A loose federation of distributed, typed datasets
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400 <h2 id="toc-title">On this page</h2>
401
402 <ul>
403 <li><a href="#atdata.Packable" id="toc-atdata.Packable" class="nav-link active" data-scroll-target="#atdata.Packable">Packable</a>
404 <ul class="collapse">
405 <li><a href="#examples" id="toc-examples" class="nav-link" data-scroll-target="#examples">Examples</a></li>
406 <li><a href="#attributes" id="toc-attributes" class="nav-link" data-scroll-target="#attributes">Attributes</a></li>
407 <li><a href="#methods" id="toc-methods" class="nav-link" data-scroll-target="#methods">Methods</a>
408 <ul class="collapse">
409 <li><a href="#atdata.Packable.from_bytes" id="toc-atdata.Packable.from_bytes" class="nav-link" data-scroll-target="#atdata.Packable.from_bytes">from_bytes</a></li>
410 <li><a href="#atdata.Packable.from_data" id="toc-atdata.Packable.from_data" class="nav-link" data-scroll-target="#atdata.Packable.from_data">from_data</a></li>
411 </ul></li>
412 </ul></li>
413 </ul>
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418
419
420
421
422
423<section id="atdata.Packable" class="level1">
424<h1>Packable</h1>
425<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>Packable()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
426<p>Structural protocol for packable sample types.</p>
427<p>This protocol allows classes decorated with <code>@packable</code> to be recognized as valid types for lens transformations and schema operations, even though the decorator doesn’t change the class’s nominal type at static analysis time.</p>
428<p>Both <code>PackableSample</code> subclasses and <code>@packable</code>-decorated classes satisfy this protocol structurally.</p>
429<p>The protocol captures the full interface needed for: - Lens type transformations (as_wds, from_data) - Schema publishing (class introspection via dataclass fields) - Serialization/deserialization (packed, from_bytes)</p>
430<section id="examples" class="level2 doc-section doc-section-examples">
431<h2 class="doc-section doc-section-examples anchored" data-anchor-id="examples">Examples</h2>
432<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="op">@</span>packable</span>
433<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>... <span class="kw">class</span> MySample:</span>
434<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>... name: <span class="bu">str</span></span>
435<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>... value: <span class="bu">int</span></span>
436<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>...</span>
437<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="op">>>></span> <span class="kw">def</span> process(sample_type: Type[Packable]) <span class="op">-></span> <span class="va">None</span>:</span>
438<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a>... <span class="co"># Type checker knows sample_type has from_bytes, packed, etc.</span></span>
439<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a>... instance <span class="op">=</span> sample_type.from_bytes(data)</span>
440<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a>... <span class="bu">print</span>(instance.packed)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
441</section>
442<section id="attributes" class="level2">
443<h2 class="anchored" data-anchor-id="attributes">Attributes</h2>
444<table class="caption-top table">
445<thead>
446<tr class="header">
447<th>Name</th>
448<th>Description</th>
449</tr>
450</thead>
451<tbody>
452<tr class="odd">
453<td><a href="#atdata.Packable.as_wds">as_wds</a></td>
454<td>WebDataset-compatible representation with <strong>key</strong> and msgpack.</td>
455</tr>
456<tr class="even">
457<td><a href="#atdata.Packable.packed">packed</a></td>
458<td>Pack this sample’s data into msgpack bytes.</td>
459</tr>
460</tbody>
461</table>
462</section>
463<section id="methods" class="level2">
464<h2 class="anchored" data-anchor-id="methods">Methods</h2>
465<table class="caption-top table">
466<thead>
467<tr class="header">
468<th>Name</th>
469<th>Description</th>
470</tr>
471</thead>
472<tbody>
473<tr class="odd">
474<td><a href="#atdata.Packable.from_bytes">from_bytes</a></td>
475<td>Create instance from raw msgpack bytes.</td>
476</tr>
477<tr class="even">
478<td><a href="#atdata.Packable.from_data">from_data</a></td>
479<td>Create instance from unpacked msgpack data dictionary.</td>
480</tr>
481</tbody>
482</table>
483<section id="atdata.Packable.from_bytes" class="level3">
484<h3 class="anchored" data-anchor-id="atdata.Packable.from_bytes">from_bytes</h3>
