File size: 4,545 Bytes
b2cb4a0 | 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 | #!/usr/bin/env python3
"""Preflight checks for the packaged SimpleFold ModelScope layout."""
from __future__ import annotations
import argparse
import importlib
import sys
from pathlib import Path
ROOT = Path(__file__).resolve().parents[1]
if str(ROOT) not in sys.path:
sys.path.insert(0, str(ROOT))
REQUIRED_FILES = [
"README.md",
"configuration.json",
"requirements_dcu.txt",
"env_install.sh",
"config/train.yaml",
"config/base_train.yaml",
"config/base_eval.yaml",
"config/model/architecture/foldingdit_100M.yaml",
"config/model/architecture/foldingdit_1.6B.yaml",
"config/model/architecture/plddt_module.yaml",
"scripts/run_inference.py",
"scripts/inference.py",
"scripts/train.py",
"scripts/train_fsdp.py",
"scripts/evaluate.py",
"scripts/process_data.py",
"scripts/tokenize_data.py",
"examples/minimal.fasta",
"modules/models/simplefold/flow.py",
"modules/datapipes/simplefold/processor/protein_processor.py",
"modules/utils/simplefold/esm_utils.py",
"modules/datapipes/boltz_data_pipeline/types.py",
"modules/models/esm/pretrained.py",
]
REQUIRED_WEIGHTS = [
"simplefold_100M.ckpt",
"simplefold_360M.ckpt",
"simplefold_700M.ckpt",
"simplefold_1.1B.ckpt",
"simplefold_1.6B.ckpt",
"simplefold_3B.ckpt",
"plddt.ckpt",
"plddt_module_1.6B.ckpt",
"ccd.pkl",
"boltz1_conf.ckpt",
]
OPTIONAL_ESM_WEIGHTS = [
"esm_models/esm2_t36_3B_UR50D.pt",
"esm_models/esm2_t36_3B_UR50D-contact-regression.pt",
]
def ok(message: str) -> None:
print(f"[OK] {message}")
def warn(message: str) -> None:
print(f"[WARN] {message}")
def fail(message: str) -> None:
print(f"[FAIL] {message}")
raise SystemExit(1)
def check_files() -> None:
missing = [path for path in REQUIRED_FILES if not (ROOT / path).exists()]
if missing:
fail("Missing required files: " + ", ".join(missing))
ok("Required package files are present")
def check_weights(strict: bool) -> None:
missing = []
placeholders = []
for name in REQUIRED_WEIGHTS:
path = ROOT / "weight" / name
if not path.exists():
missing.append(name)
elif path.stat().st_size < 1024:
placeholders.append(name)
if missing:
fail("Missing weight files: " + ", ".join(missing))
if placeholders:
message = (
"These files look like link/placeholder files and must be replaced "
"before real inference/training: " + ", ".join(placeholders)
)
if strict:
fail(message)
warn(message)
else:
ok("Required SimpleFold weights look like real files")
missing_esm = [name for name in OPTIONAL_ESM_WEIGHTS if not (ROOT / "weight" / name).exists()]
if missing_esm:
warn(
"ESM-2 3B local weights are not present. Put them under weight/esm_models "
"before running inference: " + ", ".join(missing_esm)
)
else:
ok("Local ESM-2 3B files are present")
def check_imports(strict: bool) -> None:
modules = [
"modules.models.simplefold.flow",
"modules.models.simplefold.torch.architecture",
"modules.datapipes.simplefold.processor.protein_processor",
"modules.utils.simplefold.esm_utils",
"modules.datapipes.boltz_data_pipeline.types",
"modules.models.esm.pretrained",
]
missing_dependencies = []
for module_name in modules:
try:
importlib.import_module(module_name)
except ModuleNotFoundError as exc:
missing_dependencies.append(f"{module_name}: {exc.name}")
if missing_dependencies:
message = (
"Some imports need external Python dependencies. Install requirements_dcu.txt "
"and rerun with --strict-imports for a full check: "
+ "; ".join(missing_dependencies)
)
if strict:
fail(message)
warn(message)
else:
ok("Bundled Python modules import successfully")
def main() -> None:
parser = argparse.ArgumentParser(description="Check packaged SimpleFold runtime files.")
parser.add_argument("--strict-weights", action="store_true")
parser.add_argument("--strict-imports", action="store_true")
args = parser.parse_args()
check_files()
check_weights(strict=args.strict_weights)
check_imports(strict=args.strict_imports)
ok("SimpleFold package preflight finished")
if __name__ == "__main__":
main()
|