refactor() : update doc (#184)

ltelab · May 8, 2023 · 2960369 · 2960369
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diff --git a/disdrodb/l0/io.py b/disdrodb/l0/io.py
@@ -946,7 +946,18 @@ def _check_pre_existing_station_data(campaign_dir, product_level, station_name,
 
 
 def check_processed_dir(processed_dir):
-    # Check input, format and validity of the directory path
+    """Check input, format and validity of the directory path
+
+    Parameters
+    ----------
+    processed_dir : str
+        Path of the processed directory
+
+    Returns
+    -------
+    str
+        Path of the processed directory
+    """
     processed_dir = _check_is_processed_dir(processed_dir)
     return processed_dir
 

diff --git a/disdrodb/l0/issue.py b/disdrodb/l0/issue.py
@@ -33,17 +33,53 @@
 
 
 def is_numpy_array_string(arr):
-    """Check if the numpy array contains strings."""
+    """Check if the numpy array contains strings
+
+    Parameters
+    ----------
+    arr : numpy array
+        Numpy array to check.
+    """
+
     dtype = arr.dtype.type
     return dtype == np.str_ or dtype == np.unicode_
 
 
 def is_numpy_array_datetime(arr):
+    """Check if the numpy array contains datetime64
+
+    Parameters
+    ----------
+    arr : numpy array
+        Numpy array to check.
+
+    Returns
+    -------
+    numpy array
+        Numpy array checked.
+    """
     return arr.dtype.type == np.datetime64
 
 
 def _check_timestep_datetime_accuracy(timesteps, unit="s"):
-    """Check the accuracy of the numpy datetime array."""
+    """Check the accuracy of the numpy datetime array.
+
+    Parameters
+    ----------
+    timesteps : numpy array
+        Numpy array to check.
+    unit : str, optional
+        Unit, by default "s"
+
+    Returns
+    -------
+    numpy array
+        Numpy array checked.
+
+    Raises
+    ------
+    ValueError
+    """
     if not timesteps.dtype == f"<M8[{unit}]":
         msg = f"The timesteps does not have datetime64 {unit} accuracy."
         log_error(logger, msg=msg, verbose=False)

diff --git a/disdrodb/l0/l0_processing.py b/disdrodb/l0/l0_processing.py
@@ -91,6 +91,8 @@ def _generate_l0a(
     parallel,
     issue_dict={},
 ):
+    """Generate L0A file from raw file."""
+
     from disdrodb.l0.io import get_L0A_fpath
     from disdrodb.l0.l0a_processing import (
         process_raw_file,

diff --git a/docs/source/api/disdrodb.l0.rst b/docs/source/api/disdrodb.l0.rst
@@ -28,6 +28,14 @@ disdrodb.l0.check\_metadata module
    :undoc-members:
    :show-inheritance:
 
+disdrodb.l0.check\_readers module
+---------------------------------
+
+.. automodule:: disdrodb.l0.check_readers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 disdrodb.l0.check\_standards module
 -----------------------------------
 

diff --git a/docs/source/metadata.rst b/docs/source/metadata.rst
@@ -27,6 +27,21 @@ There are 7 metadata keys for which is mandatory to specify the value :
     to process the data, you specify the reader name ``GPM/IFLOODS``.
 
 
+
+
+To check the validity of the metadata YAML files, run the following code:
+
+.. code-block:: python
+
+    from disdrodb.l0 import check_archive_metadata_compliance, check_archive_metadata_geolocation
+
+    disdrodb_dir = "<...>/DISDRODB"
+    check_archive_metadata_compliance(disdrodb_dir)
+    check_archive_metadata_geolocation(disdrodb_dir)
+
+
+
+
 The list of the standard metadata keys and their description is provided here below:
 
