @@ def _define_disdrodb_data_url(zenodo_host, deposit_id, filename):
 
 def _upload_file_to_zenodo(filepath: str, metadata_filepath: str, sandbox: bool) -> None:
     """Upload a file to a Zenodo bucket."""
-
     # Read metadata
     metadata = read_yaml(metadata_filepath)
     data_source = metadata["data_source"]

disdrodb/issue/__init__.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Created on Sat Nov 11 01:12:40 2023
+Created on Sat Nov 11 01:12:40 2023.
 
 @author: ghiggi
 """

disdrodb/issue/checks.py

@@ -35,7 +35,6 @@ def _is_numpy_array_string(arr):
     arr : numpy array
         Numpy array to check.
     """
-
     dtype = arr.dtype.type
     return dtype in (np.str_, np.unicode_)
 
@@ -148,7 +147,6 @@ def check_timesteps(timesteps):
 
 def _check_time_period_nested_list_format(time_periods):
     """Check that the time_periods is a list of list of length 2."""
-
     if not isinstance(time_periods, list):
         msg = "'time_periods' must be a list'"
         log_error(logger, msg=msg, verbose=False)

disdrodb/issue/reader.py

@@ -28,6 +28,8 @@
 
 
 class NoDatesSafeLoader(yaml.SafeLoader):
+    """A YAML loader that does not parse dates."""
+
     @classmethod
     def remove_implicit_resolver(cls, tag_to_remove):
         """
@@ -47,7 +49,7 @@ def remove_implicit_resolver(cls, tag_to_remove):
 
 
 def _load_yaml_without_date_parsing(filepath):
-    "Read a YAML file without converting automatically date string to datetime."
+    """Read a YAML file without converting automatically date string to datetime."""
     NoDatesSafeLoader.remove_implicit_resolver("tag:yaml.org,2002:timestamp")
     with open(filepath) as f:
         dictionary = yaml.load(f, Loader=NoDatesSafeLoader)

disdrodb/issue/writer.py

@@ -30,7 +30,7 @@
 
 
 def _write_issue_docs(f):
-    """Provide template for issue.yml"""
+    """Provide template for issue.yml."""
     f.write("""# This file is used to store timesteps/time periods with wrong/corrupted observation.
 # The specified timesteps are dropped during the L0 processing.
 # The time format used is the isoformat : YYYY-mm-dd HH:MM:SS.