fix: pin pytantan to 0.1.3 and add defensive lazy import

CITATION.cff

@@ -18,4 +18,4 @@ keywords:
   - consensus gene models
 license: BSD-2-Clause
 version: version = "26.5.22"
-date-released: '2026-05-23'
+date-released: '2026-05-24'

Dockerfile

@@ -4,7 +4,7 @@
 
 ARG PIXI_VERSION=0.67.0
 ARG UBUNTU_VERSION=22.04
-ARG PYTANTAN_VERSION=0.1.4
+ARG PYTANTAN_VERSION=0.1.3
 
 # ---------------------------------------------------------------------------
 # Stage 1: build — resolve + install the pixi environment from pixi.lock
@@ -21,53 +21,44 @@ COPY funannotate2 ./funannotate2
 # Install from the lockfile; no-op if the lockfile already matches.
 RUN pixi install --locked
 
-# Rebuild pytantan from source with all SIMD backends disabled.
+# Rebuild pytantan from source with AVX2 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.
+# Background: pytantan's PyPI wheels ship with AVX2 SIMD enabled, which SIGILLs
+# on x86_64 CPUs that lack AVX2 (notably Rosetta 2 on Apple Silicon, and some
+# pre-Haswell servers). We pin to v0.1.3 — this is the last release with a
+# straightforward CMake gate, where setting HAVE_AVX2=OFF and clearing the
+# AVX2_C_FLAGS cache variable is sufficient to produce a portable build.
 #
-# 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.
+# scikit-build-core (pytantan's build backend) reads SKBUILD_CMAKE_ARGS as a
+# semicolon-separated CMake list and passes it directly to the inner cmake
+# invocation, bypassing the env-var filtering that affects CMAKE_ARGS.
 ARG PYTANTAN_VERSION
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
         git build-essential cmake zlib1g-dev binutils ca-certificates && \
     rm -rf /var/lib/apt/lists/*
-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= \
+RUN SKBUILD_CMAKE_ARGS="-DHAVE_AVX2:BOOL=OFF;-DAVX2_C_FLAGS:STRING=" \
+    /app/.pixi/envs/default/bin/pip install \
+        --no-deps --no-cache-dir --force-reinstall \
         "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.
+# Verify the rebuild was effective: no avx2.*.so module should be present in
+# the platform/ directory, and no shipped .so should contain AVX/AVX2/AVX512
+# vector instructions (ymm/zmm register references). SSE4 on x86_64 is fine
+# under Rosetta 2 and is left enabled. 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: $SIMD_MODS"; \
-        exit 1; \
+    if [ -d "$PT_DIR/platform" ]; then ls -la "$PT_DIR/platform/"; fi; \
+    if [ -d "$PT_DIR/platform" ]; then \
+        AVX_MODS=$(ls "$PT_DIR/platform/" | grep -E '^avx[0-9]*\.' || true); \
+        if [ -n "$AVX_MODS" ]; then \
+            echo "ERROR: AVX platform modules were built despite HAVE_AVX2=OFF: $AVX_MODS"; \
+            exit 1; \
+        fi; \
     fi; \
     BAD=""; \
     for so in $(find "$PT_DIR" -maxdepth 2 -name '*.so'); do \
@@ -78,7 +69,7 @@ RUN set -eux; \
         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__)"
+    "$PY" -c "import pytantan; from pytantan.lib import 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 && \

funannotate2/fastx.py

@@ -4,7 +4,6 @@
 
 import pyfastx
 from natsort import natsorted
-from pytantan.lib import RepeatFinder, default_scoring_matrix
 
 
 def softmask_fasta(
@@ -39,6 +38,20 @@ def softmask_fasta(
     Returns:
         None
     """
+    # pytantan is imported lazily: its compiled extension uses CPU-specific
+    # SIMD that can SIGILL on hosts without AVX2 (notably Rosetta 2 on Apple
+    # Silicon). Deferring the import keeps unrelated funannotate2 subcommands
+    # usable when pytantan is broken or absent.
+    try:
+        from pytantan.lib import RepeatFinder, default_scoring_matrix
+    except ImportError as e:
+        raise RuntimeError(
+            "pytantan is required for softmasking but could not be imported "
+            "(it may be missing or built with incompatible SIMD flags). "
+            "Install a working pytantan build, or pre-softmask the assembly "
+            "with an external repeat masker before running funannotate2. "
+            f"Underlying error: {e}"
+        ) from e
     # set default scoring matrix
     matrix = default_scoring_matrix(protein, match_score, mismatch_cost)
     repeat_finder = RepeatFinder(

funannotate2/predict.py

@@ -241,7 +241,16 @@ def predict(args):
             "Genome assembly is not softmasked, running pytantan to quickly softmask repeats"
         )
         os.rename(GenomeFasta, GenomeFasta + ".original")
-        softmask_fasta(GenomeFasta + ".original", GenomeFasta)
+        try:
+            softmask_fasta(GenomeFasta + ".original", GenomeFasta)
+        except (RuntimeError, ImportError) as e:
+            os.rename(GenomeFasta + ".original", GenomeFasta)
+            logger.critical(
+                f"Softmasking with pytantan failed: {e}\n"
+                "Pre-softmask the assembly with an external repeat masker "
+                "(e.g. tantan, RepeatMasker, or red) and rerun."
+            )
+            raise SystemExit(1)
         stats, bad_names, nuc_errors, contigs = analyzeAssembly(
             GenomeFasta,
             maskedRegions,

pixi.toml

@@ -52,8 +52,10 @@ funannotate2 = { path = ".", editable = false }
 "funannotate2-addons" = "*"
 helixerlite = "*"
 annorefine = ">=2026.2.9"
-# pytantan: bioconda lags at 0.1.3; pull 0.1.4+ from PyPI
-pytantan = ">=0.1.4"
+# pytantan: pinned to 0.1.3 from PyPI; the 0.1.4 wheel/SIMD dispatch has been
+# unreliable on x86_64 hosts without AVX2 (notably Rosetta 2 on Apple Silicon).
+# The Docker image rebuilds this from source with AVX2 disabled.
+pytantan = "==0.1.3"
 
 
 [tasks]

pyproject.toml

@@ -23,7 +23,7 @@ dependencies = [
     "requests",
     "gb-io>=0.3.2",
     "json-repair",
-    "pytantan>=0.1.4",
+    "pytantan>=0.1.3",
     "psutil",
     "annorefine>=2026.2.9"
 ]