fix: pin pytantan to 0.1.3 and add defensive lazy import

[nextgenusfs]

Summary

Belt-and-braces fix for the recurring Illegal instruction SIGILL when running the funannotate2 Docker image under Rosetta 2 on Apple Silicon. Combines a known-working pytantan version with defensive import handling so that even a broken pytantan installation can no longer take down the entire CLI.

Changes

1. Pin pytantan to v0.1.3

• pyproject.toml: pytantan>=0.1.4 → pytantan>=0.1.3
• pixi.toml: pytantan = ">=0.1.4" → pytantan = "==0.1.3"
• pixi.lock: regenerated via pixi update pytantan (now resolves to 0.1.3)

v0.1.3 was the last release with a straightforward CMake gate where HAVE_AVX2=OFF is sufficient to produce a portable build. v0.1.4's runtime SIMD dispatch added complexity without giving us anything we use — funannotate2 only consumes RepeatFinder and default_scoring_matrix, which are identical in both versions.

2. Restore the proven Dockerfile recipe

RUN SKBUILD_CMAKE_ARGS="-DHAVE_AVX2:BOOL=OFF;-DAVX2_C_FLAGS:STRING=" \
    pip install --no-deps --no-cache-dir --force-reinstall \
        "pytantan @ git+https://github.com/althonos/pytantan.git@v${PYTANTAN_VERSION}"

SKBUILD_CMAKE_ARGS is scikit-build-core's own env var (semicolon-separated CMake list) and is passed directly into the inner cmake invocation, bypassing the env-var filtering that affected previous attempts with CMAKE_ARGS. The objdump + file-presence guards are retained as cheap insurance — they will fail the build loudly if any AVX2 instructions sneak in.

3. Defensive lazy import in funannotate2/fastx.py

Moved from pytantan.lib import RepeatFinder, default_scoring_matrix from module top into softmask_fasta(), wrapped in try/except ImportError → raises a descriptive RuntimeError. As a result:

• funannotate2 --help, funannotate2 install, etc. never crash even if pytantan is broken in the user's environment.
• Only an actual softmasking call surfaces an error, and the message is actionable.

4. Graceful handling in funannotate2/predict.py

Wrapped the softmask_fasta() call in try/except (RuntimeError, ImportError):

• Restores the original FASTA on failure (no half-renamed state).
• Logs a critical message pointing at external repeat maskers as a workaround.
• Exits cleanly with code 1.

Validation

• All 15 existing tests in tests/unit/test_predict.py + test_fastx.py pass.
• All 16 tests in test_predict_functions.py, test_predict_comprehensive.py, test_fastx_additional.py, test_fastx_more.py pass.
• Verified manually that funannotate2.fastx imports cleanly with pytantan blocked at the meta-path level, and that softmask_fasta() then raises a descriptive RuntimeError only when invoked.

Post-merge action

The docker.yml workflow only publishes :latest on release tags or manual workflow_dispatch. After merging this PR, run Actions → Build and Publish Docker Image → Run workflow on main (with push=true) to republish :latest with the working v0.1.3 image.

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