fix(docker): force pytantan to build without any SIMD backends

Dockerfile

@@ -21,21 +21,65 @@ COPY funannotate2 ./funannotate2
 # Install from the lockfile; no-op if the lockfile already matches.
 RUN pixi install --locked
 
-# Rebuild pytantan from source with AVX2 disabled (SSE4-only baseline).
-# The PyPI/bioconda wheel ships with AVX2 SIMD which SIGILLs on CPUs that lack
-# it — notably Rosetta 2 on Apple Silicon — and AVX2 gives no meaningful win
-# for this pipeline. `pip` uses build isolation, so scikit-build-core/cython/
-# scoring-matrices are pulled in transparently; we only need the C/C++ toolchain.
+# Rebuild pytantan from source with all SIMD backends disabled.
+#
+# Background: pytantan's wheels ship with AVX2 enabled, and prior to v0.1.4
+# the generic path was also polluted with AVX2 flags via `add_compile_options`
+# in the project-level CMakeLists.txt. Either way, on x86_64 CPUs without AVX2
+# (notably Rosetta 2 on Apple Silicon) any code path that executes an AVX2
+# instruction raises SIGILL. The runtime-dispatch added in v0.1.4 does not
+# help us here because we want a build that is portable to *any* x86_64.
+#
+# pytantan's CMakeLists.txt uses FindAVX2/FindSSE4/FindNEON which auto-detect
+# on the build host (GitHub Actions runners have AVX2), so we have to force
+# the HAVE_* flags OFF. Pre-defining them in FindAVX2.cmake's `if((DEFINED ...))`
+# guard short-circuits detection entirely.
+#
+# We pass these via pip's `--config-settings=cmake.define.*` rather than
+# CMAKE_ARGS/SKBUILD_CMAKE_ARGS env vars, since that route goes directly into
+# scikit-build-core's parser and is not subject to env-var filtering.
 ARG PYTANTAN_VERSION
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
-        git build-essential cmake zlib1g-dev ca-certificates && \
+        git build-essential cmake zlib1g-dev binutils ca-certificates && \
     rm -rf /var/lib/apt/lists/*
-RUN CMAKE_ARGS="-DHAVE_AVX2=OFF -DAVX2_C_FLAGS= -DHAVE_SSE4=OFF -DSSE4_C_FLAGS= -DHAVE_NEON=OFF -DNEON_C_FLAGS=" \
-    /app/.pixi/envs/default/bin/pip install --no-deps --force-reinstall \
+RUN /app/.pixi/envs/default/bin/pip install \
+        --no-deps --no-cache-dir --force-reinstall -v \
+        --config-settings=cmake.define.HAVE_AVX2=OFF \
+        --config-settings=cmake.define.HAVE_SSE4=OFF \
+        --config-settings=cmake.define.HAVE_NEON=OFF \
+        --config-settings=cmake.define.AVX2_C_FLAGS= \
+        --config-settings=cmake.define.SSE4_C_FLAGS= \
+        --config-settings=cmake.define.NEON_C_FLAGS= \
         "pytantan @ git+https://github.com/althonos/pytantan.git@v${PYTANTAN_VERSION}" && \
     rm -rf /root/.cache/pip
 
+# Verify the rebuild was effective: only `generic` should be present in the
+# platform/ directory and neither lib.*.so nor generic.*.so should contain
+# any AVX/AVX2 instructions (no `ymm`/`zmm` register references, no `vex`-
+# encoded vector ops). Fail the build loudly otherwise so we never ship an
+# image that SIGILLs at import time.
+RUN set -eux; \
+    PY=/app/.pixi/envs/default/bin/python; \
+    PT_DIR=$("$PY" -c 'import pytantan, os; print(os.path.dirname(pytantan.__file__))'); \
+    echo "pytantan installed at: $PT_DIR"; \
+    ls -la "$PT_DIR/platform/"; \
+    SIMD_MODS=$(ls "$PT_DIR/platform/" | grep -E '^(avx2|sse4|neon)\.' || true); \
+    if [ -n "$SIMD_MODS" ]; then \
+        echo "ERROR: SIMD platform modules were built despite HAVE_*=OFF: $SIMD_MODS"; \
+        exit 1; \
+    fi; \
+    BAD=""; \
+    for so in $(find "$PT_DIR" -maxdepth 2 -name '*.so'); do \
+        if objdump -d -M intel --no-show-raw-insn "$so" 2>/dev/null \
+            | grep -Eq '\b(ymm[0-9]+|zmm[0-9]+|vpbroadcast|vextracti128|vinserti128)\b'; then \
+            echo "ERROR: $so contains AVX/AVX2 instructions"; \
+            BAD="${BAD} ${so}"; \
+        fi; \
+    done; \
+    if [ -n "$BAD" ]; then exit 1; fi; \
+    "$PY" -c "import pytantan; from pytantan import Alphabet, RepeatFinder, default_scoring_matrix; print('pytantan smoke test OK', pytantan.__version__)"
+
 # Pre-generate an activation script so the final image doesn't need pixi.
 RUN mkdir -p /app/bin && \
     { echo '#!/bin/bash'; \