From d45bfa375ba13baa4b5fb9f106b52ebc01e3d51e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 1 Sep 2023 19:33:43 +0000
Subject: [PATCH] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/probeinterface/generator.py | 22 ++++++-----
 src/probeinterface/io.py        | 22 ++++++++---
 src/probeinterface/library.py   |  6 +--
 src/probeinterface/probe.py     | 66 ++++++++++++++++++---------------
 src/probeinterface/utils.py     |  4 +-
 src/probeinterface/wiring.py    |  4 +-
 6 files changed, 72 insertions(+), 52 deletions(-)

diff --git a/src/probeinterface/generator.py b/src/probeinterface/generator.py
index f690b1d..cd3f8e6 100644
--- a/src/probeinterface/generator.py
+++ b/src/probeinterface/generator.py
@@ -10,7 +10,7 @@
 from .utils import combine_probes
 
 
-def generate_dummy_probe(elec_shapes:str ="circle"):
+def generate_dummy_probe(elec_shapes: str = "circle"):
     """
     Generate a dummy probe with 3 columns and 32 contacts.
     Mainly used for testing and examples.
@@ -72,7 +72,7 @@ def generate_dummy_probe_group():
     return probegroup
 
 
-def generate_tetrode(r:float=10):
+def generate_tetrode(r: float = 10):
     """
     Generate a tetrode Probe.
     Parameters
@@ -92,13 +92,13 @@ def generate_tetrode(r:float=10):
 
 
 def generate_multi_columns_probe(
-    num_columns:int=3,
-    num_contact_per_column:int =10,
-    xpitch:float=20,
-    ypitch:float=20,
+    num_columns: int = 3,
+    num_contact_per_column: int = 10,
+    xpitch: float = 20,
+    ypitch: float = 20,
     y_shift_per_column=None,
-    contact_shapes:str="circle",
-    contact_shape_params:dict={"radius": 6},
+    contact_shapes: str = "circle",
+    contact_shape_params: dict = {"radius": 6},
 ):
     """Generate a Probe with several columns.
 
@@ -150,7 +150,9 @@ def generate_multi_columns_probe(
     return probe
 
 
-def generate_linear_probe(num_elec: int =16, ypitch:float=20, contact_shapes:str="circle", contact_shape_params:dict={"radius": 6}):
+def generate_linear_probe(
+    num_elec: int = 16, ypitch: float = 20, contact_shapes: str = "circle", contact_shape_params: dict = {"radius": 6}
+):
     """Generate a one-column linear probe.
 
     Parameters
@@ -184,7 +186,7 @@ def generate_linear_probe(num_elec: int =16, ypitch:float=20, contact_shapes:str
     return probe
 
 
-def generate_multi_shank(num_shank:int=2, shank_pitch:list=[150, 0], **kargs):
+def generate_multi_shank(num_shank: int = 2, shank_pitch: list = [150, 0], **kargs):
     """Generate a multi-shank probe.
     Internally, calls generate_multi_columns_probe and combine_probes.
 
diff --git a/src/probeinterface/io.py b/src/probeinterface/io.py
index f60dca4..5499af9 100644
--- a/src/probeinterface/io.py
+++ b/src/probeinterface/io.py
@@ -32,7 +32,7 @@ def _probeinterface_format_check_version(d):
     pass
 
 
-def read_probeinterface(file:Union[str, Path])-> ProbeGroup:
+def read_probeinterface(file: Union[str, Path]) -> ProbeGroup:
     """
     Read probeinterface JSON-based format.
 