 
@@ -70,17 +85,3 @@ The list of the standard metadata keys and their description is provided here be
    :file: ./metadata_csv/Data_Attribution.csv
    :widths: auto
    :header-rows: 1
-
-
-
-
-
-To check the validity of the metadata YAML files, run the following code:
-
-.. code-block:: python
-
-    from disdrodb.l0 import check_archive_metadata_compliance, check_archive_metadata_geolocation
-
-    disdrodb_dir = "<...>/DISDRODB"
-    check_archive_metadata_compliance(disdrodb_dir)
-    check_archive_metadata_geolocation(disdrodb_dir)
diff --git a/docs/source/overview.rst b/docs/source/overview.rst
@@ -74,122 +74,3 @@ The current software structure is described below:
 | 📜 README.md
 | 📜 readthedocs.yml
 | 📜 requirements.txt
-
-
-
-
-Description of the disdrodb files and folders
-================================================
-
-The disdrodb folder contains the core software to process raw data files to DISDRODB L0 products. Here is a description of the files and folders:
-
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| Type  | Folder / files name                | Description                                                                                                  |
-+=======+====================================+==============================================================================================================+
-| 📁    | api                                | Contains some generic functions                                                                              |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | checks.py                          | Basic checks on paths                                                                                        |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | info.py                            | DISDRODB File Information and parser                                                                         |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | io.py                              | Input output fuctions                                                                                        |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | metadata.py                        | Operation on metadata stations files                                                                         |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📁    | data_transfer                      | Contains scripts to upload or download stations's data                                                       |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | download_data.py                   | Functions to download stations' raw data                                                                     |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | upload_data.py                     | Functions to upload to Zenodo stations' raw data                                                             |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📁    | l0                                 | Contains the software to produce the DISDRODB L0 products                                                    |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | check_configs.py                   | Contain functionsChecking the sensorConfigs YAML files                                                       |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | check_metadata.py                  | Contain functionsChecking the metadata YAML files                                                            |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | check_standards.py                 | Contain functionsChecking that DISDRODB standards are met                                                    |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | io.py                              | Core functions to read/write files andCreate/remove directories                                              |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | issue.py                           | Code to manage the issues YAML files and exclude erroneous time steps during L0 processing                   |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | l0_processing.py                   | Contain the functions to process raw data files to L0A and L0B                                               |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | l0_reader.py                       | Contain the functions to check and retrieve the DISDRODB readers                                             |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | l0a_processing.py                  | Contain the functions to process raw data files to L0A format (Parquet)                                      |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | l0b_concat.py                      | Contain the functions to concatenate multiple L0B files into a single L0B netCDF                             |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | l0b_processing.py                  | Contain the functions to process raw data files to L0B format (netCDF4)                                      |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | l0b_processing.py                  | Contain the functions to run the DISDRODB L0 processing                                                      |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | metadata.py                        | Code to read/write the metadata YAML files                                                                   |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | standards.py                       | Contain the functions to encode the L0 sensor specifications defined in L0.configs                           |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | summary.py                         | Contain the functions to define a summary for each station                                                   |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | template_tools.py                  | Helpers to Create DISDRODB readers                                                                           |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📁    | configs                            | Contains the specifications of various types of disdrometers                                                 |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📁    | <sensor_name>                      | Name of the sensor (e.g. OTT_Parsivel, OTT_Parsivel2, Thies_LPM, RD_80)                                      |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | *.yml                              | YAML files defining sensorCharacteristics (e.g. diameter and velocity bins)                                  |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📁    | manuals                            | Folder for the  Official disdrometers documentation                                                          |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | *.pdf                              | Official disdrometers documentation                                                                          |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📁    | readers                            | Folder that contains all the readers functions                                                               |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📁    | <data_source>                      | e.g. GPM, ARM, EPFL, ...                                                                                     |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | <reader_name>.py                   | Readers to transform raw data into DISDRODB L0 products                                                      |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📁    | scripts                            | Contains a set of python scripts to beCalled from the terminal to launch the L0 processing                   |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | run_disdrodb_l0_station.py         | Script launching the L0 processing for a specific station                                                    |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | run_disdrodb_l0                    | Script launching the L0 processing for specific portion of the DISDRODB archive                              |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | run_disdrodb_l0a.py                | Script to run the L0A processing of DISDRODB stations                                                        |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | run_disdrodb_l0a_station.py        | Script to run the L0A processing of a specific DISDRODB station from the terminal                            |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | run_disdrodb_l0b.py                | Script to run the L0B processing of DISDRODB stations                                                        |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | run_disdrodb_l0b_station.py        | Script to run the L0B processing of a specific DISDRODB station from the terminal                            |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | run_disdrodb_l0b_concat.py         | Script to run the L0BConcatenation of available DISDRODB stations                                            |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | run_disdrodb_l0b_concat_station.py | Script toConcatenate all L0B files of a specific DISDRODB station into a single netCDF                       |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📁    | l1                                 | Code not yet implemented. It willContain software to homogenize and qualityCheck DISDRODB L0 products        |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📁    | l2                                 | Code not yet implemented. It willContain software to produce DISDRODB L2 products (i.e. DSD parameters, ...) |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📁    | tests                              | Folder containing the tests (readers and unit tests)                                                         |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📁    | utils                              | Folder to gather small, reusable functions orClasses                                                         |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | logger.py                          | Logger functions                                                                                             |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | scripts.py                         | Utility functions to run python scripts into the terminal                                                    |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-| 📜    | netcdf.py                          | Utility function toCheck and merge/concat multiple netCDF4 files                                             |
-+-------+------------------------------------+--------------------------------------------------------------------------------------------------------------+
-
-
-
-Description of the other folders
-================================================
-
-Some other folder are included in the DISDRODB repository. Here is a short description of their content:
-
-* data : sample data to test the DISDRODB L0 l0_processing
-* docs : documentation of the DISDRODB L0 processing
-* tutorials : Jupyter notebooks to illustrate the DISDRODB L0 processing