V0.2.1 (#30)

* update environment, change to pyproject.toml convention * update test and score list in readme * update environment * update environment
INM-6 · Dec 21, 2023 · 773dda4 · 773dda4
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diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright (c) 2018, NetworkUnit authors and contributors
+Copyright (c) 2018-2023, NetworkUnit 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:
@@ -7,4 +7,4 @@ Redistribution and use in source and binary forms, with or without modification,
 * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
 * Neither the names of the copyright holders nor the names of the contributors may be used to endorse or promote products derived from this software without specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/README.rst b/README.rst
@@ -58,53 +58,60 @@ accessible via the launch-binder button at the top.
 
 Overview of tests
 -----------------
-===================================     =======================     ===================================================
+===================================     =======================     ======================================================
 Class name                              Parent class                Prediction measure
-===================================     =======================     ===================================================
+===================================     =======================     ======================================================
 two_sample_test                         \-                          \-
+firing_rate_test                        two_sample_test             firing rates
+isi_variation_test                      two_sample_test             inter-spike-intervals, their CV, CV2, LV, or LVR
+covariance_test                         two_sample_test             covariances
 correlation_test                        two_sample_test             \-
 correlation_dist_test                   correlation_test            correlation coefficients
 correlation_matrix_test                 correlation_test            correlation coefficient matrix
+avg_std_correlation_test                correlation_test            avg or std of correlation coefficients
 generalized_correlation_matrix_test     correlation_matrix_test     matrix of derived cross-correlation measures
 eigenvalue_test                         correlation_test            eigenvalues of the correlation coefficient matrix
-covariance_test                         two_sample_test             covariances
-firing_rate_test                        two_sample_test             firing rates
-isi_variation_test                      two_sample_test             inter-spike-intervals, their CV, or LV
+power_spectrum_test                     two_sample_test             power spectral density values
+freqband_power_test                     power_spectrum_test         power spectral density values in frequency band
+timescale_test                          two_sample_test             spike train timescale
 graph_centrality_helperclass            sciunit.Test                graph centrality measures of given adjacency matrix
-===================================     =======================     ===================================================
+joint_test                              two_sample_test             joining other test classes for multivariate evaluation
+===================================     =======================     ======================================================
 
 Inheritance order in case of multiple inheritance for derived test classes:
 
-.. code:: python
+.. code:: Python
 
-    class new_test(sciunit.TestM2M, graph_centrality_helperclass, <base_test_class>)
+   class new_test(sciunit.TestM2M, graph_centrality_helperclass, <base_test_class>)
 
 
 Overview of scores
 ------------------
 
-================    ===============================     ===================
-Class name          Test name                           Comparison measure
-================    ===============================     ===================
-students_t          Student't test                      sample mean
-ks_distance         Kolmogorov-Smirnov test             sample distribution
-kl_divergence       Kullback-Leibler divergence         sample entropy
-mwu_statistic       Mann-Whitney U test                 rank sum
-levene_score        Levene's test                       sample variance
-effect_size         Effect size                         standardized mean
-best_effect_size    Bayesian estimation effect size     standardized mean
-================    ===============================     ===================
+====================    ===============================     ===========================
+Class name              Test name                           Comparison measure
+====================    ===============================     ===========================
+students_t              Student't test                      sample mean
+ks_distance             Kolmogorov-Smirnov test             sample distribution
+kl_divergence           Kullback-Leibler divergence         sample entropy
+mwu_statistic           Mann-Whitney U test                 rank sum
+levene_score            Levene's test                       sample variance
+effect_size             Effect size                         standardized mean
+best_effect_size        Bayesian estimation effect size     standardized mean
+wasserstein_distance    Wasserstein Distance                multivariate score distance
+eigenangle              Eigenangle Test                     eigenangle similarity
+====================    ===============================     ===========================
 
