doc updates [skip ci]

dev/_sources/auto_examples/intro/checking_validity_of_a_pag.rst.txt

@@ -144,7 +144,7 @@ To check if the constructed PAG is a valid one in pywhy-graphs, we can simply do
  .. code-block:: none
 
     ConditioningSetSelection.PDS
-    Context(observed_variables={'G', 'S', 'I', 'PSH', 'L'}, latent_variables=set(), state_variables={}, init_graph=<networkx.classes.graph.Graph object at 0x7efb5d9de890>, included_edges=<networkx.classes.graph.Graph object at 0x7efb5d9def90>, excluded_edges=<networkx.classes.graph.Graph object at 0x7efb5d9df3d0>, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
+    Context(observed_variables={'PSH', 'S', 'L', 'G', 'I'}, latent_variables=set(), state_variables={}, init_graph=<networkx.classes.graph.Graph object at 0x7f88f0a2a250>, included_edges=<networkx.classes.graph.Graph object at 0x7f88f0a2a950>, excluded_edges=<networkx.classes.graph.Graph object at 0x7f88f0a2ad90>, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
     True
 
 
@@ -180,7 +180,7 @@ relationship. As such, the resulting graph is no longer a valid PAG.
  .. code-block:: none
 
     ConditioningSetSelection.PDS
-    Context(observed_variables={'G', 'S', 'I', 'PSH', 'L'}, latent_variables=set(), state_variables={}, init_graph=<networkx.classes.graph.Graph object at 0x7efb5d9feb10>, included_edges=<networkx.classes.graph.Graph object at 0x7efb5d9ff210>, excluded_edges=<networkx.classes.graph.Graph object at 0x7efb5d9ff650>, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
+    Context(observed_variables={'PSH', 'S', 'L', 'G', 'I'}, latent_variables=set(), state_variables={}, init_graph=<networkx.classes.graph.Graph object at 0x7f88f0a32750>, included_edges=<networkx.classes.graph.Graph object at 0x7f88f0a32e50>, excluded_edges=<networkx.classes.graph.Graph object at 0x7f88f0a33290>, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
     False
 
 
@@ -195,7 +195,7 @@ References
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 1.257 seconds)
+   **Total running time of the script:** (0 minutes 1.206 seconds)
 
 **Estimated memory usage:**  167 MB
 

dev/_sources/auto_examples/intro/inducing_path.rst.txt

@@ -241,7 +241,7 @@ References
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 1.323 seconds)
+   **Total running time of the script:** (0 minutes 1.294 seconds)
 
 **Estimated memory usage:**  165 MB
 

dev/_sources/auto_examples/intro/intro_causal_graphs.rst.txt

@@ -169,7 +169,7 @@ Here, we will simulate some data to understand causal graphs in the context of S
 
  .. code-block:: none
 
-    Fitting causal models:   0%|          | 0/5 [00:00<?, ?it/s]    Fitting causal mechanism of node x:   0%|          | 0/5 [00:00<?, ?it/s]    Fitting causal mechanism of node y:   0%|          | 0/5 [00:00<?, ?it/s]    Fitting causal mechanism of node z:   0%|          | 0/5 [00:00<?, ?it/s]    Fitting causal mechanism of node w:   0%|          | 0/5 [00:00<?, ?it/s]    Fitting causal mechanism of node xy:   0%|          | 0/5 [00:00<?, ?it/s]    Fitting causal mechanism of node xy: 100%|██████████| 5/5 [00:00<00:00, 713.00it/s]
+    Fitting causal models:   0%|          | 0/5 [00:00<?, ?it/s]    Fitting causal mechanism of node x:   0%|          | 0/5 [00:00<?, ?it/s]    Fitting causal mechanism of node y:   0%|          | 0/5 [00:00<?, ?it/s]    Fitting causal mechanism of node z:   0%|          | 0/5 [00:00<?, ?it/s]    Fitting causal mechanism of node w:   0%|          | 0/5 [00:00<?, ?it/s]    Fitting causal mechanism of node xy:   0%|          | 0/5 [00:00<?, ?it/s]    Fitting causal mechanism of node xy: 100%|██████████| 5/5 [00:00<00:00, 749.30it/s]
        z  xy  w  x  y
     0  1   1  1  1  1
     1  1   1  2  2  3
@@ -183,7 +183,7 @@ Here, we will simulate some data to understand causal graphs in the context of S
     y     [1, 3, 2, 0]
     dtype: object
 
