Update docstring as per numpy style format

ioos · Aug 7, 2024 · 4d8285e · 4d8285e
1 parent 5c974e6
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Showing 6 changed files with 250 additions and 172 deletions.
diff --git a/ioos_qc/argo.py b/ioos_qc/argo.py
@@ -24,12 +24,14 @@ def pressure_increasing_test(inp):
 
     Ref: ARGO QC Manual: 8. Pressure increasing test
 
-    Args
-    ----
-        inp: Pressure values as a numeric numpy array or a list of numbers.
+    Parameters
+    ----------
+    inp 
+        Pressure values as a numeric numpy array or a list of numbers.
 
     Returns
     -------
+    flag_arr
         A masked array of flag values equal in size to that of the input.
 
     """
@@ -68,25 +70,31 @@ def speed_test(
     Missing and masked data is flagged as UNKNOWN.
 
     If this test fails, it typically means that either a position or time is bad data,
-     or that a platform is mislabeled.
+    or that a platform is mislabeled.
 
     Ref: ARGO QC Manual: 5. Impossible speed test
 
-    Args
-    ----
-        lon: Longitudes as a numeric numpy array or a list of numbers.
-        lat: Latitudes as a numeric numpy array or a list of numbers.
-        tinp: Time data as a sequence of datetime objects compatible with pandas DatetimeIndex.
-              This includes numpy datetime64, python datetime objects and pandas Timestamp object.
-              ie. pd.DatetimeIndex([datetime.utcnow(), np.datetime64(), pd.Timestamp.now()]
-              If anything else is passed in the format is assumed to be seconds since the unix epoch.
-        suspect_threshold: A float value representing a speed, in meters per second.
-           Speeds exceeding this will be flagged as SUSPECT.
-        fail_threshold: A float value representing a speed, in meters per second.
-           Speeds exceeding this will be flagged as FAIL.
+    Parameters
+    ----------
+    lon
+        Longitudes as a numeric numpy array or a list of numbers.
+    lat
+        Latitudes as a numeric numpy array or a list of numbers.
+    tinp
+        Time data as a sequence of datetime objects compatible with pandas DatetimeIndex.
+        This includes numpy datetime64, python datetime objects and pandas Timestamp object.
+        ie. pd.DatetimeIndex([datetime.utcnow(), np.datetime64(), pd.Timestamp.now()])
+        If anything else is passed in the format is assumed to be seconds since the unix epoch.
+    suspect_threshold
+        A float value representing a speed, in meters per second.
+        Speeds exceeding this will be flagged as SUSPECT.
+    fail_threshold
+        A float value representing a speed, in meters per second.
+        Speeds exceeding this will be flagged as FAIL.
 
     Returns
     -------
+    flag_arr
         A masked array of flag values equal in size to that of the input.
 
     """

diff --git a/ioos_qc/axds.py b/ioos_qc/axds.py
@@ -39,22 +39,25 @@ def valid_range_test(
     treated as inclusive and the second span valid is treated as exclusive. To change this
     behavior you can use the parameters `start_inclusive` and `end_inclusive`.
 
-    Args
-    ----
-        inp (Sequence[any]): Data as a sequence of objects compatible with the fail_span objects
-        fail_span (Tuple[any, any]): 2-tuple range which to flag outside data as FAIL. Objects
-            should be of equal format to that of the inp parameter as they will be checked for
-            equality without type conversion.
-        dtype (np.dtype): Optional. If your data is not already numpy-typed you can specify its
-            dtype here.
-        start_inclusive (bool): Optional. If the starting span value should be inclusive (True) or
-            exclusive (False).
-        end_inclusive (bool): Optional. If the ending span value should be inclusive (True) or
-            exclusive (False).
+    Parameters
+    ----------
+    inp (Sequence[any])
+        Data as a sequence of objects compatible with the fail_span objects
+    fail_span (Tuple[any, any])
+        2-tuple range which to flag outside data as FAIL. Objects
+        should be of equal format to that of the inp parameter as they will be checked for
+        equality without type conversion.
+    dtype (np.dtype)
+        Optional. If your data is not already numpy-typed you can specify its dtype here.
+    start_inclusive (bool)
+        Optional. If the starting span value should be inclusive (True) or exclusive (False).
+    end_inclusive (bool)
+        Optional. If the ending span value should be inclusive (True) or exclusive (False).
 
     Returns
     -------
-        np.ma.core.MaskedArray: A masked array of flag values equal in size to that of the input.
+    np.ma.core.MaskedArray
+        A masked array of flag values equal in size to that of the input.
 
     """
     # Numpy array inputs

diff --git a/ioos_qc/config.py b/ioos_qc/config.py
@@ -5,7 +5,8 @@
 
 Attributes
 ----------
-    tw (namedtuple): The TimeWindow namedtuple definition
+tw (namedtuple)
+    The TimeWindow namedtuple definition
 
 """
 
@@ -182,9 +183,10 @@ def run(self, **passedkwargs):
 def extract_calls(source) -> List[Call]:
     """Extracts call objects from a source object.
 
