Move OneTaxonomy to the @extantape scope and ExtantApe repo

.github/workflows/ci.yml

@@ -30,7 +30,7 @@ jobs:
       # Builds the example Payload site, starts it with a throwaway in-memory database on the runner, and checks it
       # over HTTP with sign-in cookies. About a minute.
       - name: Example site smoke test
-        run: pnpm --filter @captiveorigins/onetaxonomy-payload-example smoke
+        run: pnpm --filter @extantape/onetaxonomy-payload-example smoke
       # The OneOrigin brand copy (brand/oneorigin/) must match brand/oneorigin.lock, and the CSS built from it must be current.
       # The source is OnePhylogeny's docs/oneorigin/; the check warns, without failing, when it has moved ahead of the copy.
       - name: OneOrigin brand check

.github/workflows/release.yml

@@ -1,5 +1,5 @@
 # Release: pushing a version tag (vX.Y.Z) builds, tests and *stages* every OneTaxonomy package on npm.
-# Nothing goes public until the maintainer npm account approves each with 2FA
+# Nothing goes public until the mdgilardi npm account, which owns the @extantape scope, approves each with 2FA
 # (npmjs.com → your avatar → Staged Packages → Approve, or `npm stage approve <id>`).
 # No token is stored: npm trusted publishing (OIDC) lets only this workflow stage.
 name: Release
@@ -27,14 +27,14 @@ jobs:
           GH_TOKEN: ${{ github.token }}
         run: |
           test "$(gh api repos/${{ github.repository }} -q .description)" = "$(node -p "require('./package.json').description")" \
-            || { echo "::error::GitHub's description differs from package.json: sync it (npm run packages:sync in captive-origins) and re-tag."; exit 1; }
+            || { echo "::error::GitHub's description differs from package.json: copy the description to GitHub and re-tag."; exit 1; }
       - name: Tag matches every package
         run: for p in packages/*/; do test "${GITHUB_REF_NAME#v}" = "$(node -p "require('./${p}package.json').version")"; done
       - run: pnpm build && pnpm typecheck && pnpm test
       - name: Stage on npm
         run: |
           VERSION=$(node -p "require('./packages/core/package.json').version")
-          # payload (@captiveorigins/payload-plugin-onetaxonomy) isn't staged: its first npm version is published by hand
+          # payload (@extantape/payload-plugin-onetaxonomy) isn't staged: its first npm version is published by hand
           # by the owner, and trusted publishing is set up after that. Add it here then.
           for p in $(ls packages | grep -v -x payload); do
             NAME=$(node -p "require('./packages/$p/package.json').name")

README.md

@@ -2,9 +2,9 @@
 
 A source-available framework for importing, curating, browsing and publishing **scientifically faithful** taxonomic classifications and phylogenetic trees: for developers, and for teachers, museums, researchers and animal keepers who don't write code.
 
-Part of the [OneOrigin suite](https://github.com/CaptiveOrigins/onephylogeny/blob/main/docs/oneorigin/README.md): independent tools, with no subscriptions, that work alone or together.
+Part of the [OneOrigin suite](https://github.com/ExtantApe/OnePhylogeny/blob/main/docs/oneorigin/README.md): independent tools, with no subscriptions, that work alone or together.
 
-> **Status: early (Phase 1, milestone 4 of 8).** The pure TypeScript core, the importers (Newick, NEXUS, phyloXML, CSV/TSV checklists, Darwin Core Archives, OneTaxonomy JSON) and curated selective imports with coverage reports, views with undo/redo, layouts and the React explorer work and are tested (see `apps/playground`). A first Mac app (`apps/studio`) opens these files and saves views. Profiles and the Studio's project files are planned, and the Payload plugin has its first four parts (snapshots, views, import jobs, proposals and a small read API, tested on an in-memory database) and a small example site (`apps/payload-example`); see [the phase plan](docs/architecture/phase-plan.md). The five `@captiveorigins/onetaxonomy-*` packages are on npm as alpha versions; the Payload plugin isn't yet.
+> **Status: early (Phase 1, milestone 4 of 8).** The pure TypeScript core, the importers (Newick, NEXUS, phyloXML, CSV/TSV checklists, Darwin Core Archives, OneTaxonomy JSON) and curated selective imports with coverage reports, views with undo/redo, layouts and the React explorer work and are tested (see `apps/playground`). A first Mac app (`apps/studio`) opens these files and saves views. Profiles and the Studio's project files are planned, and the Payload plugin has its first four parts (snapshots, views, import jobs, proposals and a small read API, tested on an in-memory database) and a small example site (`apps/payload-example`); see [the phase plan](docs/architecture/phase-plan.md). The five `onetaxonomy-*` packages are on npm as alpha versions, under `@extantape` from 0.1.0-alpha.4; the Payload plugin isn't yet.
 
