Merge pull request #25 from NeuralEnsemble/development

Latest dev -> master - removed py2 support

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
 

.gitignore

@@ -20,3 +20,4 @@ doc/_build
 
 *.egg-info/
 dist/
+arm64

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2014, Neurotune authors and contributors
+Copyright (c) 2023, Neurotune authors and contributors
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

neurotune/__init__.py

@@ -1 +1 @@
-__version__ = "0.2.5"
+__version__ = "0.2.6"

neurotune/utils.py

@@ -4,10 +4,12 @@
 
 """
 
+from __future__ import annotations
 import math
 import numpy as np
+
 try:
-    from typing import List, Dict, Bool, Union
+    import typing
 except ImportError:
     pass
 
@@ -17,16 +19,15 @@
 
 
 def plot_generation_evolution(
-    sim_var_names,
-    target_values={},
-    individuals_file_name="../data/ga_individuals.csv",
-    show_plot_already=True,
-    save_to_file=False,
-    save_to_file_scatter=False,
-    save_to_file_hist=False,
-    title_prefix="",
-):
-    # type: (List, Dict, str, Bool, Union[Bool, str], Union[Bool, str], Union[Bool, str], str) -> None
+    sim_var_names: list,
+    target_values: dict = {},
+    individuals_file_name: str = "../data/ga_individuals.csv",
+    show_plot_already: bool = True,
+    save_to_file: typing.Union[bool, str] = False,
+    save_to_file_scatter: bool = False,
+    save_to_file_hist: bool = False,
+    title_prefix: str = "",
+) -> None:
     """Plot generation evolution related graphs.
 
     :param sim_var_names: names of variables
@@ -145,15 +146,19 @@ def plot_generation_evolution(
         0.40,
         0.01,
         "Generation (%i individuals, offset slightly; larger circle => fitter)"
-        % (population_total)
+        % (population_total),
     )
     for i in range(val_num):
 
         var_name = sim_var_names[i]
 
-        pyplot.subplot(nrows, ncols, i + 1, xlabel="Generation",
-                       ylabel="{} ({})".format(var_name.split('/')[-2],
-                                               var_name.split('/')[-1]))
+        pyplot.subplot(
+            nrows,
+            ncols,
+            i + 1,
+            xlabel="Generation",
+            ylabel="{} ({})".format(var_name.split("/")[-2], var_name.split("/")[-1]),
+        )
         pyplot.title(var_name)
         if target_values is not None and sim_var_names[i] in target_values:
             value = target_values[sim_var_names[i]]
@@ -164,7 +169,7 @@ def plot_generation_evolution(
         pyplot.scatter(generations_offset, vals[i], s=sizes[i], c=colours[i], alpha=0.4)
 
     if save_to_file_scatter:
-        pyplot.savefig(save_to_file_scatter, dpi=300, bbox_inches='tight')
+        pyplot.savefig(save_to_file_scatter, dpi=300, bbox_inches="tight")
 
     fig2 = pyplot.figure()
     pyplot.get_current_fig_manager().set_window_title(
@@ -183,26 +188,28 @@ def plot_generation_evolution(
         0.40,
         0.01,
         "Generation (%i individuals, offset slightly; larger circle => fitter)"
-        % (population_total)
+        % (population_total),
     )
 
     if save_to_file:
-        pyplot.savefig(save_to_file, dpi=300, bbox_inches='tight')
+        pyplot.savefig(save_to_file, dpi=300, bbox_inches="tight")
 
     fig3 = pyplot.figure()
     pyplot.get_current_fig_manager().set_window_title(
-        title_prefix + " Histograms over %i generations of %s" %
-        (generations_total, sim_var_names)
+        title_prefix
+        + " Histograms over %i generations of %s" % (generations_total, sim_var_names)
     )
 
     pyplot.subplots_adjust(hspace=0.4)
     for i in range(val_num):
 
-        var_name = (sim_var_names[i])
-        ax = pyplot.subplot(nrows, ncols, i + 1,
-                            xlabel="{} ({})".format(var_name.split('/')[-2],
-                                                    var_name.split('/')[-1])
-                            )
+        var_name = sim_var_names[i]
+        ax = pyplot.subplot(
+            nrows,
+            ncols,
+            i + 1,
+            xlabel="{} ({})".format(var_name.split("/")[-2], var_name.split("/")[-1]),
+        )
         pyplot.title(var_name)
 
         for generation in generations:
@@ -217,7 +224,7 @@ def plot_generation_evolution(
             ax.plot(xs, hist, color=(shade, shade, shade))
 
     if save_to_file_hist:
-        pyplot.savefig(save_to_file_hist, dpi=300, bbox_inches='tight')
+        pyplot.savefig(save_to_file_hist, dpi=300, bbox_inches="tight")
 
     if show_plot_already:
         pyplot.show()

setup.py

@@ -6,13 +6,17 @@
     if line.startswith("__version__"):
         version = line.split("=")[1].strip()[1:-1]
 
+long_description = open("README.md").read()
+
 setup(
     name="neurotune",
     version=version,
     packages=["neurotune"],
     author="Michael Vella, Padraig Gleeson",
     author_email="mv333@cam.ac.uk, p.gleeson@gmail.com",
     description="A Python library for optimising neuronal models",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
     license="BSD",
     install_requires=["scipy", "inspyred", "pyelectro"],
     url="https://github.com/NeuralEnsemble/neurotune",
@@ -22,11 +26,12 @@
         "License :: OSI Approved :: BSD License",
         "Natural Language :: English",
         "Operating System :: OS Independent",
-        "Programming Language :: Python :: 2.7",
         "Programming Language :: Python :: 3",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
         "Topic :: Scientific/Engineering",
     ],
 )

test.sh

@@ -1,6 +1,8 @@
 set -e
 
-rm -rf examples/*/x86_64/
+pip install .
+
+rm -rf examples/*/x86_64/ examples/*/arm64
 
 #### Requires NEURON
 cd examples/example_1