Merge pull request #82 from jakobrunge/developer

Developer

README.md

@@ -14,7 +14,7 @@ Tigramite is a causal time series analysis python package. It allows to
  efficiently reconstruct causal graphs from high-dimensional time series datasets and model the obtained causal dependencies for causal mediation and prediction analyses. Causal discovery is based on linear as well as non-parametric conditional independence tests applicable to discrete or continuously-valued time series.  Also includes functions for high-quality plots of the results. Please cite the following papers depending on which method you use:
 
 - PCMCI: J. Runge, P. Nowack, M. Kretschmer, S. Flaxman, D. Sejdinovic, Detecting and quantifying causal associations in large nonlinear time series datasets. Sci. Adv. 5, eaau4996 (2019). https://advances.sciencemag.org/content/5/11/eaau4996
-- PCMCI+: J. Runge (2020): Discovering contemporaneous and lagged causal relations in autocorrelated nonlinear time series datasets. https://arxiv.org/abs/2003.03685
+- PCMCI+: J. Runge (2020): Discovering contemporaneous and lagged causal relations in autocorrelated nonlinear time series datasets. Proceedings of the 36th Conference on Uncertainty in Artificial Intelligence, UAI 2020,Toronto, Canada, 2019, AUAI Press, 2020. http://auai.org/uai2020/proceedings/579_main_paper.pdf
 - Generally: J. Runge (2018): Causal Network Reconstruction from Time Series: From Theoretical Assumptions to Practical Estimation. Chaos: An Interdisciplinary Journal of Nonlinear Science 28 (7): 075310. https://aip.scitation.org/doi/10.1063/1.5025050
 - Nature Communications Perspective paper: https://www.nature.com/articles/s41467-019-10105-3
 - Mediation class: J. Runge et al. (2015): Identifying causal gateways and mediators in complex spatio-temporal systems. Nature Communications, 6, 8502. http://doi.org/10.1038/ncomms9502

docs/_build/html/_modules/abc.html

@@ -93,7 +93,7 @@ <h1>Source code for abc</h1><div class="highlight"><pre>
 
     <span class="n">__isabstractmethod__</span> <span class="o">=</span> <span class="kc">True</span>
 
-    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">callable</span><span class="p">):</span>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">callable</span><span class="p">):</span>
         <span class="n">callable</span><span class="o">.</span><span class="n">__isabstractmethod__</span> <span class="o">=</span> <span class="kc">True</span>
         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">callable</span><span class="p">)</span>
 
@@ -116,7 +116,7 @@ <h1>Source code for abc</h1><div class="highlight"><pre>
 
     <span class="n">__isabstractmethod__</span> <span class="o">=</span> <span class="kc">True</span>
 
-    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">callable</span><span class="p">):</span>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">callable</span><span class="p">):</span>
         <span class="n">callable</span><span class="o">.</span><span class="n">__isabstractmethod__</span> <span class="o">=</span> <span class="kc">True</span>
         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">callable</span><span class="p">)</span>
 
@@ -153,11 +153,11 @@ <h1>Source code for abc</h1><div class="highlight"><pre>
 
 
 <span class="k">try</span><span class="p">:</span>
-    <span class="kn">from</span> <span class="nn">_abc</span> <span class="k">import</span> <span class="p">(</span><span class="n">get_cache_token</span><span class="p">,</span> <span class="n">_abc_init</span><span class="p">,</span> <span class="n">_abc_register</span><span class="p">,</span>
+    <span class="kn">from</span> <span class="nn">_abc</span> <span class="kn">import</span> <span class="p">(</span><span class="n">get_cache_token</span><span class="p">,</span> <span class="n">_abc_init</span><span class="p">,</span> <span class="n">_abc_register</span><span class="p">,</span>
                       <span class="n">_abc_instancecheck</span><span class="p">,</span> <span class="n">_abc_subclasscheck</span><span class="p">,</span> <span class="n">_get_dump</span><span class="p">,</span>
                       <span class="n">_reset_registry</span><span class="p">,</span> <span class="n">_reset_caches</span><span class="p">)</span>
 <span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
-    <span class="kn">from</span> <span class="nn">_py_abc</span> <span class="k">import</span> <span class="n">ABCMeta</span><span class="p">,</span> <span class="n">get_cache_token</span>
+    <span class="kn">from</span> <span class="nn">_py_abc</span> <span class="kn">import</span> <span class="n">ABCMeta</span><span class="p">,</span> <span class="n">get_cache_token</span>
     <span class="n">ABCMeta</span><span class="o">.</span><span class="vm">__module__</span> <span class="o">=</span> <span class="s1">&#39;abc&#39;</span>
 <span class="k">else</span><span class="p">:</span>
     <span class="k">class</span> <span class="nc">ABCMeta</span><span class="p">(</span><span class="nb">type</span><span class="p">):</span>
@@ -173,7 +173,7 @@ <h1>Source code for abc</h1><div class="highlight"><pre>
 <span class="sd">        implementations defined by the registering ABC be callable (not</span>
 <span class="sd">        even via super()).</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">def</span> <span class="nf">__new__</span><span class="p">(</span><span class="n">mcls</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">bases</span><span class="p">,</span> <span class="n">namespace</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+        <span class="k">def</span> <span class="fm">__new__</span><span class="p">(</span><span class="n">mcls</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">bases</span><span class="p">,</span> <span class="n">namespace</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
             <span class="bp">cls</span> <span class="o">=</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__new__</span><span class="p">(</span><span class="n">mcls</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">bases</span><span class="p">,</span> <span class="n">namespace</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
             <span class="n">_abc_init</span><span class="p">(</span><span class="bp">cls</span><span class="p">)</span>
             <span class="k">return</span> <span class="bp">cls</span>
@@ -185,24 +185,24 @@ <h1>Source code for abc</h1><div class="highlight"><pre>
 <span class="sd">            &quot;&quot;&quot;</span>
             <span class="k">return</span> <span class="n">_abc_register</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">subclass</span><span class="p">)</span>
 
