A loose federation of distributed, typed datasets
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401
402 <ul>
403 <li><a href="#atdata.AbstractIndex" id="toc-atdata.AbstractIndex" class="nav-link active" data-scroll-target="#atdata.AbstractIndex">AbstractIndex</a>
404 <ul class="collapse">
405 <li><a href="#optional-extensions" id="toc-optional-extensions" class="nav-link" data-scroll-target="#optional-extensions">Optional Extensions</a></li>
406 <li><a href="#examples" id="toc-examples" class="nav-link" data-scroll-target="#examples">Examples</a></li>
407 <li><a href="#attributes" id="toc-attributes" class="nav-link" data-scroll-target="#attributes">Attributes</a></li>
408 <li><a href="#methods" id="toc-methods" class="nav-link" data-scroll-target="#methods">Methods</a>
409 <ul class="collapse">
410 <li><a href="#atdata.AbstractIndex.decode_schema" id="toc-atdata.AbstractIndex.decode_schema" class="nav-link" data-scroll-target="#atdata.AbstractIndex.decode_schema">decode_schema</a></li>
411 <li><a href="#atdata.AbstractIndex.get_dataset" id="toc-atdata.AbstractIndex.get_dataset" class="nav-link" data-scroll-target="#atdata.AbstractIndex.get_dataset">get_dataset</a></li>
412 <li><a href="#atdata.AbstractIndex.get_schema" id="toc-atdata.AbstractIndex.get_schema" class="nav-link" data-scroll-target="#atdata.AbstractIndex.get_schema">get_schema</a></li>
413 <li><a href="#atdata.AbstractIndex.insert_dataset" id="toc-atdata.AbstractIndex.insert_dataset" class="nav-link" data-scroll-target="#atdata.AbstractIndex.insert_dataset">insert_dataset</a></li>
414 <li><a href="#atdata.AbstractIndex.list_datasets" id="toc-atdata.AbstractIndex.list_datasets" class="nav-link" data-scroll-target="#atdata.AbstractIndex.list_datasets">list_datasets</a></li>
415 <li><a href="#atdata.AbstractIndex.list_schemas" id="toc-atdata.AbstractIndex.list_schemas" class="nav-link" data-scroll-target="#atdata.AbstractIndex.list_schemas">list_schemas</a></li>
416 <li><a href="#atdata.AbstractIndex.publish_schema" id="toc-atdata.AbstractIndex.publish_schema" class="nav-link" data-scroll-target="#atdata.AbstractIndex.publish_schema">publish_schema</a></li>
417 </ul></li>
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428
429<section id="atdata.AbstractIndex" class="level1">
430<h1>AbstractIndex</h1>
431<div class="sourceCode" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>AbstractIndex()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
432<p>Protocol for index operations - implemented by LocalIndex and AtmosphereIndex.</p>
433<p>This protocol defines the common interface for managing dataset metadata: - Publishing and retrieving schemas - Inserting and listing datasets - (Future) Publishing and retrieving lenses</p>
434<p>A single index can hold datasets of many different sample types. The sample type is tracked via schema references, not as a generic parameter on the index.</p>
435<section id="optional-extensions" class="level2 doc-section doc-section-optional-extensions">
436<h2 class="doc-section doc-section-optional-extensions anchored" data-anchor-id="optional-extensions">Optional Extensions</h2>
437<p>Some index implementations support additional features: - <code>data_store</code>: An AbstractDataStore for reading/writing dataset shards. If present, <code>load_dataset</code> will use it for S3 credential resolution.</p>
438</section>
439<section id="examples" class="level2 doc-section doc-section-examples">
440<h2 class="doc-section doc-section-examples anchored" data-anchor-id="examples">Examples</h2>
441<div class="sourceCode" id="cb2"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="op">>>></span> <span class="kw">def</span> publish_and_list(index: AbstractIndex) <span class="op">-></span> <span class="va">None</span>:</span>
442<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>... <span class="co"># Publish schemas for different types</span></span>
443<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>... schema1 <span class="op">=</span> index.publish_schema(ImageSample, version<span class="op">=</span><span class="st">"1.0.0"</span>)</span>
444<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>... schema2 <span class="op">=</span> index.publish_schema(TextSample, version<span class="op">=</span><span class="st">"1.0.0"</span>)</span>
