Add new tests

.pre-commit-config.yaml

@@ -1,12 +1,12 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.10.0
     hooks:
     -   id: black
         files: ^src/

doc/library.rst

@@ -18,10 +18,10 @@ How to contribute
 
 TODO: explain with more details
 
-  1. Generate the JSON file with probeinterface function (or directly
+  1. Generate the JSON file with probeinterface (or directly
       with another language)
-  2. Generate an image with `plot_probe`
-  3. Clone with gin client the `probeinterface_library repo <https://github.com/SpikeInterface/probeinterface_library>`_
-  4. Put files in the right place.
-  5. Push to a branch with git client
-  6. Make a pull request on the gin portal (like a github PR)
+  2. Generate an image of the probe with the `plot_probe` function in probeinterface
+  3. Clone the `probeinterface_library repo <https://github.com/SpikeInterface/probeinterface_library>`_
+  4. Put the JSON file and image into the correct folder or make a new folder (following the format of the repo)
+  5. Push to one of your branches with a git client
+  6. Make a pull request to the main repo

examples/ex_11_automatic_wiring.py

@@ -56,3 +56,16 @@
 
 
 plt.show()
+
+"""
+Available wiring "pathways"
+---------------------------
+
+The available pathways can be found in the `probeinterface.wiring <>`_ module.
+
+The following pathways are available:
+"""
+
+from probeinterface import get_available_pathways
+
+print(get_available_pathways())

src/probeinterface/generator.py

@@ -2,23 +2,25 @@
 This module contains useful helper functions for generating probes.
 
 """
-
+from __future__ import annotations
 import numpy as np
 
+from typing import Optional
+
 from .probe import Probe
 from .probegroup import ProbeGroup
 from .utils import combine_probes
 
 
-def generate_dummy_probe(elec_shapes="circle"):
+def generate_dummy_probe(elec_shapes: str = "circle") -> Probe:
     """
     Generate a dummy probe with 3 columns and 32 contacts.
     Mainly used for testing and examples.
 
     Parameters
     ----------
-    elec_shapes : str, optional
-        Shape of the electrodes, by default 'circle'
+    elec_shapes : str, , by default 'circle'
+        Shape of the electrodes with possibilities of ('circle', 'square', 'rect')
 
     Returns
     -------
@@ -49,7 +51,7 @@ def generate_dummy_probe(elec_shapes="circle"):
     return probe
 
 
-def generate_dummy_probe_group():
+def generate_dummy_probe_group() -> ProbeGroup:
     """
     Generate a ProbeGroup with 2 probes.
     Mainly used for testing and examples.
@@ -72,10 +74,13 @@ def generate_dummy_probe_group():
     return probegroup
 
 
-def generate_tetrode(r=10):
+def generate_tetrode(r: float = 10) -> Probe:
     """
     Generate a tetrode Probe.
-
+    Parameters
+    ----------
+    r: float
+        The distance multiplier for the positions
     Returns
     -------
     probe : Probe
@@ -89,32 +94,35 @@ def generate_tetrode(r=10):
 
 
 def generate_multi_columns_probe(
-    num_columns=3,
-    num_contact_per_column=10,
-    xpitch=20,
-    ypitch=20,
-    y_shift_per_column=None,
-    contact_shapes="circle",
-    contact_shape_params={"radius": 6},
-):
+    num_columns: int = 3,
+    num_contact_per_column: int = 10,
+    xpitch: float = 20,
+    ypitch: float = 20,
+    y_shift_per_column: Optional[np.array | list] = None,
+    contact_shapes: str = "circle",
+    contact_shape_params: dict = {"radius": 6},
+) -> Probe:
     """Generate a Probe with several columns.
 
     Parameters
     ----------
-    num_columns : int, optional
-        Number of columns, by default 3
-    num_contact_per_column : int, optional
-        Number of contacts per column, by default 10
-    xpitch : float, optional
-        Pitch in x direction, by default 20
-    ypitch : float, optional
-        Pitch in y direction, by default 20
+    num_columns : int, by default 3
+        Number of columns
+    num_contact_per_column : int, by default 10
+        Number of contacts per column
+    xpitch : float, by default 20
+        Pitch in x direction
+    ypitch : float, by default 20
+        Pitch in y direction
     y_shift_per_column : array-like, optional
         Shift in y direction per column. It needs to have the same length as num_columns, by default None
-    contact_shapes : str, optional
-        Shape of the contacts ('circle', 'rect', 'square'), by default 'circle'
-    contact_shape_params : dict, optional
-        Parameters for the shape, by default {'radius': 6}
+    contact_shapes : str, by default 'circle'
+        Shape of the contacts ('circle', 'rect', 'square')
+    contact_shape_params : dict, default {'radius': 6}
+        Parameters for the shape.
+        For circle: {"radius": float}
+        For square: {"width": float}
+        For rectangle: {"width": float, "height": float}
 
     Returns
     -------
@@ -144,19 +152,24 @@ def generate_multi_columns_probe(
     return probe
 
 
-def generate_linear_probe(num_elec=16, ypitch=20, contact_shapes="circle", contact_shape_params={"radius": 6}):
+def generate_linear_probe(
+    num_elec: int = 16, ypitch: float = 20, contact_shapes: str = "circle", contact_shape_params: dict = {"radius": 6}
+) -> Probe:
     """Generate a one-column linear probe.
 
     Parameters
     ----------
-    num_elec : int, optional
+    num_elec : int
         Number of electrodes, by default 16
-    ypitch : float, optional
+    ypitch : float
         Pitch in y direction, by default 20
-    contact_shapes : str, optional
-        Shape of the contacts ('circle', 'rect', 'square'), by default 'circle'
-    contact_shape_params : dict, optional
-        Parameters for the shape, by default {'radius': 6}
+    contact_shapes : str, default 'circle'
+        Shape of the contacts ('circle', 'rect', 'square')
+    contact_shape_params : dict, default {'radius': 6}
+        Parameters for the shape.
+        For circle: {"radius": float}
+        For square: {"width": float}
+        For rectangle: {"width": float, "height": float}
 
     Returns
     -------
@@ -175,15 +188,15 @@ def generate_linear_probe(num_elec=16, ypitch=20, contact_shapes="circle", conta
     return probe
 
 
-def generate_multi_shank(num_shank=2, shank_pitch=[150, 0], **kargs):
+def generate_multi_shank(num_shank: int = 2, shank_pitch: list = [150, 0], **kargs) -> Probe:
     """Generate a multi-shank probe.
     Internally, calls generate_multi_columns_probe and combine_probes.
 
     Parameters
     ----------
-    num_shank : int, optional
-        Number of shanks, by default 2
-    shank_pitch : list, optional
+    num_shank : int, default 2
+        Number of shanks
+    shank_pitch : list, default [150,0]
         Distance between shanks, by default [150, 0]
 
     Returns