return bool instead of np.bool_
#4074
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Beautiful! I believe I have seen issues related to this at some point. I just did a global search (re pattern pymatgen/src/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py Lines 716 to 727 in ea7c339 pymatgen/src/pymatgen/core/surface.py Lines 308 to 321 in ea7c339 The following might return pymatgen/src/pymatgen/analysis/interfaces/zsl.py Lines 317 to 330 in ea7c339 |
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I did some messy The Slightly updated list: |
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I think this script can be adapted later to handle a more thorough check of serialization bugs caused by custom import pytest
import inspect
import pkgutil
import importlib
import pymatgen
import numpy as np
triggered = set()
def log_numpy_return(func, path_name, name):
def wrapper(*args_, **kwargs_):
result = func(*args_, **kwargs_)
if isinstance(result, np.generic):
# print(f"Function '{name}' in '{path_name}' returned a NumPy generic object")
triggered.add(f"Function '{name}' in '{path_name}' returned a NumPy generic object")
return result
return wrapper
def wrap_func(path, name, func, path_name):
setattr(path, name, log_numpy_return(func, path_name, name))
def get_all_functions(package):
"""
Get all functions and methods from a package and its submodules.
"""
functions = dict()
for module_info in pkgutil.walk_packages(package.__path__, prefix=f"{package.__name__}."):
try:
# Dynamically import the module
module = importlib.import_module(module_info.name)
# Get all functions in the module
for name, func_ in inspect.getmembers(module, inspect.isfunction):
source_module = func_.__module__
if package.__name__ not in source_module: continue
functions[f"{module.__name__}.{name}"] = (module, name, func_, source_module)
# Get all the methods in the module
for class_name, obj in inspect.getmembers(module, inspect.isclass):
source_module = obj.__module__
if package.__name__ not in source_module: continue
for name2, method_ in inspect.getmembers(obj, inspect.isfunction):
functions[f"{module.__name__}.{class_name}.{name2}"] = (obj, name2, method_, f"{source_module}.{class_name}")
except Exception as e:
# Handle modules that cannot be imported or have issues
print(f"Failed to inspect {module_info.name}: {e}")
return functions
funcs = get_all_functions(pymatgen)
for v in funcs.values():
wrap_func(*v)
# Run pytest
pytest.main(['-v', '-s'])
print("Triggered:")
print(triggered)
# write triggerd to file
with open("triggered.txt", "w") as f:
f.write("\n".join(triggered)) |
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Ok I went through the list and found ones where a user will plausibly serialize into a DB. |
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Summary
The return signature of this function is currently
np.bool_which can cause serialization problems with older atomate1 workflows.Changed to
boolinstead.