 ## Principles
 
@@ -20,12 +20,12 @@ The full rules are in [scientific invariants](docs/architecture/scientific-invar
 
 | Package | What it does | Status |
 | --- | --- | --- |
-| [`@captiveorigins/onetaxonomy-core`](packages/core) | Records, validation, bounded traversal, MRCA, tri-state monophyly, curated selections, coverage reports, snapshot checksums and diffs, views (actions, undo/redo, filters, highlights, projection), JSON Schema. No dependencies; runs anywhere. | Working |
-| [`@captiveorigins/onetaxonomy-import`](packages/import) | Source adapters (CSV/TSV, Darwin Core Archive, JSON, Newick, NEXUS, phyloXML), reconciliation, selective imports, community presets | Working |
-| [`@captiveorigins/onetaxonomy-layout`](packages/layout) | Rectangular, phylogram/time (only when valid), radial and sunburst layouts as plain coordinates | Working |
-| [`@captiveorigins/onetaxonomy-react`](packages/react) | Server-renderable SVG tree, accessible keyboard outline, explorer (undo/redo, drag, overlays, inspector, clade selector, SVG/PNG/JSON exports), lesson player | Working |
-| [`@captiveorigins/onetaxonomy-education`](packages/education) | Lesson decks (scenes, cameras, annotations, reveals) and worksheets with answers computed from the data | Working |
-| [`@captiveorigins/payload-plugin-onetaxonomy`](packages/payload) | Payload plugin: sealed snapshots checked by checksum, staged and published, views pinned to them, import jobs that turn source files into staged snapshots, people's own proposals that a curator can accept into a new staged version, a bounded read API (name search, ancestors, descendants, MRCA, coverage, projected views, exports) behind the host's access rules, with optional tenant scope, and admin panels for publishing, import progress and deciding on proposals | Early (M7 parts 1 to 5): tested on Payload with an in-memory MongoDB and in the example site on this machine, not yet in a deployed site. Not on npm |
+| [`@extantape/onetaxonomy-core`](packages/core) | Records, validation, bounded traversal, MRCA, tri-state monophyly, curated selections, coverage reports, snapshot checksums and diffs, views (actions, undo/redo, filters, highlights, projection), JSON Schema. No dependencies; runs anywhere. | Working |
+| [`@extantape/onetaxonomy-import`](packages/import) | Source adapters (CSV/TSV, Darwin Core Archive, JSON, Newick, NEXUS, phyloXML), reconciliation, selective imports, community presets | Working |
+| [`@extantape/onetaxonomy-layout`](packages/layout) | Rectangular, phylogram/time (only when valid), radial and sunburst layouts as plain coordinates | Working |
+| [`@extantape/onetaxonomy-react`](packages/react) | Server-renderable SVG tree, accessible keyboard outline, explorer (undo/redo, drag, overlays, inspector, clade selector, SVG/PNG/JSON exports), lesson player | Working |
+| [`@extantape/onetaxonomy-education`](packages/education) | Lesson decks (scenes, cameras, annotations, reveals) and worksheets with answers computed from the data | Working |
+| [`@extantape/payload-plugin-onetaxonomy`](packages/payload) | Payload plugin: sealed snapshots checked by checksum, staged and published, views pinned to them, import jobs that turn source files into staged snapshots, people's own proposals that a curator can accept into a new staged version, a bounded read API (name search, ancestors, descendants, MRCA, coverage, projected views, exports) behind the host's access rules, with optional tenant scope, and admin panels for publishing, import progress and deciding on proposals | Early (M7 parts 1 to 5): tested on Payload with an in-memory MongoDB and in the example site on this machine, not yet in a deployed site. Not on npm |
 | [`apps/studio`](apps/studio) | OneTaxonomy for Mac (Tauri 2): open checklists, Darwin Core Archives, Newick, NEXUS and phyloXML trees and snapshots; browse them; collapse weak branches, add a tree to an open checklist and link its tips to taxa (proposed by exact name, confirmed by you), compare two trees, and reroot or midpoint-root as a new tree; save views and sealed snapshots (never over the file that was opened), and save and open `.onetaxonomy` bundles (a documented ZIP with a manifest and checksums) | 0.1.0 on GitHub Releases. Not notarized, and it can't update itself yet |
 | [`apps/payload-example`](apps/payload-example) | A small Payload and Next.js site that uses the plugin: two roles, public pages that draw published views on the server, and proposals that record people by id, with a public handle shown beside it. Runs on your machine with a throwaway in-memory database | An example. Checked over HTTP by its smoke test; nobody has clicked through its admin yet |
 
