Merge pull request #29 from XENONnT/mybinder

Example Notebook
XENONnT · Dec 28, 2021 · f1a3d87 · f1a3d87
2 parents be93136 + f98c22b
commit f1a3d87
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diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -26,13 +26,26 @@ jobs:
     - name: Checkout repo
       uses: actions/checkout@v2
     - name: Install dependencies
-      uses: py-actions/py-dependency-install@v2
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest coverage coveralls
+        pip install -r requirements.txt
+    - name: Install GOFevaluation
+      run: |
+        pip install .
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        flake8 . --count --select=F5,F6,F7,F8,F9,E1,E2,E3,E5,E7,E9,W291 --max-line-length=100 --show-source --statistics
     - name: Test with pytest
       run: |
         pytest
+    - name: Coveralls
+      # Make the coverage report and upload
+      env:
+        NUMBA_DISABLE_JIT: 1
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        coverage run --source=GOFevaluation setup.py test -v
+        coveralls --service=github
+
diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,4 @@ build
 dist
 __pycache__
 .eggs
+gofevaluation_tutorial.py
diff --git a/GOFevaluation/evaluator_base.py b/GOFevaluation/evaluator_base.py
@@ -1,7 +1,8 @@
 import numpy as np
 import scipy.stats as sps
 import warnings
-from GOFevaluation import equiprobable_histogram, apply_irregular_binning, plot_equiprobable_histogram, check_sample_sanity
+from GOFevaluation import (equiprobable_histogram, apply_irregular_binning,
+                           plot_equiprobable_histogram, check_sample_sanity)
 
 
 class EvaluatorBase(object):
@@ -19,9 +20,9 @@ def __repr__(self):
 
     def __str__(self):
         args = [self._name]
-        if self.gof:
+        if self.gof is not None:
             args.append(f'gof = {self.gof}')
-        if self.pvalue:
+        if self.pvalue is not None:
             args.append(f'p-value = {self.pvalue}')
         args_str = "\n".join(args)
         return f'{self.__class__.__module__}\n{args_str}'

diff --git a/GOFevaluation/evaluators_nd.py b/GOFevaluation/evaluators_nd.py
@@ -108,7 +108,7 @@ class BinnedChi2GOF(EvaluatorBaseBinned):
         initialise with .bin_equiprobable(...)
             :param data_sample: sample of unbinned data
             :type data_sample: array_like, n-Dimensional
-            :param reference_sample: sample of unbinned reference 
+            :param reference_sample: sample of unbinned reference
                 (should have >50 samples than the data sample so that
                 statistical fluctuations are negligible.)
             :type reference_sample: array_like, n-Dimensional
@@ -178,7 +178,7 @@ class PointToPointGOF(EvaluatorBaseSample):
     :type data_sample: array_like, n-Dimensional
     :param reference_sample: sample of unbinned reference
     :type reference_sample: array_like, n-Dimensional
-    :param w_func: weighting function to use for the GOF measure. 
+    :param w_func: weighting function to use for the GOF measure.
         Defaults to 'log'. Other options are:
         'x2', 'x', '1/x'
     :type w_func' str, optional

diff --git a/GOFevaluation/gof_test.py b/GOFevaluation/gof_test.py
@@ -55,6 +55,8 @@ def __init__(self, gof_list, **kwargs):
         for gof_str in self.gof_list:
             if gof_str in self.allowed_gof_str:
                 func = eval(gof_str)
+                self.gofs[gof_str] = None
+                self.pvalues[gof_str] = None
             else:
                 allowed_str = ", ".join(
                     ['"' + str(p) + '"' for p in self.allowed_gof_str])
@@ -71,13 +73,13 @@ def __repr__(self):
         return f'{self.__class__.__module__}:\n{self.__dict__}'
 
