[build]: isort, pylint, mypy ran across files since type checking is …

…now working in openseize, still pylint complaints but all test passing

src/openseize/demos/demopaths.py

@@ -13,8 +13,8 @@
 import reprlib
 
 # wget missing stubs & request usage here is very limited
-import requests # type: ignore
-import wget # type: ignore
+import requests  # type: ignore
+import wget  # type: ignore
 
 from openseize.file_io.dialogs import message
 

src/openseize/file_io/bases.py

@@ -162,7 +162,6 @@ def __init__(self, path: typing.Union[str, Path], mode: str, **kwargs: str
         self.path = Path(path)
         self.mode = mode
         self.kwargs = kwargs
-        self._fobj = None
         self.open()
 
     def open(self):
@@ -255,7 +254,6 @@ def __init__(self, path: typing.Union[str, Path], mode: str) -> None:
 
         self.path = Path(path)
         self.mode = mode
-        self._fobj = None
 
     def __enter__(self):
         """Return instance as target variable of this context."""
@@ -271,6 +269,8 @@ def __exit__(self, exc_type, exc_value, traceback):
 
         if self._fobj:
             self._fobj.close()
+            # closed file links not pickleable so reassign file obj.
+            self._fobj = None
 
     @abc.abstractmethod
     def write(self, *args, **kwargs) -> None:
@@ -348,19 +348,19 @@ def open(self, path: Path) -> typing.Tuple[typing.IO, typing.Iterable]:
         """Opens a file at path returning a file handle & row iterator."""
 
     @abc.abstractmethod
-    def label(self, row: typing.Iterable) -> str:
+    def label(self, row) -> str:
         """Reads the annotation label at row in this file."""
 
     @abc.abstractmethod
-    def time(self, row: typing.Iterable) -> float:
+    def time(self, row) -> float:
         """Reads annotation time in secs from recording start at row."""
 
     @abc.abstractmethod
-    def duration(self, row: typing.Iterable) -> float:
+    def duration(self, row) -> float:
         """Returns the duration of the annotated event in secs."""
 
     @abc.abstractmethod
-    def channel(self, row: typing.Iterable) -> typing.Union[int, str]:
+    def channel(self, row) -> typing.Union[int, str]:
         """Returns the channel this annotated event was detected on."""
 
     def read(self,

src/openseize/file_io/edf.py

@@ -100,8 +100,7 @@
 
 import copy
 from pathlib import Path
-from typing import (cast, Dict, Generator, List, Optional, Sequence, Tuple,
-                    Union)
+from typing import cast, Dict, Generator, List, Optional, Sequence, Tuple, Union
 
 import numpy as np
 import numpy.typing as npt
@@ -379,7 +378,7 @@ def shape(self) -> Tuple[int, ...]:
         return len(self.channels), max(self.header.samples)
 
     def _decipher(self,
-                  arr: np.ndarray,
+                  arr: npt.NDArray,
                   channels: Sequence[int],
                   axis: int = -1,
     ):
@@ -480,7 +479,7 @@ def _records(self, a: int, b: int):
         return arr
 
     def _padstack(self,
-                  arrs: Sequence[np.ndarray],
+                  arrs: Sequence[npt.NDArray],
                   value: float,
                   axis: int = 0
     ):
@@ -641,9 +640,9 @@ def _write_header(self, header: Header) -> None:
                 self._fobj.write(bytestr)
 
     def _records(self,
-                 data: Union[np.ndarray, Reader],
+                 data: Union[npt.NDArray, Reader],
                  channels: Sequence[int]
-    ) -> Generator[List[np.ndarray], None, None]:
+    ) -> Generator[List[npt.NDArray], None, None]:
         """Yields 1-D arrays, one per channel, to write to a data record.
 
         Args:
@@ -697,7 +696,8 @@ def _encipher(self, arrs: Sequence):
             results.append(arr)
         return results
 
-    def _validate(self, header: Header, data: np.ndarray) -> None:
+    def _validate(self, header: Header, data: Union[npt.NDArray, Reader],
+    ) -> None:
         """Ensures the number of samples is divisible by the number of
         records.
 
