File size: 3,142 Bytes
0161e74 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 | """
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()
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