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Update gh-pages to output generated at b5ed19f
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@deeenes
deeenes committed Sep 28, 2023
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2 changes: 1 addition & 1 deletion .buildinfo
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 6638dbd7184cb550a48603f73a4a13d4
config: df110aff3167443fdfe3094198dfb16a
tags: 645f666f9bcd5a90fca523b33c5a78b7
4 changes: 2 additions & 2 deletions _modules/index.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &#8212; pypath 0.15.8 documentation</title>
<title>Overview: module code &#8212; pypath 0.15.9 documentation</title>



Expand Down Expand Up @@ -710,8 +710,8 @@ <h1>All modules for which code is available</h1>
<li><a href="pypath/share/session.html">pypath.share.session</a></li>
<li><a href="pypath/share/settings.html">pypath.share.settings</a></li>
<li><a href="pypath/utils/go.html">pypath.utils.go</a></li>
<li><a href="pypath/utils/homology.html">pypath.utils.homology</a></li>
<li><a href="pypath/utils/mapping.html">pypath.utils.mapping</a></li>
<li><a href="pypath/utils/orthology.html">pypath.utils.orthology</a></li>
<li><a href="pypath/utils/pdb.html">pypath.utils.pdb</a></li>
<li><a href="pypath/utils/proteomicsdb.html">pypath.utils.proteomicsdb</a></li>
<li><a href="pypath/utils/pyreact.html">pypath.utils.pyreact</a></li>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath &#8212; pypath 0.15.8 documentation</title>
<title>pypath &#8212; pypath 0.15.9 documentation</title>



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2 changes: 1 addition & 1 deletion _modules/pypath/core/annot.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.core.annot &#8212; pypath 0.15.8 documentation</title>
<title>pypath.core.annot &#8212; pypath 0.15.9 documentation</title>



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2 changes: 1 addition & 1 deletion _modules/pypath/core/attrs.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.core.attrs &#8212; pypath 0.15.8 documentation</title>
<title>pypath.core.attrs &#8212; pypath 0.15.9 documentation</title>



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2 changes: 1 addition & 1 deletion _modules/pypath/core/common.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.core.common &#8212; pypath 0.15.8 documentation</title>
<title>pypath.core.common &#8212; pypath 0.15.9 documentation</title>



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2 changes: 1 addition & 1 deletion _modules/pypath/core/complex.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.core.complex &#8212; pypath 0.15.8 documentation</title>
<title>pypath.core.complex &#8212; pypath 0.15.9 documentation</title>



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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.core.entity &#8212; pypath 0.15.8 documentation</title>
<title>pypath.core.entity &#8212; pypath 0.15.9 documentation</title>



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90 changes: 45 additions & 45 deletions _modules/pypath/core/enz_sub.html
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2 changes: 1 addition & 1 deletion _modules/pypath/core/evidence.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.core.evidence &#8212; pypath 0.15.8 documentation</title>
<title>pypath.core.evidence &#8212; pypath 0.15.9 documentation</title>



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14 changes: 7 additions & 7 deletions _modules/pypath/core/interaction.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.core.interaction &#8212; pypath 0.15.8 documentation</title>
<title>pypath.core.interaction &#8212; pypath 0.15.9 documentation</title>



Expand Down Expand Up @@ -534,7 +534,7 @@ <h1>Source code for pypath.core.interaction</h1><div class="highlight"><pre>
<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity</span>
<span class="kn">import</span> <span class="nn">pypath.core.attrs</span> <span class="k">as</span> <span class="nn">attrs_mod</span>
<span class="kn">import</span> <span class="nn">pypath.utils.homology</span> <span class="k">as</span> <span class="nn">homology</span>
<span class="kn">import</span> <span class="nn">pypath.utils.orthology</span> <span class="k">as</span> <span class="nn">orthology</span>

<span class="n">_logger</span> <span class="o">=</span> <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;interaction&#39;</span><span class="p">)</span>
<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
Expand Down Expand Up @@ -2546,7 +2546,7 @@ <h1>Source code for pypath.core.interaction</h1><div class="highlight"><pre>
<span class="k">return</span> <span class="n">new</span></div>


<span class="k">def</span> <span class="nf">homology_translate_one</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">id_a</span><span class="p">,</span> <span class="n">id_b</span><span class="p">,</span> <span class="n">taxon</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">orthology_translate_one</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">id_a</span><span class="p">,</span> <span class="n">id_b</span><span class="p">,</span> <span class="n">taxon</span><span class="p">):</span>

<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
<span class="n">ids</span> <span class="o">=</span> <span class="p">{</span>
Expand All @@ -2572,29 +2572,29 @@ <h1>Source code for pypath.core.interaction</h1><div class="highlight"><pre>
<span class="p">)</span>


<span class="k">def</span> <span class="nf">homology_translate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">taxon</span><span class="p">,</span> <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">orthology_translate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">taxon</span><span class="p">,</span> <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>

<span class="n">exclude</span> <span class="o">=</span> <span class="n">exclude</span> <span class="ow">or</span> <span class="nb">set</span><span class="p">()</span>
<span class="n">exclude</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>

