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popsim-consortium · Jan 21, 2025 · afa5137 · afa5137
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diff --git a/main/_images/sec_catalog_anapla_models_mallardblackduck_2l19.png b/main/_images/sec_catalog_anapla_models_mallardblackduck_2l19.png
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diff --git a/main/_images/sec_catalog_homsap_models_americanadmixture_4b18.png b/main/_images/sec_catalog_homsap_models_americanadmixture_4b18.png
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diff --git a/main/_images/sec_catalog_homsap_models_outofafricaarchaicadmixture_5r19.png b/main/_images/sec_catalog_homsap_models_outofafricaarchaicadmixture_5r19.png
diff --git a/.../sec_catalog_homsap_models_outofafricaextendedneandertaladmixturepulse_3i21.png b/.../sec_catalog_homsap_models_outofafricaextendedneandertaladmixturepulse_3i21.png
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diff --git a/main/_modules/stdpopsim/genomes.html b/main/_modules/stdpopsim/genomes.html
@@ -821,14 +821,17 @@ <h1>Source code for stdpopsim.genomes</h1><div class="highlight"><pre>
 <span class="sd">        object is added more than once.</span>
 
 <span class="sd">        For instance, if we do</span>
-<span class="sd">        ```</span>
-<span class="sd">        a1 = np.array([[0, 100]])</span>
-<span class="sd">        a2 = np.array([[50, 120]])</span>
-<span class="sd">        contig.add_dfe(a1, dfe1)</span>
-<span class="sd">        contig.add_dfe(a2, dfe2)</span>
-<span class="sd">        ```</span>
-<span class="sd">        then ``dfe1`` applies to the region from 0 to 50 and ``dfe2`` applies</span>
-<span class="sd">        to the region from 50 to 120.</span>
+
+<span class="sd">        .. code-block:: python</span>
+
+<span class="sd">            a1 = np.array([[0, 100]])</span>
+<span class="sd">            a2 = np.array([[50, 120]])</span>
+<span class="sd">            contig.add_dfe(a1, dfe1)</span>
+<span class="sd">            contig.add_dfe(a2, dfe2)</span>
+
+<span class="sd">        then ``dfe1`` applies to the region from 0 to 50 (including 0 but not</span>
+<span class="sd">        50) and ``dfe2`` applies to the region from 50 to 120 (including 50 but</span>
+<span class="sd">        not 120).</span>
 
 <span class="sd">        Any of the ``intervals`` that fall outside of the contig will be</span>
 <span class="sd">        clipped to the contig boundaries. If no ``intervals`` overlap the</span>

diff --git a/main/api.html b/main/api.html
@@ -642,15 +642,16 @@ <h2>Quick reference<a class="headerlink" href="#quick-reference" title="Link to
 carries its own MutationTypes: no mutation types are shared between
 DFEs added by different calls to <code class="docutils literal notranslate"><span class="pre">add_dfe(</span> <span class="pre">)</span></code>, even if the same DFE
 object is added more than once.</p>
-<p>For instance, if we do
-<code class="docutils literal notranslate"><span class="pre">`</span>
-<span class="pre">a1</span> <span class="pre">=</span> <span class="pre">np.array([[0,</span> <span class="pre">100]])</span>
-<span class="pre">a2</span> <span class="pre">=</span> <span class="pre">np.array([[50,</span> <span class="pre">120]])</span>
-<span class="pre">contig.add_dfe(a1,</span> <span class="pre">dfe1)</span>
-<span class="pre">contig.add_dfe(a2,</span> <span class="pre">dfe2)</span>
-<span class="pre">`</span></code>
-then <code class="docutils literal notranslate"><span class="pre">dfe1</span></code> applies to the region from 0 to 50 and <code class="docutils literal notranslate"><span class="pre">dfe2</span></code> applies
-to the region from 50 to 120.</p>
+<p>For instance, if we do</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">a1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">100</span><span class="p">]])</span>
+<span class="n">a2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">50</span><span class="p">,</span> <span class="mi">120</span><span class="p">]])</span>
+<span class="n">contig</span><span class="o">.</span><span class="n">add_dfe</span><span class="p">(</span><span class="n">a1</span><span class="p">,</span> <span class="n">dfe1</span><span class="p">)</span>
+<span class="n">contig</span><span class="o">.</span><span class="n">add_dfe</span><span class="p">(</span><span class="n">a2</span><span class="p">,</span> <span class="n">dfe2</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>then <code class="docutils literal notranslate"><span class="pre">dfe1</span></code> applies to the region from 0 to 50 (including 0 but not
+50) and <code class="docutils literal notranslate"><span class="pre">dfe2</span></code> applies to the region from 50 to 120 (including 50 but
+not 120).</p>
 <p>Any of the <code class="docutils literal notranslate"><span class="pre">intervals</span></code> that fall outside of the contig will be
 clipped to the contig boundaries. If no <code class="docutils literal notranslate"><span class="pre">intervals</span></code> overlap the
 contig, an “empty” DFE will be added with a warning.</p>

diff --git a/main/cli_arguments.html b/main/cli_arguments.html
@@ -691,7 +691,7 @@ <h4>Named Arguments<a class="headerlink" href="#named-arguments_repeat4" title="
 <p>Default: <code class="docutils literal notranslate"><span class="pre">False</span></code></p>
 </dd>
 <dt><kbd>-c, --chromosome</kbd></dt>
-<dd><p>Possible choices: CM009931.2, 1, NC_037638.1, CM009932.2, NC_037639.1, 2, CM009933.2, NC_037640.1, 3, CM009934.2, NC_037641.1, 4, CM009935.2, NC_037642.1, 5, CM009936.2, NC_037643.1, 6, CM009937.2, NC_037644.1, 7, CM009938.2, NC_037645.1, 8, CM009939.2, 9, NC_037646.1, CM009940.2, NC_037647.1, 10, CM009941.2, 11, NC_037648.1, CM009942.2, 12, NC_037649.1, CM009943.2, 13, NC_037650.1, CM009944.2, NC_037651.1, 14, CM009945.2, NC_037652.1, 15, CM009946.2, NC_037653.1, 16, CM009947.2, MT, NC_001566.1</p>
+<dd><p>Possible choices: CM009931.2, 1, NC_037638.1, CM009932.2, NC_037639.1, 2, CM009933.2, 3, NC_037640.1, CM009934.2, NC_037641.1, 4, CM009935.2, NC_037642.1, 5, CM009936.2, NC_037643.1, 6, CM009937.2, NC_037644.1, 7, CM009938.2, 8, NC_037645.1, CM009939.2, 9, NC_037646.1, CM009940.2, NC_037647.1, 10, CM009941.2, 11, NC_037648.1, CM009942.2, 12, NC_037649.1, CM009943.2, 13, NC_037650.1, CM009944.2, NC_037651.1, 14, CM009945.2, NC_037652.1, 15, CM009946.2, NC_037653.1, 16, CM009947.2, NC_001566.1, MT</p>
 <p>Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: CM009931.2, CM009932.2, CM009933.2, CM009934.2, CM009935.2, CM009936.2, CM009937.2, CM009938.2, CM009939.2, CM009940.2, CM009941.2, CM009942.2, CM009943.2, CM009944.2, CM009945.2, CM009946.2, CM009947.2. Default=None.</p>
 </dd>
 <dt><kbd>-L, --length</kbd></dt>