Skip to content
TDA Bioinformatics Foundry
Packages Environments Molds Papers Tags
Glossary Design

Shared substrate · local expression

The surfaces this Foundry is made from.

The shared cases come from @galaxy-foundry/site-kit; this page supplies no alternate palette. Every header, note frame, reference card, and licence surface below is therefore wearing the same warm editorial system as the rest of the TDA Foundry.

Beside them are the pieces that belong here alone: filtration, persistence-barcode punctuation, point-cloud fingerprints, graph-like breadcrumbs, and this corpus's own reference kinds.

Shared 8

Component groups supplied and maintained by site-kit.

Instance 5

Groups derived from TDA vocabulary and local visual components.

site-kit ContentNote 2 cases · inline site-kit TagChips 2 cases · inline site-kit ReferenceContract 8 cases · inline site-kit LicenseBadge 6 cases · inline site-kit LicenseFileBody 4 cases · inline site-kit SiteHeader 6 cases · isolated site-kit SiteFooter 2 cases · inline site-kit SiteShell 2 cases · document tda ReferenceContract 1 case · inline tda FiltrationHero 1 case · isolated tda PersistenceDivider 1 case · inline tda PointCloudFingerprint 1 case · inline tda TopologyBreadcrumb 1 case · inline
Shared component

ContentNote

The invariant page frame around an instance-specific typed note.

Shared case

Body owns its heading

Most corpus notes already begin with H1; the frame supplies navigation, summary, tags, and the article boundary without duplicating it.

content-note/body-heading
← Packages
method/persistent-laplacian

A package profile whose Markdown body owns its title.

A short note body makes the frame visible without inventing a second content model for the gallery.

Shared case

Frame owns its heading

A design record whose body starts directly in prose asks the shared frame to render its title and summary.

content-note/frame-heading

Content-reader architecture

Why content mechanics are shared and the content model is local.

A short note body makes the frame visible without inventing a second content model for the gallery.

Shared component

TagChips

Controlled vocabulary shown as links only when an instance has a browse route.

Shared case

Browsable tags

An established content site links each chip through the one route prefix the instance supplies.

tag-chips/linked
method/persistent-laplacian
Shared case

Tags before browse exists

A partial content site shows controlled metadata without claiming a destination it has not built.

tag-chips/unlinked
method/persistent-laplacian
Shared component

ReferenceContract

A note's typed reference manifest, rendered against the contract it was authored under.

Shared case

A single reference

The baseline: a kind with a destination, four inherited chips, no authored prose.

reference-contract/one-reference
contract

Reference Loading

Typed references describe what casting consumes, and when the generated skill should load each artifact.

Mold Trimming reads

The authored note a skill is cast from.

RuntimeUpfrontVerbatimCast Validated
Shared case

With authored detail

Purpose, trigger and verification are the author's prose, not vocabulary. They open the detail list under the chips.

reference-contract/authored-detail
contract

Reference Loading

Typed references describe what casting consumes, and when the generated skill should load each artifact.

Mold Trimming reads

The authored note a skill is cast from.

BothOn DemandSidecarCorpus Observed
Purpose
Supplies the parameter table the generated skill fills in.
Trigger
The user asks to trim reads.
Shared case

A kind with nowhere to go

The kind pill is a link only when its term carries an href. Without one it is a span — because an anchor with no href is not focusable, not clickable, and announced as plain text, while wearing the same pill styling as the real links beside it.

reference-contract/kind-without-destination
contract

Reference Loading

Typed references describe what casting consumes, and when the generated skill should load each artifact.

Research Trimming reads

Background synthesis an instance holds but does not publish.

Cast TimeUpfrontVerbatimCorpus Observed
Shared case

Provisional evidence

The chip is coloured by the standing its term DECLARES, not by a list of term names in a selector. `hypothesis` also requires a verification, and the detail row wears the same standing's colour.

reference-contract/provisional-evidence
contract

Reference Loading

Typed references describe what casting consumes, and when the generated skill should load each artifact.

Mold Trimming reads

The authored note a skill is cast from.

RuntimeUpfrontVerbatimHypothesis
Verify
Cast the skill and check the parameter table survives the round trip.
Shared case

A ref that resolves to nothing

A resolver returning a target with no href means the note is named and not there. It renders as marked text rather than as a link to nowhere.

reference-contract/dangling-ref
contract

Reference Loading

Typed references describe what casting consumes, and when the generated skill should load each artifact.

Mold a-note-that-moved

The authored note a skill is cast from.

RuntimeUpfrontVerbatimCorpus Observed
Shared case

A term outside the vocabulary

Should never reach a page — the schema refuses it at build. If one does, it renders as itself with the reason attached, rather than throwing on a reader or rendering as a blank chip that looks like a term with a short label.

reference-contract/unregistered-term
contract

Reference Loading

Typed references describe what casting consumes, and when the generated skill should load each artifact.