485<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>Packable.from_bytes(bs)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
486<p>Create instance from raw msgpack bytes.</p>
487</section>
488<section id="atdata.Packable.from_data" class="level3">
489<h3 class="anchored" data-anchor-id="atdata.Packable.from_data">from_data</h3>
490<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>Packable.from_data(data)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
491<p>Create instance from unpacked msgpack data dictionary.</p>
492
493
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500 window.document.addEventListener("DOMContentLoaded", function (event) {
501 // Ensure there is a toggle, if there isn't float one in the top right
502 if (window.document.querySelector('.quarto-color-scheme-toggle') === null) {
503 const a = window.document.createElement('a');
504 a.classList.add('top-right');
505 a.classList.add('quarto-color-scheme-toggle');
506 a.href = "";
507 a.onclick = function() { try { window.quartoToggleColorScheme(); } catch {} return false; };
508 const i = window.document.createElement("i");
509 i.classList.add('bi');
510 a.appendChild(i);
511 window.document.body.appendChild(a);
512 }
513 setColorSchemeToggle(hasAlternateSentinel())
514 const icon = "";
515 const anchorJS = new window.AnchorJS();
516 anchorJS.options = {
517 placement: 'right',
518 icon: icon
519 };
520 anchorJS.add('.anchored');
521 const isCodeAnnotation = (el) => {
522 for (const clz of el.classList) {
523 if (clz.startsWith('code-annotation-')) {
524 return true;
525 }
526 }
527 return false;
528 }
529 const onCopySuccess = function(e) {
530 // button target
531 const button = e.trigger;
532 // don't keep focus
533 button.blur();
534 // flash "checked"
535 button.classList.add('code-copy-button-checked');
536 var currentTitle = button.getAttribute("title");
537 button.setAttribute("title", "Copied!");
538 let tooltip;
539 if (window.bootstrap) {
540 button.setAttribute("data-bs-toggle", "tooltip");
541 button.setAttribute("data-bs-placement", "left");
542 button.setAttribute("data-bs-title", "Copied!");
543 tooltip = new bootstrap.Tooltip(button,
544 { trigger: "manual",
545 customClass: "code-copy-button-tooltip",
546 offset: [0, -8]});
547 tooltip.show();
548 }
549 setTimeout(function() {
550 if (tooltip) {
551 tooltip.hide();
552 button.removeAttribute("data-bs-title");
553 button.removeAttribute("data-bs-toggle");
554 button.removeAttribute("data-bs-placement");
555 }
556 button.setAttribute("title", currentTitle);
557 button.classList.remove('code-copy-button-checked');
558 }, 1000);
559 // clear code selection
560 e.clearSelection();
561 }
562 const getTextToCopy = function(trigger) {
563 const codeEl = trigger.previousElementSibling.cloneNode(true);
564 for (const childEl of codeEl.children) {
565 if (isCodeAnnotation(childEl)) {
566 childEl.remove();
567 }
568 }
569 return codeEl.innerText;
570 }
571 const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
572 text: getTextToCopy
573 });
574 clipboard.on('success', onCopySuccess);
575 if (window.document.getElementById('quarto-embedded-source-code-modal')) {
576 const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
577 text: getTextToCopy,
578 container: window.document.getElementById('quarto-embedded-source-code-modal')
579 });
580 clipboardModal.on('success', onCopySuccess);
581 }
582 var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
583 var mailtoRegex = new RegExp(/^mailto:/);
584 var filterRegex = new RegExp("https:\/\/github\.com\/your-org\/atdata");
585 var isInternal = (href) => {
586 return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
587 }
588 // Inspect non-navigation links and adorn them if external
589 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)');
590 for (var i=0; i<links.length; i++) {
591 const link = links[i];
592 if (!isInternal(link.href)) {
593 // undo the damage that might have been done by quarto-nav.js in the case of
594 // links that we want to consider external
595 if (link.dataset.originalHref !== undefined) {
596 link.href = link.dataset.originalHref;
597 }
598 }
599 }
600 function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
601 const config = {
602 allowHTML: true,
603 maxWidth: 500,
604 delay: 100,
605 arrow: false,
606 appendTo: function(el) {
607 return el.parentElement;
608 },
609 interactive: true,
610 interactiveBorder: 10,
611 theme: 'quarto',
612 placement: 'bottom-start',
613 };
614 if (contentFn) {
615 config.content = contentFn;
616 }
617 if (onTriggerFn) {
618 config.onTrigger = onTriggerFn;
619 }
620 if (onUntriggerFn) {
621 config.onUntrigger = onUntriggerFn;
622 }
623 window.tippy(el, config);
624 }
