Fix pixi resolver: pytantan from PyPI, bump buscolite, drop Dockerfile source rebuild

[nextgenusfs]

Problem

After #56 merged, main received a dependency bump (3bfa9baa) that landed pyproject.toml with pytantan>=0.1.4 and buscolite>=26.2.22. That broke the Docker build because:

1. pytantan: bioconda only ships 0.1.3. pixi.toml had pytantan = "*" under conda [dependencies], so pixi would never try PyPI for it — the pyproject.toml floor of >=0.1.4 from the local funannotate2 sdist was unsatisfiable.
2. buscolite: pixi.toml still pinned >=26.1.26 under conda [dependencies], but the local funannotate2 sdist (via pyproject.toml) now requires >=26.2.22. Pixi's conda-vs-PyPI pin reconciliation raised an unsatisfiable-requirements error on pixi lock --check.
3. Dockerfile: It was rebuilding pytantan from git source with AVX2 disabled, using PYTANTAN_VERSION=0.1.3 — now redundant since 0.1.4 comes from PyPI as a wheel.

Changes

pixi.toml

• Remove pytantan = "*" from conda [dependencies].
• Add pytantan = ">=0.1.4" to [pypi-dependencies].
• Bump conda-side buscolite = ">=26.1.26" → ">=26.2.22" to match pyproject.toml.

pixi.lock

Regenerated in a linux/amd64 pixi container (pixi's build dispatch can't resolve on osx-arm64 for this linux-64-only workspace). Packages changed:

• pytantan 0.1.3 (bioconda) → 0.1.4 (PyPI wheel cp311-abi3-manylinux_2_24_x86_64)
• archspec 0.2.5, scoring-matrices 0.3.4 → moved to PyPI alongside pytantan (same versions)
• buscolite 26.1.26 → 26.4.22 (bioconda)

Dockerfile

• Drop ARG PYTANTAN_VERSION=0.1.3 (top-level and the build-stage duplicate).
• Drop the apt-get install git build-essential cmake zlib1g-dev ca-certificates step — it only existed for the pytantan source rebuild.
• Drop the SKBUILD_CMAKE_ARGS=... pip install --no-deps --force-reinstall "pytantan @ git+..." step.
• Build stage is now: COPY + pixi install --locked + entrypoint shell-hook.

Diff stat: 3 files changed, 36 insertions(+), 72 deletions(-)

Verification

$ grep -n pytantan pixi.toml pixi.lock
pixi.toml:52:# pytantan: bioconda lags at 0.1.3; pull 0.1.4+ from PyPI
pixi.toml:53:pytantan = ">=0.1.4"
pixi.lock: ... pytantan-0.1.4-cp311-abi3-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

$ grep -nE "pytantan|PYTANTAN_VERSION|SKBUILD_CMAKE_ARGS|build-essential|cmake|zlib1g-dev" Dockerfile
(no matches)

$ docker run --rm --platform=linux/amd64 -v "$PWD":/work -w /work ghcr.io/prefix-dev/pixi:0.67.0 pixi lock --check
Lock-file was already up-to-date

Risk notes

• AVX2 baseline: The prior build disabled AVX2 in pytantan for compatibility (Rosetta 2, pre-Haswell Xeons). Upstream pytantan 0.1.4 uses runtime archspec dispatch, but the x86_64 wheel may still ship AVX2 code paths that SIGILL on non-AVX2 CPUs. If a crash report comes in from such a host, the source-rebuild pattern can be re-introduced behind a build arg (preserved in git history from commit 1a7e3356).
• Lock regeneration workflow: pixi lock can't be run natively on osx-arm64 for this workspace (linux-64-only, plus the local funannotate2 sdist needs a matching-platform Python in pixi's build dispatch). Use docker run --rm --platform=linux/amd64 -v "$PWD":/work -w /work ghcr.io/prefix-dev/pixi:0.67.0 pixi lock or rely on CI.

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

[nextgenusfs]

Update: CI failures resolved in b75fc6c7

After the buscolite pin fix in 1cc8fe26, the resolver error was gone but the Run unit tests step started failing on Py 3.9/3.10/3.11 (Linux) and Py 3.11 (macOS), while 3.12/3.13 kept passing. The GitHub Actions raw log truncates at ~68 KB and cut off before pytest's actual output, so the real traceback wasn't visible.

Diagnosis

The published pytantan 0.1.4 wheels were the culprit. 3.12/3.13 resolve to the same cp311-abi3 wheel as 3.11 yet passed, which points to an ABI- or build-specific defect in the prebuilt wheels rather than a bug in pytantan itself.

Fix in b75fc6c7

• Dockerfile: restored the pre-Suppress repetitive GeneMark license banner in training/predict logs #56 source-rebuild block, bumped to v0.1.4 — ARG PYTANTAN_VERSION=0.1.4, apt-get install git build-essential cmake zlib1g-dev ca-certificates, and SKBUILD_CMAKE_ARGS="-DHAVE_AVX2:BOOL=OFF;-DAVX2_C_FLAGS:STRING=" pip install --no-deps --force-reinstall "pytantan @ git+https://github.com/althonos/pytantan.git@v0.1.4".
• .github/workflows/tests.yml: added cmake to the Linux apt install and the macOS conda install, and set PIP_NO_BINARY: pytantan on the Install dependencies step so every matrix Python compiles pytantan from sdist.

pixi.lock and pixi.toml are unchanged — pixi still resolves pytantan 0.1.4 from PyPI; the pip --force-reinstall in the Docker build replaces the wheel with the source-compiled version.

Result

Run 24796874131 on b75fc6c7 — all 6 jobs green:

Job	1cc8fe26	b75fc6c7
ubuntu-latest, 3.9	❌	✅
ubuntu-latest, 3.10	❌	✅
ubuntu-latest, 3.11	❌	✅
ubuntu-latest, 3.12	✅	✅
ubuntu-latest, 3.13	✅	✅
macos-latest, 3.11	❌	✅

Trade-off: each CI job now compiles pytantan from sdist, adding ~10–20s to Install dependencies. Worth it for reliability until the upstream wheels are fixed.