Update latest documentation

latest/generated/sgkit.save_dataset.html

@@ -679,7 +679,7 @@
 <h1>sgkit.save_dataset<a class="headerlink" href="#sgkit-save-dataset" title="Permalink to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="sgkit.save_dataset">
-<span class="sig-prename descclassname"><span class="pre">sgkit.</span></span><span class="sig-name descname"><span class="pre">save_dataset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ds</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">store</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">storage_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auto_rechunk</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#sgkit.save_dataset" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.</span></span><span class="sig-name descname"><span class="pre">save_dataset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ds</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">store</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">storage_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">auto_rechunk</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zarr_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#sgkit.save_dataset" title="Permalink to this definition">#</a></dt>
 <dd><p>Save a dataset to Zarr storage.</p>
 <p>This function is a thin wrapper around <a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.to_zarr.html#xarray.Dataset.to_zarr" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">xarray.Dataset.to_zarr()</span></code></a>
 that uses sensible defaults and makes it easier to use in a pipeline.</p>

latest/generated/sgkit.variables.call_dosage_spec.html

@@ -679,7 +679,7 @@
 <h1>sgkit.variables.call_dosage_spec<a class="headerlink" href="#sgkit-variables-call-dosage-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.call_dosage_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">call_dosage_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='call_dosage',</span> <span class="pre">__doc__='\nDosages,</span> <span class="pre">encoded</span> <span class="pre">as</span> <span class="pre">floats,</span> <span class="pre">with</span> <span class="pre">NaN</span> <span class="pre">indicating</span> <span class="pre">a</span> <span class="pre">missing</span> <span class="pre">value.\nDosages</span> <span class="pre">can</span> <span class="pre">represent</span> <span class="pre">one</span> <span class="pre">of</span> <span class="pre">several</span> <span class="pre">possible</span> <span class="pre">quantities,</span> <span class="pre">e.g.:\n-</span> <span class="pre">Alternate</span> <span class="pre">allele</span> <span class="pre">counts\n-</span> <span class="pre">Recessive</span> <span class="pre">or</span> <span class="pre">dominant</span> <span class="pre">allele</span> <span class="pre">encodings\n-</span> <span class="pre">True</span> <span class="pre">dosages</span> <span class="pre">as</span> <span class="pre">computed</span> <span class="pre">from</span> <span class="pre">imputed</span> <span class="pre">or</span> <span class="pre">probabilistic</span> <span class="pre">variant</span> <span class="pre">calls\n-</span> <span class="pre">Any</span> <span class="pre">other</span> <span class="pre">custom</span> <span class="pre">encoding</span> <span class="pre">in</span> <span class="pre">a</span> <span class="pre">user-defined</span> <span class="pre">variable\n',</span> <span class="pre">kind={'i',</span> <span class="pre">'u',</span> <span class="pre">'f'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('variants',</span> <span class="pre">'samples'))</span></em><a class="headerlink" href="#sgkit.variables.call_dosage_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">call_dosage_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='call_dosage',</span> <span class="pre">__doc__='\nDosages,</span> <span class="pre">encoded</span> <span class="pre">as</span> <span class="pre">floats,</span> <span class="pre">with</span> <span class="pre">NaN</span> <span class="pre">indicating</span> <span class="pre">a</span> <span class="pre">missing</span> <span class="pre">value.\nDosages</span> <span class="pre">can</span> <span class="pre">represent</span> <span class="pre">one</span> <span class="pre">of</span> <span class="pre">several</span> <span class="pre">possible</span> <span class="pre">quantities,</span> <span class="pre">e.g.:\n-</span> <span class="pre">Alternate</span> <span class="pre">allele</span> <span class="pre">counts\n-</span> <span class="pre">Recessive</span> <span class="pre">or</span> <span class="pre">dominant</span> <span class="pre">allele</span> <span class="pre">encodings\n-</span> <span class="pre">True</span> <span class="pre">dosages</span> <span class="pre">as</span> <span class="pre">computed</span> <span class="pre">from</span> <span class="pre">imputed</span> <span class="pre">or</span> <span class="pre">probabilistic</span> <span class="pre">variant</span> <span class="pre">calls\n-</span> <span class="pre">Any</span> <span class="pre">other</span> <span class="pre">custom</span> <span class="pre">encoding</span> <span class="pre">in</span> <span class="pre">a</span> <span class="pre">user-defined</span> <span class="pre">variable\n',</span> <span class="pre">kind={'i',</span> <span class="pre">'f',</span> <span class="pre">'u'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('variants',</span> <span class="pre">'samples'))</span></em><a class="headerlink" href="#sgkit.variables.call_dosage_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Dosages, encoded as floats, with NaN indicating a missing value.
 Dosages can represent one of several possible quantities, e.g.:
 - Alternate allele counts