625 const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
626 for (var i=0; i<noterefs.length; i++) {
627 const ref = noterefs[i];
628 tippyHover(ref, function() {
629 // use id or data attribute instead here
630 let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
631 try { href = new URL(href).hash; } catch {}
632 const id = href.replace(/^#\/?/, "");
633 const note = window.document.getElementById(id);
634 if (note) {
635 return note.innerHTML;
636 } else {
637 return "";
638 }
639 });
640 }
641 const xrefs = window.document.querySelectorAll('a.quarto-xref');
642 const processXRef = (id, note) => {
643 // Strip column container classes
644 const stripColumnClz = (el) => {
645 el.classList.remove("page-full", "page-columns");
646 if (el.children) {
647 for (const child of el.children) {
648 stripColumnClz(child);
649 }
650 }
651 }
652 stripColumnClz(note)
653 if (id === null || id.startsWith('sec-')) {
654 // Special case sections, only their first couple elements
655 const container = document.createElement("div");
656 if (note.children && note.children.length > 2) {
657 container.appendChild(note.children[0].cloneNode(true));
658 for (let i = 1; i < note.children.length; i++) {
659 const child = note.children[i];
660 if (child.tagName === "P" && child.innerText === "") {
661 continue;
662 } else {
663 container.appendChild(child.cloneNode(true));
664 break;
665 }
666 }
667 if (window.Quarto?.typesetMath) {
668 window.Quarto.typesetMath(container);
669 }
670 return container.innerHTML
671 } else {
672 if (window.Quarto?.typesetMath) {
673 window.Quarto.typesetMath(note);
674 }
675 return note.innerHTML;
676 }
677 } else {
678 // Remove any anchor links if they are present
679 const anchorLink = note.querySelector('a.anchorjs-link');
680 if (anchorLink) {
681 anchorLink.remove();
682 }
683 if (window.Quarto?.typesetMath) {
684 window.Quarto.typesetMath(note);
685 }
686 if (note.classList.contains("callout")) {
687 return note.outerHTML;
688 } else {
689 return note.innerHTML;
690 }
691 }
692 }
693 for (var i=0; i<xrefs.length; i++) {
694 const xref = xrefs[i];
695 tippyHover(xref, undefined, function(instance) {
696 instance.disable();
697 let url = xref.getAttribute('href');
698 let hash = undefined;
699 if (url.startsWith('#')) {
700 hash = url;
701 } else {
702 try { hash = new URL(url).hash; } catch {}
703 }
704 if (hash) {
705 const id = hash.replace(/^#\/?/, "");
706 const note = window.document.getElementById(id);
707 if (note !== null) {
708 try {
709 const html = processXRef(id, note.cloneNode(true));
710 instance.setContent(html);
711 } finally {
712 instance.enable();
713 instance.show();
714 }
715 } else {
716 // See if we can fetch this
717 fetch(url.split('#')[0])
718 .then(res => res.text())
719 .then(html => {
720 const parser = new DOMParser();
721 const htmlDoc = parser.parseFromString(html, "text/html");
722 const note = htmlDoc.getElementById(id);
723 if (note !== null) {
724 const html = processXRef(id, note);
725 instance.setContent(html);
726 }
727 }).finally(() => {
728 instance.enable();
729 instance.show();
730 });
731 }
732 } else {
733 // See if we can fetch a full url (with no hash to target)
734 // This is a special case and we should probably do some content thinning / targeting
735 fetch(url)
736 .then(res => res.text())
737 .then(html => {
738 const parser = new DOMParser();
739 const htmlDoc = parser.parseFromString(html, "text/html");
740 const note = htmlDoc.querySelector('main.content');
741 if (note !== null) {
742 // This should only happen for chapter cross references
743 // (since there is no id in the URL)
744 // remove the first header
745 if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
746 note.children[0].remove();
747 }
748 const html = processXRef(null, note);
749 instance.setContent(html);
750 }
751 }).finally(() => {
752 instance.enable();
753 instance.show();
754 });
755 }
756 }, function(instance) {
757 });
758 }
759 let selectedAnnoteEl;
760 const selectorForAnnotation = ( cell, annotation) => {
761 let cellAttr = 'data-code-cell="' + cell + '"';
762 let lineAttr = 'data-code-annotation="' + annotation + '"';
763 const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
764 return selector;
765 }
766 const selectCodeLines = (annoteEl) => {
767 const doc = window.document;
768 const targetCell = annoteEl.getAttribute("data-target-cell");
769 const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
770 const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
771 const lines = annoteSpan.getAttribute("data-code-lines").split(",");
772 const lineIds = lines.map((line) => {
773 return targetCell + "-" + line;
774 })
775 let top = null;
776 let height = null;