445<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>...</span>
446<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a>... <span class="co"># Insert datasets of different types</span></span>
447<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a>... index.insert_dataset(image_ds, name<span class="op">=</span><span class="st">"images"</span>)</span>
448<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a>... index.insert_dataset(text_ds, name<span class="op">=</span><span class="st">"texts"</span>)</span>
449<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a>...</span>
450<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a>... <span class="co"># List all datasets (mixed types)</span></span>
451<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a>... <span class="cf">for</span> entry <span class="kw">in</span> index.list_datasets():</span>
452<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a>... <span class="bu">print</span>(<span class="ss">f"</span><span class="sc">{</span>entry<span class="sc">.</span>name<span class="sc">}</span><span class="ss"> -> </span><span class="sc">{</span>entry<span class="sc">.</span>schema_ref<span class="sc">}</span><span class="ss">"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
453</section>
454<section id="attributes" class="level2">
455<h2 class="anchored" data-anchor-id="attributes">Attributes</h2>
456<table class="caption-top table">
457<thead>
458<tr class="header">
459<th>Name</th>
460<th>Description</th>
461</tr>
462</thead>
463<tbody>
464<tr class="odd">
465<td><a href="#atdata.AbstractIndex.data_store">data_store</a></td>
466<td>Optional data store for reading/writing shards.</td>
467</tr>
468<tr class="even">
469<td><a href="#atdata.AbstractIndex.datasets">datasets</a></td>
470<td>Lazily iterate over all dataset entries in this index.</td>
471</tr>
472<tr class="odd">
473<td><a href="#atdata.AbstractIndex.schemas">schemas</a></td>
474<td>Lazily iterate over all schema records in this index.</td>
475</tr>
476</tbody>
477</table>
478</section>
479<section id="methods" class="level2">
480<h2 class="anchored" data-anchor-id="methods">Methods</h2>
481<table class="caption-top table">
482<thead>
483<tr class="header">
484<th>Name</th>
485<th>Description</th>
486</tr>
487</thead>
488<tbody>
489<tr class="odd">
490<td><a href="#atdata.AbstractIndex.decode_schema">decode_schema</a></td>
491<td>Reconstruct a Python Packable type from a stored schema.</td>
492</tr>
493<tr class="even">
494<td><a href="#atdata.AbstractIndex.get_dataset">get_dataset</a></td>
495<td>Get a dataset entry by name or reference.</td>
496</tr>
497<tr class="odd">
498<td><a href="#atdata.AbstractIndex.get_schema">get_schema</a></td>
499<td>Get a schema record by reference.</td>
500</tr>
501<tr class="even">
502<td><a href="#atdata.AbstractIndex.insert_dataset">insert_dataset</a></td>
503<td>Insert a dataset into the index.</td>
504</tr>
505<tr class="odd">
506<td><a href="#atdata.AbstractIndex.list_datasets">list_datasets</a></td>
507<td>Get all dataset entries as a materialized list.</td>
508</tr>
509<tr class="even">
510<td><a href="#atdata.AbstractIndex.list_schemas">list_schemas</a></td>
511<td>Get all schema records as a materialized list.</td>
512</tr>
513<tr class="odd">
514<td><a href="#atdata.AbstractIndex.publish_schema">publish_schema</a></td>
515<td>Publish a schema for a sample type.</td>
516</tr>
517</tbody>
518</table>
519<section id="atdata.AbstractIndex.decode_schema" class="level3">
520<h3 class="anchored" data-anchor-id="atdata.AbstractIndex.decode_schema">decode_schema</h3>
521<div class="sourceCode" id="cb3"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>AbstractIndex.decode_schema(ref)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
522<p>Reconstruct a Python Packable type from a stored schema.</p>
523<p>This method enables loading datasets without knowing the sample type ahead of time. The index retrieves the schema record and dynamically generates a Packable class matching the schema definition.</p>
524<section id="parameters" class="level4 doc-section doc-section-parameters">