latest/generated/sgkit.variables.stat_Fst_spec.html

@@ -679,7 +679,7 @@
 <h1>sgkit.variables.stat_Fst_spec<a class="headerlink" href="#sgkit-variables-stat-fst-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.stat_Fst_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_Fst_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_Fst',</span> <span class="pre">__doc__='Fixation</span> <span class="pre">index</span> <span class="pre">(Fst)</span> <span class="pre">between</span> <span class="pre">pairs</span> <span class="pre">of</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=3,</span> <span class="pre">dims=({'windows',</span> <span class="pre">'variants'},</span> <span class="pre">'cohorts_0',</span> <span class="pre">'cohorts_1'))</span></em><a class="headerlink" href="#sgkit.variables.stat_Fst_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_Fst_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_Fst',</span> <span class="pre">__doc__='Fixation</span> <span class="pre">index</span> <span class="pre">(Fst)</span> <span class="pre">between</span> <span class="pre">pairs</span> <span class="pre">of</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=3,</span> <span class="pre">dims=({'variants',</span> <span class="pre">'windows'},</span> <span class="pre">'cohorts_0',</span> <span class="pre">'cohorts_1'))</span></em><a class="headerlink" href="#sgkit.variables.stat_Fst_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Fixation index (Fst) between pairs of cohorts.</p>
 </dd></dl>
 

latest/generated/sgkit.variables.stat_Tajimas_D_spec.html

@@ -679,7 +679,7 @@
 <h1>sgkit.variables.stat_Tajimas_D_spec<a class="headerlink" href="#sgkit-variables-stat-tajimas-d-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.stat_Tajimas_D_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_Tajimas_D_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_Tajimas_D',</span> <span class="pre">__doc__='Tajima’s</span> <span class="pre">D</span> <span class="pre">for</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=2,</span> <span class="pre">dims=({'windows',</span> <span class="pre">'variants'},</span> <span class="pre">'cohorts'))</span></em><a class="headerlink" href="#sgkit.variables.stat_Tajimas_D_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_Tajimas_D_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_Tajimas_D',</span> <span class="pre">__doc__='Tajima’s</span> <span class="pre">D</span> <span class="pre">for</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=2,</span> <span class="pre">dims=({'variants',</span> <span class="pre">'windows'},</span> <span class="pre">'cohorts'))</span></em><a class="headerlink" href="#sgkit.variables.stat_Tajimas_D_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Tajima’s D for cohorts.</p>
 </dd></dl>
 

latest/generated/sgkit.variables.stat_divergence_spec.html

@@ -679,7 +679,7 @@
 <h1>sgkit.variables.stat_divergence_spec<a class="headerlink" href="#sgkit-variables-stat-divergence-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.stat_divergence_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_divergence_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_divergence',</span> <span class="pre">__doc__='Genetic</span> <span class="pre">divergence</span> <span class="pre">between</span> <span class="pre">pairs</span> <span class="pre">of</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=3,</span> <span class="pre">dims=({'windows',</span> <span class="pre">'variants'},</span> <span class="pre">'cohorts_0',</span> <span class="pre">'cohorts_1'))</span></em><a class="headerlink" href="#sgkit.variables.stat_divergence_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_divergence_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_divergence',</span> <span class="pre">__doc__='Genetic</span> <span class="pre">divergence</span> <span class="pre">between</span> <span class="pre">pairs</span> <span class="pre">of</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=3,</span> <span class="pre">dims=({'variants',</span> <span class="pre">'windows'},</span> <span class="pre">'cohorts_0',</span> <span class="pre">'cohorts_1'))</span></em><a class="headerlink" href="#sgkit.variables.stat_divergence_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Genetic divergence between pairs of cohorts.</p>
 </dd></dl>
 

