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Automated doc build for refs/heads/main
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PopSim-bot committed Dec 12, 2024
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8 changes: 8 additions & 0 deletions main/_modules/stdpopsim/citations.html
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Expand Up @@ -81,6 +81,7 @@ <h1>Source code for stdpopsim.citations</h1><div class="highlight"><pre>
<span class="sd">citation information associated with different entities derived from the</span>
<span class="sd">literature that are used within a simulation.</span>
<span class="sd">&quot;&quot;&quot;</span>

<span class="kn">import</span> <span class="nn">collections</span>
<span class="kn">import</span> <span class="nn">urllib.request</span>

Expand Down Expand Up @@ -189,6 +190,13 @@ <h1>Source code for stdpopsim.citations</h1><div class="highlight"><pre>
<span class="n">author</span><span class="o">=</span><span class="s2">&quot;Adrion et al.&quot;</span><span class="p">,</span>
<span class="n">reasons</span><span class="o">=</span><span class="p">{</span><span class="n">CiteReason</span><span class="o">.</span><span class="n">STDPOPSIM</span><span class="p">},</span>
<span class="p">)</span>

<span class="n">_catalog_citation</span> <span class="o">=</span> <span class="n">Citation</span><span class="p">(</span>
<span class="n">doi</span><span class="o">=</span><span class="s2">&quot;https://doi.org/10.7554/eLife.84874&quot;</span><span class="p">,</span>
<span class="n">year</span><span class="o">=</span><span class="s2">&quot;2023&quot;</span><span class="p">,</span>
<span class="n">author</span><span class="o">=</span><span class="s2">&quot;Lauterbur et al.&quot;</span><span class="p">,</span>
<span class="n">reasons</span><span class="o">=</span><span class="p">{</span><span class="n">CiteReason</span><span class="o">.</span><span class="n">STDPOPSIM</span><span class="p">},</span>
<span class="p">)</span>
</pre></div>

</div>
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24 changes: 20 additions & 4 deletions main/_modules/stdpopsim/engines.html
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Expand Up @@ -198,9 +198,24 @@ <h1>Source code for stdpopsim.engines</h1><div class="highlight"><pre>
<span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span>
<span class="s2">&quot;The demographic model has mutation rate &quot;</span>
<span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">demographic_model</span><span class="o">.</span><span class="n">mutation_rate</span><span class="si">}</span><span class="s2">, but this simulation used the &quot;</span>
<span class="sa">f</span><span class="s2">&quot;contig&#39;s mutation rate </span><span class="si">{</span><span class="n">contig</span><span class="o">.</span><span class="n">mutation_rate</span><span class="si">}</span><span class="s2">. Diversity levels &quot;</span>
<span class="s2">&quot;may be different than expected for this species. For details see &quot;</span>
<span class="s2">&quot;documentation at &quot;</span>
<span class="s2">&quot;contig&#39;s mutation rate &quot;</span>
<span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">contig</span><span class="o">.</span><span class="n">mutation_rate</span><span class="si">}</span><span class="s2">. &quot;</span>
<span class="s2">&quot;Diversity levels may be different than expected for this species. &quot;</span>
<span class="s2">&quot;For details see documentation at &quot;</span>
<span class="s2">&quot;https://popsim-consortium.github.io/stdpopsim-docs/stable/tutorial.html&quot;</span>
<span class="p">)</span>

<span class="k">def</span> <span class="nf">_warn_recombination_rate_mismatch</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">contig</span><span class="p">,</span> <span class="n">demographic_model</span><span class="p">):</span>
<span class="k">if</span> <span class="n">demographic_model</span><span class="o">.</span><span class="n">recombination_rate</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">math</span><span class="o">.</span><span class="n">isclose</span><span class="p">(</span>
<span class="n">demographic_model</span><span class="o">.</span><span class="n">recombination_rate</span><span class="p">,</span> <span class="n">contig</span><span class="o">.</span><span class="n">recombination_map</span><span class="o">.</span><span class="n">mean_rate</span>
<span class="p">):</span>
<span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span>
<span class="s2">&quot;The demographic model has recombination rate &quot;</span>
<span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">demographic_model</span><span class="o">.</span><span class="n">recombination_rate</span><span class="si">}</span><span class="s2">, but this simulation used the &quot;</span>
<span class="s2">&quot;contig&#39;s recombination rate &quot;</span>
<span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">contig</span><span class="o">.</span><span class="n">recombination_map</span><span class="o">.</span><span class="n">mean_rate</span><span class="si">}</span><span class="s2">. &quot;</span>
<span class="s2">&quot;Patterns of linkage may be different than expected for this species. &quot;</span>
<span class="s2">&quot;For details see documentation at &quot;</span>
<span class="s2">&quot;https://popsim-consortium.github.io/stdpopsim-docs/stable/tutorial.html&quot;</span>
<span class="p">)</span></div>

Expand Down Expand Up @@ -337,6 +352,7 @@ <h1>Source code for stdpopsim.engines</h1><div class="highlight"><pre>
<span class="c1"># TODO: remove this after a release or two. See #745.</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_warn_zigzag</span><span class="p">(</span><span class="n">demographic_model</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_warn_mutation_rate_mismatch</span><span class="p">(</span><span class="n">contig</span><span class="p">,</span> <span class="n">demographic_model</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_warn_recombination_rate_mismatch</span><span class="p">(</span><span class="n">contig</span><span class="p">,</span> <span class="n">demographic_model</span><span class="p">)</span>

<span class="n">rng</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">default_rng</span><span class="p">(</span><span class="n">seed</span><span class="p">)</span>
<span class="n">seeds</span> <span class="o">=</span> <span class="n">rng</span><span class="o">.</span><span class="n">integers</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="o">**</span><span class="mi">31</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
Expand All @@ -354,7 +370,7 @@ <h1>Source code for stdpopsim.engines</h1><div class="highlight"><pre>
<span class="p">)</span>
<span class="k">elif</span> <span class="p">(</span><span class="n">gc_frac</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="n">gc_frac</span> <span class="o">&gt;</span> <span class="mf">0.0</span><span class="p">):</span>
<span class="c1"># the recombination map is a map of double-stranded breaks,</span>
<span class="c1"># so we need to separate out GC from crossovers</span>
<span class="c1"># so we need to separate out gene conversion from crossing-over</span>
<span class="n">gc_rate</span> <span class="o">=</span> <span class="n">contig</span><span class="o">.</span><span class="n">recombination_map</span><span class="o">.</span><span class="n">mean_rate</span> <span class="o">*</span> <span class="n">gc_frac</span> <span class="o">/</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">gc_frac</span><span class="p">)</span>
<span class="n">recombination_map</span> <span class="o">=</span> <span class="n">msprime</span><span class="o">.</span><span class="n">RateMap</span><span class="p">(</span>
<span class="n">position</span><span class="o">=</span><span class="n">recombination_map</span><span class="o">.</span><span class="n">position</span><span class="p">,</span>
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