525<h4 class="doc-section doc-section-parameters anchored" data-anchor-id="parameters">Parameters</h4>
526<table class="caption-top table">
527<thead>
528<tr class="header">
529<th>Name</th>
530<th>Type</th>
531<th>Description</th>
532<th>Default</th>
533</tr>
534</thead>
535<tbody>
536<tr class="odd">
537<td>ref</td>
538<td><a href="`str`">str</a></td>
539<td>Schema reference string (local:// or at://).</td>
540<td><em>required</em></td>
541</tr>
542</tbody>
543</table>
544</section>
545<section id="returns" class="level4 doc-section doc-section-returns">
546<h4 class="doc-section doc-section-returns anchored" data-anchor-id="returns">Returns</h4>
547<table class="caption-top table">
548<thead>
549<tr class="header">
550<th>Name</th>
551<th>Type</th>
552<th>Description</th>
553</tr>
554</thead>
555<tbody>
556<tr class="odd">
557<td></td>
558<td><a href="`typing.Type`">Type</a>[<a href="`atdata._protocols.Packable`">Packable</a>]</td>
559<td>A dynamically generated Packable class with fields matching</td>
560</tr>
561<tr class="even">
562<td></td>
563<td><a href="`typing.Type`">Type</a>[<a href="`atdata._protocols.Packable`">Packable</a>]</td>
564<td>the schema definition. The class can be used with</td>
565</tr>
566<tr class="odd">
567<td></td>
568<td><a href="`typing.Type`">Type</a>[<a href="`atdata._protocols.Packable`">Packable</a>]</td>
569<td><code>Dataset[T]</code> to load and iterate over samples.</td>
570</tr>
571</tbody>
572</table>
573</section>
574<section id="raises" class="level4 doc-section doc-section-raises">
575<h4 class="doc-section doc-section-raises anchored" data-anchor-id="raises">Raises</h4>
576<table class="caption-top table">
577<thead>
578<tr class="header">
579<th>Name</th>
580<th>Type</th>
581<th>Description</th>
582</tr>
583</thead>
584<tbody>
585<tr class="odd">
586<td></td>
587<td><a href="`KeyError`">KeyError</a></td>
588<td>If schema not found.</td>
589</tr>
590<tr class="even">
591<td></td>
592<td><a href="`ValueError`">ValueError</a></td>
593<td>If schema cannot be decoded (unsupported field types).</td>
594</tr>
595</tbody>
596</table>
597</section>
598<section id="examples-1" class="level4 doc-section doc-section-examples">
599<h4 class="doc-section doc-section-examples anchored" data-anchor-id="examples-1">Examples</h4>
600<div class="sourceCode" id="cb4"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="op">>>></span> entry <span class="op">=</span> index.get_dataset(<span class="st">"my-dataset"</span>)</span>
601<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="op">>>></span> SampleType <span class="op">=</span> index.decode_schema(entry.schema_ref)</span>
602<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a><span class="op">>>></span> ds <span class="op">=</span> Dataset[SampleType](entry.data_urls[<span class="dv">0</span>])</span>
603<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a><span class="op">>>></span> <span class="cf">for</span> sample <span class="kw">in</span> ds.ordered():</span>
604<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a>... <span class="bu">print</span>(sample) <span class="co"># sample is instance of SampleType</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
605</section>
606</section>
607<section id="atdata.AbstractIndex.get_dataset" class="level3">
608<h3 class="anchored" data-anchor-id="atdata.AbstractIndex.get_dataset">get_dataset</h3>
609<div class="sourceCode" id="cb5"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>AbstractIndex.get_dataset(ref)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
610<p>Get a dataset entry by name or reference.</p>
611<section id="parameters-1" class="level4 doc-section doc-section-parameters">
612<h4 class="doc-section doc-section-parameters anchored" data-anchor-id="parameters-1">Parameters</h4>
613<table class="caption-top table">
614<thead>
615<tr class="header">
616<th>Name</th>
617<th>Type</th>
618<th>Description</th>
619<th>Default</th>
620</tr>
621</thead>
622<tbody>
623<tr class="odd">
624<td>ref</td>
625<td><a href="`str`">str</a></td>
626<td>Dataset name, path, or full reference string.</td>
627<td><em>required</em></td>
628</tr>
629</tbody>
630</table>
631</section>
632<section id="returns-1" class="level4 doc-section doc-section-returns">
