Changelog

2.0.0 — 2026-09-24 (corrected release)

At the maintainer's explicit request, this corrected 2.0.0 consolidates the initial 2.0.0 and the subsequently published 2.0.1 and 3.0.0. The original 2.0.0 is archived as archive/v2.0.0-original, retaining its original sources, release assets, attribution, and licenses. The former 3.0.0 is archived as archive/v3.0.0-before-correction with its original contents. Both archived releases are marked as prereleases; their release IDs and asset hashes are preserved. The historical v2.0.1 tag remains. These short-lived versions are superseded by this corrected release. This is a documented one-time version correction, not a claim that those versions were never published.

This release also incorporates the previously unpublished 1.0.1 cleanup; there was no separate 1.0.1 release.

• Removes the VIGIL visual example, editable sources, supporting files, and documentation from the current public package, along with its CC BY-NC 4.0 license notice. The privately maintained example is outside this distribution.
• Removes the previously documented build_example.py vigil case and bundled VIGIL paths. Users of that example cannot use those paths or that command with this corrected package. All nine skills and the remaining examples are retained.
• Retains licenses and attribution for the remaining material, including ShareAlike examples and embedded fonts; the package remains mixed-license. Earlier distributed VIGIL copies retain their attribution and CC BY-NC 4.0 terms. This removal does not relicense them.
• Redraws the collective-cell schematic around complementary modeling choices, retained detail, and coarse-graining. Removes the misleading resolution axis and clarifies the captions and primary-source context.
• Separates single-site cellular automata from multisite Cellular Potts cells, and individual-cell phase fields from spatially averaged tissue density.
• Computes physical vectors from the illustrated force law and chemical field; labels model-dependency links separately from forces.
• Applies the maintainer's minimal README wording and removes installation instructions. Retains SVG examples, editable sources, and links to their scientific context and the third-party notices.
• Renames the collection from Theoretical Biophysics Modeling Skills to Computational Modeling Skills, and the plugin/extension identifier from theoretical-biophysics-modeling-skills to computational-modeling-skills. This is a breaking package identity change; the eight individual skill names remain unchanged.
• Adds paper-reproduce as the ninth skill, with its reviewed operational references, target-card validator, and current decision diagram. Development notes and superseded diagrams remain outside the distribution.
• Adds portable root plugin metadata, Codex and Claude repository catalogs, and package logo assets. The package contains no MCP server, app, hook, or automatic installation action.
• Documents scoped handoffs between modeling and documentation, notebooks and visualization, and schematic design and request clarification. Existing approvals and the coordinating skill's requested outputs remain authoritative.
• Changes qualified skill invocations from theoretical-biophysics-modeling-skills:<skill-name> to computational-modeling-skills:<skill-name>. For example, theoretical-biophysics-modeling-skills:model-documentation becomes computational-modeling-skills:model-documentation. Update saved qualified invocations when adopting the renamed package.
• Moves the derived local checkout to public/computational-modeling-skills/. The current GitHub hosting address remains https://github.com/surajinacademia/theoretical-biophysics-modeling-skills until the owner renames the remote repository. No installation or registration changes are performed by this local rename.
• Limits the distribution to skills and their runtime dependencies, supporting material, package metadata, and licensing information.
• Removes development tests and evaluation suites, the development-only check_model_doc.py checker, and unused build files.
• Routes five manual TikZ recipes through the private build workflow.
• Publishes quantitative PDF outputs through private staging and opened output directories; assembles the gallery from private inputs before publishing it. File replacements are atomic individually, not as a multi-file transaction.
• Rejects escaped or comment-obfuscated SVG CSS, unsupported style properties and functions, and SMIL animation; requires UTF-8 XML and rejects invalid XML control characters. Rejects nonregular TeX source/include files without blocking on FIFOs.
• Preserves the original eight skill names and remaining diagram creator credits and third-party license terms. The published v1.0.0 release and its history remain unchanged.

1.0.0

First stable eight-skill collection. This establishes the compatibility contract in VERSIONING.md.

• Retains computational modeling, model documentation, schematic design, and request clarification.
• Adds scientific notebooks, linear stability analysis, data visualization, and a portable single-job CPU Slurm workflow.
• Removes gotcha from the current package; this does not erase prior releases or repository history. Private skills are outside this release.
• Aligns platform manifest versions and documents mixed licensing, per-example diagram attribution, notebook provenance, and font notices. VIGIL remains CC BY-NC 4.0; share-alike examples retain their applicable terms.