latest/generated/sgkit.variables.stat_diversity_spec.html

@@ -679,7 +679,7 @@
 <h1>sgkit.variables.stat_diversity_spec<a class="headerlink" href="#sgkit-variables-stat-diversity-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.stat_diversity_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_diversity_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_diversity',</span> <span class="pre">__doc__='Genetic</span> <span class="pre">diversity</span> <span class="pre">(also</span> <span class="pre">known</span> <span class="pre">as</span> <span class="pre">&quot;Tajima’s</span> <span class="pre">pi&quot;)</span> <span class="pre">for</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=2,</span> <span class="pre">dims=({'windows',</span> <span class="pre">'variants'},</span> <span class="pre">'cohorts'))</span></em><a class="headerlink" href="#sgkit.variables.stat_diversity_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_diversity_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_diversity',</span> <span class="pre">__doc__='Genetic</span> <span class="pre">diversity</span> <span class="pre">(also</span> <span class="pre">known</span> <span class="pre">as</span> <span class="pre">&quot;Tajima’s</span> <span class="pre">pi&quot;)</span> <span class="pre">for</span> <span class="pre">cohorts.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=2,</span> <span class="pre">dims=({'variants',</span> <span class="pre">'windows'},</span> <span class="pre">'cohorts'))</span></em><a class="headerlink" href="#sgkit.variables.stat_diversity_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Genetic diversity (also known as “Tajima’s pi”) for cohorts.</p>
 </dd></dl>
 

latest/generated/sgkit.variables.stat_observed_heterozygosity_spec.html

@@ -679,7 +679,7 @@
 <h1>sgkit.variables.stat_observed_heterozygosity_spec<a class="headerlink" href="#sgkit-variables-stat-observed-heterozygosity-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.stat_observed_heterozygosity_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_observed_heterozygosity_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_observed_heterozygosity',</span> <span class="pre">__doc__='\nObserved</span> <span class="pre">heterozygosity</span> <span class="pre">for</span> <span class="pre">cohorts.\n',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=2,</span> <span class="pre">dims=({'windows',</span> <span class="pre">'variants'},</span> <span class="pre">'cohorts'))</span></em><a class="headerlink" href="#sgkit.variables.stat_observed_heterozygosity_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_observed_heterozygosity_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_observed_heterozygosity',</span> <span class="pre">__doc__='\nObserved</span> <span class="pre">heterozygosity</span> <span class="pre">for</span> <span class="pre">cohorts.\n',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=2,</span> <span class="pre">dims=({'variants',</span> <span class="pre">'windows'},</span> <span class="pre">'cohorts'))</span></em><a class="headerlink" href="#sgkit.variables.stat_observed_heterozygosity_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Observed heterozygosity for cohorts.</p>
 </dd></dl>
 

latest/generated/sgkit.variables.stat_pbs_spec.html

@@ -679,7 +679,7 @@
 <h1>sgkit.variables.stat_pbs_spec<a class="headerlink" href="#sgkit-variables-stat-pbs-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.stat_pbs_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_pbs_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_pbs',</span> <span class="pre">__doc__='Population</span> <span class="pre">branching</span> <span class="pre">statistic</span> <span class="pre">for</span> <span class="pre">cohort</span> <span class="pre">triples.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=4,</span> <span class="pre">dims=({'windows',</span> <span class="pre">'variants'},</span> <span class="pre">'cohorts_0',</span> <span class="pre">'cohorts_1',</span> <span class="pre">'cohorts_2'))</span></em><a class="headerlink" href="#sgkit.variables.stat_pbs_spec" title="Permalink to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">stat_pbs_spec</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">ArrayLikeSpec(default_name='stat_pbs',</span> <span class="pre">__doc__='Population</span> <span class="pre">branching</span> <span class="pre">statistic</span> <span class="pre">for</span> <span class="pre">cohort</span> <span class="pre">triples.',</span> <span class="pre">kind='f',</span> <span class="pre">ndim=4,</span> <span class="pre">dims=({'variants',</span> <span class="pre">'windows'},</span> <span class="pre">'cohorts_0',</span> <span class="pre">'cohorts_1',</span> <span class="pre">'cohorts_2'))</span></em><a class="headerlink" href="#sgkit.variables.stat_pbs_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Population branching statistic for cohort triples.</p>
 </dd></dl>