     def __str__(self):
-        args = ['GoF measures: ' + ", ".join(self.gof_list)]
-        if self.gofs:
-            gofs_str = ", ".join([str(g) for g in self.gofs.values()])
-            args.append('gofs = ' + gofs_str)
-        if self.pvalues:
-            pvalues_str = ", ".join([str(p) for p in self.pvalues.values()])
-            args.append('p-values = ' + pvalues_str)
+        args = ['GOF measures: ' + ", ".join(self.gof_list)] + ['\n']
+        for key, gof in self.gofs.items():
+            pval = self.pvalues[key]
+            results_str = '\033[1m' + key + '\033[0m' + '\n'
+            results_str += f'gof = {gof}\n'
+            results_str += f'p-value = {pval}\n'
+            args.append(results_str)
         args_str = "\n".join(args)
         return f'{self.__class__.__module__}\n{args_str}'
 
@@ -134,6 +136,7 @@ def get_pvalues(self, **kwargs):
             specific_kwargs = self._get_specific_kwargs(func, kwargs)
             pvalue = func(**specific_kwargs)
             self.pvalues[key] = pvalue
+            self.gofs[key] = self.gof_objects[key].gof
             kwargs_used += specific_kwargs.keys()
         self._check_kwargs_used(kwargs_used, kwargs)
         return self.pvalues
diff --git a/GOFevaluation/utils.py b/GOFevaluation/utils.py
@@ -63,10 +63,10 @@ def _get_equiprobable_binning(reference_sample, n_partitions, order=None):
         [1, 0] : first bin y then bin x for each partition in y
         if None, the natural order, i.e. [0, 1] is used. For 1D just put None.
     :type order: list, optional
-    :return: Returns bin_edges. 
+    :return: Returns bin_edges.
         1D: list of bin edges
-        2D: For order [0, 1]([1, 0]) these are the bin edges in x(y) and y(x) 
-        respectively. bin_edges[1] is a list of bin edges corresponding to the 
+        2D: For order [0, 1]([1, 0]) these are the bin edges in x(y) and y(x)
+        respectively. bin_edges[1] is a list of bin edges corresponding to the
         partitions defined in bin_edges[0].
     :rtype: list of arrays
     :raises ValueError: when an unknown order is passed.

diff --git a/HISTORY.md b/HISTORY.md
@@ -1,3 +1,7 @@
 v0.1.0
 ===================
-* Release as a python package
+* Multiple GOF tests (binned and unbinned) can be performed (#1, #5, #10, #12, #13)
+* The p-value is calculated based on toy sampling from the reference or a permutation test (#2, #14)
+* A wrapper class makes it convenient to perform multiple GOF tests in parallel (#19)
+* An equiprobable binning algorithm is implemented. The binning can be applied upon initialisation of the GOF object and a few visualization tools are provided. (#25, #26)
+* CI workflow implemented (#7)
diff --git a/README.md b/README.md
@@ -1,6 +1,10 @@
 # GOFevaluation
 Evaluate the Goodness-of-Fit (GoF) for binned or unbinned data.  
 ![Test package](https://github.com/XENONnT/GOFevaluation/actions/workflows/python-package.yml/badge.svg)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/XENONnT/GOFevaluation/HEAD)
+[![PyPI version shields.io](https://img.shields.io/pypi/v/GOFevaluation.svg)](https://pypi.python.org/pypi/GOFevaluation/)
+[![CodeFactor](https://www.codefactor.io/repository/github/xenonnt/gofevaluation/badge)](https://www.codefactor.io/repository/github/xenonnt/gofevaluation)
+[![Coverage Status](https://coveralls.io/repos/github/XENONnT/GOFevaluation/badge.svg?branch=master)](https://coveralls.io/github/XENONnT/GOFevaluation?branch=master) 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5626909.svg)](https://doi.org/10.5281/zenodo.5626909)
 
 This GoF suite comprises the possibility to calculate different 1D / nD, binned / two-sample (unbinned) GoF measures and the corresponding p-value. A list of implemented measures is given below. 
@@ -19,6 +23,12 @@ This GoF suite comprises the possibility to calculate different 1D / nD, binned
 
