configure

#!/usr/bin/env bash
# Detect CPU SIMD backend (SSE / NEON), rewrite p7_config.h + esl_config.h vector
# sections, and emit build-config.mk for GNU make.
#
# Usage:
#   ./configure [--with-impl=sse|neon|auto] [--help]
#
# Default --with-impl=auto uses uname -m (aarch64/arm64 -> neon, x86* -> sse).

set -euo pipefail

die() { echo "[configure] ERROR: $*" >&2; exit 1; }

command -v awk >/dev/null 2>&1 || die "awk is required to run configure (POSIX awk is enough)."

ROOT="$(cd "$(dirname "$0")" && pwd)"
WITH_IMPL="auto"

while [[ $# -gt 0 ]]; do
  case "$1" in
    --help|-h)
      cat <<'EOF'
Usage: ./configure [--with-impl=sse|neon|auto]

  --with-impl=auto   Detect from uname -m (default)
  --with-impl=sse    Intel/AMD SSE2 implementation (impl_sse, esl_sse.c)
  --with-impl=neon   ARM NEON implementation (impl_neon, esl_neon.c)

Generates build-config.mk and updates vector macro blocks in:
  src/p7_config.h
  easel/esl_config.h
(requires POSIX awk)

Then run: make
EOF
      exit 0
      ;;
    --with-impl=*)
      WITH_IMPL="${1#*=}"
      shift
      ;;
    *)
      die "unknown option: $1 (try --help)"
      ;;
  esac
done

machine="$(uname -m 2>/dev/null || echo unknown)"

pick_impl() {
  case "${WITH_IMPL}" in
    auto)
      case "${machine}" in
        aarch64|arm64) echo neon ;;
        x86_64|amd64|i386|i686|i86pc) echo sse ;;
        *)
          die "unsupported machine '${machine}' for --with-impl=auto. Set --with-impl=sse or --with-impl=neon explicitly."
          ;;
      esac
      ;;
    sse|neon) echo "${WITH_IMPL}" ;;
    *) die "invalid --with-impl=${WITH_IMPL} (use sse, neon, or auto)" ;;
  esac
}

IMPL="$(pick_impl)"

if [[ ! -d "${ROOT}/src/impl_${IMPL}" ]]; then
  die "missing ${ROOT}/src/impl_${IMPL} — copy impl_${IMPL} from hmmer-3.4/src before building."
fi

if [[ "${IMPL}" == neon && ! -f "${ROOT}/easel/esl_neon.c" ]]; then
  die "missing easel/esl_neon.c — copy from hmmer-3.4/easel before building."
fi
if [[ "${IMPL}" == sse && ! -f "${ROOT}/easel/esl_sse.c" ]]; then
  die "missing easel/esl_sse.c"
fi

# Compiler flags for SIMD translation units (impl_* + easel simd)
SIMD_CFLAGS=""
case "${IMPL}" in
  sse)
    # Match typical HMMER/gcc behavior; clang accepts -msse2 on x86.
    SIMD_CFLAGS="-msse2"
    ;;
  neon)
    # -mfpu=neon is for 32-bit ARM (GCC). Do not match arm64 — that prefix matches arm* and
    # breaks Apple/clang (aarch64 always has NEON; -mfpu is invalid for arm64-apple-darwin).
    case "${machine}" in
      armv7*|armv6*|armv5*|armv4*)
        SIMD_CFLAGS="-mfpu=neon"
        ;;
      *)
        SIMD_CFLAGS=""
        ;;
    esac
    ;;
esac

# Inner blocks (between SLEDGE_VECTOR markers, exclusive of marker lines)
p7_inner_sse='/* #undef eslENABLE_NEON */
#define eslENABLE_SSE 1
/* #undef eslENABLE_VMX */'

p7_inner_neon='#define eslENABLE_NEON 1
/* #undef eslENABLE_SSE */
/* #undef eslENABLE_VMX */'

esl_inner_sse='#define eslENABLE_SSE 1
/* #undef eslENABLE_SSE4 */
/* #undef eslENABLE_AVX */
/* #undef eslENABLE_AVX512 */
/* #undef eslENABLE_NEON */
/* #undef eslENABLE_VMX */

