Fix CPU-baseline SIGILLs under Rosetta 2 (apt augustus + pytantan no-SIMD)

[nextgenusfs]

Summary

The bioconda augustus 3.5.0 binary is built with a modern x86_64 microarch baseline (AVX2/BMI2) and SIGILLs (rc=-4) under Rosetta 2 on Apple Silicon and on pre-Haswell x86_64 hardware. Inside the linux/amd64 docker image this caused every augustus invocation on a Mac to silently die, manifesting downstream as a buscolite run with 0 hits across 6,654 BUSCO models.

This PR switches the Docker image to install augustus from Ubuntu apt instead of bioconda. Ubuntu noble ships augustus 3.5.0+dfsg built against the generic x86_64 baseline, so it runs on every host the image can land on (real amd64 and Rosetta 2 alike).

Changes

• Dockerfile

  • Bump UBUNTU_VERSION 22.04 -> 24.04 (noble — required for augustus 3.5.0 from apt; jammy only has 3.4.0).
  • apt-install augustus augustus-data in the final stage.
  • Repoint AUGUSTUS_CONFIG_PATH to /usr/share/augustus/config. funannotate2/config.py auto-derives AUGUSTUS_BASE=/usr/share/augustus/scripts, where the apt package installs new_species.pl, optimize_augustus.pl, etc.

• pixi.toml

  • Drop augustus from [dependencies].
  • Move buscolite from [dependencies] to [pypi-dependencies]. Its bioconda recipe hard-depends on augustus; its PyPI wheel does not. This prevents conda from transitively pulling augustus back in.
  • On osx-arm64 augustus is no longer installed at all — the funannotate2 CLI is exercised on Mac via the dockerized image, so this is intentional.

• pixi.lock

  • Regenerated. Zero augustus entries; buscolite-26.4.22-py3-none-any.whl now from PyPI on both linux-64 and osx-arm64.

• funannotate2/train.py

  • Re-enable the augustus PPX self-test in buscolite() by removing the check_augustus=False override. Paired with the companion buscolite PR (nextgenusfs/buscolite diagnose-augustus-sigill) that classifies signal deaths with a Rosetta/AVX hint, a future binary mismatch will now fail loudly at the first augustus call instead of silently producing 0 hits.

Verification

• pixi install succeeds on osx-arm64.
• buscolite imports from .pixi/envs/default/lib/python3.11/site-packages/buscolite.
• No augustus binaries in .pixi/envs/default/bin/.
• Docker build / runtime test against Rosetta 2 still needs to happen before merging.

Related

• Companion PR (required): buscolite diagnose-augustus-sigill.
• Root-cause sibling: pytantan SIMD/AVX2 SIGILL under Rosetta 2 (already merged on this branch as commit 0f39d033).

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Pull Request opened by Augment Code with guidance from the PR author