added a _seen set to avoid infinite recursions due to function arguments; also, applied pbc_diff to neighbors in tetrahedral order

Reviewed-on: #2

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "mdevaluate"
-version = "24.06"
+version = "24.02"
 dependencies = [
     "mdanalysis",
     "pandas",

src/mdevaluate/__init__.py

@@ -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(

src/mdevaluate/autosave.py

@@ -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

src/mdevaluate/checksum.py

@@ -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())
@@ -73,17 +113,19 @@ def checksum(*args, csum=None):
         elif isinstance(arg, FunctionType):
             csum.update(strip_comments(inspect.getsource(arg)).encode())
             c = inspect.getclosurevars(arg)
-            for v in {**c.nonlocals, **c.globals}.values():
+            merged = {**c.nonlocals, **c.globals}
+            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:

src/mdevaluate/coordinates.py

@@ -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

src/mdevaluate/correlation.py

@@ -13,95 +13,9 @@ from .pbc import pbc_diff, pbc_points
 from .coordinates import Coordinates, CoordinateFrame, displacements_without_drift
 
 
-def _is_multi_selector(selection):
-    if len(selection) == 0:
-        return False
-    elif (
-        isinstance(selection[0], int)
-        or isinstance(selection[0], bool)
-        or isinstance(selection[0], np.integer)
-        or isinstance(selection[0], np.bool_)
-    ):
-        return False
-    else:
-        for indices in selection:
-            if len(indices) == 0:
-                continue
-            elif (
-                isinstance(indices[0], int)
-                or isinstance(indices[0], bool)
-                or isinstance(indices[0], np.integer)
-                or isinstance(indices[0], np.bool_)
-            ):
-                return True
-            else:
-                raise ValueError(
-                    "selector has more than two dimensions or does not "
-                    "contain int or bool types"
-                )
-
-
-def _calc_correlation(
-    frames: Coordinates,
-    start_frame: CoordinateFrame,
-    function: Callable,
-    selection: np.ndarray,
-    shifted_idx: np.ndarray,
-) -> np.ndarray:
-    if len(selection) == 0:
-        correlation = np.zeros(len(shifted_idx))
-    else:
-        start = start_frame[selection]
-        correlation = np.array(
-            [
-                function(start, frames[frame_index][selection])
-                for frame_index in shifted_idx
-            ]
-        )
-    return correlation
-
-
-def _calc_correlation_multi(
-    frames: Coordinates,
-    start_frame: CoordinateFrame,
-    function: Callable,
-    selection: np.ndarray,
-    shifted_idx: np.ndarray,
-) -> np.ndarray:
-    correlations = np.zeros((len(selection), len(shifted_idx)))
-    for i, frame_index in enumerate(shifted_idx):
-        frame = frames[frame_index]
-        for j, current_selection in enumerate(selection):
-            if len(selection) == 0:
-                correlations[j, i] = 0
-            else:
-                correlations[j, i] = function(
-                    start_frame[current_selection], frame[current_selection]
-                )
-    return correlations
-
-
-def _average_correlation(result):
-    averaged_result = []
-    for n in range(result.shape[1]):
-        clean_result = []
-        for entry in result[:, n]:
-            if np.all(entry == 0):
-                continue
-            else:
-                clean_result.append(entry)
-        averaged_result.append(np.average(np.array(clean_result), axis=0))
-    return np.array(averaged_result)
-
-
-def _average_correlation_multi(result):
-    clean_result = []
-    for entry in result:
-        if np.all(entry == 0):
-            continue
-        else:
-            clean_result.append(entry)
-    return np.average(np.array(clean_result), axis=0)
+def log_indices(first: int, last: int, num: int = 100) -> np.ndarray:
+    ls = np.logspace(0, np.log10(last - first + 1), num=num)
+    return np.unique(np.int_(ls) - 1 + first)
 