@@ -732,7 +732,7 @@ def _progress(self, record_idx: int) -> None:
     # pylint: disable-next=arguments-differ
     def write(self,
               header: Header,
-              data: Union[np.ndarray, Reader],
+              data: Union[npt.NDArray, Reader],
               channels: Sequence[int],
               verbose: bool = True,
               ) -> None:

src/openseize/filtering/bases.py

@@ -7,11 +7,15 @@
 from typing import Optional, Sequence, Tuple, Union
 
 import numpy as np
+import numpy.typing as npt
 import scipy.signal as sps
+
 from openseize.core import mixins
 from openseize.core import numerical as nm
-from openseize.core.producer import Producer, producer
-from openseize.filtering.mixins import FIRViewer, IIRViewer
+from openseize.core.producer import Producer
+from openseize.core.producer import producer
+from openseize.filtering.mixins import FIRViewer
+from openseize.filtering.mixins import IIRViewer
 
 
 class IIR(abc.ABC, IIRViewer, mixins.ViewInstance):
@@ -53,10 +57,10 @@ class IIR(abc.ABC, IIRViewer, mixins.ViewInstance):
     """
 
     def __init__(self,
-                 fpass: Union[float, Sequence[float]],
-                 fstop: Union[float, Sequence[float]],
+                 fpass: Union[float, Sequence[float], npt.NDArray],
+                 fstop: Union[float, Sequence[float], npt.NDArray],
                  gpass: float,
-                 gstop: float,
+                 gstop: Union[float, None],
                  fs: float,
                  fmt: str,
     ) -> None:
@@ -141,12 +145,12 @@ def _build(self):
                              output=self.fmt, fs=self.fs)
 
     def __call__(self,
-                 data: Union[Producer, np.ndarray],
+                 data: Union[Producer, npt.NDArray],
                  chunksize: int,
                  axis: int = -1,
                  dephase: bool = True,
-                 zi: Optional[np.ndarray] = None,
-                 **kwargs) -> Union[Producer, np.ndarray]:
+                 zi: Optional[npt.NDArray] = None,
+                 **kwargs) -> Union[Producer, npt.NDArray]:
         """Apply this filter to an ndarray or producer of ndarrays.
 
         Args:
@@ -180,19 +184,16 @@ def __call__(self,
 
         if self.fmt == 'sos':
             if dephase:
-                filtfunc = nm.sosfiltfilt
+                genfunc = partial(nm.sosfiltfilt, pro, self.coeffs, axis)
             else:
-                filtfunc = nm.sosfilt
+                genfunc = partial(nm.sosfilt, pro, self.coeffs, axis, zi) 
 
         if self.fmt == 'ba':
             if dephase:
-                filtfunc = nm.filtfilt
+                genfunc = partial(nm.filtfilt, pro, self.coeffs, axis)
             else:
-                filtfunc = nm.lfilter
+                genfunc = partial(nm.lfilter, pro, self.coeffs, axis, zi) 
 
-        # zi is ignored if filtfunc is a forward/backward filter
-        genfunc = partial(filtfunc, pro, self.coeffs, axis, zi=zi)
-
         # build producer from a generating function
         result = producer(genfunc, chunksize, axis, shape=pro.shape)
 
@@ -344,11 +345,11 @@ def _build(self, **kwargs):
                           scale=True, fs=self.fs, **kwargs)
 
     def __call__(self,
-                 data: Union[Producer, np.ndarray],
+                 data: Union[Producer, npt.NDArray],
                  chunksize: int,
                  axis: int = -1,
                  mode: str = 'same',
-                 **kwargs) -> Union[Producer, np.ndarray]:
+                 **kwargs) -> Union[Producer, npt.NDArray]:
         """Apply this filter to an ndarray or producer of ndarrays.
 
         Args:

src/openseize/filtering/fir.py

@@ -45,6 +45,7 @@
 
 import numpy as np
 import scipy.signal as sps
+
 from openseize.filtering.bases import FIR
 
 

src/openseize/filtering/iir.py

@@ -37,6 +37,7 @@
 
 import numpy as np
 import scipy.signal as sps
+
 from openseize.filtering.bases import IIR
 
 
@@ -384,10 +385,10 @@ def __init__(self, fstop: float, width: float, fs:float) -> None:
         """
 
         fpass = np.array([fstop - width / 2, fstop + width / 2])
-        fstop = np.array([fstop, fstop])
+        fstops = np.array([fstop, fstop])
         self.width = width
         # gpass is 3dB, gstop is determined by width
-        super().__init__(fpass, fstop, gpass=3, gstop=None, fs=fs, fmt='ba')
+        super().__init__(fpass, fstops, gpass=3, gstop=None, fs=fs, fmt='ba')
 
     @property
     def order(self):