@@ -35,11 +35,11 @@ The full rules are in [scientific invariants](docs/architecture/scientific-invar
 pnpm install
 pnpm build
 pnpm test
-pnpm --filter @captiveorigins/onetaxonomy-examples start
+pnpm --filter @extantape/onetaxonomy-examples start
 ```
 
 ```js
-import { assessTaxon, indexDataset } from '@captiveorigins/onetaxonomy-core'
+import { assessTaxon, indexDataset } from '@extantape/onetaxonomy-core'
 
 const data = indexDataset(snapshot)
 const result = assessTaxon(data.classification('traditional'), 'c:reptilia', data.phylogeny('archelosauria'))
@@ -49,7 +49,7 @@ const result = assessTaxon(data.classification('traditional'), 'c:reptilia', dat
 Curate a selective import from a checklist (see `examples/selective-import.mjs`):
 
 ```js
-import { csvAdapter, selectiveImport, toSnapshot } from '@captiveorigins/onetaxonomy-import'
+import { csvAdapter, selectiveImport, toSnapshot } from '@extantape/onetaxonomy-import'
 
 const read = await csvAdapter({ source: mySource }).read(csvText)        // Darwin Core column names by default
 const full = toSnapshot(read, { id: 'my-checklist', version: '2026-03', createdAt })
@@ -68,4 +68,4 @@ const { snapshot, coverage } = selectiveImport(full, {
 
 ## License
 
-[PolyForm Noncommercial 1.0.0](https://polyformproject.org/licenses/noncommercial/1.0.0) for the software: free for noncommercial use, with attribution; commercial use needs a separate license from Captive Origins. Versions published before this change remain under MIT. Data you import keeps its own license; OneTaxonomy records it with every snapshot.
+[PolyForm Noncommercial 1.0.0](https://polyformproject.org/licenses/noncommercial/1.0.0) for the software: free for noncommercial use, with attribution; commercial use needs a separate license from EXTANT APE. Versions published before this change remain under MIT. Data you import keeps its own license; OneTaxonomy records it with every snapshot.

RELEASING.md

@@ -4,12 +4,12 @@ One description everywhere: each `package.json` (`description`, `keywords`) is t
 
 1. Bump the same `version` in every `packages/*/package.json` (lockstep, ADR 0007), update `CHANGELOG.md`, commit as `Release x.y.z`, tag `vx.y.z`, and push the commit and the tag.
 2. The Release workflow builds, tests and **stages** every package on npm (trusted publishing, no stored token). Prereleases go to the `alpha` dist-tag once a package has a stable version; before that they are also `latest`.
-3. The maintainer account approves each with 2FA: npmjs.com → avatar → **Staged Packages** → **Approve**, or `npm stage list` then `npm stage approve <id>`. Only then are they public.
+3. The `mdgilardi` npm account, which owns the `@extantape` scope, approves each with 2FA: npmjs.com → avatar → **Staged Packages** → **Approve**, or `npm stage list` then `npm stage approve <id>`. Only then are they public.
 
-`@captiveorigins/payload-plugin-onetaxonomy` (`packages/payload`) moves in lockstep but isn't staged yet: the Release workflow skips it until the owner has published its first version by hand and set up its trust. Then remove `grep -v -x payload` from the workflow's stage step.
+`@extantape/payload-plugin-onetaxonomy` (`packages/payload`) moves in lockstep but isn't staged yet: the Release workflow skips it until the owner has published its first version by hand and set up its trust. Then remove `grep -v -x payload` from the workflow's stage step.
 
 The first version of each package is published by hand (`pnpm publish --access public` in each `packages/*` folder, `core` first; pnpm turns `workspace:^` into the real version), because npm can only trust a workflow for a package that exists; then, once per package:
 