777 let parent = null;
778 if (lineIds.length > 0) {
779 //compute the position of the single el (top and bottom and make a div)
780 const el = window.document.getElementById(lineIds[0]);
781 top = el.offsetTop;
782 height = el.offsetHeight;
783 parent = el.parentElement.parentElement;
784 if (lineIds.length > 1) {
785 const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
786 const bottom = lastEl.offsetTop + lastEl.offsetHeight;
787 height = bottom - top;
788 }
789 if (top !== null && height !== null && parent !== null) {
790 // cook up a div (if necessary) and position it
791 let div = window.document.getElementById("code-annotation-line-highlight");
792 if (div === null) {
793 div = window.document.createElement("div");
794 div.setAttribute("id", "code-annotation-line-highlight");
795 div.style.position = 'absolute';
796 parent.appendChild(div);
797 }
798 div.style.top = top - 2 + "px";
799 div.style.height = height + 4 + "px";
800 div.style.left = 0;
801 let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
802 if (gutterDiv === null) {
803 gutterDiv = window.document.createElement("div");
804 gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
805 gutterDiv.style.position = 'absolute';
806 const codeCell = window.document.getElementById(targetCell);
807 const gutter = codeCell.querySelector('.code-annotation-gutter');
808 gutter.appendChild(gutterDiv);
809 }
810 gutterDiv.style.top = top - 2 + "px";
811 gutterDiv.style.height = height + 4 + "px";
812 }
813 selectedAnnoteEl = annoteEl;
814 }
815 };
816 const unselectCodeLines = () => {
817 const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
818 elementsIds.forEach((elId) => {
819 const div = window.document.getElementById(elId);
820 if (div) {
821 div.remove();
822 }
823 });
824 selectedAnnoteEl = undefined;
825 };
826 // Handle positioning of the toggle
827 window.addEventListener(
828 "resize",
829 throttle(() => {
830 elRect = undefined;
831 if (selectedAnnoteEl) {
832 selectCodeLines(selectedAnnoteEl);
833 }
834 }, 10)
835 );
836 function throttle(fn, ms) {
837 let throttle = false;
838 let timer;
839 return (...args) => {
840 if(!throttle) { // first call gets through
841 fn.apply(this, args);
842 throttle = true;
843 } else { // all the others get throttled
844 if(timer) clearTimeout(timer); // cancel #2
845 timer = setTimeout(() => {
846 fn.apply(this, args);
847 timer = throttle = false;
848 }, ms);
849 }
850 };
851 }
852 // Attach click handler to the DT
853 const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
854 for (const annoteDlNode of annoteDls) {
855 annoteDlNode.addEventListener('click', (event) => {
856 const clickedEl = event.target;
857 if (clickedEl !== selectedAnnoteEl) {
858 unselectCodeLines();
859 const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
860 if (activeEl) {
861 activeEl.classList.remove('code-annotation-active');
862 }
863 selectCodeLines(clickedEl);
864 clickedEl.classList.add('code-annotation-active');
865 } else {
866 // Unselect the line
867 unselectCodeLines();
868 clickedEl.classList.remove('code-annotation-active');
869 }
870 });
871 }
872 const findCites = (el) => {
873 const parentEl = el.parentElement;
874 if (parentEl) {
875 const cites = parentEl.dataset.cites;
876 if (cites) {
877 return {
878 el,
879 cites: cites.split(' ')
880 };
881 } else {
882 return findCites(el.parentElement)
883 }
884 } else {
885 return undefined;
886 }
887 };
888 var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
889 for (var i=0; i<bibliorefs.length; i++) {
890 const ref = bibliorefs[i];
891 const citeInfo = findCites(ref);
892 if (citeInfo) {
893 tippyHover(citeInfo.el, function() {
894 var popup = window.document.createElement('div');
895 citeInfo.cites.forEach(function(cite) {
896 var citeDiv = window.document.createElement('div');
897 citeDiv.classList.add('hanging-indent');
898 citeDiv.classList.add('csl-entry');
899 var biblioDiv = window.document.getElementById('ref-' + cite);
900 if (biblioDiv) {
901 citeDiv.innerHTML = biblioDiv.innerHTML;
902 }
903 popup.appendChild(citeDiv);
904 });
905 return popup.innerHTML;
906 });
907 }
908 }
909 });
910 </script>
911</div> <!-- /content -->
912<footer class="footer">
913 <div class="nav-footer">
914 <div class="nav-footer-left">
915<p>Built with <a href="https://quarto.org/">Quarto</a></p>
916</div>
917 <div class="nav-footer-center">
918
919 <div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/your-org/atdata/edit/main/api/Packable-protocol.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>
920 <div class="nav-footer-right">
921<p>MIT License</p>
922</div>
923 </div>
924</footer>
925
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