633<h4 class="doc-section doc-section-returns anchored" data-anchor-id="returns-1">Returns</h4>
634<table class="caption-top table">
635<thead>
636<tr class="header">
637<th>Name</th>
638<th>Type</th>
639<th>Description</th>
640</tr>
641</thead>
642<tbody>
643<tr class="odd">
644<td></td>
645<td><a href="`atdata._protocols.IndexEntry`">IndexEntry</a></td>
646<td>IndexEntry for the dataset.</td>
647</tr>
648</tbody>
649</table>
650</section>
651<section id="raises-1" class="level4 doc-section doc-section-raises">
652<h4 class="doc-section doc-section-raises anchored" data-anchor-id="raises-1">Raises</h4>
653<table class="caption-top table">
654<thead>
655<tr class="header">
656<th>Name</th>
657<th>Type</th>
658<th>Description</th>
659</tr>
660</thead>
661<tbody>
662<tr class="odd">
663<td></td>
664<td><a href="`KeyError`">KeyError</a></td>
665<td>If dataset not found.</td>
666</tr>
667</tbody>
668</table>
669</section>
670</section>
671<section id="atdata.AbstractIndex.get_schema" class="level3">
672<h3 class="anchored" data-anchor-id="atdata.AbstractIndex.get_schema">get_schema</h3>
673<div class="sourceCode" id="cb6"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>AbstractIndex.get_schema(ref)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
674<p>Get a schema record by reference.</p>
675<section id="parameters-2" class="level4 doc-section doc-section-parameters">
676<h4 class="doc-section doc-section-parameters anchored" data-anchor-id="parameters-2">Parameters</h4>
677<table class="caption-top table">
678<thead>
679<tr class="header">
680<th>Name</th>
681<th>Type</th>
682<th>Description</th>
683<th>Default</th>
684</tr>
685</thead>
686<tbody>
687<tr class="odd">
688<td>ref</td>
689<td><a href="`str`">str</a></td>
690<td>Schema reference string (local:// or at://).</td>
691<td><em>required</em></td>
692</tr>
693</tbody>
694</table>
695</section>
696<section id="returns-2" class="level4 doc-section doc-section-returns">
697<h4 class="doc-section doc-section-returns anchored" data-anchor-id="returns-2">Returns</h4>
698<table class="caption-top table">
699<thead>
700<tr class="header">
701<th>Name</th>
702<th>Type</th>
703<th>Description</th>
704</tr>
705</thead>
706<tbody>
707<tr class="odd">
708<td></td>
709<td><a href="`dict`">dict</a></td>
710<td>Schema record as a dictionary with fields like ‘name’, ‘version’,</td>
711</tr>
712<tr class="even">
713<td></td>
714<td><a href="`dict`">dict</a></td>
715<td>‘fields’, etc.</td>
716</tr>
717</tbody>
718</table>
719</section>
720<section id="raises-2" class="level4 doc-section doc-section-raises">
721<h4 class="doc-section doc-section-raises anchored" data-anchor-id="raises-2">Raises</h4>
722<table class="caption-top table">
723<thead>
724<tr class="header">
725<th>Name</th>
726<th>Type</th>
727<th>Description</th>
728</tr>
729</thead>
730<tbody>
731<tr class="odd">
732<td></td>
733<td><a href="`KeyError`">KeyError</a></td>
734<td>If schema not found.</td>
735</tr>
736</tbody>
737</table>
738</section>
739</section>
740<section id="atdata.AbstractIndex.insert_dataset" class="level3">
741<h3 class="anchored" data-anchor-id="atdata.AbstractIndex.insert_dataset">insert_dataset</h3>
742<div class="sourceCode" id="cb7"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>AbstractIndex.insert_dataset(ds, <span class="op">*</span>, name, schema_ref<span class="op">=</span><span class="va">None</span>, <span class="op">**</span>kwargs)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
743<p>Insert a dataset into the index.</p>
744<p>The sample type is inferred from <code>ds.sample_type</code>. If schema_ref is not provided, the schema may be auto-published based on the sample type.</p>
745<section id="parameters-3" class="level4 doc-section doc-section-parameters">
746<h4 class="doc-section doc-section-parameters anchored" data-anchor-id="parameters-3">Parameters</h4>
747<table class="caption-top table">
748<thead>
749<tr class="header">
750<th>Name</th>
751<th>Type</th>
752<th>Description</th>
753<th>Default</th>
754</tr>
755</thead>
756<tbody>
757<tr class="odd">
758<td>ds</td>
759<td><a href="`atdata.dataset.Dataset`">Dataset</a></td>
760<td>The Dataset to register in the index (any sample type).</td>