 
 @autosave_data(2)
@@ -114,82 +28,113 @@ def shifted_correlation(
     window: float = 0.5,
     average: bool = True,
     points: int = 100,
-) -> tuple[np.ndarray, np.ndarray]:
-    """Compute a time-dependent correlation function for a given trajectory.
-
-    To improve statistics, multiple (possibly overlapping) windows will be
-    layed over the whole trajectory and the correlation is computed for them separately.
-    The start frames of the windows are spaced linearly over the valid region of
-    the trajectory (skipping frames in the beginning given by skip parameter).
-
-    The points within each window are spaced logarithmically.
-
-    Only a certain subset of the given atoms may be selected for each window
-    individually using a selector function.
-
-    Note that this function is specifically optimized for multi selectors, which select
-    multiple selection sets per window, for which the correlation is to be computed
-    separately.
-
-
-    Arguments
-    ---------
-    function:
-        The (correlation) function to evaluate.
-        Should be of the form (CoordinateFrame, CoordinateFrame) -> float
-
-    frames:
-        Trajectory to evaluate on
-
-    selector: (optional)
-        Selection function so select only certain selection sets for each start frame.
-        Should be of the form
-            (CoordinateFrame) -> list[A]
-        where A is something you can index an ndarray with.
-        For example a list of indices or a bool array.
-        Must return the same number of selection sets for every frame.
-
-    segments:
-        Number of start frames
-
-    skip:
-        Percentage of trajectory to skip from the start
-
-    window:
-        Length of each segment given as percentage of trajectory
-
-    average:
-        Whether to return averaged results.
-        See below for details on the returned ndarray.
-
-    points:
-        Number of points per segment
-
-
-    Returns
-    -------
-    times: ndarray
-        1d array of time differences to start frame
-    result: ndarray
-        2d ndarray of averaged (or non-averaged) correlations.
-
-        When average==True (default) the returned array will be of the shape (S, P)
-        where S is the number of selection sets and P the number of points per window.
-        For selection sets that where empty for all start frames all data points will be
-        zero.
-
-        When average==False the returned array will be of shape (W, S) with
-        dtype=object. The elements are either ndarrays of shape (P,) containing the
-        correlation data for the specific window and selection set or None if the
-        corresponding selection set was empty.
-        W is the number of segments (windows).
-        S and P are the same as for average==True.
-
+) -> (np.ndarray, np.ndarray):
     """
+    Calculate the time series for a correlation function.
+
+    The times at which the correlation is calculated are determined by
+    a logarithmic distribution.
+
+    Args:
+        function: The function that should be correlated
+        frames: The coordinates of the simulation data
+        selector (opt.):
+                    A function that returns the indices depending on
+                    the staring frame for which particles the
+                    correlation should be calculated.
+        segments (int, opt.):
+                    The number of segments the time window will be
+                    shifted
+        skip (float, opt.):
+                    The fraction of the trajectory that will be skipped
+                    at the beginning, if this is None the start index
+                    of the frames slice will be used, which defaults
+                    to 0.1.
+        window (float, opt.):
+                    The fraction of the simulation the time series will
+                    cover
+        average (bool, opt.):
+                    If True, returns averaged correlation function
+        points (int, opt.):
+                    The number of timeshifts for which the correlation
+                    should be calculated
+    Returns:
+        tuple:
+            A list of length N that contains the timeshiftes of the frames at which
+            the time series was calculated and a numpy array of shape (segments, N)
+            that holds the (non-avaraged) correlation data
+
+    Example:
+        Calculating the mean square displacement of a coordinate object
+        named ``coords``:
+
+        >>> time, data = shifted_correlation(msd, coords)
+    """
+
+    def get_correlation(
+        frames: CoordinateFrame,
+        start_frame: CoordinateFrame,
+        index: np.ndarray,
+        shifted_idx: np.ndarray,
+    ) -> np.ndarray:
+        if len(index) == 0:
+            correlation = np.zeros(len(shifted_idx))
+        else:
+            start = frames[start_frame][index]
+            correlation = np.array(
+                [function(start, frames[frame][index]) for frame in shifted_idx]
+            )
+        return correlation
+
+    def apply_selector(
+        start_frame: CoordinateFrame,
+        frames: CoordinateFrame,
+        idx: np.ndarray,
+        selector: Optional[Callable] = None,
+    ):
+        shifted_idx = idx + start_frame
+
+        if selector is None:
+            index = np.arange(len(frames[start_frame]))
+            return get_correlation(frames, start_frame, index, shifted_idx)
+        else:
+            index = selector(frames[start_frame])
+            if len(index) == 0:
+                return np.zeros(len(shifted_idx))
+
+            elif (
+                isinstance(index[0], int)
+                or isinstance(index[0], bool)
+                or isinstance(index[0], np.integer)
+                or isinstance(index[0], np.bool_)
+            ):
+                return get_correlation(frames, start_frame, index, shifted_idx)
+            else:
+                correlations = []
+                for ind in index:
+                    if len(ind) == 0:
+                        correlations.append(np.zeros(len(shifted_idx)))
+
+                    elif (
+                        isinstance(ind[0], int)
+                        or isinstance(ind[0], bool)
+                        or isinstance(ind[0], np.integer)
+                        or isinstance(ind[0], np.bool_)
+                    ):
+                        correlations.append(
+                            get_correlation(frames, start_frame, ind, shifted_idx)
+                        )
+                    else:
+                        raise ValueError(
+                            "selector has more than two dimensions or does not "
+                            "contain int or bool types"
+                        )
+                return correlations
+
     if 1 - skip < window:
         window = 1 - skip
 