Mold Trimming reads

The authored note a skill is cast from.

RuntimeUpfrontVerbatimvibes
Shared case

Several references

The grid is auto-fit at a 17rem minimum, so how many columns appear is decided by the width the gallery gives it and not by the count. Narrow the window here.

reference-contract/several-references
contract

Reference Loading

Typed references describe what casting consumes, and when the generated skill should load each artifact.

Mold Trimming reads

The authored note a skill is cast from.

RuntimeUpfrontVerbatimCast Validated
Research a-note-that-moved

Background synthesis an instance holds but does not publish.

Cast TimeUpfrontSidecarCorpus Observed
Mold Trimming reads

The authored note a skill is cast from.

BothOn DemandVerbatimHypothesis
Trigger
A workflow declares a trimming step.
Verify
Confirm the step appears in a cast run.
Research Trimming reads

Background synthesis an instance holds but does not publish.

RuntimeUpfrontSidecarCast Validated
Shared case

No references

The component renders NOTHING — not an empty card, not a heading with an empty grid. A note with no typed references gets no section, so this specimen is deliberately blank and the gallery should say so rather than look broken.

reference-contract/no-references
Shared component

LicenseBadge

What a licence permits, as chips, from the id a note declares.

Shared case

Redistributable

The baseline. `MIT` is also 1 of the 23 rows whose name equals its id, which is why rendering the id instead of the name looked right for sixteen notes.

license-badge/verbatim-ok
MIT verbatim OK
Shared case

Redistributable, and copyleft

The third chip appears only when the row calls for it. Copyleft is a property of the licence and not of the policy — a reader has to be able to see both at once.

license-badge/copyleft
GPL 3.0 verbatim OK copyleft
Shared case

Not redistributable

The chip that has to be distinguishable from `verbatim OK` at a glance, because it means the opposite thing. Its colour is a token: as a raw hex in two repositories nothing could change it and nothing could break it either.

license-badge/own-words-only
CC BY-NC 4.0 own-words only
Shared case

A LicenseRef, not an SPDX id

Why the badge renders `name` rather than the id: `LicenseRef-arXiv-nonexclusive-distrib-1.0` is a pill that teaches a reader nothing. The id stays reachable as the chip's title.

license-badge/custom-ref
arXiv non-exclusive distribution 1.0 own-words only
Shared case

A LicenseRef nobody has curated

The same deny-by-default policy as the specimen below, and deliberately not the same name. This licence IS resolved — an author identified it and used the escape hatch — so labelling it `unresolved / missing` reports a real licence as an absent one, and reproaches the note that did the right thing. Its terms are still unknown, which is why the policy chip does not soften.

license-badge/uncurated-ref
yale-non-commercial own-words only
Shared case

An id the table does not have

Deny-by-default, rendered. An unknown id resolves to the default row — own-words-only, flagged a defect — rather than to a gap, because a conservative chip beats a blank where a licence should be.

license-badge/unresolved
unresolved / missing own-words only
Shared component

LicenseFileBody

What one vendored licence copy governs, who redistributes under it, and its text.

Shared case

One copy, one licence

The baseline, and the URLs in the text are the case worth looking at: a licence is the one document a reader most plausibly wants to leave, and the canonical terms are what they are leaving for.

license-file-body/one-license

CC-BY-4.0 verbatim OK

attribution (title/author/source/license/changes)

Redistributed by (2)

  • trimming-reads CC-BY-4.0
  • aligning-reads CC-BY-4.0

License text

Permission is granted to redistribute this text verbatim.
The canonical terms are at https://creativecommons.org/licenses/by/4.0/ and
questions go to https://example.org/contact — this copy is a courtesy.
Shared case

One copy, several licences

A copy is keyed by SOURCE, so what it governs has more than one answer: the users' own ids, deduped and resolved. Both instances derived this the same way, which is why the derivation ships rather than the list.

license-file-body/several-licenses

Apache-2.0 verbatim OK

attribution + notice + preserve NOTICE

MIT verbatim OK

attribution + license notice

Redistributed by (3)

  • a-note MIT
  • another-note Apache-2.0
  • a-third-note MIT

License text

Permission is granted to redistribute this text verbatim.
The canonical terms are at https://creativecommons.org/licenses/by/4.0/ and
questions go to https://example.org/contact — this copy is a courtesy.
Shared case

Users that declare no id

The policy section disappears entirely rather than rendering empty. Nothing was resolved because nothing was declared, and a row of chips derived from no ids would be an answer the notes never gave.

license-file-body/no-declared-license

Redistributed by (1)

  • a-note-with-no-license

License text

Permission is granted to redistribute this text verbatim.
The canonical terms are at https://creativecommons.org/licenses/by/4.0/ and
questions go to https://example.org/contact — this copy is a courtesy.
Shared case

Text with nothing to leave for

The other half of the URL cut. Everything outside a match is emitted verbatim, whitespace included — reflowing a redistributed licence is exactly what the obligation forbids.

license-file-body/no-links-in-the-text

LicenseRef-all-rights-reserved own-words only

citation only

Redistributed by (1)

  • a-manuscript LicenseRef-all-rights-reserved

License text

All rights reserved.