 ```bash
-npm trust github <package-name> --repo CaptiveOrigins/onetaxonomy --file release.yml --allow-stage-publish --yes
+npm trust github <package-name> --repo ExtantApe/OneTaxonomy --file release.yml --allow-stage-publish --yes
 ```

apps/payload-example/README.md

@@ -1,6 +1,6 @@
 # OneTaxonomy Payload example
 
-A small Payload and Next.js site that uses [`@captiveorigins/payload-plugin-onetaxonomy`](../../packages/payload). It shows the plugin set up the way a real site would: accounts with two roles, public pages that draw published views, import jobs over uploaded files, and proposals that record a person by an id, with a public handle shown beside it and no email address.
+A small Payload and Next.js site that uses [`@extantape/payload-plugin-onetaxonomy`](../../packages/payload). It shows the plugin set up the way a real site would: accounts with two roles, public pages that draw published views, import jobs over uploaded files, and proposals that record a person by an id, with a public handle shown beside it and no email address.
 
 > **Status: an example, not a product.** It runs on this machine only, on a throwaway in-memory MongoDB, with made-up accounts and the repository's illustrative fixtures. Tested: 74 checks over HTTP with sign-in cookies (`pnpm smoke`, in CI), on `next dev` and on the built site, with Payload 3.93 and Next.js 16; the admin's panels clicked through in headless Chrome as the curator, in light and dark (`pnpm click-through`, 40 checks, not in CI: it needs Chrome and the network); and the three public pages looked at in headless Chrome by hand, in light and dark, at desktop width and at 520 px. Not tested: a screen reader, Safari, Firefox, a phone, Postgres or SQLite, or a deployed site.
 
@@ -24,7 +24,7 @@ From the repository root, with Node 22 or later and pnpm:
 ```bash
 pnpm install
 pnpm build      # the packages the site uses
-pnpm --filter @captiveorigins/onetaxonomy-payload-example dev
+pnpm --filter @extantape/onetaxonomy-payload-example dev
 ```
 
 The first run downloads a MongoDB binary (about 140 MB on a Mac, kept in `~/.cache/mongodb-binaries`). Then it prints the site's address, the two accounts and a password made up for this run:
@@ -48,7 +48,7 @@ Stop it with Ctrl-C. The database and the uploaded files go with it: every run s
 ## Check it
 
 ```bash
-pnpm --filter @captiveorigins/onetaxonomy-payload-example smoke
+pnpm --filter @extantape/onetaxonomy-payload-example smoke
 ```
 
 This builds the site, starts it on a free port with its own database, and sends it requests the way a browser would. It takes about 15 seconds on a recent Mac. It checks that:
@@ -76,7 +76,7 @@ This builds the site, starts it on a free port with its own database, and sends
 ### In a browser
 