<span class="k">for</span> <span class="n">new_a</span><span class="p">,</span> <span class="n">new_b</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
<span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">identifier</span><span class="p">,)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">taxon</span> <span class="ow">in</span> <span class="n">exclude</span> <span class="k">else</span>
<span class="n">homology</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
<span class="n">orthology</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
<span class="n">source_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
<span class="n">target</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">,</span>
<span class="n">source</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">taxon</span><span class="p">,</span>
<span class="p">),</span>
<span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">identifier</span><span class="p">,)</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">taxon</span> <span class="ow">in</span> <span class="n">exclude</span> <span class="k">else</span>
<span class="n">homology</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
<span class="n">orthology</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
<span class="n">source_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
<span class="n">target</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">,</span>
<span class="n">source</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">taxon</span><span class="p">,</span>
<span class="p">),</span>
<span class="p">):</span>

<span class="k">yield</span> <span class="bp">self</span><span class="o">.</span><span class="n">homology_translate_one</span><span class="p">(</span>
<span class="k">yield</span> <span class="bp">self</span><span class="o">.</span><span class="n">orthology_translate_one</span><span class="p">(</span>
<span class="n">id_a</span> <span class="o">=</span> <span class="n">new_a</span><span class="p">,</span>
<span class="n">id_b</span> <span class="o">=</span> <span class="n">new_b</span><span class="p">,</span>
<span class="n">taxon</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">,</span>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.core.intercell &#8212; pypath 0.15.8 documentation</title>
<title>pypath.core.intercell &#8212; pypath 0.15.9 documentation</title>



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4 changes: 2 additions & 2 deletions _modules/pypath/core/network.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.core.network &#8212; pypath 0.15.8 documentation</title>
<title>pypath.core.network &#8212; pypath 0.15.9 documentation</title>



Expand Down Expand Up @@ -4798,7 +4798,7 @@ <h1>Source code for pypath.core.network</h1><div class="highlight"><pre>
<span class="n">n_ia_translated</span> <span class="o">+=</span> <span class="n">ia_translated</span>

<span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
<span class="s1">&#39;Homology translation ready. &#39;</span>
<span class="s1">&#39;Orthology translation ready. &#39;</span>
<span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> out of </span><span class="si">%u</span><span class="s1"> interactions (</span><span class="si">%.02f%%</span><span class="s1">), &#39;</span>
<span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> out of </span><span class="si">%u</span><span class="s1"> entities (</span><span class="si">%.02f%%</span><span class="s1">) &#39;</span>
<span class="s1">&#39;have been translated.&#39;</span> <span class="o">%</span> <span class="p">(</span>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.inputs &#8212; pypath 0.15.8 documentation</title>
<title>pypath.inputs &#8212; pypath 0.15.9 documentation</title>



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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.inputs.abs &#8212; pypath 0.15.8 documentation</title>
<title>pypath.inputs.abs &#8212; pypath 0.15.9 documentation</title>



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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.inputs.acsn &#8212; pypath 0.15.8 documentation</title>
<title>pypath.inputs.acsn &#8212; pypath 0.15.9 documentation</title>



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2 changes: 1 addition & 1 deletion _modules/pypath/inputs/adhesome.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.inputs.adhesome &#8212; pypath 0.15.8 documentation</title>
<title>pypath.inputs.adhesome &#8212; pypath 0.15.9 documentation</title>



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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.inputs.adrecs &#8212; pypath 0.15.8 documentation</title>
<title>pypath.inputs.adrecs &#8212; pypath 0.15.9 documentation</title>



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2 changes: 1 addition & 1 deletion _modules/pypath/inputs/almen2009.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.inputs.almen2009 &#8212; pypath 0.15.8 documentation</title>
<title>pypath.inputs.almen2009 &#8212; pypath 0.15.9 documentation</title>



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6 changes: 3 additions & 3 deletions _modules/pypath/inputs/baccin2019.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.inputs.baccin2019 &#8212; pypath 0.15.8 documentation</title>
<title>pypath.inputs.baccin2019 &#8212; pypath 0.15.9 documentation</title>



Expand Down Expand Up @@ -518,7 +518,7 @@ <h1>Source code for pypath.inputs.baccin2019</h1><div class="highlight"><pre>
<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
<span class="kn">import</span> <span class="nn">pypath.utils.homology</span> <span class="k">as</span> <span class="nn">homology_mod</span>
<span class="kn">import</span> <span class="nn">pypath.utils.orthology</span> <span class="k">as</span> <span class="nn">orthology_mod</span>
<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>

Expand Down Expand Up @@ -552,7 +552,7 @@ <h1>Source code for pypath.inputs.baccin2019</h1><div class="highlight"><pre>

<span class="n">uniprots</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
<span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
<span class="n">homology_mod</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
<span class="n">orthology_mod</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
<span class="n">uniprot</span><span class="p">,</span>
<span class="n">target</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
<span class="n">source</span> <span class="o">=</span> <span class="mi">10090</span><span class="p">,</span>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.inputs.biogps &#8212; pypath 0.15.8 documentation</title>
<title>pypath.inputs.biogps &#8212; pypath 0.15.9 documentation</title>



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2 changes: 1 addition & 1 deletion _modules/pypath/inputs/biogrid.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>pypath.inputs.biogrid &#8212; pypath 0.15.8 documentation</title>
<title>pypath.inputs.biogrid &#8212; pypath 0.15.9 documentation</title>



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