-        <span class="k">def</span> <span class="nf">__instancecheck__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">instance</span><span class="p">):</span>
+        <span class="k">def</span> <span class="fm">__instancecheck__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">instance</span><span class="p">):</span>
             <span class="sd">&quot;&quot;&quot;Override for isinstance(instance, cls).&quot;&quot;&quot;</span>
             <span class="k">return</span> <span class="n">_abc_instancecheck</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">instance</span><span class="p">)</span>
 
-        <span class="k">def</span> <span class="nf">__subclasscheck__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">subclass</span><span class="p">):</span>
+        <span class="k">def</span> <span class="fm">__subclasscheck__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">subclass</span><span class="p">):</span>
             <span class="sd">&quot;&quot;&quot;Override for issubclass(subclass, cls).&quot;&quot;&quot;</span>
             <span class="k">return</span> <span class="n">_abc_subclasscheck</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">subclass</span><span class="p">)</span>
 
         <span class="k">def</span> <span class="nf">_dump_registry</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
             <span class="sd">&quot;&quot;&quot;Debug helper to print the ABC registry.&quot;&quot;&quot;</span>
-            <span class="nb">print</span><span class="p">(</span><span class="n">f</span><span class="s2">&quot;Class: </span><span class="si">{cls.__module__}</span><span class="s2">.</span><span class="si">{cls.__qualname__}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">file</span><span class="p">)</span>
-            <span class="nb">print</span><span class="p">(</span><span class="n">f</span><span class="s2">&quot;Inv. counter: {get_cache_token()}&quot;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">file</span><span class="p">)</span>
+            <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Class: </span><span class="si">{</span><span class="bp">cls</span><span class="o">.</span><span class="vm">__module__</span><span class="si">}</span><span class="s2">.</span><span class="si">{</span><span class="bp">cls</span><span class="o">.</span><span class="vm">__qualname__</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">file</span><span class="p">)</span>
+            <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Inv. counter: </span><span class="si">{</span><span class="n">get_cache_token</span><span class="p">()</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">file</span><span class="p">)</span>
             <span class="p">(</span><span class="n">_abc_registry</span><span class="p">,</span> <span class="n">_abc_cache</span><span class="p">,</span> <span class="n">_abc_negative_cache</span><span class="p">,</span>
              <span class="n">_abc_negative_cache_version</span><span class="p">)</span> <span class="o">=</span> <span class="n">_get_dump</span><span class="p">(</span><span class="bp">cls</span><span class="p">)</span>
-            <span class="nb">print</span><span class="p">(</span><span class="n">f</span><span class="s2">&quot;_abc_registry: </span><span class="si">{_abc_registry!r}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">file</span><span class="p">)</span>
-            <span class="nb">print</span><span class="p">(</span><span class="n">f</span><span class="s2">&quot;_abc_cache: </span><span class="si">{_abc_cache!r}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">file</span><span class="p">)</span>
-            <span class="nb">print</span><span class="p">(</span><span class="n">f</span><span class="s2">&quot;_abc_negative_cache: </span><span class="si">{_abc_negative_cache!r}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">file</span><span class="p">)</span>
-            <span class="nb">print</span><span class="p">(</span><span class="n">f</span><span class="s2">&quot;_abc_negative_cache_version: </span><span class="si">{_abc_negative_cache_version!r}</span><span class="s2">&quot;</span><span class="p">,</span>
+            <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;_abc_registry: </span><span class="si">{</span><span class="n">_abc_registry</span><span class="si">!r}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">file</span><span class="p">)</span>
+            <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;_abc_cache: </span><span class="si">{</span><span class="n">_abc_cache</span><span class="si">!r}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">file</span><span class="p">)</span>
+            <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;_abc_negative_cache: </span><span class="si">{</span><span class="n">_abc_negative_cache</span><span class="si">!r}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">file</span><span class="p">)</span>
+            <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;_abc_negative_cache_version: </span><span class="si">{</span><span class="n">_abc_negative_cache_version</span><span class="si">!r}</span><span class="s2">&quot;</span><span class="p">,</span>
                   <span class="n">file</span><span class="o">=</span><span class="n">file</span><span class="p">)</span>
 
         <span class="k">def</span> <span class="nf">_abc_registry_clear</span><span class="p">(</span><span class="bp">cls</span><span class="p">):</span>