761<td><em>required</em></td>
762</tr>
763<tr class="even">
764<td>name</td>
765<td><a href="`str`">str</a></td>
766<td>Human-readable name for the dataset.</td>
767<td><em>required</em></td>
768</tr>
769<tr class="odd">
770<td>schema_ref</td>
771<td><a href="`typing.Optional`">Optional</a>[<a href="`str`">str</a>]</td>
772<td>Optional explicit schema reference. If not provided, the schema may be auto-published or inferred from ds.sample_type.</td>
773<td><code>None</code></td>
774</tr>
775<tr class="even">
776<td>**kwargs</td>
777<td></td>
778<td>Additional backend-specific options.</td>
779<td><code>{}</code></td>
780</tr>
781</tbody>
782</table>
783</section>
784<section id="returns-3" class="level4 doc-section doc-section-returns">
785<h4 class="doc-section doc-section-returns anchored" data-anchor-id="returns-3">Returns</h4>
786<table class="caption-top table">
787<thead>
788<tr class="header">
789<th>Name</th>
790<th>Type</th>
791<th>Description</th>
792</tr>
793</thead>
794<tbody>
795<tr class="odd">
796<td></td>
797<td><a href="`atdata._protocols.IndexEntry`">IndexEntry</a></td>
798<td>IndexEntry for the inserted dataset.</td>
799</tr>
800</tbody>
801</table>
802</section>
803</section>
804<section id="atdata.AbstractIndex.list_datasets" class="level3">
805<h3 class="anchored" data-anchor-id="atdata.AbstractIndex.list_datasets">list_datasets</h3>
806<div class="sourceCode" id="cb8"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>AbstractIndex.list_datasets()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
807<p>Get all dataset entries as a materialized list.</p>
808<section id="returns-4" class="level4 doc-section doc-section-returns">
809<h4 class="doc-section doc-section-returns anchored" data-anchor-id="returns-4">Returns</h4>
810<table class="caption-top table">
811<thead>
812<tr class="header">
813<th>Name</th>
814<th>Type</th>
815<th>Description</th>
816</tr>
817</thead>
818<tbody>
819<tr class="odd">
820<td></td>
821<td><a href="`list`">list</a>[<a href="`atdata._protocols.IndexEntry`">IndexEntry</a>]</td>
822<td>List of IndexEntry for each dataset.</td>
823</tr>
824</tbody>
825</table>
826</section>
827</section>
828<section id="atdata.AbstractIndex.list_schemas" class="level3">
829<h3 class="anchored" data-anchor-id="atdata.AbstractIndex.list_schemas">list_schemas</h3>
830<div class="sourceCode" id="cb9"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>AbstractIndex.list_schemas()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
831<p>Get all schema records as a materialized list.</p>
832<section id="returns-5" class="level4 doc-section doc-section-returns">
833<h4 class="doc-section doc-section-returns anchored" data-anchor-id="returns-5">Returns</h4>
834<table class="caption-top table">
835<thead>
836<tr class="header">
837<th>Name</th>
838<th>Type</th>
839<th>Description</th>
840</tr>
841</thead>
842<tbody>
843<tr class="odd">
844<td></td>
845<td><a href="`list`">list</a>[<a href="`dict`">dict</a>]</td>
846<td>List of schema records as dictionaries.</td>
847</tr>
848</tbody>
849</table>
850</section>
851</section>
852<section id="atdata.AbstractIndex.publish_schema" class="level3">
853<h3 class="anchored" data-anchor-id="atdata.AbstractIndex.publish_schema">publish_schema</h3>
854<div class="sourceCode" id="cb10"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>AbstractIndex.publish_schema(sample_type, <span class="op">*</span>, version<span class="op">=</span><span class="st">'1.0.0'</span>, <span class="op">**</span>kwargs)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
855<p>Publish a schema for a sample type.</p>
856<p>The sample_type is accepted as <code>type</code> rather than <code>Type[Packable]</code> to support <code>@packable</code>-decorated classes, which satisfy the Packable protocol at runtime but cannot be statically verified by type checkers.</p>
857<section id="parameters-4" class="level4 doc-section doc-section-parameters">
858<h4 class="doc-section doc-section-parameters anchored" data-anchor-id="parameters-4">Parameters</h4>
859<table class="caption-top table">
860<thead>
861<tr class="header">
862<th>Name</th>
863<th>Type</th>
864<th>Description</th>
865<th>Default</th>
866</tr>
867</thead>
868<tbody>
