"""
Bootstrap scDFM imports by creating missing __init__.py files and loading
its modules under a 'scdfm_src' prefix in sys.modules.

This module MUST be imported before any CCFM src imports.
"""

import sys
import os
import types

_SCDFM_ROOT = os.path.normpath(
    os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "scDFM")
)

# Directories in scDFM that need __init__.py to be proper packages
_DIRS_NEEDING_INIT = [
    "src",
    "src/models",
    "src/models/origin",
    "src/data_process",
    "src/tokenizer",
    "src/script",
    "src/models/perturbation",
]


def _ensure_init_files():
    """Create missing __init__.py files in scDFM so it can be imported as packages."""
    created = []
    for d in _DIRS_NEEDING_INIT:
        init_path = os.path.join(_SCDFM_ROOT, d, "__init__.py")
        if not os.path.exists(init_path):
            with open(init_path, "w") as f:
                f.write("# Auto-created by CCFM bootstrap\n")
            created.append(init_path)
    return created


def bootstrap():
    """Load scDFM's src package as 'scdfm_src' in sys.modules."""
    if "scdfm_src" in sys.modules:
        return  # Already bootstrapped

    # Create missing __init__.py files
    _ensure_init_files()

    # Save CCFM's src modules
    saved = {}
    for key in list(sys.modules.keys()):
        if key == "src" or key.startswith("src."):
            saved[key] = sys.modules.pop(key)

    # Add scDFM root to path
    sys.path.insert(0, _SCDFM_ROOT)

    try:
        # Import scDFM modules (their relative imports work now)
        import src as scdfm_src_pkg
        import src.models
        import src.models.origin
        import src.models.origin.blocks
        import src.models.origin.layers
        import src.models.origin.model
        import src.flow_matching
        import src.flow_matching.path
        import src.flow_matching.path.path
        import src.flow_matching.path.path_sample
        import src.flow_matching.path.affine
        import src.flow_matching.path.scheduler
        import src.flow_matching.path.scheduler.scheduler
        # Skip src.flow_matching.ot (requires 'ot' package, not needed for CCFM)
        import src.utils
        import src.utils.utils
        import src.tokenizer
        import src.tokenizer.gene_tokenizer
        # Skip src.data_process (has heavy deps like bs4, rdkit)
        # We handle data loading separately in CCFM

        # Re-register all under scdfm_src.* prefix
        for key in list(sys.modules.keys()):
            if key == "src" or key.startswith("src."):
                new_key = "scdfm_" + key
                sys.modules[new_key] = sys.modules[key]

    finally:
        # Remove scDFM's src.* entries
        for key in list(sys.modules.keys()):
            if (key == "src" or key.startswith("src.")) and not key.startswith("scdfm_"):
                del sys.modules[key]

        # Restore CCFM's src modules
        for key, mod in saved.items():
            sys.modules[key] = mod

        # Remove scDFM from front of path
        if _SCDFM_ROOT in sys.path:
            sys.path.remove(_SCDFM_ROOT)


bootstrap()