Update latest documentation

latest/api.html

@@ -1070,7 +1070,7 @@ <h2>Utilities<a class="headerlink" href="#utilities" title="Permalink to this he
 <td><p>Variance explained by each principal component.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="generated/sgkit.variables.sample_pca_explained_variance_ratio_spec.html#sgkit.variables.sample_pca_explained_variance_ratio_spec" title="sgkit.variables.sample_pca_explained_variance_ratio_spec"><code class="xref py py-obj docutils literal notranslate"><span class="pre">variables.sample_pca_explained_variance_ratio_spec</span></code></a></p></td>
-<td><p>Ratio of variance explained to total variance for each principal component, i.e. <code class="docutils literal notranslate"><span class="pre">dask_ml.decomposition.TruncatedSVD.explained_variance_ratio_</span></code>.</p></td>
+<td><p>Ratio of variance explained to total variance for each principal component, i.e. <code class="docutils literal notranslate"><span class="pre">sgkit.stats.truncated_svd.TruncatedSVD.explained_variance_ratio_</span></code>.</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="generated/sgkit.variables.sample_pca_loading_spec.html#sgkit.variables.sample_pca_loading_spec" title="sgkit.variables.sample_pca_loading_spec"><code class="xref py py-obj docutils literal notranslate"><span class="pre">variables.sample_pca_loading_spec</span></code></a></p></td>
 <td><p>PCA loadings defined as principal axes scaled by square root of eigenvalues.</p></td>

latest/generated/sgkit.Fst.html

@@ -687,7 +687,7 @@ <h1>sgkit.Fst<a class="headerlink" href="#sgkit-fst" title="Permalink to this he
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><dl class="simple">
-<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Genotype call dataset.</p>
+<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Genotype call dataset.</p>
 </dd>
 <dt><strong>estimator</strong> <span class="classifier"><span class="annotation terse"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> | <a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.13)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">None</span></code></a></span><span class="annotation full"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Optional" title="(in Python v3.13)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Optional</span></code></a>[<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>]</span> (default: <code class="docutils literal notranslate"><span class="pre">None</span></code>)</span></dt></dt><dd><p>Determines the formula to use for computing Fst.
 If None (the default), or <code class="docutils literal notranslate"><span class="pre">Hudson</span></code>, Fst is calculated
@@ -709,7 +709,7 @@ <h1>sgkit.Fst<a class="headerlink" href="#sgkit-fst" title="Permalink to this he
 </dl>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
 <dd class="field-odd"><p><p>:

latest/generated/sgkit.Garud_H.html

@@ -688,7 +688,7 @@ <h1>sgkit.Garud_H<a class="headerlink" href="#sgkit-garud-h" title="Permalink to
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><dl class="simple">
-<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Genotype call dataset.</p>
+<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Genotype call dataset.</p>
 </dd>
 <dt><strong>call_genotype</strong> <span class="classifier"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Hashable" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Hashable</span></code></a> (default: <code class="docutils literal notranslate"><span class="pre">'call_genotype'</span></code>)</span></dt></dt><dd><p>Input variable name holding call_genotype as defined by
 <a class="reference internal" href="sgkit.variables.call_genotype_spec.html#sgkit.variables.call_genotype_spec" title="sgkit.variables.call_genotype_spec"><code class="xref py py-data docutils literal notranslate"><span class="pre">sgkit.variables.call_genotype_spec</span></code></a>.
@@ -709,7 +709,7 @@ <h1>sgkit.Garud_H<a class="headerlink" href="#sgkit-garud-h" title="Permalink to
 </dl>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
 <dd class="field-odd"><p><p>:

latest/generated/sgkit.Tajimas_D.html

@@ -687,7 +687,7 @@ <h1>sgkit.Tajimas_D<a class="headerlink" href="#sgkit-tajimas-d" title="Permalin
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><dl class="simple">
-<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Genotype call dataset.</p>
+<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Genotype call dataset.</p>
 </dd>
 <dt><strong>variant_allele_count</strong> <span class="classifier"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Hashable" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Hashable</span></code></a> (default: <code class="docutils literal notranslate"><span class="pre">'variant_allele_count'</span></code>)</span></dt></dt><dd><p>Variant allele count variable to use or calculate. Defined by
 <a class="reference internal" href="sgkit.variables.variant_allele_count_spec.html#sgkit.variables.variant_allele_count_spec" title="sgkit.variables.variant_allele_count_spec"><code class="xref py py-data docutils literal notranslate"><span class="pre">sgkit.variables.variant_allele_count_spec</span></code></a>.
@@ -707,7 +707,7 @@ <h1>sgkit.Tajimas_D<a class="headerlink" href="#sgkit-tajimas-d" title="Permalin
 </dl>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
 <dd class="field-odd"><p><p>:

latest/generated/sgkit.Weir_Goudet_beta.html

@@ -695,7 +695,7 @@ <h1>sgkit.Weir_Goudet_beta<a class="headerlink" href="#sgkit-weir-goudet-beta" t
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><dl class="simple">
-<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Genotype call dataset.</p>
+<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Genotype call dataset.</p>
 </dd>
 <dt><strong>stat_identity_by_state</strong> <span class="classifier"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Hashable" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Hashable</span></code></a> (default: <code class="docutils literal notranslate"><span class="pre">'stat_identity_by_state'</span></code>)</span></dt></dt><dd><p>Input variable name holding stat_identity_by_state as defined
 by <a class="reference internal" href="sgkit.variables.stat_identity_by_state_spec.html#sgkit.variables.stat_identity_by_state_spec" title="sgkit.variables.stat_identity_by_state_spec"><code class="xref py py-data docutils literal notranslate"><span class="pre">sgkit.variables.stat_identity_by_state_spec</span></code></a>.
@@ -710,7 +710,7 @@ <h1>sgkit.Weir_Goudet_beta<a class="headerlink" href="#sgkit-weir-goudet-beta" t
 </dl>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
 <dd class="field-odd"><p><p>:

latest/generated/sgkit.call_allele_frequencies.html

@@ -684,7 +684,7 @@ <h1>sgkit.call_allele_frequencies<a class="headerlink" href="#sgkit-call-allele-
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><dl class="simple">
-<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Dataset containing genotype calls.</p>
+<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Dataset containing genotype calls.</p>
 </dd>
 <dt><strong>call_allele_count</strong> <span class="classifier"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Hashable" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Hashable</span></code></a> (default: <code class="docutils literal notranslate"><span class="pre">'call_allele_count'</span></code>)</span></dt></dt><dd><p>Input variable name holding call_allele_count as defined by
 <a class="reference internal" href="sgkit.variables.call_allele_count_spec.html#sgkit.variables.call_allele_count_spec" title="sgkit.variables.call_allele_count_spec"><code class="xref py py-data docutils literal notranslate"><span class="pre">sgkit.variables.call_allele_count_spec</span></code></a>.
@@ -699,7 +699,7 @@ <h1>sgkit.call_allele_frequencies<a class="headerlink" href="#sgkit-call-allele-
 </dl>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
 <dd class="field-odd"><p><p>:

latest/generated/sgkit.cohort_allele_frequencies.html

@@ -684,7 +684,7 @@ <h1>sgkit.cohort_allele_frequencies<a class="headerlink" href="#sgkit-cohort-all
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><dl class="simple">
-<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Dataset containing genotype calls.</p>
+<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Dataset containing genotype calls.</p>
 </dd>
 <dt><strong>cohort_allele_count</strong> <span class="classifier"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Hashable" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Hashable</span></code></a> (default: <code class="docutils literal notranslate"><span class="pre">'cohort_allele_count'</span></code>)</span></dt></dt><dd><p>Input variable name holding cohort_allele_count as defined by
 <a class="reference internal" href="sgkit.variables.cohort_allele_count_spec.html#sgkit.variables.cohort_allele_count_spec" title="sgkit.variables.cohort_allele_count_spec"><code class="xref py py-data docutils literal notranslate"><span class="pre">sgkit.variables.cohort_allele_count_spec</span></code></a>.
@@ -699,7 +699,7 @@ <h1>sgkit.cohort_allele_frequencies<a class="headerlink" href="#sgkit-cohort-all
 </dl>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
 <dd class="field-odd"><p><p>:

latest/generated/sgkit.convert_call_to_index.html

@@ -684,7 +684,7 @@ <h1>sgkit.convert_call_to_index<a class="headerlink" href="#sgkit-convert-call-t
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><dl class="simple">
-<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Dataset containing genotype calls.</p>
+<dt><strong>ds</strong> <span class="classifier"><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></span></dt></dt><dd><p>Dataset containing genotype calls.</p>
 </dd>
 <dt><strong>call_genotype</strong> <span class="classifier"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Hashable" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Hashable</span></code></a> (default: <code class="docutils literal notranslate"><span class="pre">'call_genotype'</span></code>)</span></dt></dt><dd><p>Input variable name holding call_genotype as defined by
 <a class="reference internal" href="sgkit.variables.call_genotype_spec.html#sgkit.variables.call_genotype_spec" title="sgkit.variables.call_genotype_spec"><code class="xref py py-data docutils literal notranslate"><span class="pre">sgkit.variables.call_genotype_spec</span></code></a>.
@@ -698,7 +698,7 @@ <h1>sgkit.convert_call_to_index<a class="headerlink" href="#sgkit-convert-call-t
 </dl>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.10.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html#xarray.Dataset" title="(in xarray v2024.11.1.dev0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Dataset</span></code></a></p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
 <dd class="field-odd"><p><p>: