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ProtCross 0.1.3

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@GeraltZeroZhong GeraltZeroZhong released this 30 Jun 11:22
v0.1.3
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Learn about vigilant mode.

Summary

ProtCross 0.1.3 is a release-preparation and user-facing hardening release. It focuses on making clean installs, prediction outputs, training entry points, runtime assets, and repository layout reliable before broader distribution.

Highlights

  • protcross is now the canonical package name, with deprecated evopoint_da compatibility aliases retained for 0.1.x users.
  • protcross predict now writes a downstream-friendly result package by default: annotated structure, extended scores TSV, pocket JSON, and summary JSON.
  • Prediction outputs now include pocket centers, residue lists, probabilities/scores, residue counts, asset version, threshold, clustering metadata, truncation metadata, and output paths.
  • Structure writeback is safer for docking/MD workflows: scored protein residues are handled explicitly, altloc atoms are updated consistently, HETATM collisions are avoided, and multi-model warnings are recorded.
  • Runtime asset resolution is centralized and now supports manifest metadata, SHA verification, refresh, offline mode, explicit overrides, and clearer cache behavior.
  • Original 0.1.0-era paper reproduction scripts are archived under reproduction/legacy/; the main README now focuses on maintained 0.1.3 workflows.
  • Root-level runtime assets and placeholder data are removed from source control. Assets are downloaded, supplied explicitly, or read from cache.
  • Release packaging now includes source package data, CI, wheel/sdist smoke checks, and deprecated import compatibility tests.

Validation

  • PR CI on main: passed
  • conda run -n pyg5070 pytest -q: 95 passed
  • python -m build: passed
  • python -m twine check dist/*: passed
  • Clean wheel install and CLI help smoke: passed
  • PyPI upload: https://pypi.org/project/protcross/0.1.3/

Notes

This package release ships code only. The default runtime asset bundle remains the stable 0.1.2 checkpoint/PCA bundle and is installed through protcross setup-assets or automatically during prediction unless offline mode is requested.

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