add ruff, redo deps v0.12.3

siplab-gt · Dec 1, 2023 · f9baeac · f9baeac
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diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -50,8 +50,8 @@ my_function(a, b='B'):
 ```
 
 ## Style
-We will use Black formatting. The easiest way is to enable Black as the formatter in 
-your IDE with auto-formatting on save.
+We will use Black-style formatting, as implemented (faster) by Ruff.
+The easiest way is to enable Ruff as the formatter in your IDE with auto-formatting on save.
 
 ## Linting
 I was going to lint using flake8 but then I realized, this is a small research code package! We don't need super pretty, consistent code. Just try to follow Python conventions and use Black.

diff --git a/README.md b/README.md
@@ -3,6 +3,7 @@
 
 [![Tests](https://github.com/kjohnsen/cleosim/actions/workflows/test.yml/badge.svg)](https://github.com/kjohnsen/cleosim/actions/workflows/test.yml)
 [![Documentation Status](https://readthedocs.org/projects/cleosim/badge/?version=latest)](https://cleosim.readthedocs.io/en/latest/?badge=latest)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 
 <h1>
@@ -80,9 +81,7 @@ The `ldsCtrlEst` library implements adaptive linear dynamical system-based contr
 </p>
 
 ### 📃 Publications
-[**Cleo: A testbed for bridging model and experiment by
-simulating closed-loop stimulation, electrode recording,
-and optophysiology**](https://www.biorxiv.org/content/10.1101/2023.01.27.525963)<br>
+[**Cleo: A testbed for bridging model and experiment by simulating closed-loop stimulation, electrode recording, and optophysiology**](https://www.biorxiv.org/content/10.1101/2023.01.27.525963)<br>
 K.A. Johnsen, N.A. Cruzado, Z.C. Menard, A.A. Willats, A.S. Charles, and C.J. Rozell. *bioRxiv*, 2023.
 
 [**CLOC Tools: A Library of Tools for Closed-Loop Neuroscience**](https://github.com/cloctools/tools-for-neuro-control-manuscript)<br>

diff --git a/cleo/coords.py b/cleo/coords.py
@@ -59,7 +59,7 @@ def assign_coords_grid_rect_prism(
     z = np.linspace(zlim[0], zlim[1], shape[2])
 
     x, y, z = np.meshgrid(x, y, z, indexing="ij")
-    assign_xyz(neuron_group, x, y, z)
+    assign_xyz(neuron_group, x, y, z, unit=unit)
 
 
 def assign_coords_rand_rect_prism(

diff --git a/cleo/light/light.py b/cleo/light/light.py
@@ -186,9 +186,7 @@ def viz_params(
         x, y, z = xyz_from_rθz(r, theta, zc, coords, end)
         density_factor = 3
         cyl_vol = np.pi * r_thresh**2 * zc_thresh
-        markersize_um = ((cyl_vol / n_points_per_source * density_factor)) ** (
-            1 / 3
-        ) / um
+        markersize_um = (cyl_vol / n_points_per_source * density_factor) ** (1 / 3) / um
         intensity_scale = (1e3 / n_points_per_source) ** (1 / 3)
         return coords_from_xyz(x, y, z), markersize_um, intensity_scale
 

diff --git a/cleo/light/two_photon.py b/cleo/light/two_photon.py
@@ -3,11 +3,11 @@
 import numpy as np
 from attrs import define
 from brian2 import Quantity
-from brian2.units import um, nmeter
+from brian2.units import nmeter, um
 from nptyping import NDArray
 
 from cleo.coords import concat_coords, coords_from_ng, coords_from_xyz
-from cleo.light import LightModel, Light
+from cleo.light import Light, LightModel
 from cleo.utilities import uniform_cylinder_rθz, xyz_from_rθz
 
 
@@ -59,9 +59,7 @@ def viz_params(
         # m x n x 3
         density_factor = 3
         cyl_vol = np.pi * r_thresh**2 * zc_thresh
-        markersize_um = ((cyl_vol / n_points_per_source * density_factor)) ** (
-            1 / 3
-        ) / um
+        markersize_um = (cyl_vol / n_points_per_source * density_factor) ** (1 / 3) / um
         intensity_scale = (1000 / n_points_per_source) ** (1 / 3)
         return coords_from_xyz(x, y, z), markersize_um, intensity_scale
 

diff --git a/cleo/utilities.py b/cleo/utilities.py
@@ -1,19 +1,18 @@
 """Assorted utilities for developers."""
+import warnings
 from collections.abc import MutableMapping
 
-from matplotlib import pyplot as plt
-
-from brian2 import np, second, Quantity
-from brian2.groups.group import get_dtype
+import neo
+import quantities as pq
+from brian2 import Quantity, np, second
 from brian2.equations.equations import (
-    Equations,
     DIFFERENTIAL_EQUATION,
-    SUBEXPRESSION,
     PARAMETER,
+    SUBEXPRESSION,
+    Equations,
 )
-import neo
-import quantities as pq
-
+from brian2.groups.group import get_dtype
+from matplotlib import pyplot as plt
 
 rng = np.random.default_rng()
 """supposed to be the central random number generator, but not yet used everywhere"""