    Reproduced here by permission.
Shared component

SiteFooter

The closing bar: the copyright mark, the repository, and whatever else an instance links.

Shared case

Repository only

The repository is the one link the footer always has, so an empty `footerLinks` is a complete footer rather than a missing one.

site-footer/repository-only
© Galaxy Workflow Foundry
GitHub
Shared case

With instance links

Footer links render before GitHub, in the order the identity lists them.

site-footer/with-links
© Galaxy Workflow Foundry
AboutLicenses GitHub
TDA component

ReferenceContract

Every reference kind this Foundry declares, derived from its contract so a new kind cannot arrive unseen.

TDA case

Environment

A runnable biopixi fixture and its declared bundled companions.

tda-reference-kinds/environment
contract

Reference Loading

Typed references describe what casting consumes, and when the generated skill should load each artifact.

Environment [[gallery-environment]]

A runnable biopixi fixture and its declared bundled companions.

RuntimeUpfrontVerbatimCorpus Observed
TDA component

PersistenceDivider

A deterministic barcode used as punctuation between conceptual sections.

TDA case

Persistent section break

One interval receives the persistent accent, turning a divider into domain-specific hierarchy without adding prose.

tda-persistence-divider/section-punctuation
TDA component

PointCloudFingerprint

Seeded geometric marginalia that gives each surface a stable visual fingerprint.

TDA case

Seeded point cloud

The same semantic seed always yields the same points, neighborhood edges, and highlighted loop.

tda-point-cloud-fingerprint/stable-fingerprint
TDA component

TopologyBreadcrumb

Back navigation drawn as connected nodes, paired with a deterministic point-cloud signature.

TDA case

Connected reading path

The ordinary collection-to-note relationship is expressed as a tiny graph without weakening breadcrumb semantics.

tda-topology-breadcrumb/method-detail
  1. Methods
  2. Persistent homology
Shared component

SiteHeader

The dark bar: wordmark, derived navigation, search box, theme toggle. Its isolated surface receives a real route rather than a second copy on this document.

Shared case

Everything fits

No "More" button, and the overflow script is not shipped at all — an instance whose destinations all fit is the intended state, not a stub.

site-header/everything-fits
Open site-header/everything-fits full width
Shared case

More than fits

One list and a cut point, not two lists: which destinations exist and which of them fit are different questions, and only the second is about the header's width.

site-header/overflows
Open site-header/overflows full width
Shared case

Reading a section that overflowed

The "More" button itself lights up when the reader is inside a destination it holds — otherwise the section they are in has no marker anywhere on the bar.

site-header/active-under-more
Open site-header/active-under-more full width
Shared case

Reading beneath a destination

A destination is active on its own page and on everything beneath it, so a note page keeps its section marked.

site-header/active-below-a-section
Open site-header/active-below-a-section full width
Shared case

A path that merely starts the same

Compared on whole path segments: on `/tags/`, a `/tag/` destination stays dark. String-prefix matching lights up both, and the bug is invisible until an instance happens to own both routes.

site-header/sibling-prefix
Open site-header/sibling-prefix full width
Shared case

A long wordmark

Why `navVisible` is not a number to copy from a sibling instance: the same count that fits beside "Foundry" wraps beside a longer name. Measure it against a built page.

site-header/long-wordmark
Open site-header/long-wordmark full width
Shared component

SiteShell

The whole document: head, header, the reading column, footer. Its document surface receives a real route rather than a second copy on this document.

Shared case

A page in the index

The default, and defaulted TRUE on purpose: `<main>` carries the Pagefind attribute. Marking one page is what removes every unmarked page from the index, so a route one forgotten prop away from unfindable is the failure this default exists to refuse.

site-shell/searchable
Open site-shell/searchable full width
Shared case

A page kept out of the index

Opting out is per page and is the only thing that makes an absence a decision. A gallery route is itself a fair candidate — its text is component names and prop values, which nobody is searching the corpus for.

site-shell/unsearchable
Open site-shell/unsearchable full width
TDA component

FiltrationHero

The interactive frontispiece: a point cloud becomes a complex and leaves one persistent loop. Its isolated surface receives a real route rather than a second copy on this document.

TDA case

Structure across scale

The range control makes filtration tangible while the copy connects multiscale structure to the Foundry workflow.

tda-filtration-hero/stable-loop
Open tda-filtration-hero/stable-loop full width
© Topological Data Analysis Bioinformatics Foundry
GitHub