@@ -175,7 +175,10 @@ def read_BIDS_probe(folder: Union[str, Path], prefix: Optional[str] = None) -> P
         if "contact_shapes" not in df_probe:
             df_probe["contact_shapes"] = "circle"
             df_probe["radius"] = 1
-            print(f"There is no contact shape provided for probe {probe_id}, a " f"dummy circle with 1um radius will be used.")
+            print(
+                f"There is no contact shape provided for probe {probe_id}, a "
+                f"dummy circle with 1um radius will be used."
+            )
 
         if "x" not in df_probe:
             df_probe["x"] = np.arange(len(df_probe.index), dtype=float)
@@ -186,7 +189,8 @@ def read_BIDS_probe(folder: Union[str, Path], prefix: Optional[str] = None) -> P
         if "y" not in df_probe:
             df_probe["y"] = 0.0
             print(
-                f"There is no y coordinate provided for probe {probe_id}, a " f"dummy constant y coordinate will be used."
+                f"There is no y coordinate provided for probe {probe_id}, a "
+                f"dummy constant y coordinate will be used."
             )
 
         if "si_units" not in df_probe:
@@ -290,7 +294,7 @@ def read_BIDS_probe(folder: Union[str, Path], prefix: Optional[str] = None) -> P
     return probegroup
 
 
-def write_BIDS_probe(folder: Union[str, Path], probe_or_probegroup: Union[Probe, ProbeGroup], prefix:str=""):
+def write_BIDS_probe(folder: Union[str, Path], probe_or_probegroup: Union[Probe, ProbeGroup], prefix: str = ""):
     """
     Write to probe and contact formats as proposed
     for ephy BIDS extension (tsv & json based).
@@ -577,7 +581,13 @@ def read_3brain(file: Union[str, Path], mea_pitch: float = 42, electrode_width:
     return probe
 
 
-def write_prb(file:str, probegroup:ProbeGroup, total_nb_channels:Optional[int]=None, radius:Optional[float]=None, group_mode:str="by_probe"):
+def write_prb(
+    file: str,
+    probegroup: ProbeGroup,
+    total_nb_channels: Optional[int] = None,
+    radius: Optional[float] = None,
+    group_mode: str = "by_probe",
+):
     """
     Write ProbeGroup into a prb file.
 
@@ -656,7 +666,7 @@ def write_prb(file:str, probegroup:ProbeGroup, total_nb_channels:Optional[int]=N
         f.write("}\n")
 
 
-def read_csv(file:Union[str, Path]):
+def read_csv(file: Union[str, Path]):
     """
     Return a 2 or 3 columns csv file with contact positions
     """
diff --git a/src/probeinterface/library.py b/src/probeinterface/library.py
index 20c0b15..07fc791 100644
--- a/src/probeinterface/library.py
+++ b/src/probeinterface/library.py
@@ -25,7 +25,7 @@
 cache_folder = Path(os.path.expanduser("~")) / ".config" / "probeinterface" / "library"
 
 
-def download_probeinterface_file(manufacturer:str, probe_name:str):
+def download_probeinterface_file(manufacturer: str, probe_name: str):
     """Download the probeinterface file to the cache directory.
     Note that the file is itself a ProbeGroup but on the repo each file
     represents one probe.
@@ -45,7 +45,7 @@ def download_probeinterface_file(manufacturer:str, probe_name:str):
         f.write(dist.read())
 
 
-def get_from_cache(manufacturer:str, probe_name:str)-> Optional["Probe"]:
+def get_from_cache(manufacturer: str, probe_name: str) -> Optional["Probe"]:
     """
     Get Probe from local cache
 
@@ -72,7 +72,7 @@ def get_from_cache(manufacturer:str, probe_name:str)-> Optional["Probe"]:
         return probe
 
 
-def get_probe(manufacturer:str, probe_name:str)-> "Probe":
+def get_probe(manufacturer: str, probe_name: str) -> "Probe":
     """
     Get probe from ProbeInterface library
 
diff --git a/src/probeinterface/probe.py b/src/probeinterface/probe.py
index ff11258..a32f1d7 100644
--- a/src/probeinterface/probe.py
+++ b/src/probeinterface/probe.py
@@ -16,7 +16,7 @@ class Probe:
 
     """
 
-    def __init__(self, ndim:int=2, si_units:int="um"):
+    def __init__(self, ndim: int = 2, si_units: int = "um"):
         """
         Some attributes are protected and have to be set with setters:
           * set_contacts(...)
@@ -91,7 +91,7 @@ def contact_ids(self):
     def shank_ids(self):
         return self._shank_ids
 