/* #undef eslHAVE_NEON_AARCH64 */'

if [[ "${IMPL}" == neon ]] && [[ "${machine}" == aarch64 || "${machine}" == arm64 ]]; then
  esl_inner_neon='/* #undef eslENABLE_SSE */
/* #undef eslENABLE_SSE4 */
/* #undef eslENABLE_AVX */
/* #undef eslENABLE_AVX512 */
#define eslENABLE_NEON 1
/* #undef eslENABLE_VMX */

#define eslHAVE_NEON_AARCH64 1'
else
  esl_inner_neon='#define eslENABLE_NEON 1
/* #undef eslENABLE_SSE */
/* #undef eslENABLE_SSE4 */
/* #undef eslENABLE_AVX */
/* #undef eslENABLE_AVX512 */
/* #undef eslENABLE_VMX */

/* #undef eslHAVE_NEON_AARCH64 */'
fi

patch_vector_block() {
  local file="$1"
  local inner="$2"
  local innerfile outfile
  innerfile="${TMPDIR:-/tmp}/sledge_cfg_$$.inner"
  outfile="${TMPDIR:-/tmp}/sledge_cfg_$$.out"
  trap 'rm -f "$innerfile" "$outfile"' EXIT
  printf '%s\n' "$inner" >"$innerfile" || die "failed to write temp file"

  # POSIX awk: replace lines between markers (exclusive) with inner text; no Perl needed.
  awk -v innerfile="$innerfile" '
    BEGIN {
      while ((getline line < innerfile) > 0)
        inner = inner line "\n"
      close(innerfile)
    }
    index($0, "/* === SLEDGE_VECTOR_BEGIN === */") {
      print
      printf "%s", inner
      skipping = 1
      next
    }
    skipping {
      if (index($0, "/* === SLEDGE_VECTOR_END === */") > 0) {
        print
        skipping = 0
      }
      next
    }
    { print }
  ' "$file" >"$outfile" || die "awk failed on ${file}"
  mv "$outfile" "$file" || die "failed to install patched ${file}"
  rm -f "$innerfile"
  trap - EXIT
}

if [[ "${IMPL}" == sse ]]; then
  patch_vector_block "${ROOT}/src/p7_config.h" "${p7_inner_sse}"
  patch_vector_block "${ROOT}/easel/esl_config.h" "${esl_inner_sse}"
  EASEL_SIMD_SRC="easel/esl_sse.c"
else
  patch_vector_block "${ROOT}/src/p7_config.h" "${p7_inner_neon}"
  patch_vector_block "${ROOT}/easel/esl_config.h" "${esl_inner_neon}"
  EASEL_SIMD_SRC="easel/esl_neon.c"
fi

# Same basenames as upstream impl_*/Makefile (excluding mpi.c — not used by sledge binaries)
IMPL_CFILES="decoding.c fwdback.c io.c ssvfilter.c msvfilter.c null2.c optacc.c stotrace.c vitfilter.c p7_omx.c p7_oprofile.c"
HMMER_IMPL_SRCS=""
for f in ${IMPL_CFILES}; do
  HMMER_IMPL_SRCS="${HMMER_IMPL_SRCS} src/impl_${IMPL}/${f}"
done

cat > "${ROOT}/build-config.mk" <<EOF
# Generated by ./configure — do not edit.
# Regenerate: ./configure

IMPL_CHOICE := ${IMPL}
IMPLDIR := impl_${IMPL}
SIMD_CFLAGS := ${SIMD_CFLAGS}
EASEL_SIMD_SRC := ${EASEL_SIMD_SRC}

HMMER_IMPL_SRCS :=${HMMER_IMPL_SRCS}
EOF

echo "[configure] machine=${machine} impl=${IMPL} SIMD_CFLAGS='${SIMD_CFLAGS}'"
echo "[configure] wrote ${ROOT}/build-config.mk"
echo "[configure] updated vector blocks in src/p7_config.h and easel/esl_config.h"
echo "[configure] Next: make"