869<tr class="odd">
870<td>sample_type</td>
871<td><a href="`type`">type</a></td>
872<td>A Packable type (PackableSample subclass or <span class="citation" data-cites="packable-decorated">@packable-decorated</span>). Validated at runtime via the <span class="citation" data-cites="runtime_checkable">@runtime_checkable</span> Packable protocol.</td>
873<td><em>required</em></td>
874</tr>
875<tr class="even">
876<td>version</td>
877<td><a href="`str`">str</a></td>
878<td>Semantic version string for the schema.</td>
879<td><code>'1.0.0'</code></td>
880</tr>
881<tr class="odd">
882<td>**kwargs</td>
883<td></td>
884<td>Additional backend-specific options.</td>
885<td><code>{}</code></td>
886</tr>
887</tbody>
888</table>
889</section>
890<section id="returns-6" class="level4 doc-section doc-section-returns">
891<h4 class="doc-section doc-section-returns anchored" data-anchor-id="returns-6">Returns</h4>
892<table class="caption-top table">
893<thead>
894<tr class="header">
895<th>Name</th>
896<th>Type</th>
897<th>Description</th>
898</tr>
899</thead>
900<tbody>
901<tr class="odd">
902<td></td>
903<td><a href="`str`">str</a></td>
904<td>Schema reference string:</td>
905</tr>
906<tr class="even">
907<td></td>
908<td><a href="`str`">str</a></td>
909<td>- Local: ‘local://schemas/{module.Class}<span class="citation" data-cites="version">@version</span>’</td>
910</tr>
911<tr class="odd">
912<td></td>
913<td><a href="`str`">str</a></td>
914<td>- Atmosphere: ‘at://did:plc:…/ac.foundation.dataset.sampleSchema/…’</td>
915</tr>
916</tbody>
917</table>
918
919
920</section>
921</section>
922</section>
923</section>
924
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1011 var filterRegex = new RegExp("https:\/\/github\.com\/your-org\/atdata");
1012 var isInternal = (href) => {
1013 return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
1014 }
1015 // Inspect non-navigation links and adorn them if external
1016 var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
1017 for (var i=0; i<links.length; i++) {
1018 const link = links[i];
1019 if (!isInternal(link.href)) {
1020 // undo the damage that might have been done by quarto-nav.js in the case of
1021 // links that we want to consider external
1022 if (link.dataset.originalHref !== undefined) {
1023 link.href = link.dataset.originalHref;
1024 }
1025 }
1026 }
1027 function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
1028 const config = {
1029 allowHTML: true,
1030 maxWidth: 500,
1031 delay: 100,
1032 arrow: false,
1033 appendTo: function(el) {
1034 return el.parentElement;
1035 },
1036 interactive: true,
1037 interactiveBorder: 10,
1038 theme: 'quarto',
1039 placement: 'bottom-start',
1040 };
1041 if (contentFn) {
1042 config.content = contentFn;
1043 }
1044 if (onTriggerFn) {
1045 config.onTrigger = onTriggerFn;
1046 }
1047 if (onUntriggerFn) {
1048 config.onUntrigger = onUntriggerFn;
1049 }
1050 window.tippy(el, config);
1051 }
1052 const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
1053 for (var i=0; i<noterefs.length; i++) {
1054 const ref = noterefs[i];
1055 tippyHover(ref, function() {
1056 // use id or data attribute instead here
1057 let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
1058 try { href = new URL(href).hash; } catch {}
1059 const id = href.replace(/^#\/?/, "");
1060 const note = window.document.getElementById(id);
1061 if (note) {
1062 return note.innerHTML;
1063 } else {
1064 return "";
1065 }
1066 });
1067 }
1068 const xrefs = window.document.querySelectorAll('a.quarto-xref');
1069 const processXRef = (id, note) => {
1070 // Strip column container classes
1071 const stripColumnClz = (el) => {
1072 el.classList.remove("page-full", "page-columns");
1073 if (el.children) {
1074 for (const child of el.children) {
1075 stripColumnClz(child);
1076 }
1077 }
1078 }
1079 stripColumnClz(note)
1080 if (id === null || id.startsWith('sec-')) {
1081 // Special case sections, only their first couple elements
1082 const container = document.createElement("div");
1083 if (note.children && note.children.length > 2) {
1084 container.appendChild(note.children[0].cloneNode(true));
1085 for (let i = 1; i < note.children.length; i++) {
1086 const child = note.children[i];
1087 if (child.tagName === "P" && child.innerText === "") {