-    def get_title(self)->str:
+    def get_title(self) -> str:
         if self.contact_positions is None:
             txt = "Undefined probe"
         else:
@@ -132,14 +132,14 @@ def check_annotations(self):
         if "first_index" in d:
             assert d["first_index"] in (0, 1)
 
-    def get_contact_count(self)->int:
+    def get_contact_count(self) -> int:
         """
         Return the number of contacts on the probe.
         """
         assert self.contact_positions is not None
         return len(self.contact_positions)
 
-    def get_shank_count(self)->int:
+    def get_shank_count(self) -> int:
         """
         Return the number of shanks for this probe.
         """
@@ -212,7 +212,7 @@ def set_contacts(self, positions, shapes="circle", shape_params={"radius": 10},
             shape_params = [shape_params] * n
         self._contact_shape_params = np.array(shape_params)
 
-    def set_planar_contour(self, contour_polygon:list):
+    def set_planar_contour(self, contour_polygon: list):
         """Set the planar countour (the shape) of the probe.
 
         Parameters
@@ -225,7 +225,7 @@ def set_planar_contour(self, contour_polygon:list):
             raise ValueError("contour_polygon.shape[1] and ndim do not match!")
         self.probe_planar_contour = contour_polygon
 
-    def create_auto_shape(self, probe_type:str="tip", margin:float=20.0):
+    def create_auto_shape(self, probe_type: str = "tip", margin: float = 20.0):
         """Create planar contour automatically based on probe contact positions.
 
         Parameters
@@ -280,7 +280,7 @@ def create_auto_shape(self, probe_type:str="tip", margin:float=20.0):
 
         self.set_planar_contour(polygon)
 
-    def set_device_channel_indices(self, channel_indices:Sequence[int]):
+    def set_device_channel_indices(self, channel_indices: Sequence[int]):
         """
         Manually set the device channel indices.
 
@@ -298,7 +298,7 @@ def set_device_channel_indices(self, channel_indices:Sequence[int]):
         if self._probe_group is not None:
             self._probe_group.check_global_device_wiring_and_ids()
 
-    def wiring_to_device(self, pathway:str, channel_offset:int=0):
+    def wiring_to_device(self, pathway: str, channel_offset: int = 0):
         """
         Automatically set device_channel_indices based on a pathway.
 
@@ -315,7 +315,7 @@ def wiring_to_device(self, pathway:str, channel_offset:int=0):
 
         wire_probe(self, pathway, channel_offset=channel_offset)
 
-    def set_contact_ids(self, contact_ids:Sequence[Union[int, float, str]]):
+    def set_contact_ids(self, contact_ids: Sequence[Union[int, float, str]]):
         """
         Set contact ids. Channel ids are converted to strings.
         Contact ids must be **unique** for the **Probe**
@@ -339,7 +339,7 @@ def set_contact_ids(self, contact_ids:Sequence[Union[int, float, str]]):
         if self._probe_group is not None:
             self._probe_group.check_global_device_wiring_and_ids()
 
-    def set_shank_ids(self, shank_ids:Sequence[Union[int, float, str]]):
+    def set_shank_ids(self, shank_ids: Sequence[Union[int, float, str]]):
         """
         Set shank ids.
 
@@ -385,7 +385,7 @@ def copy(self):
         # channel_indices are not copied
         return other
 
-    def to_3d(self, axes:str="xz"):
+    def to_3d(self, axes: str = "xz"):
         """
         Transform 2d probe to 3d probe.
 
@@ -422,7 +422,7 @@ def to_3d(self, axes:str="xz"):
 
         return probe3d
 
-    def to_2d(self, axes:str="xy"):
+    def to_2d(self, axes: str = "xy"):
         """
         Transform 3d probe to 2d probe.
 
