v0.6.0 -> master (#182)

* prepare v0.6.0

* fix codacy complaints

* fix tests

* remove raw directive from README

README.rst

@@ -37,21 +37,12 @@ However, interactions between the device electronics and the retinal
 neurophysiology result in perceptual distortions that may severely limit the
 quality of the generated visual experience:
 
-.. raw:: html
-
-   <div style="width: 100%; margin: 0; padding: 0 30%">
-    <div style="float: right; width: 20%; text-align: center">
-      Predicted percept
-    </div>
-    <div style="width: 20%; text-align: center">
-      Input stimulus
-    </div>
-  </div>
-
 .. image:: https://raw.githubusercontent.com/pulse2percept/pulse2percept/master/doc/_static/boston-train-combined.gif
    :align: center
    :alt: Input stimulus and predicted percept
 
+*(left: input stimulus, right: predicted percept)*
+
 Built on the NumPy and SciPy stacks, `pulse2percept`_ provides an open-source
 implementation of a number of computational models for state-of-the-art
 `visual prostheses`_ (also known as the 'bionic eye'),

doc/index.rst

@@ -48,14 +48,14 @@ pulse2percept |version| documentation
 
 .. include:: ../README.rst
    :start-line: 28
-   :end-line: 79
+   :end-line: 70
 
 Installation
 ============
 
 .. include:: ../README.rst
-   :start-line: 82
-   :end-line: 101
+   :start-line: 73
+   :end-line: 92
 
 Detailed instructions for different platforms can be found in our
 :ref:`Installation Guide <install>`.

doc/install.rst

@@ -161,8 +161,8 @@ Dependencies
 ------------
 
 .. include:: ../README.rst
-   :start-line: 115
-   :end-line: 148
+   :start-line: 105
+   :end-line: 139
 
 Obtaining the latest code from GitHub
 -------------------------------------
@@ -217,7 +217,8 @@ Obtaining the latest code from GitHub
 Building pulse2percept
 ----------------------
 
-Assuming you are still in the root directory of the git clone, type:
+Assuming you are still in the root directory of the git clone, type
+(note the ``.``):
 
 .. code-block:: bash
 

doc/users/release_notes.rst

@@ -9,7 +9,7 @@ Release Notes
     pulse2percept 0.4.3 is the last release to support Python 2.7 and 3.4.
     pulse2percept 0.5+ require **Python 3.5 or newer**.
 
-v0.6.0 (2020, planned)
+v0.6.0 (2020-05-05)
 ----------------------
 
 Highlights
@@ -19,7 +19,8 @@ Highlights
 *   New implants: :py:class:`~pulse2percept.implants.BVA24` (:pull:`161`)
 *   New models: :py:class:`~pulse2percept.models.ScoreboardModel` (:pull:`96`),
     :py:class:`~pulse2percept.models.AxonMapModel` (:pull:`96`),
-    :py:class:`~pulse2percept.models.Nanduri2012Model` (:pull:`168`)
+    :py:class:`~pulse2percept.models.Nanduri2012Model` (:pull:`168`),
+    :py:class:`~pulse2percept.models.Horsager2009Model` (:pull:`180`)
 *   New stimuli: :py:class:`~pulse2percept.stimuli.BiphasicPulseTrain`,
     :py:class:`~pulse2percept.stimuli.AsymmetricBiphasicPulse`,
     :py:class:`~pulse2percept.stimuli.AsymmetricBiphasicPulseTrain`
@@ -57,13 +58,18 @@ Backward-incompatible changes
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 *  Times are now specified in milliseconds.
-*  The ``TimeSeries`` object is deprecated. Please use 
-   :py:class:`~pulse2percept.stimuli.Stimulus` instead.
 *  The ``Simulation`` object has been removed. Please directly
    :ref:`instantiate a model <topics-models>` instead.
 *  ``pulse2percept.retina``: use :py:mod:`~pulse2percept.models` instead
 *  ``pulse2percept.files``: use :py:mod:`~pulse2percept.io` instead
 
+Deprecations
+^^^^^^^^^^^^
+
+*  ``TimeSeries``: use :py:class:`~pulse2percept.stimuli.Stimulus` instead
+*  Old pulses got renamed to ``LegacyMonophasicPulse``, ``LegacyBiphasicPulse``
+   and ``LegacyPulseTrain``
+
 v0.5.2 (2020-02-25)
 -------------------
 

pulse2percept/datasets/horsager2009.py

@@ -1,5 +1,4 @@
 """`load_horsager2009`, `VariableDuration`"""
-import numpy as np
 from os.path import dirname, join
 
 try:

pulse2percept/models/base.py

@@ -8,7 +8,7 @@
 from ..implants import ProsthesisSystem
 from ..stimuli import Stimulus
 from ..percepts import Percept
-from ..utils import PrettyPrint, Frozen, FreezeError, GridXY, parfor, bisect
+from ..utils import PrettyPrint, Frozen, FreezeError, GridXY, bisect
 
 
 class NotBuiltError(ValueError, AttributeError):

pulse2percept/models/tests/test_horsager2009.py

@@ -3,7 +3,7 @@
 import pytest
 
 from pulse2percept.implants import ProsthesisSystem, PointSource
-from pulse2percept.stimuli import Stimulus, BiphasicPulse, BiphasicPulseTrain
+from pulse2percept.stimuli import BiphasicPulse, BiphasicPulseTrain
 from pulse2percept.percepts import Percept
 from pulse2percept.models import Horsager2009Model, Horsager2009Temporal
 from pulse2percept.utils import FreezeError
@@ -74,8 +74,6 @@ def test_Horsager2009Model():
     with pytest.raises(FreezeError):
         model.rho = 100
 
