configure

#!/bin/bash
# Configure script for FastQDesign R package
# Builds fastF binary during R CMD INSTALL or devtools::install()
# Search order: LD_LIBRARY_PATH -> pkg-config -> common paths

set -e

# Find R from micromamba environment if not in PATH
if ! command -v cmake &> /dev/null; then
    R_LIB_BIN=$(R --quiet --no-save -e 'cat(dirname(R.home()), "/bin", sep="")' 2>/dev/null | tr -d ' ')
    if [ -d "$R_LIB_BIN" ]; then
        export PATH="$R_LIB_BIN:$PATH"
    fi
fi

echo "=== Building fastF binary ==="

# Get package root directory
PKG_ROOT="$(cd "$(dirname "$0")" && pwd)"
BUILD_DIR="$PKG_ROOT/build"
CMAKE_DIR="$PKG_ROOT"
INST_BIN="$PKG_ROOT/inst/bin"

# Create directories
mkdir -p "$BUILD_DIR"
mkdir -p "$INST_BIN"

# Helper function to find library in LD_LIBRARY_PATH
find_in_ld_path() {
    local lib_name="$1"
    local ld_path="$LD_LIBRARY_PATH"
    [ -z "$ld_path" ] && ld_path="/lib:/lib64:/usr/lib:/usr/local/lib"
    
    IFS=':' read -ra PATHS <<< "$ld_path"
    for path in "${PATHS[@]}"; do
        if [ -f "$path/lib${lib_name}.so" ] || [ -f "$path/lib${lib_name}.a" ]; then
            echo "$path"
            return 0
        fi
    done
    return 1
}

# Initialize flags
CFLAGS=""
LDFLAGS=""
LIBS=""

# 1. Find htslib
# Priority: LD_LIBRARY_PATH -> pkg-config -> common paths
HTSLIB_FOUND=false
HTSLIB_PATH=""

# Check LD_LIBRARY_PATH first
if [ -n "$LD_LIBRARY_PATH" ]; then
    for path in $(echo "$LD_LIBRARY_PATH" | tr ':' ' '); do
        if [ -f "$path/libhts.so" ] || [ -f "$path/libhts.a" ]; then
            HTSLIB_PATH=$(dirname "$path")
            break
        fi
    done
fi

# Also check /usr/local/lib
if [ -z "$HTSLIB_PATH" ] && [ -f "/usr/local/lib/libhts.so" ]; then
    HTSLIB_PATH="/usr/local/lib"
fi

# Check micromamba/conda environment paths
if [ -z "$HTSLIB_PATH" ]; then
    # Check MAMBA_ROOT_PREFIX (micromamba) or CONDA_PREFIX
    for env_root in "$MAMBA_ROOT_PREFIX" "$CONDA_PREFIX" "$MAMBA_PREFIX"; do
        if [ -n "$env_root" ] && [ -d "$env_root" ]; then
            if [ -f "$env_root/lib/libhts.so" ] || [ -f "$env_root/lib/libhts.a" ]; then
                HTSLIB_PATH="$env_root/lib"
                break
            fi
            if [ -f "$env_root/lib64/libhts.so" ] || [ -f "$env_root/lib64/libhts.a" ]; then
                HTSLIB_PATH="$env_root/lib64"
                break
            fi
        fi
        # Also check common micromamba locations
        if [ -d "/home/runner/micromamba/envs" ]; then
            for env_dir in /home/runner/micromamba/envs/*/; do
                if [ -f "${env_dir}lib/libhts.so" ] || [ -f "${env_dir}lib/libhts.a" ]; then
                    HTSLIB_PATH="${env_dir}lib"
                    break 2
                fi
                if [ -f "${env_dir}lib64/libhts.so" ] || [ -f "${env_dir}lib64/libhts.a" ]; then
                    HTSLIB_PATH="${env_dir}lib64"
                    break 2
                fi
            done
        fi
    done
fi

# Check common paths (including CI environments)
if [ -z "$HTSLIB_PATH" ]; then
    for path in \
        /usr/local \
        /hpc/apps/htslib/1.22.1 \
        /usr \
        /opt/htslib \
        ~/anaconda3 \
        ~/miniconda3 \
        /home/runner; do
        if [ -f "$path/lib/libhts.so" ] || [ -f "$path/lib/libhts.a" ]; then
            HTSLIB_PATH="$path/lib"
            break
        fi
        if [ -f "$path/lib64/libhts.so" ] || [ -f "$path/lib64/libhts.a" ]; then
            HTSLIB_PATH="$path/lib64"
            break
        fi
    done
fi