 ```bash
-pnpm --filter @captiveorigins/onetaxonomy-payload-example click-through
+pnpm --filter @extantape/onetaxonomy-payload-example click-through
 ```
 
 This builds the site, starts it the same way, opens a Chrome or Chromium already on the machine with no window and a throwaway profile, signs in as the curator and does what a curator would: publishes a snapshot with the keyboard, changes and saves a draft view, runs the three import jobs, renames a finished one with Payload's own Save, accepts a proposal into a new version, pastes a sealed snapshot into the new-snapshot form, and publishes it with Payload's own status field. It takes about two minutes. It checks what the panels say at each step, what was sent, that the form under a panel doesn't repeat it, that the panel's parts are spaced apart as the browser lays them out, and that no page asks any site but this one, apart from Payload's code editor.

apps/payload-example/app/(payload)/admin/importMap.js

@@ -1,14 +1,14 @@
-import { SnapshotPanel as SnapshotPanel_577f3b5b503ff777fe77b01de8cacfa5 } from '@captiveorigins/payload-plugin-onetaxonomy/client'
-import { ViewPanel as ViewPanel_577f3b5b503ff777fe77b01de8cacfa5 } from '@captiveorigins/payload-plugin-onetaxonomy/client'
-import { ImportPanel as ImportPanel_577f3b5b503ff777fe77b01de8cacfa5 } from '@captiveorigins/payload-plugin-onetaxonomy/client'
-import { ProposalPanel as ProposalPanel_577f3b5b503ff777fe77b01de8cacfa5 } from '@captiveorigins/payload-plugin-onetaxonomy/client'
+import { SnapshotPanel as SnapshotPanel_6db27829aa354dff1e248cee79348b1f } from '@extantape/payload-plugin-onetaxonomy/client'
+import { ViewPanel as ViewPanel_6db27829aa354dff1e248cee79348b1f } from '@extantape/payload-plugin-onetaxonomy/client'
+import { ImportPanel as ImportPanel_6db27829aa354dff1e248cee79348b1f } from '@extantape/payload-plugin-onetaxonomy/client'
+import { ProposalPanel as ProposalPanel_6db27829aa354dff1e248cee79348b1f } from '@extantape/payload-plugin-onetaxonomy/client'
 import { CollectionCards as CollectionCards_f9c02e79a4aed9a3924487c0cd4cafb1 } from '@payloadcms/next/rsc'
 
 /** @type import('payload').ImportMap */
 export const importMap = {
-  "@captiveorigins/payload-plugin-onetaxonomy/client#SnapshotPanel": SnapshotPanel_577f3b5b503ff777fe77b01de8cacfa5,
-  "@captiveorigins/payload-plugin-onetaxonomy/client#ViewPanel": ViewPanel_577f3b5b503ff777fe77b01de8cacfa5,
-  "@captiveorigins/payload-plugin-onetaxonomy/client#ImportPanel": ImportPanel_577f3b5b503ff777fe77b01de8cacfa5,
-  "@captiveorigins/payload-plugin-onetaxonomy/client#ProposalPanel": ProposalPanel_577f3b5b503ff777fe77b01de8cacfa5,
+  "@extantape/payload-plugin-onetaxonomy/client#SnapshotPanel": SnapshotPanel_6db27829aa354dff1e248cee79348b1f,
+  "@extantape/payload-plugin-onetaxonomy/client#ViewPanel": ViewPanel_6db27829aa354dff1e248cee79348b1f,
+  "@extantape/payload-plugin-onetaxonomy/client#ImportPanel": ImportPanel_6db27829aa354dff1e248cee79348b1f,
+  "@extantape/payload-plugin-onetaxonomy/client#ProposalPanel": ProposalPanel_6db27829aa354dff1e248cee79348b1f,
   "@payloadcms/next/rsc#CollectionCards": CollectionCards_f9c02e79a4aed9a3924487c0cd4cafb1
 }

apps/payload-example/app/(site)/layout.tsx

@@ -1,4 +1,4 @@
-import '@captiveorigins/onetaxonomy-react/styles.css'
+import '@extantape/onetaxonomy-react/styles.css'
 import './site.css'
 
 import type { Metadata } from 'next'

apps/payload-example/app/(site)/site.css

@@ -1,4 +1,4 @@
-/* The example site's own page styles. The trees are styled by @captiveorigins/onetaxonomy-react/styles.css. */
+/* The example site's own page styles. The trees are styled by @extantape/onetaxonomy-react/styles.css. */
 :root {
   --ink: #4c312c;
   --text: #1d2330;

apps/payload-example/app/(site)/views/[id]/ViewFigure.tsx

@@ -1,5 +1,5 @@
-import type { Highlight, LayoutKind, Projection } from '@captiveorigins/onetaxonomy-core'
-import { layoutFor, TreeOutline, treeViewBox, TreeView } from '@captiveorigins/onetaxonomy-react'
+import type { Highlight, LayoutKind, Projection } from '@extantape/onetaxonomy-core'
+import { layoutFor, TreeOutline, treeViewBox, TreeView } from '@extantape/onetaxonomy-react'
 
 /** The parts of a stored view the drawing needs. */
 export type StoredView = { layout: { kind: LayoutKind }; highlights: Highlight[] }

apps/payload-example/app/(site)/views/[id]/page.tsx

@@ -1,4 +1,4 @@
-import { projectedView } from '@captiveorigins/payload-plugin-onetaxonomy'
+import { projectedView } from '@extantape/payload-plugin-onetaxonomy'
 import config from '@payload-config'
 import type { Metadata } from 'next'
 import { notFound } from 'next/navigation'