 Overview of model classes
 -------------------------
 
-===================     ===================     ===============        ==================================
+===================     ===================     =====================  ==================================
 Model name              Capability              Parent class           Purpose
-===================     ===================     ===============        ==================================
+===================     ===================     =====================  ==================================
 loaded_spiketrains      ProducesSpikeTrains     sciunit.RunnableModel  loading simulated spiking data
 stochastic_activity     ProducesSpikeTrains     sciunit.RunnableModel  generating stochastic spiking data
 nest_simulation         ProducesSpikeTrains     sciunit.RunnableModel  template for NEST models
-===================     ===================     ===============        ==================================
+===================     ===================     =====================  ==================================
 
 Other validation test repositories
 ----------------------------------

diff --git a/environment.yml b/environment.yml
@@ -1,9 +1,7 @@
 name: networkunit_env
 channels:
-  - damianavila82
   - defaults
 dependencies:
-  - rise
   - pip
   - pip:
     - jupyter==1.0.0

diff --git a/networkunit/VERSION b/networkunit/VERSION
@@ -1 +1 @@
-0.2.0dev
+0.2.1
diff --git a/networkunit/scores/best_effect_size.py b/networkunit/scores/best_effect_size.py
@@ -1,3 +1,7 @@
+"""
+The Baysian Estimation Effect Size  is introduced in Kruschke, J. (2012)
+doi:10.1037/a0029146
+"""
 from __future__ import division
 import numpy as np
 import sciunit
@@ -16,8 +20,6 @@
 class best_effect_size(sciunit.Score):
     """
     Baysian Estimation Effect Size according to  Kruschke, J. (2012)
-    'Bayesian estimation supersedes the t-test',
-    Journal of Experimental Psychology
 
     Requires the test parameters:
         mcmc_iter : int (default 110000)

diff --git a/networkunit/scores/eigenangle.py b/networkunit/scores/eigenangle.py
@@ -1,6 +1,9 @@
+"""
+The Eigenangle Test is introduced in Gutzen, Grün, Denker (2023) 
+doi:10.1016/j.biosystems.2022.104813
+"""
 import numpy as np
 from scipy.linalg import eigh
-from scipy.special import binom
 from scipy.integrate import quad
 import matplotlib.pyplot as plt
 import seaborn as sns
@@ -18,7 +21,7 @@ class eigenangle(sciunit.Score):
     similar non-random elements by calculating the significance of the angles
     between the corresponding eigenvectors.
     Either the bin_size or the number of bins must be provides to perform the
-    signficnace test.
+    significance test.
     """
     score = np.nan
 

diff --git a/networkunit/tests/timescale_test.py b/networkunit/tests/timescale_test.py
@@ -44,7 +44,7 @@ def generate_prediction(self, model):
 
     def calc_timescales(self, spiketrain):
         if len(spiketrain.times) >= self.params['min_spikecount']:
-            bst = BinnedSpikeTrain(st, bin_size=self.params['bin_size'])
+            bst = BinnedSpikeTrain(spiketrain, bin_size=self.params['bin_size'])
             tau = timescale(bst, self.params['tau_max'])
             tau = tau.rescale('ms').magnitude
         else:

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,68 @@
+[project]
+name = "networkunit"
+description = "A SciUnit library for validation testing of spiking networks."
+version = "0.2.1"
+readme = "README.rst"
+authors = [
+    { name = "NetworkUnit authors and contributors", email = "[email protected]" }
+]
+
+requires-python = ">=3.8"
+dependencies = [
+    "nbconvert == 7.12.0", #remove when updating sciunit version
+    "sciunit == 0.2.7",
+    "elephant >= 0.7.0",
+    "neo >= 0.9",
+    "networkx >= 2.1",
+    "tabulate >= 0.8.2",
+    "seaborn >= 0.8.1",
+    "numpy >= 1.15.3",
+    "opencv-python"
+]
+
+[metadata]
+description-file = "README.md"
+classifiers = [
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: BSD-3-Clause",
+    "Programming Language :: Python :: 3",
+    "Topic :: Software Development :: Libraries :: Python Modules"
+]
+
+[project.urls]
+"Homepage" = "https://github.com/INM-6/networkunit"
+"Bug Tracker" = "https://github.com/INM-6/networkunit/issues"
+
+[project.scripts]
+
+[project.optional-dependencies]
+dev = [
+    "black",
+    "bump2version",
+    "flake8",
+    "mypy",
+    "pre-commit",
+    "pydocstyle",
+    "pylint",
+    "pytest",
+    "pytest-black",
+    "pytest-cov",
+    "pytest-flake8",
+    "pytest-mypy",
+    "pytest-pydocstyle",
+    "pytest-pylint",
+    "pytest-xdist",
+]
+doc = [
+    "sphinx",
+    "sphinx-autodoc-typehints",
+    "numpydoc>=1.1.0",
+    "sphinx-tabs>=1.3.0",
+    "sphinx-argparse>=0.4.0",
+    "pygments",
+    "recommonmark",
+]
+
+[build-system]
+build-backend = "flit_core.buildapi"
+requires = ["flit_core >=3.2,<4"]
diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.py b/setup.py
@@ -1,48 +1,6 @@
-# -*- coding: utf-8 -*-
+# encoding: utf8
+'Packaging configuration.'
 
-from setuptools import setup
-import os
-import sys
+from setuptools import setup        # type: ignore
 
-long_description = open("README.rst").read()
-with open('requirements.txt', 'r') as fp:
-    install_requires = fp.read()
-extras_require = {}
-for extra in ['docs']:
-    with open('requirements-{0}.txt'.format(extra)) as fp:
-        extras_require[extra] = fp.read()
-
-setup(
-    name="networkunit",
-    version='0.2.0',
-    packages=['networkunit', 'figures', 'examples'],
-    package_data={'networkunit':[
-        os.path.join('tests','*.py'),
-        os.path.join('models','*.py'),
-        os.path.join('models/backends','*.py'),
-        os.path.join('capabilities','*.py'),
-        os.path.join('scores','*.py'),
-        os.path.join('plots','*.py'),
-        'VERSION'],
-        'figures':['*.png'],
-        'examples':['*.py', '*.ipynb']
-        },
-    install_requires=install_requires,
-    extras_require=extras_require,
-
-    author="NetworkUnit authors and contributors",
-    author_email="[email protected]",
-    description="A SciUnit library for validation testing of neural network models.",
-    long_description=long_description,
-    license="BSD",
-    url='https://github.com/INM-6/NetworkUnit',
-    classifiers=[
-        'Development Status :: 3 - Alpha',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: BSD License',
-        'Natural Language :: English',
-        'Operating System :: OS Independent',
-        'Programming Language :: Python :: 2',
-        'Programming Language :: Python :: 3',
-        'Topic :: Scientific/Engineering']
-)
+setup()     # everything configured via pyproject.toml
diff --git a/tox.ini b/tox.ini
@@ -0,0 +1,22 @@
+[pytest]
+addopts = -n 0 --doctest-modules --pycodestyle --mypy --pylint --pylint-rcfile=.pylintrc --pydocstyle --cov --ignore=conda --ignore=env --ignore=.git --ignore=__pycache__
+
+[pycodestyle]
+count = False
+#ignore = E226,E302,E41
+exclude = .git/, .snakemake/, .pytest_cache/, sync-test-env/, conda/, env/
+max-line-length = 120
+statistics = True
+
+# as suggested by pylint docs for joint usage with other tools
+# http://pylint.pycqa.org/en/latest/faq.html?highlight=pylintrc#i-am-using-another-popular-linter-alongside-pylint-which-messages-should-i-disable-to-avoid-duplicates
+
+[pylint]
+options = unneeded-not, line-too-long, unnecessary-semicolon, trailing-whitespace, missing-final-newline, bad-indentation, multiple-statements, bare-except
+
+[pydocstyle]
+convention = numpy
+add-ignore = D300
+
+[mypy]
+exclude = .git/, .snakemake/, .pytest_cache/, sync-test-env/, conda/, env/