Update latest documentation

latest/generated/sgkit.variables.call_dosage_spec.html

@@ -748,7 +748,7 @@
 <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={'u',</span> <span class="pre">'i',</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={'f',</span> <span class="pre">'i',</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.interval_contig_name_spec.html

@@ -748,7 +748,7 @@
 <h1>sgkit.variables.interval_contig_name_spec<a class="headerlink" href="#sgkit-variables-interval-contig-name-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.interval_contig_name_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">interval_contig_name_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='interval_contig_name',</span> <span class="pre">__doc__='Interval</span> <span class="pre">contig</span> <span class="pre">name.</span> <span class="pre">Must</span> <span class="pre">match</span> <span class="pre">a</span> <span class="pre">contig</span> <span class="pre">defined</span> <span class="pre">in</span> <span class="pre">the</span> <span class="pre">``contigs``</span> <span class="pre">attribute.',</span> <span class="pre">kind={'S',</span> <span class="pre">'U',</span> <span class="pre">'O'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=None)</span></em><a class="headerlink" href="#sgkit.variables.interval_contig_name_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">interval_contig_name_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='interval_contig_name',</span> <span class="pre">__doc__='Interval</span> <span class="pre">contig</span> <span class="pre">name.</span> <span class="pre">Must</span> <span class="pre">match</span> <span class="pre">a</span> <span class="pre">contig</span> <span class="pre">defined</span> <span class="pre">in</span> <span class="pre">the</span> <span class="pre">``contigs``</span> <span class="pre">attribute.',</span> <span class="pre">kind={'U',</span> <span class="pre">'S',</span> <span class="pre">'O'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=None)</span></em><a class="headerlink" href="#sgkit.variables.interval_contig_name_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Interval contig name. Must match a contig defined in the <code class="docutils literal notranslate"><span class="pre">contigs</span></code> attribute.</p>
 </dd></dl>
 

latest/generated/sgkit.variables.parent_id_spec.html

@@ -748,7 +748,7 @@
 <h1>sgkit.variables.parent_id_spec<a class="headerlink" href="#sgkit-variables-parent-id-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.parent_id_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">parent_id_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='parent_id',</span> <span class="pre">__doc__='\nUnique</span> <span class="pre">identifiers</span> <span class="pre">of</span> <span class="pre">parent</span> <span class="pre">samples</span> <span class="pre">matching</span> <span class="pre">those</span> <span class="pre">in\n:data:`sgkit.variables.sample_id_spec`.\n',</span> <span class="pre">kind={'S',</span> <span class="pre">'U',</span> <span class="pre">'O'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('samples',</span> <span class="pre">'parents'))</span></em><a class="headerlink" href="#sgkit.variables.parent_id_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">parent_id_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='parent_id',</span> <span class="pre">__doc__='\nUnique</span> <span class="pre">identifiers</span> <span class="pre">of</span> <span class="pre">parent</span> <span class="pre">samples</span> <span class="pre">matching</span> <span class="pre">those</span> <span class="pre">in\n:data:`sgkit.variables.sample_id_spec`.\n',</span> <span class="pre">kind={'U',</span> <span class="pre">'S',</span> <span class="pre">'O'},</span> <span class="pre">ndim=2,</span> <span class="pre">dims=('samples',</span> <span class="pre">'parents'))</span></em><a class="headerlink" href="#sgkit.variables.parent_id_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Unique identifiers of parent samples matching those in
 <a class="reference internal" href="sgkit.variables.sample_id_spec.html#sgkit.variables.sample_id_spec" title="sgkit.variables.sample_id_spec"><code class="xref py py-data docutils literal notranslate"><span class="pre">sgkit.variables.sample_id_spec</span></code></a>.</p>
 </dd></dl>