1088 continue;
1089 } else {
1090 container.appendChild(child.cloneNode(true));
1091 break;
1092 }
1093 }
1094 if (window.Quarto?.typesetMath) {
1095 window.Quarto.typesetMath(container);
1096 }
1097 return container.innerHTML
1098 } else {
1099 if (window.Quarto?.typesetMath) {
1100 window.Quarto.typesetMath(note);
1101 }
1102 return note.innerHTML;
1103 }
1104 } else {
1105 // Remove any anchor links if they are present
1106 const anchorLink = note.querySelector('a.anchorjs-link');
1107 if (anchorLink) {
1108 anchorLink.remove();
1109 }
1110 if (window.Quarto?.typesetMath) {
1111 window.Quarto.typesetMath(note);
1112 }
1113 if (note.classList.contains("callout")) {
1114 return note.outerHTML;
1115 } else {
1116 return note.innerHTML;
1117 }
1118 }
1119 }
1120 for (var i=0; i<xrefs.length; i++) {
1121 const xref = xrefs[i];
1122 tippyHover(xref, undefined, function(instance) {
1123 instance.disable();
1124 let url = xref.getAttribute('href');
1125 let hash = undefined;
1126 if (url.startsWith('#')) {
1127 hash = url;
1128 } else {
1129 try { hash = new URL(url).hash; } catch {}
1130 }
1131 if (hash) {
1132 const id = hash.replace(/^#\/?/, "");
1133 const note = window.document.getElementById(id);
1134 if (note !== null) {
1135 try {
1136 const html = processXRef(id, note.cloneNode(true));
1137 instance.setContent(html);
1138 } finally {
1139 instance.enable();
1140 instance.show();
1141 }
1142 } else {
1143 // See if we can fetch this
1144 fetch(url.split('#')[0])
1145 .then(res => res.text())
1146 .then(html => {
1147 const parser = new DOMParser();
1148 const htmlDoc = parser.parseFromString(html, "text/html");
1149 const note = htmlDoc.getElementById(id);
1150 if (note !== null) {
1151 const html = processXRef(id, note);
1152 instance.setContent(html);
1153 }
1154 }).finally(() => {
1155 instance.enable();
1156 instance.show();
1157 });
1158 }
1159 } else {
1160 // See if we can fetch a full url (with no hash to target)
1161 // This is a special case and we should probably do some content thinning / targeting
1162 fetch(url)
1163 .then(res => res.text())
1164 .then(html => {
1165 const parser = new DOMParser();
1166 const htmlDoc = parser.parseFromString(html, "text/html");
1167 const note = htmlDoc.querySelector('main.content');
1168 if (note !== null) {
1169 // This should only happen for chapter cross references
1170 // (since there is no id in the URL)
1171 // remove the first header
1172 if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
1173 note.children[0].remove();
1174 }
1175 const html = processXRef(null, note);
1176 instance.setContent(html);
1177 }
1178 }).finally(() => {
1179 instance.enable();
1180 instance.show();
1181 });
1182 }
1183 }, function(instance) {
1184 });
1185 }
1186 let selectedAnnoteEl;
1187 const selectorForAnnotation = ( cell, annotation) => {
1188 let cellAttr = 'data-code-cell="' + cell + '"';
1189 let lineAttr = 'data-code-annotation="' + annotation + '"';
1190 const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
1191 return selector;
1192 }
1193 const selectCodeLines = (annoteEl) => {
1194 const doc = window.document;
1195 const targetCell = annoteEl.getAttribute("data-target-cell");
1196 const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
1197 const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
1198 const lines = annoteSpan.getAttribute("data-code-lines").split(",");
1199 const lineIds = lines.map((line) => {
1200 return targetCell + "-" + line;
1201 })
1202 let top = null;
1203 let height = null;
1204 let parent = null;
1205 if (lineIds.length > 0) {
1206 //compute the position of the single el (top and bottom and make a div)
1207 const el = window.document.getElementById(lineIds[0]);
1208 top = el.offsetTop;
1209 height = el.offsetHeight;
1210 parent = el.parentElement.parentElement;
1211 if (lineIds.length > 1) {
1212 const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
1213 const bottom = lastEl.offsetTop + lastEl.offsetHeight;
1214 height = bottom - top;
1215 }
1216 if (top !== null && height !== null && parent !== null) {
1217 // cook up a div (if necessary) and position it
1218 let div = window.document.getElementById("code-annotation-line-highlight");
1219 if (div === null) {
