1 Commits

9 changed files with 24 additions and 64 deletions

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@@ -16,7 +16,7 @@ from . import reader
from . import system
from . import utils
from . import extra
from .logging_util import logger
from .logging import logger
def open(

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@@ -5,7 +5,7 @@ from typing import Optional, Callable, Iterable
import numpy as np
from .checksum import checksum
from .logging_util import logger
from .logging import logger
autosave_directory: Optional[str] = None
load_autosave_data = False

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@@ -1,14 +1,9 @@
import functools
import hashlib
from .logging_util import logger
from .logging import logger
from types import ModuleType, FunctionType
import inspect
from typing import Iterable
import ast
import io
import tokenize
import re
import textwrap
import numpy as np
@@ -33,46 +28,19 @@ def version(version_nr: int, calls: Iterable = ()):
return decorator
def strip_comments(source: str) -> str:
"""Removes docstrings, comments, and irrelevant whitespace from Python source code."""
# Step 1: Remove docstrings using AST
def remove_docstrings(node):
if isinstance(node, (ast.FunctionDef, ast.AsyncFunctionDef, ast.ClassDef, ast.Module)):
if (doc := ast.get_docstring(node, clean=False)):
first_stmt = node.body[0]
if isinstance(first_stmt, ast.Expr) and isinstance(first_stmt.value, ast.Constant):
node.body.pop(0) # Remove the docstring entirely
for child in ast.iter_child_nodes(node):
remove_docstrings(child)
tree = ast.parse(textwrap.dedent(source))
remove_docstrings(tree)
code_without_docstrings = ast.unparse(tree)
# Step 2: Remove comments using tokenize
tokens = tokenize.generate_tokens(io.StringIO(code_without_docstrings).readline)
result = []
last_lineno = -1
last_col = 0
for toknum, tokval, (srow, scol), (erow, ecol), line in tokens:
if toknum == tokenize.COMMENT:
def strip_comments(s: str):
"""Strips comment lines and docstring from Python source string."""
o = ""
in_docstring = False
for l in s.split("\n"):
if l.strip().startswith(("#", '"', "'")) or in_docstring:
in_docstring = l.strip().startswith(('"""', "'''")) + in_docstring == 1
continue
if srow > last_lineno:
last_col = 0
if scol > last_col:
result.append(" " * (scol - last_col))
result.append(tokval)
last_lineno, last_col = erow, ecol
code_no_comments = ''.join(result)
# Step 3: Remove empty lines (whitespace-only or truly blank)
return "\n".join([line for line in code_no_comments.splitlines() if line.strip() != ""])
o += l + "\n"
return o
def checksum(*args, csum=None, _seen=None):
def checksum(*args, csum=None):
"""
Calculate a checksum of any object, by sha1 hash.
@@ -92,15 +60,7 @@ def checksum(*args, csum=None, _seen=None):
csum = hashlib.sha1()
csum.update(str(SALT).encode())
if _seen is None:
_seen = set()
for arg in args:
obj_id = id(arg)
if obj_id in _seen:
continue
_seen.add(obj_id)
if hasattr(arg, "__checksum__"):
logger.debug("Checksum via __checksum__: %s", str(arg))
csum.update(str(arg.__checksum__()).encode())
@@ -117,15 +77,15 @@ def checksum(*args, csum=None, _seen=None):
for key in sorted(merged): # deterministic ordering
v = merged[key]
if v is not arg:
checksum(v, csum=csum, _seen=_seen)
checksum(v, csum=csum)
elif isinstance(arg, functools.partial):
logger.debug("Checksum via partial for %s", str(arg))
checksum(arg.func, csum=csum, _seen=_seen)
checksum(arg.func, csum=csum)
for x in arg.args:
checksum(x, csum=csum, _seen=_seen)
checksum(x, csum=csum)
for k in sorted(arg.keywords.keys()):
csum.update(k.encode())
checksum(arg.keywords[k], csum=csum, _seen=_seen)
checksum(arg.keywords[k], csum=csum)
elif isinstance(arg, np.ndarray):
csum.update(arg.tobytes())
else:

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@@ -1,6 +1,6 @@
from functools import partial, wraps
from copy import copy
from .logging_util import logger
from .logging import logger
from typing import Optional, Callable, List, Tuple
import numpy as np

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@@ -431,9 +431,9 @@ def non_gaussian_parameter(
trajectory: Coordinates = None,
axis: str = "all",
) -> float:
r"""
"""
Calculate the non-Gaussian parameter.
.. math:
..math:
\alpha_2 (t) =
\frac{3}{5}\frac{\langle r_i^4(t)\rangle}{\langle r_i^2(t)\rangle^2} - 1
"""

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@@ -7,7 +7,7 @@ from numpy.typing import ArrayLike, NDArray
from itertools import product
from .logging_util import logger
from .logging import logger
if TYPE_CHECKING:
from mdevaluate.coordinates import CoordinateFrame

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@@ -19,13 +19,13 @@ import MDAnalysis
from scipy import sparse
from .checksum import checksum
from .logging_util import logger
from .logging import logger
from . import atoms
from .coordinates import Coordinates
CSR_ATTRS = ("data", "indices", "indptr")
NOJUMP_MAGIC = 2016
Group_RE = re.compile(r"\[ ([-+\w]+) \]")
Group_RE = re.compile("\[ ([-+\w]+) \]")
class NojumpError(Exception):

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@@ -14,7 +14,7 @@ from scipy.ndimage import uniform_filter1d
from scipy.interpolate import interp1d
from scipy.optimize import curve_fit
from .logging_util import logger
from .logging import logger
from .functions import kww, kww_1e