latest/generated/sgkit.variables.sample_id_spec.html

@@ -748,7 +748,7 @@
 <h1>sgkit.variables.sample_id_spec<a class="headerlink" href="#sgkit-variables-sample-id-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.sample_id_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">sample_id_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='sample_id',</span> <span class="pre">__doc__='The</span> <span class="pre">unique</span> <span class="pre">identifier</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">sample.',</span> <span class="pre">kind={'S',</span> <span class="pre">'U',</span> <span class="pre">'O'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('samples',))</span></em><a class="headerlink" href="#sgkit.variables.sample_id_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">sample_id_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='sample_id',</span> <span class="pre">__doc__='The</span> <span class="pre">unique</span> <span class="pre">identifier</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">sample.',</span> <span class="pre">kind={'U',</span> <span class="pre">'S',</span> <span class="pre">'O'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('samples',))</span></em><a class="headerlink" href="#sgkit.variables.sample_id_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>The unique identifier of the sample.</p>
 </dd></dl>
 

latest/generated/sgkit.variables.traits_spec.html

@@ -748,7 +748,7 @@
 <h1>sgkit.variables.traits_spec<a class="headerlink" href="#sgkit-variables-traits-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.traits_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">traits_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='traits',</span> <span class="pre">__doc__='\nTrait</span> <span class="pre">(for</span> <span class="pre">example</span> <span class="pre">phenotype)</span> <span class="pre">variable</span> <span class="pre">names.</span> <span class="pre">Must</span> <span class="pre">all</span> <span class="pre">be</span> <span class="pre">continuous</span> <span class="pre">and\ncorrespond</span> <span class="pre">to</span> <span class="pre">1</span> <span class="pre">or</span> <span class="pre">2D</span> <span class="pre">dataset</span> <span class="pre">variables</span> <span class="pre">of</span> <span class="pre">shape</span> <span class="pre">(samples[,</span> <span class="pre">traits]).\n2D</span> <span class="pre">trait</span> <span class="pre">arrays</span> <span class="pre">will</span> <span class="pre">be</span> <span class="pre">assumed</span> <span class="pre">to</span> <span class="pre">contain</span> <span class="pre">separate</span> <span class="pre">traits</span> <span class="pre">within</span> <span class="pre">columns\nand</span> <span class="pre">concatenated</span> <span class="pre">to</span> <span class="pre">any</span> <span class="pre">1D</span> <span class="pre">traits</span> <span class="pre">along</span> <span class="pre">the</span> <span class="pre">second</span> <span class="pre">axis</span> <span class="pre">(columns).\n',</span> <span class="pre">kind=None,</span> <span class="pre">ndim={1,</span> <span class="pre">2},</span> <span class="pre">dims=('samples',</span> <span class="pre">{None,</span> <span class="pre">'*'}))</span></em><a class="headerlink" href="#sgkit.variables.traits_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">traits_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='traits',</span> <span class="pre">__doc__='\nTrait</span> <span class="pre">(for</span> <span class="pre">example</span> <span class="pre">phenotype)</span> <span class="pre">variable</span> <span class="pre">names.</span> <span class="pre">Must</span> <span class="pre">all</span> <span class="pre">be</span> <span class="pre">continuous</span> <span class="pre">and\ncorrespond</span> <span class="pre">to</span> <span class="pre">1</span> <span class="pre">or</span> <span class="pre">2D</span> <span class="pre">dataset</span> <span class="pre">variables</span> <span class="pre">of</span> <span class="pre">shape</span> <span class="pre">(samples[,</span> <span class="pre">traits]).\n2D</span> <span class="pre">trait</span> <span class="pre">arrays</span> <span class="pre">will</span> <span class="pre">be</span> <span class="pre">assumed</span> <span class="pre">to</span> <span class="pre">contain</span> <span class="pre">separate</span> <span class="pre">traits</span> <span class="pre">within</span> <span class="pre">columns\nand</span> <span class="pre">concatenated</span> <span class="pre">to</span> <span class="pre">any</span> <span class="pre">1D</span> <span class="pre">traits</span> <span class="pre">along</span> <span class="pre">the</span> <span class="pre">second</span> <span class="pre">axis</span> <span class="pre">(columns).\n',</span> <span class="pre">kind=None,</span> <span class="pre">ndim={1,</span> <span class="pre">2},</span> <span class="pre">dims=('samples',</span> <span class="pre">{'*',</span> <span class="pre">None}))</span></em><a class="headerlink" href="#sgkit.variables.traits_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Trait (for example phenotype) variable names. Must all be continuous and
 correspond to 1 or 2D dataset variables of shape (samples[, traits]).
 2D trait arrays will be assumed to contain separate traits within columns

