Merge branch 'dev'

# Conflicts: # soundscapy/utils/_sspy_accessor.py
MitchellAcoustics · Mar 6, 2024 · c095355 · c095355
2 parents 50c1450 + 689629b
commit c095355
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diff --git a/docs/tutorials/HowToAnalyseAndRepresentSoundscapes.ipynb b/docs/tutorials/HowToAnalyseAndRepresentSoundscapes.ipynb
diff --git a/docs/tutorials/QuickStart.ipynb b/docs/tutorials/QuickStart.ipynb
diff --git a/soundscapy/__init__.py b/soundscapy/__init__.py
@@ -4,10 +4,10 @@
 
 import importlib.metadata
 
+from soundscapy import plotting
 from soundscapy.analysis._AnalysisSettings import AnalysisSettings, get_default_yaml
 from soundscapy.analysis._Binaural import Binaural
-from soundscapy.utils import _sspy_accessor, surveys
-from soundscapy.databases import isd, araus, satp
-from soundscapy import plotting
+from soundscapy.databases import araus, isd, satp
+from soundscapy.utils import surveys
 
 __version__ = importlib.metadata.version("soundscapy")
diff --git a/soundscapy/databases/isd.py b/soundscapy/databases/isd.py
@@ -135,7 +135,7 @@ def validate(
     return df, excl_df
 
 
-def _isd_select(data, select_by, condition):
+def _isd_select(data: pd.DataFrame, select_by, condition):
     """
     General function to select by ID variables.
 
