CLN: Fix pandera imports, fixes #285

src/crowsetta/formats/bbox/audbbox.py

@@ -10,7 +10,7 @@
 
 import attr
 import pandas as pd
-import pandera
+import pandera.pandas
 from pandera.typing import Series
 
 import crowsetta
@@ -97,21 +97,18 @@ def df_to_lines(df: pd.DataFrame) -> list[str]:
     return lines
 
 
-class AudBBoxSchema(pandera.DataFrameModel):
-    """A :class:`pandera.DataFrameModel
-
-    ` that
-        validates :mod:`pandas` dataframes
-        loaded from Audacity label tracks
-        in extended format, exported to txt files
-        https://manual.audacityteam.org/man/importing_and_exporting_labels.html#Extended_format_with_frequency_ranges
+class AudBBoxSchema(pandera.pandas.DataFrameModel):
+    """A :class:`pandera.pandas.DataFrameModel` that
+    validates :mod:`pandas` dataframes loaded from Audacity label tracks
+    in extended format then exported to txt files
+    https://manual.audacityteam.org/man/importing_and_exporting_labels.html#Extended_format_with_frequency_ranges
     """
 
-    begin_time_s: Series[float] = pandera.Field(coerce=True)
-    end_time_s: Series[float] = pandera.Field(coerce=True)
-    label: Series[pd.StringDtype] = pandera.Field(coerce=True)
-    low_freq_hz: Series[float] = pandera.Field(coerce=True)
-    high_freq_hz: Series[float] = pandera.Field(coerce=True)
+    begin_time_s: Series[float] = pandera.pandas.Field(coerce=True)
+    end_time_s: Series[float] = pandera.pandas.Field(coerce=True)
+    label: Series[pd.StringDtype] = pandera.pandas.Field(coerce=True)
+    low_freq_hz: Series[float] = pandera.pandas.Field(coerce=True)
+    high_freq_hz: Series[float] = pandera.pandas.Field(coerce=True)
 
     class Config:
         ordered = True

src/crowsetta/formats/bbox/raven.py

@@ -11,26 +11,23 @@
 
 import attr
 import pandas as pd
-import pandera
+import pandera.pandas
 from pandera.typing import Series
 
 import crowsetta
 from crowsetta.typing import PathLike
 
 
-class RavenSchema(pandera.DataFrameModel):
-    """A :class:`pandera.DataFrameModel
-
-    ` that validates :type:`pandas.DataFrame`s
-        loaded from a txt file, created by exporting a Selection Table
-        from Raven.
+class RavenSchema(pandera.pandas.DataFrameModel):
+    """A :class:`pandera.pandas.DataFrameModel` that validates a :type:`pandas.DataFrame`
+    loaded from a txt file, created by exporting a Selection Table from Raven.
     """
 
-    begin_time_s: Series[float] = pandera.Field()
-    end_time_s: Series[float] = pandera.Field()
-    low_freq_hz: Series[float] = pandera.Field()
-    high_freq_hz: Series[float] = pandera.Field()
-    annotation: Series[pd.StringDtype] = pandera.Field(coerce=True)
+    begin_time_s: Series[float] = pandera.pandas.Field()
+    end_time_s: Series[float] = pandera.pandas.Field()
+    low_freq_hz: Series[float] = pandera.pandas.Field()
+    high_freq_hz: Series[float] = pandera.pandas.Field()
+    annotation: Series[pd.StringDtype] = pandera.pandas.Field(coerce=True)
 
     class Config:
         # we set strict fo False

src/crowsetta/formats/seq/audseq.py

@@ -9,28 +9,24 @@
 import attr
 import numpy as np
 import pandas as pd
-import pandera
+import pandera.pandas
 from pandera.typing import Series
 
 import crowsetta
 from crowsetta.typing import PathLike
 
 
-class AudSeqSchema(pandera.DataFrameModel):
-    """A :class:`pandera.DataFrameModel
+class AudSeqSchema(pandera.pandas.DataFrameModel):
+    """A :class:`pandera.DataFrameModel` that validates a :type:`pandas.DataFrame`
+    loaded from Audacity Labeltrack annotations exported to txt files in the standard format.
 
-    `
-        that validates :type:`pandas.DataFrame`s
-        loaded from Audacity Labeltrack annotations
-        exported to txt files in the standard format.
-
-        The standard format is described here:
-        https://manual.audacityteam.org/man/importing_and_exporting_labels.html#Standard_.28default.29_format
+    The standard format is described here:
+    https://manual.audacityteam.org/man/importing_and_exporting_labels.html#Standard_.28default.29_format
     """
 
-    start_time: Optional[Series[float]] = pandera.Field()
-    end_time: Optional[Series[float]] = pandera.Field()
-    label: Series[pd.StringDtype] = pandera.Field(coerce=True)
+    start_time: Optional[Series[float]] = pandera.pandas.Field()
+    end_time: Optional[Series[float]] = pandera.pandas.Field()
+    label: Series[pd.StringDtype] = pandera.pandas.Field(coerce=True)
 
     class Config:
         ordered = True
@@ -42,7 +38,7 @@ class Config:
 class AudSeq:
     """Class meant to represent
     Audacity Labeltrack annotations
-    exported to txt files in the standard format[1]_.
+    exported to txt files in the standard format [1]_.
 
     The txt file will have 3 tab-separated columns
     that represent the start time, end time, and labels

src/crowsetta/formats/seq/generic.py

@@ -22,7 +22,7 @@
 
 import attr
 import pandas as pd
-import pandera
+import pandera.pandas
 from pandera.typing import Series
 
 import crowsetta
@@ -36,36 +36,33 @@
 """
 
 
-class GenericSeqSchema(pandera.DataFrameModel):
-    """A :class: `pandera.DataFrameModel
-
-    ` that validates
-        :type:`pandas.DataFrame`s
-        loaded from a csv file  in the ``'generic-seq'`` annotation
-        format.
+class GenericSeqSchema(pandera.pandas.DataFrameModel):
+    """A :class: `pandera.pandas.DataFrameModel` that validates
+    a :type:`pandas.DataFrame` loaded from a csv file 
+    in the ``'generic-seq'`` annotation format.
     """
 
-    label: Series[pd.StringDtype] = pandera.Field(coerce=True)
-    onset_s: Optional[Series[float]] = pandera.Field()
-    offset_s: Optional[Series[float]] = pandera.Field()
-    onset_sample: Optional[Series[int]] = pandera.Field()
-    offset_sample: Optional[Series[int]] = pandera.Field()
+    label: Series[pd.StringDtype] = pandera.pandas.Field(coerce=True)
+    onset_s: Optional[Series[float]] = pandera.pandas.Field()
+    offset_s: Optional[Series[float]] = pandera.pandas.Field()
+    onset_sample: Optional[Series[int]] = pandera.pandas.Field()
+    offset_sample: Optional[Series[int]] = pandera.pandas.Field()
 
-    notated_path: Series[str] = pandera.Field(coerce=True)
-    annot_path: Series[str] = pandera.Field(coerce=True)
-    sequence: Series[int] = pandera.Field()
-    annotation: Series[int] = pandera.Field()
+    notated_path: Series[str] = pandera.pandas.Field(coerce=True)
+    annot_path: Series[str] = pandera.pandas.Field(coerce=True)
+    sequence: Series[int] = pandera.pandas.Field()
+    annotation: Series[int] = pandera.pandas.Field()
 
-    @pandera.dataframe_check(error=ONSET_OFFSET_COLS_ERR)
+    @pandera.pandas.dataframe_check(error=ONSET_OFFSET_COLS_ERR)
     def both_onset_s_and_offset_s_if_either(cls, df: pd.DataFrame) -> bool:
         """check that, if one of {'onset_s', 'offset_s'} column is present,
         then both are present"""
         if any([col in df for col in ("onset_s", "offset_s")]):
             return all([col in df for col in ("onset_s", "offset_s")])
         else:
             return True
-
-    @pandera.dataframe_check(error=ONSET_OFFSET_COLS_ERR)
+    
+    @pandera.pandas.dataframe_check(error=ONSET_OFFSET_COLS_ERR)
     def both_onset_sample_and_offset_sample_if_either(cls, df: pd.DataFrame) -> bool:
         """check that, if one of {'onset_sample', 'offset_sample'} column is present,
         then both are present"""
@@ -74,7 +71,7 @@ def both_onset_sample_and_offset_sample_if_either(cls, df: pd.DataFrame) -> bool
         else:
             return True
 