latest/generated/sgkit.variables.variant_contig_spec.html

@@ -748,7 +748,7 @@
 <h1>sgkit.variables.variant_contig_spec<a class="headerlink" href="#sgkit-variables-variant-contig-spec" title="Permalink to this heading">#</a></h1>
 <dl class="py data">
 <dt class="sig sig-object py" id="sgkit.variables.variant_contig_spec">
-<span class="sig-prename descclassname"><span class="pre">sgkit.variables.</span></span><span class="sig-name descname"><span class="pre">variant_contig_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='variant_contig',</span> <span class="pre">__doc__='\nIndex</span> <span class="pre">corresponding</span> <span class="pre">to</span> <span class="pre">contig</span> <span class="pre">name</span> <span class="pre">for</span> <span class="pre">each</span> <span class="pre">variant.</span> <span class="pre">In</span> <span class="pre">some</span> <span class="pre">less</span> <span class="pre">common\nscenarios,</span> <span class="pre">this</span> <span class="pre">may</span> <span class="pre">also</span> <span class="pre">be</span> <span class="pre">equivalent</span> <span class="pre">to</span> <span class="pre">the</span> <span class="pre">contig</span> <span class="pre">names</span> <span class="pre">if</span> <span class="pre">the</span> <span class="pre">data\ngenerating</span> <span class="pre">process</span> <span class="pre">used</span> <span class="pre">contig</span> <span class="pre">names</span> <span class="pre">that</span> <span class="pre">were</span> <span class="pre">also</span> <span class="pre">integers.\n',</span> <span class="pre">kind={'u',</span> <span class="pre">'i'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('variants',))</span></em><a class="headerlink" href="#sgkit.variables.variant_contig_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">variant_contig_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='variant_contig',</span> <span class="pre">__doc__='\nIndex</span> <span class="pre">corresponding</span> <span class="pre">to</span> <span class="pre">contig</span> <span class="pre">name</span> <span class="pre">for</span> <span class="pre">each</span> <span class="pre">variant.</span> <span class="pre">In</span> <span class="pre">some</span> <span class="pre">less</span> <span class="pre">common\nscenarios,</span> <span class="pre">this</span> <span class="pre">may</span> <span class="pre">also</span> <span class="pre">be</span> <span class="pre">equivalent</span> <span class="pre">to</span> <span class="pre">the</span> <span class="pre">contig</span> <span class="pre">names</span> <span class="pre">if</span> <span class="pre">the</span> <span class="pre">data\ngenerating</span> <span class="pre">process</span> <span class="pre">used</span> <span class="pre">contig</span> <span class="pre">names</span> <span class="pre">that</span> <span class="pre">were</span> <span class="pre">also</span> <span class="pre">integers.\n',</span> <span class="pre">kind={'i',</span> <span class="pre">'u'},</span> <span class="pre">ndim=1,</span> <span class="pre">dims=('variants',))</span></em><a class="headerlink" href="#sgkit.variables.variant_contig_spec" title="Permalink to this definition">#</a></dt>
 <dd><p>Index corresponding to contig name for each variant. In some less common
 scenarios, this may also be equivalent to the contig names if the data
 generating process used contig names that were also integers.</p>