# Try pkg-config as last resort
if [ -z "$HTSLIB_PATH" ] && pkg-config --exists htslib 2>/dev/null; then
    HTSLIB_CFLAGS=$(pkg-config --cflags htslib 2>/dev/null || echo "")
    HTSLIB_LIBS=$(pkg-config --libs htslib 2>/dev/null || echo "")
    HTSLIB_LIBDIR=$(pkg-config --variable=libdir htslib 2>/dev/null || echo "")
    CFLAGS="$CFLAGS $HTSLIB_CFLAGS"
    LDFLAGS="$LDFLAGS -L$HTSLIB_LIBDIR"
    LIBS="$LIBS $HTSLIB_LIBS"
    HTSLIB_FOUND=true
    echo "Found htslib via pkg-config: $HTSLIB_LIBDIR"
fi

if [ -n "$HTSLIB_PATH" ]; then
    # Determine include path - try dirname/include first (conda layout), 
    # then dirname/include/htslib (some system layouts)
    HTSLIB_INCLUDE=$(dirname "$HTSLIB_PATH")/include
    if [ ! -f "$HTSLIB_INCLUDE/htslib/sam.h" ] && [ -d "$HTSLIB_INCLUDE/htslib" ]; then
        HTSLIB_INCLUDE="$HTSLIB_INCLUDE/htslib"
    fi
    CFLAGS="$CFLAGS -I$HTSLIB_INCLUDE"
    LDFLAGS="$LDFLAGS -L$HTSLIB_PATH"
    LIBS="$LIBS -lhts"
    HTSLIB_FOUND=true
    echo "Found htslib: $HTSLIB_PATH (include: $HTSLIB_INCLUDE)"
fi

if [ "$HTSLIB_FOUND" = false ]; then
    echo "ERROR: htslib not found. Please install it."
    echo "Try: sudo apt-get install libhts-dev libbz2-dev zlib1g-dev libssl-dev libsqlite3-dev"
    exit 1
fi

# 2. Find zlib
# Priority: LD_LIBRARY_PATH -> pkg-config -> fallback
if [ -n "$LD_LIBRARY_PATH" ]; then
    for path in $(echo "$LD_LIBRARY_PATH" | tr ':' ' '); do
        if [ -f "$path/libz.so" ] || [ -f "$path/libz.a" ]; then
            CFLAGS="$CFLAGS -I$(dirname "$path")/include"
            LIBS="$LIBS -L$path -lz"
            echo "Found zlib via LD_LIBRARY_PATH: $path"
            break
        fi
    done
fi

if ! echo "$LIBS" | grep -q "\-lz"; then
    if pkg-config --exists zlib 2>/dev/null; then
        ZLIB_CFLAGS=$(pkg-config --cflags zlib 2>/dev/null || echo "")
        ZLIB_LIBS=$(pkg-config --libs zlib 2>/dev/null || echo "")
        CFLAGS="$CFLAGS $ZLIB_CFLAGS"
        LIBS="$LIBS $ZLIB_LIBS"
        echo "Found zlib via pkg-config"
    else
        LIBS="$LIBS -lz"
        echo "Using fallback zlib: -lz"
    fi
fi

# 3. Find sqlite3
# Priority: LD_LIBRARY_PATH -> pkg-config -> fallback
SQLITE_FOUND=false
if [ -n "$LD_LIBRARY_PATH" ]; then
    for path in $(echo "$LD_LIBRARY_PATH" | tr ':' ' '); do
        if [ -f "$path/libsqlite3.so" ] || [ -f "$path/libsqlite3.a" ]; then
            CFLAGS="$CFLAGS -I$(dirname "$path")/include"
            LIBS="$LIBS -L$path -lsqlite3"
            SQLITE_FOUND=true
            echo "Found sqlite3 via LD_LIBRARY_PATH: $path"
            break
        fi
    done
fi

if [ "$SQLITE_FOUND" = false ]; then
    if pkg-config --exists sqlite3 2>/dev/null; then
        SQLITE_CFLAGS=$(pkg-config --cflags sqlite3 2>/dev/null || echo "")
        SQLITE_LIBS=$(pkg-config --libs sqlite3 2>/dev/null || echo "")
        CFLAGS="$CFLAGS $SQLITE_CFLAGS"
        LIBS="$LIBS $SQLITE_LIBS"
        echo "Found sqlite3 via pkg-config"
    else
        LIBS="$LIBS -lsqlite3"
        echo "Using fallback sqlite3: -lsqlite3"
    fi
fi

