Merge pull request #29 from INM-6/rtd-integration

Readthedocs integration

Author: mdenker

AUTHORS.txt

@@ -12,6 +12,7 @@ contribution, and may not be the current affiliation of a contributor.
 * Michael von Papen [1]
 * Michael Denker [1]
 * Aitor Morales-Gregorio [1][2]
+* Oliver Kloss [1]
 
 1. Institute of Neuroscience and Medicine (INM-6), Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6), Theoretical Neuroscience, Jülich Research Centre and JARA, Jülich, Germany
 2. RWTH Aachen University, Aachen, Germany

README.rst

@@ -6,6 +6,11 @@ A SciUnit_ library for validation testing of spiking networks.
 
 .. _SciUnit: https://github.com/scidash/sciunit
 
+
+
+.. image:: https://readthedocs.org/projects/networkunit/badge/?version=latest
+    :target: https://networkunit.readthedocs.io/en/latest/?badge=latest
+
 .. image:: https://mybinder.org/badge.svg
    :target: https://mybinder.org/v2/gh/INM-6/NetworkUnit/master?filepath=examples%2Findex.ipynb
    :alt: Binder Link

examples/index.ipynb

@@ -0,0 +1,136 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "sys.path.insert(0, '../')\n",
+    "from networkunit import models, tests, scores\n",
+    "import quantities as pq\n",
+    "import sciunit"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Define models\n",
+    "model_A = models.stochastic_activity('model A', rate=5*pq.Hz)\n",
+    "model_B = models.stochastic_activity('model B', rate=15*pq.Hz)\n",
+    "\n",
+    "# Define test\n",
+    "class fr_lv_jtest(tests.TestM2M, tests.joint_test):\n",
+    "    score_type = scores.ks_distance        # <- define score statistic\n",
+    "#     score_type = scores.kl_divergence\n",
+    "    params = {}\n",
+    "    test_list = [tests.firing_rate_test, tests.isi_variation_test, tests.isi_variation_test]\n",
+    "    test_params = [{}, {'variation_measure': 'lv'}, {'variation_measure': 'cv'}]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "jtest_inst = fr_lv_jtest()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(3, 100)"
+      ]
+     },
+     "execution_count": 22,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pred = jtest_inst.generate_prediction(model_A)\n",
+    "pred.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "isinstance(fr_lv_jtest, type)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "score = jtest_inst.judge([model_A, model_B])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "sciunit.scores.collections_m2m.ScoreMatrixM2M"
+      ]
+     },
+     "execution_count": 21,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "type(score)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

examples/joint_test.ipynb

@@ -0,0 +1,19 @@
+# readthedocs version
+version: 2
+
+build:
+    os: ubuntu-22.04
+    tools:
+      python: "3.9"
+
+sphinx:
+  builder: html
+  configuration: doc/conf.py
+
+
+python:
+    install:
+        - method: pip
+          path: .
+          extra_requirements:
+              - docs

readthedocs.yml

@@ -0,0 +1,5 @@
+# Packages required to build docs (in addition to requirements-tutorials.rst)
+
+jupyter>=1.0.0
+sphinx>=7.2.5
+nbsphinx>=0.9.3

requirements-docs.txt

@@ -8,6 +8,9 @@
 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",