-    <graphviz.graphs.Digraph object at 0x7efc36adc190>
+    <graphviz.graphs.Digraph object at 0x7f89021ce790>
 
 
 
@@ -307,8 +307,8 @@ in the graph. These unobserved confounders are graphically depicted with a bidir
 
  .. code-block:: none
 
-    ['z', 'x']
-    The ADMG has confounded-components: [{'y', 'x'}, {'z'}, {'w'}]
+    ['x', 'z']
+    The ADMG has confounded-components: [{'x', 'y'}, {'z'}, {'w'}]
     'z' is d-separated from 'x': True
     'z' is d-separated from 'x' given 'y': False
     'z' is d-separated from 'x' after adding a bidirected edge z<->x: False
@@ -427,7 +427,7 @@ References
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 2.607 seconds)
+   **Total running time of the script:** (0 minutes 2.782 seconds)
 
 **Estimated memory usage:**  252 MB
 

dev/_sources/auto_examples/intro/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:05.186** total execution time for 3 files **from auto_examples/intro**:
+**00:05.282** total execution time for 3 files **from auto_examples/intro**:
 
 .. container::
 
@@ -33,11 +33,11 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_intro_intro_causal_graphs.py` (``intro_causal_graphs.py``)
-     - 00:02.607
-     - 251.7
+     - 00:02.782
+     - 251.8
    * - :ref:`sphx_glr_auto_examples_intro_inducing_path.py` (``inducing_path.py``)
-     - 00:01.323
+     - 00:01.294
      - 165.1
    * - :ref:`sphx_glr_auto_examples_intro_checking_validity_of_a_pag.py` (``checking_validity_of_a_pag.py``)
-     - 00:01.257
+     - 00:01.206
      - 166.7

dev/_sources/auto_examples/mixededge/plot_mixed_edge_graph.rst.txt

@@ -154,7 +154,7 @@ Mixed Edge Graph Properties
     MixedEdgeGraph named 'IV Graph' with 3 nodes and 3 edges and 2 edge types is directed: False because there are directed edges.
     False
     ['directed', 'bidirected']
-    {'directed': <networkx.classes.digraph.DiGraph object at 0x7efb80473650>, 'bidirected': <networkx.classes.graph.Graph object at 0x7efb7ff8d090>}
+    {'directed': <networkx.classes.digraph.DiGraph object at 0x7f88f03d8110>, 'bidirected': <networkx.classes.graph.Graph object at 0x7f89021b1fd0>}
 
 
 
@@ -194,7 +194,7 @@ Mixed Edge Graph Operations on Nodes
 
  .. code-block:: none
 
-    MixedEdgeGraph named 'IV Graph' with 3 nodes and 3 edges and 2 edge types has nodes: ['X', 'Z', 'Y']
+    MixedEdgeGraph named 'IV Graph' with 3 nodes and 3 edges and 2 edge types has nodes: ['Z', 'X', 'Y']
     Graph has node A: False
     Now graph has node A: True
     Graph has node A: False
@@ -312,7 +312,7 @@ class properties. Moreover, one can specify the edge type.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 1.522 seconds)
+   **Total running time of the script:** (0 minutes 1.466 seconds)
 
 **Estimated memory usage:**  172 MB
 

dev/_sources/auto_examples/mixededge/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:01.522** total execution time for 1 file **from auto_examples/mixededge**:
+**00:01.466** total execution time for 1 file **from auto_examples/mixededge**:
 
 .. container::
 