@@ -453,7 +453,7 @@ def to_2d(self, axes:str="xy"):
 
         return probe2d
 
-    def get_contact_vertices(self)->list:
+    def get_contact_vertices(self) -> list:
         """
         Return a list of contact vertices.
         """
@@ -493,7 +493,7 @@ def get_contact_vertices(self)->list:
             vertices.append(one_vertice)
         return vertices
 
-    def move(self, translation_vector:Sequence[int]):
+    def move(self, translation_vector: Sequence[int]):
         """
         Translate the probe in one direction.
 
@@ -511,7 +511,7 @@ def move(self, translation_vector:Sequence[int]):
         if self.probe_planar_contour is not None:
             self.probe_planar_contour += translation_vector
 
-    def rotate(self, theta:float, center=None, axis=None):
+    def rotate(self, theta: float, center=None, axis=None):
         """
         Rotate the probe around a specified axis.
 
@@ -559,7 +559,7 @@ def rotate(self, theta:float, center=None, axis=None):
             new_vertices = (self.probe_planar_contour - center) @ R + center
             self.probe_planar_contour = new_vertices
 
-    def rotate_contacts(self, thetas:Union[float, Sequence[float]]):
+    def rotate_contacts(self, thetas: Union[float, Sequence[float]]):
         """
         Rotate each contact of the probe.
         Internally, it modifies the contact_plane_axes.
@@ -602,7 +602,7 @@ def rotate_contacts(self, thetas:Union[float, Sequence[float]]):
         "_shank_ids",
     ]
 
-    def to_dict(self, array_as_list:bool=False)->dict:
+    def to_dict(self, array_as_list: bool = False) -> dict:
         """Create a dictionary of all necessary attributes.
         Useful for dumping and saving to json.
 
@@ -633,7 +633,7 @@ def to_dict(self, array_as_list:bool=False)->dict:
         return d
 
     @staticmethod
-    def from_dict(d:dict):
+    def from_dict(d: dict):
         """Instantiate a Probe from a dictionary
 
         Parameters
@@ -678,7 +678,7 @@ def from_dict(d:dict):
 
         return probe
 
-    def to_numpy(self, complete:bool=False)->np.array:
+    def to_numpy(self, complete: bool = False) -> np.array:
         """
         Export to a numpy vector (structured array).
         This vector handles all contact attributes.
@@ -759,7 +759,7 @@ def to_numpy(self, complete:bool=False)->np.array:
         return arr
 
     @staticmethod
-    def from_numpy(arr:np.ndarray):
+    def from_numpy(arr: np.ndarray):
         """
         Create Probe from a complex numpy array
         see Probe.to_numpy()
@@ -830,7 +830,7 @@ def from_numpy(arr:np.ndarray):
 
         return probe
 
-    def to_dataframe(self, complete:bool=False)-> "pandas.DataFrame":
+    def to_dataframe(self, complete: bool = False) -> "pandas.DataFrame":
         """
         Export the probe to a pandas dataframe
 
@@ -854,7 +854,7 @@ def to_dataframe(self, complete:bool=False)-> "pandas.DataFrame":
         return df
 
     @staticmethod
-    def from_dataframe(df:"pandas.DataFrame"):
+    def from_dataframe(df: "pandas.DataFrame"):
         """
         Create Probe from a pandas.DataFrame
         see Probe.to_dataframe()
@@ -872,7 +872,15 @@ def from_dataframe(df:"pandas.DataFrame"):
         arr = df.to_records(index=False)
         return Probe.from_numpy(arr)
 
-    def to_image(self, values:Sequence, pixel_size:float=0.5, num_pixel:Optional[int]=None, method:str="linear", xlims:Optional[tuple]=None, ylims:Optional[tuple]=None)-> tuple[np.ndarray, tuple, tuple]:
+    def to_image(
+        self,
+        values: Sequence,
+        pixel_size: float = 0.5,
+        num_pixel: Optional[int] = None,
+        method: str = "linear",
+        xlims: Optional[tuple] = None,
+        ylims: Optional[tuple] = None,
+    ) -> tuple[np.ndarray, tuple, tuple]:
         """
         Generated a 2d (image) from a values vector with an interpolation
         into a grid mesh.
@@ -935,7 +943,7 @@ def to_image(self, values:Sequence, pixel_size:float=0.5, num_pixel:Optional[int
 
         return image, xlims, ylims
 
-    def get_slice(self, selection:np.ndarray[Union[bool, int]]):
+    def get_slice(self, selection: np.ndarray[Union[bool, int]]):
         """
         Get a copy of the Probe with a sub selection of contacts.
 