-
-def test_Horsager2009Model():
     # Model and TemporalModel give the same result
     for amp, freq in zip([136.02, 120.35, 57.71], [5, 15, 225]):
         stim = BiphasicPulseTrain(freq, amp, 0.075, interphase_dur=0.075,

pulse2percept/stimuli/pulse_trains.py

@@ -2,8 +2,6 @@
 import numpy as np
 import copy
 import logging
-from scipy.interpolate import interp1d
-
 
 from . import MIN_AMP
 from .base import TimeSeries, Stimulus

pulse2percept/stimuli/pulses.py

@@ -219,7 +219,7 @@ class AsymmetricBiphasicPulse(Stimulus):
         If True, will deliver the cathodic pulse phase before the anodic one.
     electrode : { int | string }, optional, default: 0
         Optionally, you can provide your own electrode name.
-    dt : float, optional, default: 1e-3 ms
+    dt : float, optional, default: 1e-6 ms
         Sampling time step (ms); defines the duration of the signal edge
         transitions.
 
@@ -245,7 +245,7 @@ class AsymmetricBiphasicPulse(Stimulus):
 
     def __init__(self, amp1, amp2, phase_dur1, phase_dur2, interphase_dur=0,
                  delay_dur=0, stim_dur=None, cathodic_first=True,
-                 electrode=None, dt=1e-3):
+                 electrode=None, dt=1e-6):
         if phase_dur1 <= 0:
             raise ValueError("'phase_dur1' must be greater than 0.")
         if phase_dur2 <= 0:

pulse2percept/stimuli/tests/test_pulse_trains.py

@@ -153,7 +153,7 @@ def test_BiphasicTripletTrain(amp, interphase_dur, delay_dur, cathodic_first):
     pt = BiphasicTripletTrain(freq, amp, phase_dur,
                               interphase_dur=interphase_dur,
                               delay_dur=delay_dur, stim_dur=stim_dur,
-                              cathodic_first=cathodic_first, dt=1e-6)
+                              cathodic_first=cathodic_first, dt=dt)
     for i in range(n_pulses):
         t_win = i * window_dur
         npt.assert_almost_equal(pt[0, t_win], 0)

pulse2percept/utils/optimize.py

@@ -2,7 +2,7 @@
 import logging
 
 
-def bisect(y_target, func, args=[], kwargs={}, x_lo=0, x_hi=1,
+def bisect(y_target, func, args=None, kwargs=None, x_lo=0, x_hi=1,
            x_tol=1e-6, y_tol=1e-3, max_iter=100):
     """Binary search (bisection method) to find `x` value that gives `y_target`
 
@@ -38,10 +38,19 @@ def bisect(y_target, func, args=[], kwargs={}, x_lo=0, x_hi=1,
        the conventional bisection method.
 
     """
-    assert x_lo < x_hi
-    assert x_tol > 0
-    assert y_tol > 0
-    assert max_iter > 0
+    if x_lo >= x_hi:
+        raise ValueError("x_lo (%f) must be lower than x_hi "
+                         "(%f)." % (x_lo, x_hi))
+    if x_tol <= 0:
+        raise ValueError("x_tol (%f) must be greater than zero." % x_tol)
+    if y_tol <= 0:
+        raise ValueError("y_tol (%f) must be greater than zero." % y_tol)
+    if max_iter <= 0:
+        raise ValueError("max_iter (%d) must be greater than zero." % max_iter)
+    if args is None:
+        args = []
+    if kwargs is None:
+        kwargs = {}
 
     n_iter = 1
     while n_iter < max_iter:

pulse2percept/utils/tests/test_optimize.py

@@ -1,5 +1,6 @@
 import numpy as np
 import numpy.testing as npt
+import pytest
 from pulse2percept.utils import bisect
 
 
@@ -12,3 +13,12 @@ def test_bisect():
                            max_iter=100)
             decimal = int(np.abs(np.log10(y_tol))) - 1
             npt.assert_almost_equal(func(x_mid), y_target, decimal=decimal)
+
+    with pytest.raises(ValueError):
+        bisect(0, func, x_lo=1, x_hi=0)
+    with pytest.raises(ValueError):
+        bisect(0, func, x_tol=-1)
+    with pytest.raises(ValueError):
+        bisect(0, func, y_tol=-1)
+    with pytest.raises(ValueError):
+        bisect(0, func, max_iter=0)

pulse2percept/version.py

@@ -1 +1 @@
-__version__ = '0.6.0.dev0'
+__version__ = '0.6.0'