Clade Studio 0.1.1

Clade Studio 0.1.1

A maintenance prerelease for geometry checking, bounded routing and artistic editing. This release includes the fixes reviewed in PR #1.

Fixed and improved

• Large forks count candidate enumeration against the routing work budget, avoiding unbounded pair construction. Interrupted trials restore their exact geometry, and exact work/evaluation exhaustion is disclosed.
• Shared-junction incidence checks report Incomplete when their budget expires; unchecked attachments cannot receive a Pass.
• Historical artistic copies defer QA during junction, label and waypoint dragging. Release validates the final edit; cancellation and one-step undo are retained.
• Geometry checks detect extended incident overlap and self-crossing stems, count findings beyond the bounded issue examples, and use indexed geometry for larger drawings.
• Topology inspection uses aligned, spacing-aware geometry. Readability proposals account for incomplete checks, and fitting controls use clearer names.

Project compatibility

Project format remains V4. Supported older projects preserve their stored artwork and historical QA through the original validation profiles. Current checks and exported QA use compound-v3. Older application builds may reject newly saved current-profile views; use 0.1.1 to continue editing those projects.

Downloads and quick start

Browser ZIP — clade-studio-0.1.1-browser.zip: extract and serve the folder over local HTTP. With Python 3 installed, run inside the extracted folder:

python3 -m http.server 4173 --bind 127.0.0.1

Source ZIP — clade-studio-0.1.1-source.zip: requires Node.js 22.18 or later and npm. Extract, then run:

npm ci
npm run dev

Open http://127.0.0.1:4173. Stop either server with Ctrl+C. Opening HTML directly from disk is unsupported.

Each ZIP has a companion .sha256 file and an internal release-manifest.json with file hashes and component licenses. Verify a download from its folder with:

sha256sum -c clade-studio-0.1.1-browser.zip.sha256
sha256sum -c clade-studio-0.1.1-source.zip.sha256

Verification and limitations

All 239 automated tests, strict TypeScript checking, build identity, source checksums and release-package inventories pass. Automated controller tests cover historical 600-tip drags; live browser and device-font verification were not performed for this release.

Layouts can still have contacts, clearance problems, unavailable font measurements or incomplete checks. Those findings remain Draft. Routing is a bounded heuristic, not a guarantee of an overlap-free drawing. There is no persistent autosave: save a project before closing the tab.

The project is not actively maintained. Owner development may be sporadic or absent; maintain an independent fork if you need ongoing improvements or support.

Original software is 0BSD. Bundled data retain their CC BY 4.0 or CC0 terms; see REDISTRIBUTION.md, the included notices and each archive's manifest.

Clade Studio 0.1.0

Clade Studio 0.1.0

The first release of Clade Studio: a local browser app for turning supplied trees into editable figures with sources and methods attached.

Included

• Newick import, complete-source search and a zoomable read-only Explore viewer.
• Rectangular, circular and fan cladograms; source-distance phylograms; supplied-rank classifications; and unrooted equal-angle/daylight layouts.
• Junction and label adjustments, pins, readability previews, artistic copies and Organic silhouette fitting.
• Editable V4 project saves with V1–V3 migration.
• Labeled/unlabeled SVG export packages with source mappings, QA, references and Sources & Methods.
• Offline datasets from Hug et al. (2016), Upham et al. (2019), dos Reis et al. (2018) and Kew release 4.0, plus a bundled guide.

Downloads and quick start

Browser ZIP — clade-studio-0.1.0-browser.zip: extract and serve the extracted folder over local HTTP. For example, with Python 3 installed, run this inside that folder:

python3 -m http.server 4173 --bind 127.0.0.1

Source ZIP — clade-studio-0.1.0-source.zip: requires Node.js 22.18 or later and npm. Extract, then run:

npm ci
npm run dev

Open http://127.0.0.1:4173. Stop either server with Ctrl+C. Use Guide in the app for the walkthrough. Opening the HTML directly from disk is unsupported.

Each ZIP has a companion .sha256 file and an internal release-manifest.json with file hashes and component licenses. On systems with sha256sum, verify a download from its folder with:

sha256sum -c clade-studio-0.1.0-browser.zip.sha256

Known limitations

• Layout and fitting can leave overlaps or spacing issues. Draft exports disclose unresolved geometry, font measurements and work limits; review the drawing before using it.
• There is no persistent autosave. Download a project before closing; editing images remain embedded in project files, including those inside export packages.
• One source per project. No online organism lookup, relationship inference, dated/fossil layouts, trait analysis or cross-source comparison.
• Explore is nonmetric and read-only. Its temporary viewing summaries do not change the exported drawing. Adaptive unrooted Explore is not included.
• Newick inputs are limited to 20 MB, 100,000 nodes and depth 800; project imports to 50 MB. Large inputs should be explored in full and drawn as selected subsets.
• Text depends on available browser fonts. Changed font measurements can require regeneration before export.

Original software is 0BSD. Hug and Kew data retain CC BY 4.0 terms; the included Upham and dos Reis tree components are CC0. Consult REDISTRIBUTION.md, the included notices and each archive's manifest for exact attribution and component terms.