@@ -985,7 +993,7 @@ def get_slice(self, selection:np.ndarray[Union[bool, int]]):
         return sliced_probe
 
 
-def _2d_to_3d(data2d:np.ndarray, axes:str)-> np.ndarray:
+def _2d_to_3d(data2d: np.ndarray, axes: str) -> np.ndarray:
     """
     Add a third dimension
 
@@ -1007,7 +1015,7 @@ def _2d_to_3d(data2d:np.ndarray, axes:str)-> np.ndarray:
     return data3d
 
 
-def select_axes(data:np.ndarray, axes:str="xy")->np.ndarray:
+def select_axes(data: np.ndarray, axes: str = "xy") -> np.ndarray:
     """
     Select axes in a 3d or 2d array.
 
@@ -1028,7 +1036,7 @@ def select_axes(data:np.ndarray, axes:str="xy")->np.ndarray:
     return data[:, dims]
 
 
-def _3d_to_2d(data3d:np.ndarray, axes:str="xy")-> np.ndarray:
+def _3d_to_2d(data3d: np.ndarray, axes: str = "xy") -> np.ndarray:
     """
     Reduce 3d array to 2d array on given axes.
 
@@ -1049,7 +1057,7 @@ def _3d_to_2d(data3d:np.ndarray, axes:str="xy")-> np.ndarray:
     return select_axes(data3d, axes=axes)
 
 
-def _rotation_matrix_2d(theta:float)->np.ndarray:
+def _rotation_matrix_2d(theta: float) -> np.ndarray:
     """
     Returns 2D rotation matrix
 
@@ -1067,7 +1075,7 @@ def _rotation_matrix_2d(theta:float)->np.ndarray:
     return R
 
 
-def _rotation_matrix_3d(axis:Sequence, theta:float)->np.ndarray:
+def _rotation_matrix_3d(axis: Sequence, theta: float) -> np.ndarray:
     """
     Returns 3D rotation matrix
 
diff --git a/src/probeinterface/utils.py b/src/probeinterface/utils.py
index d484580..69e23d9 100644
--- a/src/probeinterface/utils.py
+++ b/src/probeinterface/utils.py
@@ -47,7 +47,7 @@ def import_safely(module: str) -> ModuleType:
     return module_obj
 
 
-def combine_probes(probes:Probe, connect_shape:bool=True):
+def combine_probes(probes: Probe, connect_shape: bool = True):
     """
     Combine several Probe objects into a unique
     multi-shank Probe object.
@@ -102,7 +102,7 @@ def combine_probes(probes:Probe, connect_shape:bool=True):
     return multi_shank
 
 
-def generate_unique_ids(min:int, max:int, n:int, trials:int=20)-> np.array:
+def generate_unique_ids(min: int, max: int, n: int, trials: int = 20) -> np.array:
     """
     Create n unique identifiers.
     Creates `n` unique integer identifiers between `min` and `max` within a
diff --git a/src/probeinterface/wiring.py b/src/probeinterface/wiring.py
index 105c8dc..d35df7c 100644
--- a/src/probeinterface/wiring.py
+++ b/src/probeinterface/wiring.py
@@ -50,7 +50,7 @@
 # fmt: on
 
 
-def get_available_pathways()->list:
+def get_available_pathways() -> list:
     """Return available pathways
 
     Returns
@@ -61,7 +61,7 @@ def get_available_pathways()->list:
     return list(pathways.keys())
 
 
-def wire_probe(probe:"Probe", pathway:str, channel_offset:int=0):
+def wire_probe(probe: "Probe", pathway: str, channel_offset: int = 0):
     """Inplace wiring for a Probe using a pathway
 
     Parameters