Merge branch 'develop' into documentation

CONTRIBUTING.md

@@ -20,14 +20,15 @@ Please add docstrings to any new function, class or method you implement. The do
 
 ### Tests
 When implementing a new feature or fixing a bug please add meaningful tests to the files in the `tests` directory which cover the new code.
-
-### Continous integration
 For all pull requests tests are executed for the most recent python releases via
 ```
 pytest --cov=pyerrors -vv
 ```
-requiring `pytest`, `pytest-cov` and `pytest-benchmark`
-and the linter `flake8` is executed with the command
+requiring `pytest`, `pytest-cov` and `pytest-benchmark`. To get a coverage report in html run 
+```
+pytest --cov=pyerrors --cov-report html
+```
+The linter `flake8` is executed with the command
 ```
 flake8 --ignore=E501,E722 --exclude=__init__.py pyerrors
 ```

pyerrors/fits.py

@@ -402,7 +402,7 @@ def _prior_fit(x, y, func, priors, silent=False, **kwargs):
     if not silent:
         print('chisquare/d.o.f.:', output.chisquare_by_dof)
 
-    if not m.get_fmin().is_valid:
+    if not m.fmin.is_valid:
         raise Exception('The minimization procedure did not converge.')
 
     hess_inv = np.linalg.pinv(jacobian(jacobian(chisqfunc))(params))

tests/covobs_test.py

@@ -62,6 +62,9 @@ def test_covobs_name_collision():
     my_obs = pe.pseudo_Obs(2.3, 0.2, 'test')
     with pytest.raises(Exception):
         summed_obs = my_obs + covobs
+    covobs2 = pe.cov_Obs(0.3, 0.001, 'test')
+    with pytest.raises(Exception):
+        summed_obs = covobs + covobs2
 
 
 def test_covobs_replica_separator():

tests/dirac_test.py

@@ -10,3 +10,25 @@ def test_gamma_matrices():
         assert np.allclose(matrix @ matrix, np.identity(4))
         assert np.allclose(matrix, matrix.T.conj())
     assert np.allclose(pe.dirac.gamma5, pe.dirac.gamma[0] @ pe.dirac.gamma[1] @ pe.dirac.gamma[2] @ pe.dirac.gamma[3])
+
+
+def test_grid_dirac():
+    for gamma in ['Identity',
+                  'Gamma5',
+                  'GammaX',
+                  'GammaY',
+                  'GammaZ',
+                  'GammaT',
+                  'GammaXGamma5',
+                  'GammaYGamma5',
+                  'GammaZGamma5',
+                  'GammaTGamma5',
+                  'SigmaXT',
+                  'SigmaXY',
+                  'SigmaXZ',
+                  'SigmaYT',
+                  'SigmaYZ',
+                  'SigmaZT']:
+        pe.dirac.Grid_gamma(gamma)
+    with pytest.raises(Exception):
+        pe.dirac.Grid_gamma('Not a gamma matrix')

tests/obs_test.py

@@ -9,6 +9,43 @@ import pytest
 np.random.seed(0)
 
 
+def test_Obs_exceptions():
+    with pytest.raises(Exception):
+        pe.Obs([np.random.rand(10)], ['1', '2'])
+    with pytest.raises(Exception):
+        pe.Obs([np.random.rand(10)], ['1'], idl=[])
+    with pytest.raises(Exception):
+        pe.Obs([np.random.rand(10), np.random.rand(10)], ['1', '1'])
+    with pytest.raises(Exception):
+        pe.Obs([np.random.rand(10), np.random.rand(10)], ['1', 1])
+    with pytest.raises(Exception):
+        pe.Obs([np.random.rand(10)], [1])
+    with pytest.raises(Exception):
+        pe.Obs([np.random.rand(4)], ['name'])
+
+    my_obs = pe.Obs([np.random.rand(6)], ['name'])
+    my_obs._value = 0.0
+    my_obs.details()
+    with pytest.raises(Exception):
+        my_obs.plot_tauint()
+    with pytest.raises(Exception):
+        my_obs.plot_rho()
+    with pytest.raises(Exception):
+        my_obs.plot_rep_dist()
+    with pytest.raises(Exception):
+        my_obs.plot_piechart()
+    with pytest.raises(Exception):
+        my_obs.gamma_method(S='2.3')
+    with pytest.raises(Exception):
+        my_obs.gamma_method(tau_exp=2.3)
+    my_obs.gamma_method()
+    my_obs.details()
+
+    my_obs += pe.Obs([np.random.rand(6)], ['name2|r1'])
+    my_obs += pe.Obs([np.random.rand(6)], ['name2|r2'])
+    my_obs.gamma_method()
+    my_obs.details()
+
 def test_dump():
     value = np.random.normal(5, 10)
     dvalue = np.abs(np.random.normal(0, 1))
@@ -311,6 +348,7 @@ def test_overloaded_functions():
 def test_utils():
     my_obs = pe.pseudo_Obs(1.0, 0.5, 't|r01')
     my_obs += pe.pseudo_Obs(1.0, 0.5, 't|r02')
+    str(my_obs)
     for tau_exp in [0, 5]:
         my_obs.gamma_method(tau_exp=tau_exp)
         my_obs.tag = "Test description"
@@ -325,6 +363,8 @@ def test_utils():
         my_obs.plot_piechart()
         assert my_obs > (my_obs - 1)
         assert my_obs < (my_obs + 1)
+        float(my_obs)
+        str(my_obs)
 
 
 def test_cobs():