@@ -343,318 +343,3 @@ def soundscapy_describe(
     }
 
     return pd.DataFrame.from_dict(res, orient="index")
-
-
-@register_dataframe_accessor("isd")
-class ISDAccessor:
-    """Custom accessor for the International Soundscape Database (ISD) dataset
-
-    Parameters
-    ----------
-    pandas_obj : pd.DataFrame
-        Dataframe containing ISD formatted data
-
-    Attributes
-    ----------
-    _obj : pd.DataFrame
-        Dataframe containing ISD formatted data
-    _analysis_data : str
-        Date of analysis
-    _metadata : dict
-        Dictionary of metadata
-
-    Methods
-    -------
-    validate_dataset
-        Validate the dataset to ensure it is in the correct format.
-    likert_data_quality
-        Return the data quality of the PAQs
-    filter_group_ids
-        Filter the dataframe by GroupID
-    filter_location_ids
-        Filter the dataframe by LocationID
-    filter_session_ids
-        Filter the dataframe by SessionID
-    filter_record_ids
-        Filter the dataframe by RecordID
-    filter_lockdown
-        Filter the dataframe by Lockdown
-    convert_group_ids_to_index
-        Convert the GroupID column to the index
-    return_paqs
-        Return the PAQs as a dataframe
-    soundscapy_describe
-        Return a summary of the data
-    mean_responses
-        Calculate the mean responses for each PAQ
-    convert_column_to_index
-        Reassign an existing column as the dataframe index.
-    """
-
-    def __init__(self, pandas_obj):
-        self._obj = pandas_obj
-        self._analysis_data = date.today().isoformat()
-        self._metadata = {}
-
-        # raise PendingDeprecationWarning("The ISD Accessor is being deprecated.")
-
-    def validate_dataset(
-        self,
-        paq_aliases=PAQ_NAMES,
-        allow_lockdown=False,
-        allow_paq_na=False,
-        verbose=1,
-        val_range=(1, 5),
-    ):
-        """DEPRECATED - Use `soundscapy.isd.validate(data)` instead.
-
-        Validate the dataset to ensure it is in the correct format.
-
-        Parameters
-        ----------
-        paq_aliases : list, optional
-            List of aliases for the PAQ, by default PAQ_NAMES
-        allow_lockdown : bool, optional
-            Allow lockdown, by default False
-        allow_paq_na : bool, optional
-            Allow PAQ to be NA, by default False
-        verbose : int, optional
-            Print progress, by default 1
-        val_range : tuple, optional
-            Range of valid values, by default (1, 5)
-
-        Returns
-        -------
-        pandas.DataFrame
-            Validated dataframe
-        """
-        raise DeprecationWarning(
-            "The ISD accessor has been deprecated. Please use `soundscapy.isd.validate(data)` instead."
-        )
-
-    def paq_data_quality(self, verbose=0):
-        """Return the data quality of the PAQs
-
-        Parameters
-        ----------
-        verbose : int, optional
-            Print progress, by default 0
-
-        Returns
-        -------
-        pandas.DataFrame
-        """
-        raise DeprecationWarning(
-            "The ISD accessor has been deprecated. Please use `soundscapy.utils.likert_data_quality()` instead."
-        )
-        # return likert_data_quality(self._obj, verbose=verbose)
-
-    def filter_group_ids(self, group_ids):
-        """
-        Filter the dataframe by GroupID
-
-        Parameters
-        ----------
-        group_ids : list
-            List of GroupIDs to filter by
-
-        Returns
-        -------
-        pd.DataFrame
-            Filtered dataframe
-        """
-        raise DeprecationWarning(
-            "The ISD accessor has been deprecated. Please use `soundscapy.isd.select_group_ids()` instead."
-        )
-        # return self._obj.sspy.filter("GroupID", group_ids)
-
-    def filter_location_ids(self, location_ids):
-        """Filter the dataframe by LocationID
-
-        Parameters
-        ----------
-        location_ids : list
-            List of LocationIDs to filter by
-
-        Returns
-        -------
-        pd.DataFrame
-            Filtered dataframe
-        """
-        raise DeprecationWarning(
-            "The ISD accessor has been deprecated. Please use `soundscapy.isd.select_location_ids()` instead."
-        )
-        # return self._obj.sspy.filter("LocationID", location_ids)
-
-    def filter_session_ids(self, session_ids):
-        """Filter the dataframe by SessionID
-
-        Parameters
-        ----------
-        session_ids : list
-            List of SessionIDs to filter by
-
-        Returns
-        -------
-        pd.DataFrame
-            Filtered dataframe
-        """
-        raise DeprecationWarning(
-            "The ISD accessor has been deprecated. Please use `soundscapy.isd.select_session_ids()` instead."
-        )
-        # return self._obj.sspy.filter("SessionID", session_ids)
-
-    def filter_record_ids(self, record_ids):
-        """Filter the dataframe by RecordID
-
-        Parameters
-        ----------
-        record_ids : list
-            List of RecordIDs to filter by
-
-        Returns
-        -------
-        pd.DataFrame
-            Filtered dataframe
-        """
-        raise DeprecationWarning("The ISD accessor has been deprecated.")
-
-    def filter_lockdown(self, is_lockdown=False):
-        """Filter the dataframe by Lockdown
-
-        Parameters
-        ----------
-        is_lockdown : bool, optional
-            Filter by lockdown, by default False
-
-        Returns
-        -------
-        pd.DataFrame
-            Filtered dataframe
-        """
-        raise DeprecationWarning("The ISD accessor has been deprecated.")
-
-    def convert_group_ids_to_index(self, drop=False):
-        """Convert the GroupID column to the index
-
-        Parameters
-        ----------
-        drop : bool, optional
-            Drop the GroupID column, by default False
-
-        Returns
-        -------
-        pd.DataFrame
-            Dataframe with GroupID as index
-        """
-        raise DeprecationWarning("The ISD accessor has been deprecated.")
-
-    def return_paqs(self, incl_ids=True, other_cols=None):
-        """Return the PAQs as a dataframe
-
-        Parameters
-        ----------
-        incl_ids : bool, optional
-            Include the IDs, by default True
-        other_cols : list, optional
-            List of other columns to include, by default None
-
-        Returns
-        -------
-        pd.DataFrame
-            Dataframe containing the PAQs
-        """
-        raise DeprecationWarning("The ISD accessor has been deprecated.")
-
-    def location_describe(
-        self, location, type="percent", pl_threshold=0, ev_threshold=0
-    ):
-        """Return a summary of the data
-
-        Parameters
-        ----------
-        location : str
-            Location to describe
-        type : str, optional
-            Type of summary, by default "percent"
-        pl_threshold : int, optional
-            PL threshold, by default 0
-        ev_threshold : int, optional
-            EV threshold, by default 0
-
-        Returns
-        -------
-        pd.DataFrame
-            Summary of the data
-        """
-        raise DeprecationWarning(
-            "The ISD accessor has been deprecated. Please use `soundscapy.isd.describe_location()` instead."
-        )
-
-    def soundscapy_describe(self, group_by="LocationID", type="percent"):
-        """Return a summary of the data
-
-        Parameters
-        ----------
-        group_by : str, optional
-            Column to group by, by default "LocationID"
-        type : str, optional
-            Type of summary, by default "percent"
-
-        Returns
-        -------
-        pd.DataFrame
-            Summary of the data
-        """
-        raise DeprecationWarning(
-            "The ISD accessor has been deprecated. Please use `soundscapy.isd.soundscapy_describe()` instead."
-        )
-
-    def mean_responses(self, group="LocationID") -> pd.DataFrame:
-        """Calculate the mean responses for each PAQ
-
-        Parameters
-        ----------
-        df : pd.DataFrame
-            Dataframe containing ISD formatted data
-
-        Returns
-        -------
-        pd.Dataframe
-            Dataframe containing the mean responses for each PAQ
-        """
-        raise DeprecationWarning("The ISD accessor has been deprecated.")
-
-    def validate_isd(
-        self,
-        paq_aliases=None,
-        allow_lockdown=False,
-        allow_paq_na=False,
-        verbose=1,
-        val_range=(1, 5),
-    ):
-        """Validate the ISD dataset.
-
-        Parameters
-        ----------
-        df : pd.DataFrame
-            Dataframe containing ISD formatted data
-        paq_aliases : dict, optional
-            Dictionary of PAQ aliases, by default None
-        allow_lockdown : bool, optional
-            Allow lockdown PAQs?, by default False
-        allow_paq_na : bool, optional
-            Allow missing PAQs?, by default False
-        verbose : int, optional
-            Verbosity level, by default 1
-        val_range : tuple, optional
-            Range of valid values, by default (1,5)
-
-        Returns
-        -------
-        pd.DataFrame
-            Dataframe containing the validation results
-        """
-        raise DeprecationWarning(
-            "The ISD accessor has been deprecated. Please use `soundscapy.isd.validate(data)` instead."
-        )
diff --git a/soundscapy/plotting/__init__.py b/soundscapy/plotting/__init__.py
@@ -2,3 +2,4 @@
 The module ``plotting`` contains functions for plotting soundscape circumplex data and directly plotting Likert scale data.
 """
 from soundscapy.plotting.circumplex import scatter, density, jointplot
+from soundscapy.plotting import likert