Merge branch 'develop' into documentation

.github/workflows/pytest.yml

@@ -40,6 +40,7 @@ jobs:
           pip install pytest
           pip install pytest-cov
           pip install pytest-benchmark
+          pip freeze
 
       - name: Run tests
         run: pytest --cov=pyerrors -vv

.gitignore

@@ -12,3 +12,4 @@ core.*
 htmlcov
 build
 pyerrors.egg-info
+dist

pyerrors/correlators.py

@@ -602,7 +602,7 @@ class Corr:
         if variant == 'log':
             newcontent = []
             for t in range(self.T - 1):
-                if (self.content[t] is None) or (self.content[t + 1] is None):
+                if ((self.content[t] is None) or (self.content[t + 1] is None)) or (self.content[t + 1][0].value == 0):
                     newcontent.append(None)
                 else:
                     newcontent.append(self.content[t] / self.content[t + 1])
@@ -622,7 +622,7 @@ class Corr:
 
             newcontent = []
             for t in range(self.T - 1):
-                if (self.content[t] is None) or (self.content[t + 1] is None):
+                if (self.content[t] is None) or (self.content[t + 1] is None) or (self.content[t + 1][0].value == 0):
                     newcontent.append(None)
                 # Fill the two timeslices in the middle of the lattice with their predecessors
                 elif variant == 'sinh' and t in [self.T / 2, self.T / 2 - 1]:
@@ -637,7 +637,7 @@ class Corr:
         elif variant == 'arccosh':
             newcontent = []
             for t in range(1, self.T - 1):
-                if (self.content[t] is None) or (self.content[t + 1] is None) or (self.content[t - 1] is None):
+                if (self.content[t] is None) or (self.content[t + 1] is None) or (self.content[t - 1] is None) or (self.content[t][0].value == 0):
                     newcontent.append(None)
                 else:
                     newcontent.append((self.content[t + 1] + self.content[t - 1]) / (2 * self.content[t]))

setup.py

@@ -1,10 +1,16 @@
 from setuptools import setup, find_packages
 from pathlib import Path
+from distutils.util import convert_path
+
 this_directory = Path(__file__).parent
 long_description = (this_directory / "README.md").read_text()
 
+version = {}
+with open(convert_path('pyerrors/version.py')) as ver_file:
+    exec(ver_file.read(), version)
+
 setup(name='pyerrors',
-      version='2.2.0+dev',
+      version=version['__version__'],
       description='Error analysis for lattice QCD',
       long_description=long_description,
       long_description_content_type='text/markdown',

tests/correlators_test.py

@@ -1,6 +1,7 @@
 import os
 import numpy as np
 import scipy
+import matplotlib.pyplot as plt
 import pyerrors as pe
 import pytest
 
@@ -440,6 +441,7 @@ def test_spaghetti_plot():
 
     corr.spaghetti_plot(True)
     corr.spaghetti_plot(False)
+    plt.close('all')
 
 
 def _gen_corr(val, samples=2000):

tests/obs_test.py

@@ -1,6 +1,7 @@
 import autograd.numpy as np
 import os
 import copy
+import matplotlib.pyplot as plt
 import pyerrors as pe
 import pytest
 
@@ -56,6 +57,7 @@ def test_Obs_exceptions():
     one.gamma_method()
     with pytest.raises(Exception):
         one.plot_piechart()
+    plt.close('all')
 
 def test_dump():
     value = np.random.normal(5, 10)
@@ -368,6 +370,7 @@ def test_utils():
         assert my_obs < (my_obs + 1)
         float(my_obs)
         str(my_obs)
+        plt.close('all')
 
 
 def test_cobs():