 ## Installation and Set-Up
 
+### Regular installation:
+```
+pip install GOFevaluation
+```
+
+### Developer setup:
 Clone the repository:
 
 ```
@@ -37,6 +47,7 @@ python setup.py install --user
 You are now good to go!
 
 ## Usage
+The best way to start with the `GOFevaluation` package is to have a look at the tutorial notebook. If you click on the [mybinder](https://mybinder.org/v2/gh/XENONnT/GOFevaluation/HEAD) badge, you can execute the interactive notebook and give it a try yourself without the need of a local installation. 
 ### Individual GoF Measures
 Depending on your data and reference input you can initialise a `gof_object` in one of the following ways:
 ```python
@@ -84,27 +95,38 @@ gof_object.get_gofs(d_min=d_min)
 # OUTPUT:
 # OrderedDict([('ADTestTwoSampleGOF', 1.6301454042304904),
 #              ('KSTestTwoSampleGOF', 0.14),
-#              ('PointToPointGOF', 0.00048491049630050576)])
+#              ('PointToPointGOF', -0.7324060759792504)])
 
 gof_object.get_pvalues(d_min=d_min)
 # OUTPUT:
 # OrderedDict([('ADTestTwoSampleGOF', 0.08699999999999997),
 #              ('KSTestTwoSampleGOF', 0.10699999999999998),
-#              ('PointToPointGOF', 0.14300000000000002)])
+#              ('PointToPointGOF', 0.31200000000000006)])
 
 # Re-calculate p-value only for one measure:
-gof_object.get_pvalues(d_min=.3, gof_list=['PointToPointGOF'])
+gof_object.get_pvalues(d_min=.001, gof_list=['PointToPointGOF'])
 # OUTPUT:
 # OrderedDict([('ADTestTwoSampleGOF', 0.08699999999999997),
 #              ('KSTestTwoSampleGOF', 0.10699999999999998),
-#              ('PointToPointGOF', 0.03400000000000003)])
+#              ('PointToPointGOF', 0.128)])
 
