install_env.sh

#!/usr/bin/env bash
set -euo pipefail

ENV_NAME="${ENV_NAME:-biopacific}"
PYTHON_VERSION="${PYTHON_VERSION:-3.12}"

if ! command -v conda >/dev/null 2>&1; then
    echo "conda is not available in PATH." >&2
    exit 1
fi

if [[ "$(uname -s)" != "Linux" ]]; then
    echo "This installer currently supports Linux only." >&2
    exit 1
fi

CONDA_BASE="$(conda info --base)"
source "${CONDA_BASE}/etc/profile.d/conda.sh"

if conda env list | awk '{print $1}' | grep -Fxq "${ENV_NAME}"; then
    echo "Conda environment '${ENV_NAME}' already exists. Reusing it."
else
    echo "Creating conda environment '${ENV_NAME}' with Python ${PYTHON_VERSION} ..."
    conda create -n "${ENV_NAME}" "python=${PYTHON_VERSION}" -y
fi

conda activate "${ENV_NAME}"

ARCH="$(uname -m)"
HOST_TRIPLE=""
SYSROOT_PACKAGE=""
case "${ARCH}" in
    x86_64|amd64)
        HOST_TRIPLE="x86_64-conda-linux-gnu"
        SYSROOT_PACKAGE="sysroot_linux-64"
        ;;
    aarch64|arm64)
        HOST_TRIPLE="aarch64-conda-linux-gnu"
        SYSROOT_PACKAGE="sysroot_linux-aarch64"
        ;;
    *)
        echo "Unsupported Linux architecture: ${ARCH}" >&2
        exit 1
        ;;
esac

echo "Installing conda-forge compiler toolchain and sysroot into '${ENV_NAME}' ..."
conda install -n "${ENV_NAME}" -c conda-forge -y \
    compilers \
    c-compiler \
    cxx-compiler \
    binutils \
    libgcc-ng \
    libstdcxx-ng \
    "${SYSROOT_PACKAGE}"

# Reactivate so newly installed compiler activation hooks take effect.
conda deactivate
conda activate "${ENV_NAME}"

export PATH="${CONDA_PREFIX}/bin:${PATH}"

CC_CANDIDATE="${CONDA_PREFIX}/bin/${HOST_TRIPLE}-cc"
CXX_CANDIDATE="${CONDA_PREFIX}/bin/${HOST_TRIPLE}-c++"

if [[ -x "${CC_CANDIDATE}" ]]; then
    export CC="${CC_CANDIDATE}"
elif command -v "${HOST_TRIPLE}-cc" >/dev/null 2>&1; then
    export CC="$(command -v "${HOST_TRIPLE}-cc")"
fi

if [[ -x "${CXX_CANDIDATE}" ]]; then
    export CXX="${CXX_CANDIDATE}"
elif command -v "${HOST_TRIPLE}-c++" >/dev/null 2>&1; then
    export CXX="$(command -v "${HOST_TRIPLE}-c++")"
fi

if [[ -z "${CC:-}" || -z "${CXX:-}" ]]; then
    echo "Failed to locate conda compiler toolchain after installation." >&2
    exit 1
fi

if [[ -d "${CONDA_PREFIX}/${HOST_TRIPLE}/sysroot" ]]; then
    export CONDA_BUILD_SYSROOT="${CONDA_PREFIX}/${HOST_TRIPLE}/sysroot"
fi

export CMAKE_C_COMPILER="${CC}"
export CMAKE_CXX_COMPILER="${CXX}"
export CUDAHOSTCXX="${CXX}"
export CMAKE_CUDA_HOST_COMPILER="${CXX}"
export CCACHE_DISABLE=1

echo "Installing uv into '${ENV_NAME}' ..."
python -m pip install --upgrade pip
python -m pip install uv

echo "Installing core Python packages with uv ..."
uv pip install -U \
    requests \
    openai \
    beautifulsoup4 \
    selenium \
    webdriver-manager \
    numpy

echo "Installing vLLM with uv ..."
if ! uv pip install -U vllm --torch-backend=auto; then
    echo >&2
    echo "vLLM installation failed." >&2
    echo "Diagnostics:" >&2
    echo "  gcc: $(command -v gcc || true)" >&2
    echo "  g++: $(command -v g++ || true)" >&2
    echo "  CC: ${CC:-"(unset)"}" >&2
    echo "  CXX: ${CXX:-"(unset)"}" >&2
    echo "  CMAKE_C_COMPILER: ${CMAKE_C_COMPILER:-"(unset)"}" >&2
    echo "  CMAKE_CXX_COMPILER: ${CMAKE_CXX_COMPILER:-"(unset)"}" >&2
    echo "  CUDAHOSTCXX: ${CUDAHOSTCXX:-"(unset)"}" >&2
    echo "  sysroot: ${CONDA_BUILD_SYSROOT:-"(unset)"}" >&2
    echo "  gcc version: $(${CC} --version 2>/dev/null | sed -n '1p' || true)" >&2
    echo "  g++ version: $(${CXX} --version 2>/dev/null | sed -n '1p' || true)" >&2
    exit 1
fi

echo
echo "Environment ready."
echo "  active env: ${ENV_NAME}"
echo "  arch: ${ARCH}"
echo "  python: $(python --version 2>&1)"
echo "  uv: $(uv --version 2>&1)"
echo "  gcc: $(command -v gcc)"
echo "  g++: $(command -v g++)"
if [[ -n "${CC:-}" ]]; then
    echo "  CC: ${CC}"
fi
if [[ -n "${CXX:-}" ]]; then
    echo "  CXX: ${CXX}"
fi
if [[ -n "${CONDA_BUILD_SYSROOT:-}" ]]; then
    echo "  CONDA_BUILD_SYSROOT: ${CONDA_BUILD_SYSROOT}"
fi