@@ -33,5 +33,5 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_mixededge_plot_mixed_edge_graph.py` (``plot_mixed_edge_graph.py``)
-     - 00:01.522
-     - 171.7
+     - 00:01.466
+     - 171.6

dev/_sources/auto_examples/visualization/draw_and_compare_graphs_with_same_layout.rst.txt

@@ -139,7 +139,7 @@ such as `Dagitty <http://dagitty.net>`_.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.446 seconds)
+   **Total running time of the script:** (0 minutes 0.449 seconds)
 
 **Estimated memory usage:**  165 MB
 

dev/_sources/auto_examples/visualization/plot_timeseries_graphs.rst.txt

@@ -136,7 +136,7 @@ which creates a nice default layout for time-series graphs.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 1.218 seconds)
+   **Total running time of the script:** (0 minutes 1.098 seconds)
 
 **Estimated memory usage:**  165 MB
 

dev/_sources/auto_examples/visualization/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:01.664** total execution time for 2 files **from auto_examples/visualization**:
+**00:01.548** total execution time for 2 files **from auto_examples/visualization**:
 
 .. container::
 
@@ -33,8 +33,8 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_visualization_plot_timeseries_graphs.py` (``plot_timeseries_graphs.py``)
-     - 00:01.218
+     - 00:01.098
      - 165.1
    * - :ref:`sphx_glr_auto_examples_visualization_draw_and_compare_graphs_with_same_layout.py` (``draw_and_compare_graphs_with_same_layout.py``)
-     - 00:00.446
+     - 00:00.449
      - 165.1

dev/_sources/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:08.372** total execution time for 6 files **from all galleries**:
+**00:08.296** total execution time for 6 files **from all galleries**:
 
 .. container::
 
@@ -33,20 +33,20 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_intro_intro_causal_graphs.py` (``../examples/intro/intro_causal_graphs.py``)
-     - 00:02.607
-     - 251.7
+     - 00:02.782
+     - 251.8
    * - :ref:`sphx_glr_auto_examples_mixededge_plot_mixed_edge_graph.py` (``../examples/mixededge/plot_mixed_edge_graph.py``)
-     - 00:01.522
-     - 171.7
+     - 00:01.466
+     - 171.6
    * - :ref:`sphx_glr_auto_examples_intro_inducing_path.py` (``../examples/intro/inducing_path.py``)
-     - 00:01.323
+     - 00:01.294
      - 165.1
    * - :ref:`sphx_glr_auto_examples_intro_checking_validity_of_a_pag.py` (``../examples/intro/checking_validity_of_a_pag.py``)
-     - 00:01.257
+     - 00:01.206
      - 166.7
    * - :ref:`sphx_glr_auto_examples_visualization_plot_timeseries_graphs.py` (``../examples/visualization/plot_timeseries_graphs.py``)
-     - 00:01.218
+     - 00:01.098
      - 165.1
    * - :ref:`sphx_glr_auto_examples_visualization_draw_and_compare_graphs_with_same_layout.py` (``../examples/visualization/draw_and_compare_graphs_with_same_layout.py``)
-     - 00:00.446
+     - 00:00.449
      - 165.1

