Merge branch 'develop'

README.md

@@ -56,8 +56,9 @@ http://www.mis.mpg.de/preprints/2012/preprint2012_25.pdf*
 + Kraskov estimator: [*Kraskov et al., 2004, Phys Rev E 69, 066138*](https://journals.aps.org/pre/abstract/10.1103/PhysRevE.69.066138)
 + Nonuniform embedding: [*Faes et al., 2011, Phys Rev E 83, 051112*](https://journals.aps.org/pre/abstract/10.1103/PhysRevE.83.051112)
 + Faes' compensated transfer entropy: [*Faes et al., 2013, Entropy 15, 198-219*](https://www.mdpi.com/1099-4300/15/1/198)
-+ PID: [Williams & Beer, 2010, arXiv:1004.2515 [cs.IT]](http://arxiv.org/abs/1004.2515);
-  [Makkeh et al., 2020, arXiv:2002.03356 [cs.IT]](https://arxiv.org/abs/2002.03356)
++ PID: [*Williams & Beer, 2010, arXiv:1004.2515 [cs.IT]*](http://arxiv.org/abs/1004.2515);
+  [*Makkeh et al., 2021, Phys Rev E 103, 032149*](https://doi.org/10.1103/PhysRevE.103.032149);
+  [*Gutknecht et al., 2020, arXiv:2008.09535 [cs.AI]*](https://arxiv.org/abs/2008.09535)
 + PID estimators: *[Bertschinger et al., 2014, Entropy, 16(4)](https://www.mdpi.com/1099-4300/16/4/2161);
 [Makkeh et al., 2017, Entropy, 19(10)](https://www.mdpi.com/1099-4300/19/10/530);
 [Makkeh et al., 2018, Entropy, 20(271)](https://www.mdpi.com/1099-4300/20/4/271)*

README.txt

@@ -51,6 +51,8 @@ http://www.mis.mpg.de/preprints/2012/preprint2012_25.pdf*
 + Kraskov estimator: *Kraskov et al., 2004, Phys Rev E 69, 066138*
 + Nonuniform embedding: *Faes et al., 2011, Phys Rev E 83, 051112*
 + Faes' compensated transfer entropy: *Faes et al., 2013, Entropy 15, 198-219*
-+ PID: *Williams & Beer, 2010, arXiv preprint: http://arxiv.org/abs/1004.2515*
++ PID: Williams & Beer, 2010, arXiv:1004.2515 [cs.IT];
+  Makkeh et al., 2021, Phys Rev E 103, 032149;
+  Gutknecht et al., 2020, arXiv:2008.09535 [cs.AI]
 + PID estimators: *Bertschinger et al., 2014, Entropy, 16(4); Makkeh et al., 2017, Entropy, 19(10),
   Makkeh et al., 2018, Entropy, 20(271)*

idtxl/network_inference.py

@@ -78,7 +78,7 @@ def _check_source_set(self, sources, n_processes):
                 self.target, self.source_set))
 
     def _include_candidates(self, candidate_set, data):
-        """Inlcude informative candidates into the conditioning set.
+        """Include informative candidates into the conditioning set.
 
         Loop over each candidate in the candidate set and test if it has
         significant mutual information with the current value, conditional
@@ -137,7 +137,8 @@ def _include_candidates(self, candidate_set, data):
                     self._idx_to_lag([max_candidate])[0]), end='')
             try:
                 significant = stats.max_statistic(
-                    self, data, candidate_set, te_max_candidate)[0]
+                    self, data, candidate_set, te_max_candidate,
+                    conditional=self._selected_vars_realisations)[0]
             except ex.AlgorithmExhaustedError as aee:
                 # The algorithm cannot continue here, so we'll terminate the
                 # check of significance for this candidate, though those

idtxl/stats.py

@@ -395,7 +395,7 @@ def omnibus_test(analysis_setup, data):
 
 
 def max_statistic(analysis_setup, data, candidate_set, te_max_candidate,
-                  conditional=None):
+                  conditional):
     """Perform maximum statistics for one candidate source.
 
     Test if a transfer entropy value is significantly bigger than the maximum
@@ -420,10 +420,9 @@ def max_statistic(analysis_setup, data, candidate_set, te_max_candidate,
             list of indices of remaning candidates
         te_max_candidate : float
             transfer entropy value to be tested
-        conditional : numpy array [optional]
+        conditional : numpy array
             realisations of conditional, 2D numpy array where array dimensions
-            represent [realisations x variable dimension] (default=None, no
-            conditioning performed)
+            represent [realisations x variable dimension]
 
     Returns:
         bool

setup.py

@@ -10,7 +10,7 @@
     name='idtxl',
     packages=['idtxl'],
     include_package_data=True,
-    version='1.0',
+    version='1.2.2',
     description='Information Dynamics Toolkit xl',
     author='Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral',
     author_email='p.wollstadt@gmail.com',