Commit 70bf7408 authored by Tiago Peixoto's avatar Tiago Peixoto
Browse files

Fix doctests

parent 31a16689
Pipeline #203 failed with stage
in 4047 minutes and 50 seconds
...@@ -5,7 +5,7 @@ latex: ...@@ -5,7 +5,7 @@ latex:
sphinx-build -E -b latex . build sphinx-build -E -b latex . build
test: test:
OMP_NUM_THREADS=1 sphinx-build -b doctest . build sphinx-build -b doctest . build
clean: clean:
rm -rf build rm -rf build
......
...@@ -196,11 +196,11 @@ latex_elements = { ...@@ -196,11 +196,11 @@ latex_elements = {
'fontpkg': r"\usepackage{bookman}"} 'fontpkg': r"\usepackage{bookman}"}
# Example configuration for intersphinx: refer to the Python standard library. # Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'python': ('http://docs.python.org/3', None), intersphinx_mapping = {'python': ('https://docs.python.org/3', None),
'numpy': ('http://docs.scipy.org/doc/numpy', None), 'numpy': ('http://docs.scipy.org/doc/numpy', None),
'scipy': ('http://docs.scipy.org/doc/scipy/reference', None), 'scipy': ('http://docs.scipy.org/doc/scipy/reference', None),
'matplotlib': ('http://matplotlib.sourceforge.net', None), 'matplotlib': ('http://matplotlib.org', None),
'cairo': ('http://www.cairographics.org/documentation/pycairo/3/', None), 'cairo': ('https://www.cairographics.org/documentation/pycairo/3', None),
'ipython': ('http://ipython.org/ipython-doc/stable/', None), 'ipython': ('http://ipython.org/ipython-doc/stable/', None),
'panda': ('http://pandas.pydata.org/pandas-docs/stable/', None)} 'panda': ('http://pandas.pydata.org/pandas-docs/stable/', None)}
......
...@@ -506,9 +506,9 @@ example, for the American football network above, we have: ...@@ -506,9 +506,9 @@ example, for the American football network above, we have:
.. testoutput:: model-selection .. testoutput:: model-selection
:options: +NORMALIZE_WHITESPACE :options: +NORMALIZE_WHITESPACE
Non-degree-corrected DL: 1725.78502074 Non-degree-corrected DL: 1738.00660528
Degree-corrected DL: 1784.77629595 Degree-corrected DL: 1780.01146484
ln Λ: -58.9912752096 ln Λ: -42.0048595573
Hence, with a posterior odds ratio of :math:`\Lambda \sim e^{-59} \sim Hence, with a posterior odds ratio of :math:`\Lambda \sim e^{-59} \sim
10^{-25}` in favor of the non-degree-corrected model, it seems like the 10^{-25}` in favor of the non-degree-corrected model, it seems like the
...@@ -826,10 +826,9 @@ work, and we can now obtain vertex marginals on all hierarchical levels: ...@@ -826,10 +826,9 @@ work, and we can now obtain vertex marginals on all hierarchical levels:
Marginal probabilities of group memberships of the network of Marginal probabilities of group memberships of the network of
characters in the novel Les Misérables, according to the nested characters in the novel Les Misérables, according to the nested
degree-corrected SBM. The `pie fractions degree-corrected SBM. The `pie fractions <https://en.wikipedia.org/wiki/Pie_chart>`_
<https://en.wikipedia.org/wiki/Pie_chart>`_ on the nodes correspond on the nodes correspond to the probability of being in group
to the probability of being in group associated with the respective associated with the respective color.
color.
We can also obtain a marginal probability of the number of groups We can also obtain a marginal probability of the number of groups
itself, as follows. itself, as follows.
...@@ -1068,7 +1067,7 @@ evidence efficiently, as we show below, using ...@@ -1068,7 +1067,7 @@ evidence efficiently, as we show below, using
.. testoutput:: model-evidence .. testoutput:: model-evidence
Model evidence for deg_corr = True: -622.794364945 (mean field), -707.484453595 (Bethe) Model evidence for deg_corr = True: -622.794364945 (mean field), -707.484453595 (Bethe)
Model evidence for deg_corr = False: -633.276625201 (mean field), -670.113442151 (Bethe) Model evidence for deg_corr = False: -624.357861783 (mean field), -657.164066465 (Bethe)
Despite the (expected) discrepancy between both approximations, the Despite the (expected) discrepancy between both approximations, the
outcome shows a clear preference for the non-degree-corrected model. outcome shows a clear preference for the non-degree-corrected model.
...@@ -1132,8 +1131,8 @@ approach for the same network, using the nested model. ...@@ -1132,8 +1131,8 @@ approach for the same network, using the nested model.
.. testoutput:: model-evidence .. testoutput:: model-evidence
Model evidence for deg_corr = True: -530.057076507 (mean field), -702.858734133 (Bethe) Model evidence for deg_corr = True: -549.845093934 (mean field), -688.382102062 (Bethe)
Model evidence for deg_corr = False: -555.073189798 (mean field), -649.484851667 (Bethe) Model evidence for deg_corr = False: -593.581546241 (mean field), -621.257816805 (Bethe)
The results are interesting: Not only we observe a better evidence for The results are interesting: Not only we observe a better evidence for
the nested models themselves, when comparing to the evidences for the the nested models themselves, when comparing to the evidences for the
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