dev/auto_examples/intro/checking_validity_of_a_pag.html

@@ -566,7 +566,7 @@ <h2>Validity of a PAG<a class="headerlink" href="#validity-of-a-pag" title="Link
 </pre></div>
 </div>
 <div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>ConditioningSetSelection.PDS
-Context(observed_variables={&#39;G&#39;, &#39;S&#39;, &#39;I&#39;, &#39;PSH&#39;, &#39;L&#39;}, latent_variables=set(), state_variables={}, init_graph=&lt;networkx.classes.graph.Graph object at 0x7efb5d9de890&gt;, included_edges=&lt;networkx.classes.graph.Graph object at 0x7efb5d9def90&gt;, excluded_edges=&lt;networkx.classes.graph.Graph object at 0x7efb5d9df3d0&gt;, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
+Context(observed_variables={&#39;PSH&#39;, &#39;S&#39;, &#39;L&#39;, &#39;G&#39;, &#39;I&#39;}, latent_variables=set(), state_variables={}, init_graph=&lt;networkx.classes.graph.Graph object at 0x7f88f0a2a250&gt;, included_edges=&lt;networkx.classes.graph.Graph object at 0x7f88f0a2a950&gt;, excluded_edges=&lt;networkx.classes.graph.Graph object at 0x7f88f0a2ad90&gt;, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
 True
 </pre></div>
 </div>
@@ -585,7 +585,7 @@ <h2>Validity of a PAG<a class="headerlink" href="#validity-of-a-pag" title="Link
 </pre></div>
 </div>
 <div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>ConditioningSetSelection.PDS
-Context(observed_variables={&#39;G&#39;, &#39;S&#39;, &#39;I&#39;, &#39;PSH&#39;, &#39;L&#39;}, latent_variables=set(), state_variables={}, init_graph=&lt;networkx.classes.graph.Graph object at 0x7efb5d9feb10&gt;, included_edges=&lt;networkx.classes.graph.Graph object at 0x7efb5d9ff210&gt;, excluded_edges=&lt;networkx.classes.graph.Graph object at 0x7efb5d9ff650&gt;, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
+Context(observed_variables={&#39;PSH&#39;, &#39;S&#39;, &#39;L&#39;, &#39;G&#39;, &#39;I&#39;}, latent_variables=set(), state_variables={}, init_graph=&lt;networkx.classes.graph.Graph object at 0x7f88f0a32750&gt;, included_edges=&lt;networkx.classes.graph.Graph object at 0x7f88f0a32e50&gt;, excluded_edges=&lt;networkx.classes.graph.Graph object at 0x7f88f0a33290&gt;, num_distributions=1, obs_distribution=True, intervention_targets=[], symmetric_diff_map={}, sigma_map={}, f_nodes=[], num_domains=1, domain_map={}, s_nodes=[])
 False
 </pre></div>
 </div>
@@ -601,7 +601,7 @@ <h2>References<a class="headerlink" href="#references" title="Link to this headi
 </aside>
 </aside>
 </div>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.257 seconds)</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.206 seconds)</p>
 <p><strong>Estimated memory usage:</strong>  167 MB</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-intro-checking-validity-of-a-pag-py">
 <div class="sphx-glr-download sphx-glr-download-jupyter docutils container">

dev/auto_examples/intro/inducing_path.html

@@ -637,7 +637,7 @@ <h2>References<a class="headerlink" href="#references" title="Link to this headi
 </aside>
 </aside>
 </div>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.323 seconds)</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 1.294 seconds)</p>
 <p><strong>Estimated memory usage:</strong>  165 MB</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-intro-inducing-path-py">
 <div class="sphx-glr-download sphx-glr-download-jupyter docutils container">

dev/auto_examples/intro/intro_causal_graphs.html

@@ -618,7 +618,7 @@ <h2>Structural Causal Models: Simulating some data<a class="headerlink" href="#s
 Fitting causal mechanism of node z:   0%|          | 0/5 [00:00&lt;?, ?it/s]
 Fitting causal mechanism of node w:   0%|          | 0/5 [00:00&lt;?, ?it/s]
 Fitting causal mechanism of node xy:   0%|          | 0/5 [00:00&lt;?, ?it/s]
-Fitting causal mechanism of node xy: 100%|██████████| 5/5 [00:00&lt;00:00, 713.00it/s]
+Fitting causal mechanism of node xy: 100%|██████████| 5/5 [00:00&lt;00:00, 749.30it/s]
    z  xy  w  x  y
 0  1   1  1  1  1
 1  1   1  2  2  3
@@ -632,7 +632,7 @@ <h2>Structural Causal Models: Simulating some data<a class="headerlink" href="#s
 y     [1, 3, 2, 0]
 dtype: object
 