 print(gof_object)
 # OUTPUT:
 # GOFevaluation.gof_test
-# GoF measures: ADTestTwoSampleGOF, KSTestTwoSampleGOF, PointToPointGOF
-# gofs = 1.6301454042304904, 0.14, 0.00048491049630050576
-# p-values = 0.08699999999999997, 0.10699999999999998, 0.03400000000000003
+# GOF measures: ADTestTwoSampleGOF, KSTestTwoSampleGOF, PointToPointGOF
+
+
+# ADTestTwoSampleGOF
+# gof = 1.6301454042304904
+# p-value = 0.08499999999999996
+
+# KSTestTwoSampleGOF
+# gof = 0.13999999999999996
+# p-value = 0.09799999999999998
+
+# PointToPointGOF
+# gof = -0.7324060759792504
+# p-value = 0.128
 ```
 
 

diff --git a/gofevaluation_tutorial.ipynb b/gofevaluation_tutorial.ipynb
diff --git a/requirements.txt b/requirements.txt
@@ -2,5 +2,3 @@ numpy
 scipy
 sklearn
 matplotlib
-flake8
-pytest
diff --git a/tests/test_evaluators_1d.py b/tests/test_evaluators_1d.py
@@ -30,7 +30,7 @@ def test_value(self):
                               kind='cubic')
 
         # Calculate GoF 'by hand'
-        ecdf = np.arange(n_samples+1, dtype=float)/n_samples
+        ecdf = np.arange(n_samples + 1, dtype=float) / n_samples
         dn = np.abs(interp_cdf(np.sort(data)) - ecdf[:-1])
 
         # Calculate GoF
@@ -104,9 +104,9 @@ class TestPvalues(unittest.TestCase):
     def test_two_sample_value(self):
         """Test if p-value for two identical samples is 1."""
         # Fixed Standard Normal distributed data
-        data = np.array([-0.80719796,  0.39138662,  0.12886947, -0.4383365,
-                         0.88404481, 0.98167819,  1.22302837,  0.1138414,
-                         0.45974904,  0.48926863])
+        data = np.array([-0.80719796, 0.39138662, 0.12886947, -0.4383365,
+                         0.88404481, 0.98167819, 1.22302837, 0.1138414,
+                         0.45974904, 0.48926863])
 
         gof_objects = [ADTestTwoSampleGOF(data, data),
                        KSTestTwoSampleGOF(data, data),

diff --git a/tests/test_evaluators_nd.py b/tests/test_evaluators_nd.py
@@ -11,14 +11,14 @@
 class TestBinnedPoissonChi2GOF(unittest.TestCase):
     def test_dimensions(self):
         # test nD binned GOF in different dimensions:
-        for nD in range(2, 5+1):
+        for nD in range(2, 5 + 1):
             # generate uniformly distributed data points and bin data
             n_events_per_bin = 30
-            n_bins_per_dim = int(32**(1/nD))
+            n_bins_per_dim = int(32**(1 / nD))
             n_events = int(n_bins_per_dim**nD * n_events_per_bin)
 
             data_points = sps.uniform().rvs(size=[n_events, nD])
-            bin_edges = np.linspace(0, 1, n_bins_per_dim+1)
+            bin_edges = np.linspace(0, 1, n_bins_per_dim + 1)
             bin_edges = np.array([bin_edges for i in range(nD)])
             binned_data, _ = np.histogramdd(data_points, bins=bin_edges)
             binned_data_flat = binned_data.reshape(-1)
@@ -42,14 +42,14 @@ def test_dimensions(self):
 
     def test_from_binned(self):
         """Test if regular init and from_binned init give same result"""
-        for nD in range(1, 5+1):
+        for nD in range(1, 5 + 1):
             # generate uniformly distributed data points and bin data
             n_events_per_bin = 30
-            n_bins_per_dim = int(32**(1/nD))
+            n_bins_per_dim = int(32**(1 / nD))
             n_events = int(n_bins_per_dim**nD * n_events_per_bin)
 
             data_points = sps.uniform().rvs(size=[n_events, nD])
-            bin_edges = np.linspace(0, 1, n_bins_per_dim+1)
+            bin_edges = np.linspace(0, 1, n_bins_per_dim + 1)
             bin_edges = np.array([bin_edges for i in range(nD)])
             binned_data, _ = np.histogramdd(data_points, bins=bin_edges)
 
@@ -118,7 +118,7 @@ def test_distances(self):
                 data, reference)
 
             self.assertEqual(len(d_data_data), nevents_data *
-                             (nevents_data-1) / 2)
+                             (nevents_data - 1) / 2)
             self.assertEqual(len(d_data_ref), nevents_ref *
                              nevents_data)
 
@@ -141,7 +141,7 @@ def test_value(self):
         xs_a = np.array([0])[:, None]
         xs_b = np.array([1, 2])[:, None]
 
-        e_data_ref = np.log(2)/2
+        e_data_ref = np.log(2) / 2
         gofclass_ab = PointToPointGOF(xs_a, xs_b)
         # set d_min explicitly to avoid asymmetry in setting d_min
         gof_ab = gofclass_ab.get_gof(d_min=0.01)
@@ -152,14 +152,14 @@ class TestBinnedChi2GOF(unittest.TestCase):
 