-    @pandera.dataframe_check(error=ONSET_OFFSET_COLS_ERR)
+    @pandera.pandas.dataframe_check(error=ONSET_OFFSET_COLS_ERR)
     def onset_offset_s_and_ind_are_not_both_missing(cls, df: pd.DataFrame) -> bool:
         """check that at least one of the on/offset column pairs is present:
         either {'onset_s', 'offset_s'} or {'onset_sample', 'offset_sample'}"""

src/crowsetta/formats/seq/simple.py

@@ -24,26 +24,26 @@
 import attr
 import numpy as np
 import pandas as pd
-import pandera
+import pandera.pandas
 from pandera.typing import Series
 
 import crowsetta
 from crowsetta.typing import PathLike
 
 
-class SimpleSeqSchema(pandera.DataFrameModel):
-    """A :class:`pandera.DataFrameModel`
-    that validates :type:`pandas.DataFrame`s
+class SimpleSeqSchema(pandera.pandas.DataFrameModel):
+    """A :class:`pandera.pandas.DataFrameModel`
+    that validates a :type:`pandas.DataFrame`
     loaded from a csv or txt file in a 'simple-seq' format.
 
     The :meth:`SimpleSeq.from_file` loads the :type:`pandas.DataFrame`
     and makes any changes needed to get it to this format
     before validation, e.g., changing column names.
     """
 
-    onset_s: Optional[Series[float]] = pandera.Field()
-    offset_s: Optional[Series[float]] = pandera.Field()
-    label: Series[pd.StringDtype] = pandera.Field(coerce=True)
+    onset_s: Optional[Series[float]] = pandera.pandas.Field()
+    offset_s: Optional[Series[float]] = pandera.pandas.Field()
+    label: Series[pd.StringDtype] = pandera.pandas.Field(coerce=True)
 
     class Config:
         ordered = True

src/crowsetta/formats/seq/timit.py

@@ -12,29 +12,27 @@
 import attr
 import numpy as np
 import pandas as pd
-import pandera
+import pandera.pandas
 import soundfile
 from pandera.typing import Series
 
 import crowsetta
 from crowsetta.typing import PathLike
 
 
-class TimitTranscriptSchema(pandera.DataFrameModel):
-    """A :class:`pandera.DataFrameModel
+class TimitTranscriptSchema(pandera.pandas.DataFrameModel):
+    """A :class:`pandera.pandas.DataFrameModel` that validates a :type:`pandas.DataFrame`
+    loaded from a phn or wrd file in the TIMIT[1]_ transcription format.
 
-    ` that validates :type:`pandas.DataFrame`s
-        loaded from a phn or wrd file in the TIMIT[1]_ transcription format.
-
-        References
-        ----------
-        .. [1] Garofolo, John S., et al. TIMIT Acoustic-Phonetic Continuous Speech Corpus LDC93S1.
-           Web Download. Philadelphia: Linguistic Data Consortium, 1993.
+    References
+    ----------
+    .. [1] Garofolo, John S., et al. TIMIT Acoustic-Phonetic Continuous Speech Corpus LDC93S1.
+        Web Download. Philadelphia: Linguistic Data Consortium, 1993.
     """
 
-    begin_sample: Optional[Series[int]] = pandera.Field()
-    end_sample: Optional[Series[int]] = pandera.Field()
-    text: Series[pd.StringDtype] = pandera.Field(coerce=True)
+    begin_sample: Optional[Series[int]] = pandera.pandas.Field()
+    end_sample: Optional[Series[int]] = pandera.pandas.Field()
+    text: Series[pd.StringDtype] = pandera.pandas.Field(coerce=True)
 
     class Config:
         ordered = True

tests/test_formats/test_seq/test_simple.py

@@ -1,6 +1,5 @@
 import filecmp
 import inspect
-import tempfile
 
 import numpy as np
 import pandas as pd