#!/usr/bin/env bash
# Create the conda env used by Datasets/prepare_atlas.ipynb and prepare_benchmark.ipynb.
#
# Usage:
#   bash create_env.sh
#   FORCE_RECREATE=1 bash create_env.sh
#   CONDA_ENVS_PREFIX=/path/to/.conda/envs bash create_env.sh
#
# Then:
#   conda activate cyflow_datasets
#   # in Jupyter / Cursor: kernel "Python (cyflow_datasets)"

set -euo pipefail

SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
DATASETS_DIR="$(cd "${SCRIPT_DIR}/.." && pwd)"
YML_PATH="${SCRIPT_DIR}/environment.yml"
ENV_NAME="${ENV_NAME:-cyflow_datasets}"
FORCE_RECREATE="${FORCE_RECREATE:-0}"

echo "========================================================================"
echo "  CREATE DATASETS ENVIRONMENT: ${ENV_NAME}"
echo "========================================================================"
echo "Setup dir    : ${SCRIPT_DIR}"
echo "Datasets dir : ${DATASETS_DIR}"
echo ""

load_conda() {
    if command -v module >/dev/null 2>&1; then
        echo ">>> Loading cluster modules (anaconda3)..."
        module load anaconda3/2023.09-0/none-none 2>/dev/null || module load anaconda3 || true
    fi

    if ! command -v conda >/dev/null 2>&1; then
        for conda_sh in \
            "${HOME}/miniforge3/etc/profile.d/conda.sh" \
            "${HOME}/mambaforge/etc/profile.d/conda.sh" \
            "${HOME}/miniconda3/etc/profile.d/conda.sh" \
            "/opt/anaconda3/etc/profile.d/conda.sh" \
            "/opt/miniconda3/etc/profile.d/conda.sh"
        do
            if [[ -f "${conda_sh}" ]]; then
                # shellcheck source=/dev/null
                source "${conda_sh}"
                break
            fi
        done
    fi

    if ! command -v conda >/dev/null 2>&1; then
        echo "ERROR: conda not found. Install Miniforge/Anaconda or load the anaconda module."
        exit 1
    fi

    # Ensure `conda activate` works in this non-interactive shell.
    eval "$(conda shell.bash hook)"
    echo "    conda: $(command -v conda)"
    echo ""
}

env_exists() {
    conda env list | awk '{print $1}' | grep -qx "$1"
}

prepare_yml() {
    local dest="$1"
    if [[ -n "${CONDA_ENVS_PREFIX:-}" ]]; then
        grep -vE '^[[:space:]]*prefix:' "${YML_PATH}" > "${dest}"
        echo "prefix: ${CONDA_ENVS_PREFIX%/}/${ENV_NAME}" >> "${dest}"
        echo ">>> Using prefix ${CONDA_ENVS_PREFIX%/}/${ENV_NAME}"
    else
        cp "${YML_PATH}" "${dest}"
    fi
}

load_conda

if [[ "${FORCE_RECREATE}" == "1" ]] && env_exists "${ENV_NAME}"; then
    echo ">>> FORCE_RECREATE: removing existing env '${ENV_NAME}'"
    conda env remove -n "${ENV_NAME}" -y
    echo ""
fi

if env_exists "${ENV_NAME}"; then
    echo ">>> Environment '${ENV_NAME}' already exists (skip conda create)"
    echo "    Set FORCE_RECREATE=1 to rebuild."
else
    tmp_yml="$(mktemp "${TMPDIR:-/tmp}/cyflow_datasets_XXXXXX.yml")"
    prepare_yml "${tmp_yml}"
    echo ">>> Creating '${ENV_NAME}' from environment.yml"
    conda env create -n "${ENV_NAME}" -f "${tmp_yml}"
    rm -f "${tmp_yml}"
    echo "    Created: ${ENV_NAME}"
fi
echo ""

echo ">>> Registering Jupyter kernel"
conda activate "${ENV_NAME}"
python -m ipykernel install --user \
    --name "${ENV_NAME}" \
    --display-name "Python (${ENV_NAME})"
echo ""

echo ">>> Smoke-test imports (cwd=${DATASETS_DIR})"
cd "${DATASETS_DIR}"
python - <<'PY'
import importlib

mods = [
    "numpy", "pandas", "scipy", "sklearn", "yaml",
    "matplotlib", "seaborn", "anndata", "scanpy",
    "fcsparser", "scyan", "pytometry", "tableone",
    "huggingface_hub", "openpyxl", "utils_datasets",
]
failed = []
for name in mods:
    try:
        importlib.import_module(name)
        print(f"  ok  {name}")
    except Exception as exc:
        failed.append((name, exc))
        print(f"  FAIL {name}: {exc}")

if failed:
    raise SystemExit(1)
print("All imports succeeded.")
PY

echo ""
echo "========================================================================"
echo "  Activate:  conda activate ${ENV_NAME}"
echo "  Notebooks: Datasets/prepare_atlas.ipynb"
echo "             Datasets/prepare_benchmark.ipynb"
echo "  Kernel   : Python (${ENV_NAME})"
echo "========================================================================"
echo "Done."