-&lt;graphviz.graphs.Digraph object at 0x7efc36adc190&gt;
+&lt;graphviz.graphs.Digraph object at 0x7f89021ce790&gt;
 </pre></div>
 </div>
 </section>
@@ -719,8 +719,8 @@ <h2>Acyclic Directed Mixed Graphs (ADMG)<a class="headerlink" href="#acyclic-dir
 <span class="c1"># details on causal discovery (i.e. structure learning algorithms), please see that repo.</span>
 </pre></div>
 </div>
-<img src="../../_images/sphx_glr_intro_causal_graphs_002.png" srcset="../../_images/sphx_glr_intro_causal_graphs_002.png" alt="intro causal graphs" class = "sphx-glr-single-img"/><div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>[&#39;z&#39;, &#39;x&#39;]
-The ADMG has confounded-components: [{&#39;y&#39;, &#39;x&#39;}, {&#39;z&#39;}, {&#39;w&#39;}]
+<img src="../../_images/sphx_glr_intro_causal_graphs_002.png" srcset="../../_images/sphx_glr_intro_causal_graphs_002.png" alt="intro causal graphs" class = "sphx-glr-single-img"/><div class="sphx-glr-script-out highlight-none notranslate"><div class="highlight"><pre><span></span>[&#39;x&#39;, &#39;z&#39;]
+The ADMG has confounded-components: [{&#39;x&#39;, &#39;y&#39;}, {&#39;z&#39;}, {&#39;w&#39;}]
 &#39;z&#39; is d-separated from &#39;x&#39;: True
 &#39;z&#39; is d-separated from &#39;x&#39; given &#39;y&#39;: False
 &#39;z&#39; is d-separated from &#39;x&#39; after adding a bidirected edge z&lt;-&gt;x: False
@@ -801,7 +801,7 @@ <h3>References<a class="headerlink" href="#references" title="Link to this headi
 </aside>
 </aside>
 </div>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 2.607 seconds)</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 2.782 seconds)</p>
 <p><strong>Estimated memory usage:</strong>  252 MB</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-intro-intro-causal-graphs-py">
 <div class="sphx-glr-download sphx-glr-download-jupyter docutils container">

dev/auto_examples/intro/sg_execution_times.html

@@ -462,7 +462,7 @@
 
   <section id="computation-times">
 <span id="sphx-glr-auto-examples-intro-sg-execution-times"></span><h1>Computation times<a class="headerlink" href="#computation-times" title="Link to this heading">#</a></h1>
-<p><strong>00:05.186</strong> total execution time for 3 files <strong>from auto_examples/intro</strong>:</p>
+<p><strong>00:05.282</strong> total execution time for 3 files <strong>from auto_examples/intro</strong>:</p>
 <div class="docutils container">
 <style scoped>
 <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
@@ -484,15 +484,15 @@
 </thead>
 <tbody>
 <tr class="row-even"><td><p><a class="reference internal" href="intro_causal_graphs.html#sphx-glr-auto-examples-intro-intro-causal-graphs-py"><span class="std std-ref">An introduction to causal graphs and how to use them</span></a> (<code class="docutils literal notranslate"><span class="pre">intro_causal_graphs.py</span></code>)</p></td>
-<td><p>00:02.607</p></td>
-<td><p>251.7</p></td>
+<td><p>00:02.782</p></td>
+<td><p>251.8</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="inducing_path.html#sphx-glr-auto-examples-intro-inducing-path-py"><span class="std std-ref">An introduction to Inducing Paths and how to find them</span></a> (<code class="docutils literal notranslate"><span class="pre">inducing_path.py</span></code>)</p></td>
-<td><p>00:01.323</p></td>
+<td><p>00:01.294</p></td>
 <td><p>165.1</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="checking_validity_of_a_pag.html#sphx-glr-auto-examples-intro-checking-validity-of-a-pag-py"><span class="std std-ref">On PAGs and their validity</span></a> (<code class="docutils literal notranslate"><span class="pre">checking_validity_of_a_pag.py</span></code>)</p></td>
-<td><p>00:01.257</p></td>
+<td><p>00:01.206</p></td>
 <td><p>166.7</p></td>
 </tr>
 </tbody>