-    Args
-    ----
-        source ([any]): The source of Call objects, this can be a:
+    Parameters
+    ----------
+    source ([any]):
+        The source of Call objects, this can be a:
             * Call object
             * list of Call objects
             * list of objects with the 'calls' attribute
@@ -193,7 +195,8 @@ def extract_calls(source) -> List[Call]:
 
     Returns
     -------
-        List[Call]: List of extracted Call objects
+    List[Call]
+        List of extracted Call objects
 
     """
     if isinstance(source, Call):
@@ -234,9 +237,10 @@ def __init__(
         version=None,
         default_stream_key="_stream",
     ) -> None:
-        """Args
-        ----
-            source: The QC configuration representation in one of the following formats:
+        """Parameters
+        ----------
+        source:
+            The QC configuration representation in one of the following formats:
                 python dict or odict
                 JSON/YAML filepath (str or Path object)
                 JSON/YAML str
@@ -349,9 +353,10 @@ def add(self, source) -> None:
         types of objects accepted as the source parameter. The changes the internal .calls
         attribute and returns None.
 
-        Args
-        ----
-            source ([any]): The source of Call objects, this can be a:
+        Parameters
+        ----------
+        source ([any])
+            The source of Call objects, this can be a:
                 * Call object
                 * list of Call objects
                 * list of objects with the 'calls' attribute
@@ -391,10 +396,14 @@ class ContextConfig:
 
     Attributes
     ----------
-        config (odict): dict representation of the parsed ContextConfig source
-        region (GeometryCollection): A `shapely` object representing the valid geographic region
-        window (namedtuple): A TimeWindow object representing the valid time period
-        streams (odict): dict representation of the parsed Config objects
+    config (odict)
+        dict representation of the parsed ContextConfig source
+    region (GeometryCollection)
+        A `shapely` object representing the valid geographic region
+    window (namedtuple)
+        A TimeWindow object representing the valid time period
+    streams (odict)
+        dict representation of the parsed Config objects
 
     """
 
@@ -489,9 +498,10 @@ def add(self, source) -> None:
         types of objects accepted as the source parameter. The changes the internal .calls
         attribute and returns None.
 
-        Args
-        ----
-            source ([any]): The source of Call objects, this can be a:
+        Parameters
+        ----------
+        source ([any])
+            The source of Call objects, this can be a:
                 * Call object
                 * list of Call objects
                 * list of objects with the 'calls' attribute
@@ -522,17 +532,19 @@ def __init__(self, source, default_stream_key="_stream") -> None:
         stream. This just sets up a stream with the name passed in as the "default_stream_key"
         parameter.
 
-        Args
-        ----
-            source: The QC configuration representation in one of the following formats:
+        Parameters
+        ----------
+        source
+            The QC configuration representation in one of the following formats:
                 python dict or odict
                 JSON/YAML filepath (str or Path object)
                 JSON/YAML str
                 JSON/YAML StringIO
                 netCDF4/xarray filepath
                 netCDF4/xarray Dataset
                 list of Call objects
-            default_stream_key: The internal name of the stream, defaults to "_stream"
+        default_stream_key
+            The internal name of the stream, defaults to "_stream"
 
         """
         warnings.warn(

diff --git a/ioos_qc/config_creator/config_creator.py b/ioos_qc/config_creator/config_creator.py
@@ -178,12 +178,14 @@ def __str__(self) -> str:
 class QcVariableConfig(dict):
     """Used to generate a QcConfig for a specific variable.
 
-    Args
-    ----
-        path_or_dict: QcVariableConfig configuration, one of the following formats:
+    Parameters
+    ----------
+    path_or_dict
+        QcVariableConfig configuration, one of the following formats:
             python dict
             JSON filepath (str or Path object)
-        schema: JSON schema for QcVariable
+    schema
+        JSON schema for QcVariable
 
     """
 
@@ -255,12 +257,15 @@ class QcConfigCreator:
 
     Arguments
     ---------
-        creator_config (QcCreatorConfig): Configuration for datasets and variables used to create qc_config.
+    creator_config (QcCreatorConfig)
+        Configuration for datasets and variables used to create qc_config.
 
     Attributes
     ----------
-        allowed_stats (list): Specific statistics allowed to be used to configure each test.
-        allowed_operators (list): Operators allowed to used to configure each test.
+    allowed_stats (list)
+        Specific statistics allowed to be used to configure each test.
+    allowed_operators (list)
+        Operators allowed to used to configure each test.
 
     """
 
@@ -272,13 +277,15 @@ def __init__(self, creator_config) -> None:
     def create_config(self, variable_config):
         """Create QARTOD QC config given QcVariableConfig.
 
-        Args
-        ----
-            variable_config (QcVariableConfig): Config for variable to be quality controlled
+        Parameters
+        ----------
+        variable_config (QcVariableConfig)
+            Config for variable to be quality controlled
 
         Returns
         -------
-            qc_config (dict): Config for ioos_qc
+        qc_config (dict)
+            Config for ioos_qc
 
         """
         stats = self._get_stats(variable_config)
@@ -307,8 +314,8 @@ def _determine_dataset_years(self):
 
         Notes
         -----
-            - Each dataset is from a unique climatology or source,
-              so the monthly files have different years.
+        - Each dataset is from a unique climatology or source,
+            so the monthly files have different years.
 
         """
         years = {}