4 Commits

9 changed files with 64 additions and 24 deletions

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@@ -16,7 +16,7 @@ from . import reader
from . import system
from . import utils
from . import extra
from .logging import logger
from .logging_util 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 import logger
from .logging_util import logger
autosave_directory: Optional[str] = None
load_autosave_data = False

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@@ -1,9 +1,14 @@
import functools
import hashlib
from .logging import logger
from .logging_util 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
@@ -28,19 +33,46 @@ def version(version_nr: int, calls: Iterable = ()):
return decorator
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
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:
continue
o += l + "\n"
return o
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() != ""])
def checksum(*args, csum=None):
def checksum(*args, csum=None, _seen=None):
"""
Calculate a checksum of any object, by sha1 hash.
@@ -60,7 +92,15 @@ def checksum(*args, csum=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())
@@ -77,15 +117,15 @@ def checksum(*args, csum=None):
for key in sorted(merged): # deterministic ordering
v = merged[key]
if v is not arg:
checksum(v, csum=csum)
checksum(v, csum=csum, _seen=_seen)
elif isinstance(arg, functools.partial):
logger.debug("Checksum via partial for %s", str(arg))
checksum(arg.func, csum=csum)
checksum(arg.func, csum=csum, _seen=_seen)
for x in arg.args:
checksum(x, csum=csum)
checksum(x, csum=csum, _seen=_seen)
for k in sorted(arg.keywords.keys()):
csum.update(k.encode())
checksum(arg.keywords[k], csum=csum)
checksum(arg.keywords[k], csum=csum, _seen=_seen)
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 import logger
from .logging_util 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 import logger
from .logging_util 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 import logger
from .logging_util import logger
from . import atoms
from .coordinates import Coordinates
CSR_ATTRS = ("data", "indices", "indptr")
NOJUMP_MAGIC = 2016
Group_RE = re.compile("\[ ([-+\w]+) \]")
Group_RE = re.compile(r"\[ ([-+\w]+) \]")
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 import logger
from .logging_util import logger
from .functions import kww, kww_1e