# 4. Find bzip2 (needed by htslib)
# Priority: LD_LIBRARY_PATH -> pkg-config -> fallback
BZ2_FOUND=false
if [ -n "$LD_LIBRARY_PATH" ]; then
    for path in $(echo "$LD_LIBRARY_PATH" | tr ':' ' '); do
        if [ -f "$path/libbz2.so" ] || [ -f "$path/libbz2.so.1" ]; then
            LIBS="$LIBS -L$path -lbz2"
            BZ2_FOUND=true
            echo "Found bzip2 via LD_LIBRARY_PATH: $path"
            break
        fi
    done
fi

if [ "$BZ2_FOUND" = false ]; then
    if pkg-config --exists libbz2 2>/dev/null; then
        BZ2_LIBS=$(pkg-config --libs libbz2 2>/dev/null || echo "")
        LIBS="$LIBS $BZ2_LIBS"
        echo "Found libbz2 via pkg-config"
    elif pkg-config --exists bzip2 2>/dev/null; then
        BZ2_LIBS=$(pkg-config --libs bzip2 2>/dev/null || echo "")
        LIBS="$LIBS $BZ2_LIBS"
        echo "Found bzip2 via pkg-config"
    else
        LIBS="$LIBS -lbz2"
        echo "Using fallback bzip2: -lbz2"
    fi
fi

# 5. Find openssl (needed by htslib)
# Priority: LD_LIBRARY_PATH -> pkg-config -> fallback
SSL_FOUND=false
if [ -n "$LD_LIBRARY_PATH" ]; then
    for path in $(echo "$LD_LIBRARY_PATH" | tr ':' ' '); do
        if [ -f "$path/libssl.so" ] || [ -f "$path/libcrypto.so" ]; then
            LIBS="$LIBS -L$path -lssl -lcrypto"
            SSL_FOUND=true
            echo "Found openssl via LD_LIBRARY_PATH: $path"
            break
        fi
    done
fi

if [ "$SSL_FOUND" = false ]; then
    if pkg-config --exists openssl 2>/dev/null; then
        SSL_LIBS=$(pkg-config --libs openssl 2>/dev/null || echo "")
        LIBS="$LIBS $SSL_LIBS"
        echo "Found openssl via pkg-config"
    else
        LIBS="$LIBS -lssl -lcrypto"
        echo "Using fallback openssl: -lssl -lcrypto"
    fi
fi

# 6. OpenMP (usually system-installed)
if pkg-config --exists omp 2>/dev/null; then
    OMP_LIBS=$(pkg-config --libs omp 2>/dev/null || echo "")
    LIBS="$LIBS $OMP_LIBS"
    echo "Found OpenMP via pkg-config"
else
    LIBS="$LIBS -fopenmp"
    echo "Using fallback OpenMP: -fopenmp"
fi

# Add pthread
LIBS="$LIBS -lpthread"

export CFLAGS
export LDFLAGS
export LIBS

echo "CFLAGS: $CFLAGS"
echo "LDFLAGS: $LDFLAGS"
echo "LIBS: $LIBS"

# Build cmake command
CMAKE_CMD="cmake $CMAKE_DIR"
CMAKE_CMD="$CMAKE_CMD -DCMAKE_BUILD_TYPE=Release"
CMAKE_CMD="$CMAKE_CMD -DCMAKE_C_COMPILER=/usr/bin/gcc"
CMAKE_CMD="$CMAKE_CMD -DCMAKE_CXX_COMPILER=/usr/bin/g++"

echo "Running cmake..."

# Run cmake
cd "$BUILD_DIR"
$CMAKE_CMD > /dev/null 2>&1

# Build fastF
make fastF

# Copy to inst/bin if built successfully
if [ -f "$BUILD_DIR/fastF" ]; then
    cp "$BUILD_DIR/fastF" "$INST_BIN/"
    echo "fastF binary installed to inst/bin/"
    echo "=== Build complete ==="
else
    echo "ERROR: fastF build failed"
    exit 1
fi

exit 0