     def test_dimensions(self):
         # test nD binned GOF in different dimensions:
-        for nD in range(2, 5+1):
+        for nD in range(2, 5 + 1):
             # generate uniformly distributed data points and bin data
             n_events_per_bin = 30
-            n_bins_per_dim = int(32**(1/nD))
+            n_bins_per_dim = int(32**(1 / nD))
             n_events = int(n_bins_per_dim**nD * n_events_per_bin)
 
             data_points = sps.uniform().rvs(size=[n_events, nD])
-            bin_edges = np.linspace(0, 1, n_bins_per_dim+1)
+            bin_edges = np.linspace(0, 1, n_bins_per_dim + 1)
             bin_edges = np.array([bin_edges for i in range(nD)])
             binned_data, _ = np.histogramdd(data_points, bins=bin_edges)
             binned_data_flat = binned_data.reshape(-1)
@@ -187,22 +187,22 @@ def test_chi2_distribution(self):
 
         n_testvalues = 100
         model = sps.uniform()
-        for nD in range(1, 5+1):
+        for nD in range(1, 5 + 1):
             # have same number of events per bin and total number
             # of bins for all tests
             n_events_per_bin = 20
-            n_bins_per_dim = int(32**(1/nD))
+            n_bins_per_dim = int(32**(1 / nD))
             n_events = int(n_bins_per_dim**nD * n_events_per_bin)
 
-            bin_edges = np.linspace(0, 1, n_bins_per_dim+1)
+            bin_edges = np.linspace(0, 1, n_bins_per_dim + 1)
             bin_edges = np.array([bin_edges for i in range(nD)])
 
             chi2_vals = []
             for i in range(n_testvalues):
                 # generate uniformly distributed rvs with fixed random
                 # states for reproducibility
                 data_points = model.rvs(
-                    size=[n_events, nD], random_state=300+i)
+                    size=[n_events, nD], random_state=300 + i)
                 binned_data, _ = np.histogramdd(data_points, bins=bin_edges)
 
                 normed_pdf = np.ones(binned_data.shape)
@@ -228,19 +228,19 @@ def test_chi2_distribution(self):
 
             # calculate 'reduced chi2' to estimate agreement of chi2 values
             # and chi2 pdf
-            test_chi2 = np.sum((chi2_pdf-n)**2 / chi2_pdf)/n_chi2_bins
-            self.assertTrue((test_chi2 > 1/3) & (test_chi2 < 3))
+            test_chi2 = np.sum((chi2_pdf - n)**2 / chi2_pdf) / n_chi2_bins
+            self.assertTrue((test_chi2 > 1 / 3) & (test_chi2 < 3))
 
     def test_from_binned(self):
         """Test if regular init and from_binned init give same result"""
-        for nD in range(1, 5+1):
+        for nD in range(1, 5 + 1):
             # generate uniformly distributed data points and bin data
             n_events_per_bin = 15
-            n_bins_per_dim = int(32**(1/nD))
+            n_bins_per_dim = int(32**(1 / nD))
             n_events = int(n_bins_per_dim**nD * n_events_per_bin)
 
             data_points = sps.uniform().rvs(size=[n_events, nD])
-            bin_edges = np.linspace(0, 1, n_bins_per_dim+1)
+            bin_edges = np.linspace(0, 1, n_bins_per_dim + 1)
             bin_edges = np.array([bin_edges for i in range(nD)])
             binned_data, _ = np.histogramdd(data_points, bins=bin_edges)
 
@@ -299,9 +299,9 @@ def test_dimension_two_sample(self):
         d_min = .00001
         for nD in [2, 3, 4]:
             # Fixed Standard Normal distributed data
-            data = np.array([-0.80719796,  0.39138662,  0.12886947, -0.4383365,
-                             0.88404481, 0.98167819,  1.22302837,  0.1138414,
-                             0.45974904,  0.48926863])
+            data = np.array([-0.80719796, 0.39138662, 0.12886947, -0.4383365,
+                             0.88404481, 0.98167819, 1.22302837, 0.1138414,
+                             0.45974904, 0.48926863])
             data = np.vstack([data for i in range(nD)]).T
             gof_object = PointToPointGOF(data, data)
 

diff --git a/tests/test_gof_test.py b/tests/test_gof_test.py
@@ -22,7 +22,7 @@ def test_gof(self):
         model = sps.uniform
         nevents_expected = 300
         data_sample = model.rvs(size=nevents_expected)
-        reference_sample = model.rvs(size=nevents_expected*3)
+        reference_sample = model.rvs(size=nevents_expected * 3)
         bin_edges = np.linspace(0, 1, 11)
         bin_centers = (bin_edges[:-1] + bin_edges[1:]) / 2
         binned_data, _ = np.histogram(data_sample, bins=bin_edges)