1220 div = window.document.createElement("div");
1221 div.setAttribute("id", "code-annotation-line-highlight");
1222 div.style.position = 'absolute';
1223 parent.appendChild(div);
1224 }
1225 div.style.top = top - 2 + "px";
1226 div.style.height = height + 4 + "px";
1227 div.style.left = 0;
1228 let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
1229 if (gutterDiv === null) {
1230 gutterDiv = window.document.createElement("div");
1231 gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
1232 gutterDiv.style.position = 'absolute';
1233 const codeCell = window.document.getElementById(targetCell);
1234 const gutter = codeCell.querySelector('.code-annotation-gutter');
1235 gutter.appendChild(gutterDiv);
1236 }
1237 gutterDiv.style.top = top - 2 + "px";
1238 gutterDiv.style.height = height + 4 + "px";
1239 }
1240 selectedAnnoteEl = annoteEl;
1241 }
1242 };
1243 const unselectCodeLines = () => {
1244 const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
1245 elementsIds.forEach((elId) => {
1246 const div = window.document.getElementById(elId);
1247 if (div) {
1248 div.remove();
1249 }
1250 });
1251 selectedAnnoteEl = undefined;
1252 };
1253 // Handle positioning of the toggle
1254 window.addEventListener(
1255 "resize",
1256 throttle(() => {
1257 elRect = undefined;
1258 if (selectedAnnoteEl) {
1259 selectCodeLines(selectedAnnoteEl);
1260 }
1261 }, 10)
1262 );
1263 function throttle(fn, ms) {
1264 let throttle = false;
1265 let timer;
1266 return (...args) => {
1267 if(!throttle) { // first call gets through
1268 fn.apply(this, args);
1269 throttle = true;
1270 } else { // all the others get throttled
1271 if(timer) clearTimeout(timer); // cancel #2
1272 timer = setTimeout(() => {
1273 fn.apply(this, args);
1274 timer = throttle = false;
1275 }, ms);
1276 }
1277 };
1278 }
1279 // Attach click handler to the DT
1280 const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
1281 for (const annoteDlNode of annoteDls) {
1282 annoteDlNode.addEventListener('click', (event) => {
1283 const clickedEl = event.target;
1284 if (clickedEl !== selectedAnnoteEl) {
1285 unselectCodeLines();
1286 const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
1287 if (activeEl) {
1288 activeEl.classList.remove('code-annotation-active');
1289 }
1290 selectCodeLines(clickedEl);
1291 clickedEl.classList.add('code-annotation-active');
1292 } else {
1293 // Unselect the line
1294 unselectCodeLines();
1295 clickedEl.classList.remove('code-annotation-active');
1296 }
1297 });
1298 }
1299 const findCites = (el) => {
1300 const parentEl = el.parentElement;
1301 if (parentEl) {
1302 const cites = parentEl.dataset.cites;
1303 if (cites) {
1304 return {
1305 el,
1306 cites: cites.split(' ')
1307 };
1308 } else {
1309 return findCites(el.parentElement)
1310 }
1311 } else {
1312 return undefined;
1313 }
1314 };
1315 var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
1316 for (var i=0; i<bibliorefs.length; i++) {
1317 const ref = bibliorefs[i];
1318 const citeInfo = findCites(ref);
1319 if (citeInfo) {
1320 tippyHover(citeInfo.el, function() {
1321 var popup = window.document.createElement('div');
1322 citeInfo.cites.forEach(function(cite) {
1323 var citeDiv = window.document.createElement('div');
1324 citeDiv.classList.add('hanging-indent');
1325 citeDiv.classList.add('csl-entry');
1326 var biblioDiv = window.document.getElementById('ref-' + cite);
1327 if (biblioDiv) {
1328 citeDiv.innerHTML = biblioDiv.innerHTML;
1329 }
1330 popup.appendChild(citeDiv);
1331 });
1332 return popup.innerHTML;
1333 });
1334 }
1335 }
1336 });
1337 </script>
1338</div> <!-- /content -->
1339<footer class="footer">
1340 <div class="nav-footer">
1341 <div class="nav-footer-left">
1342<p>Built with <a href="https://quarto.org/">Quarto</a></p>
1343</div>
1344 <div class="nav-footer-center">
1345
1346 <div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/your-org/atdata/edit/main/api/AbstractIndex.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/your-org/atdata/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
1347 <div class="nav-footer-right">
1348<p>MIT License</p>
1349</div>
1350 </div>
1351</footer>
1352
1353
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1355
1356</body></html>