-    start_frame_indices = np.unique(
+    start_frames = np.unique(
         np.linspace(
             len(frames) * skip,
             len(frames) * (1 - window),
@@ -199,44 +144,28 @@ def shifted_correlation(
         )
     )
 
-    num_frames_per_window = int(len(frames) * window)
-    logspaced_indices = np.logspace(0, np.log10(num_frames_per_window + 1), num=points)
-    logspaced_indices = np.unique(np.int_(logspaced_indices) - 1)
-    logspaced_time = (
-        np.array([frames[i].time for i in logspaced_indices]) - frames[0].time
+    num_frames = int(len(frames) * window)
+    ls = np.logspace(0, np.log10(num_frames + 1), num=points)
+    idx = np.unique(np.int_(ls) - 1)
+    t = np.array([frames[i].time for i in idx]) - frames[0].time
+
+    result = np.array(
+        [
+            apply_selector(start_frame, frames=frames, idx=idx, selector=selector)
+            for start_frame in start_frames
+        ]
     )
 
-    if selector is None:
-        multi_selector = False
-    else:
-        selection = selector(frames[0])
-        multi_selector = _is_multi_selector(selection)
-
-    result = []
-    for start_frame_index in start_frame_indices:
-        shifted_idx = logspaced_indices + start_frame_index
-        start_frame = frames[start_frame_index]
-        if selector is None:
-            selection = np.arange(len(start_frame))
-        else:
-            selection = selector(start_frame)
-        if multi_selector:
-            result_segment = _calc_correlation_multi(
-                frames, start_frame, function, selection, shifted_idx
-            )
-        else:
-            result_segment = _calc_correlation(
-                frames, start_frame, function, selection, shifted_idx
-            )
-        result.append(result_segment)
-    result = np.array(result)
-
     if average:
-        if multi_selector:
-            result = _average_correlation_multi(result)
-        else:
-            result = _average_correlation(result)
-    return logspaced_time, result
+        clean_result = []
+        for entry in result:
+            if np.all(entry == 0):
+                continue
+            else:
+                clean_result.append(entry)
+        result = np.array(clean_result)
+        result = np.average(result, axis=0)
+    return t, result
 
 
 def msd(
@@ -255,11 +184,11 @@ def msd(
     if axis == "all":
         return (displacements**2).sum(axis=1).mean()
     elif axis == "xy" or axis == "yx":
-        return (displacements[:, [0, 1]] ** 2).sum(axis=1).mean()
+        return (displacements[:, [0, 1]]**2).sum(axis=1).mean()
     elif axis == "xz" or axis == "zx":
-        return (displacements[:, [0, 2]] ** 2).sum(axis=1).mean()
+        return (displacements[:, [0, 2]]**2).sum(axis=1).mean()
     elif axis == "yz" or axis == "zy":
-        return (displacements[:, [1, 2]] ** 2).sum(axis=1).mean()
+        return (displacements[:, [1, 2]]**2).sum(axis=1).mean()
     elif axis == "x":
         return (displacements[:, 0] ** 2).mean()
     elif axis == "y":
@@ -289,13 +218,13 @@ def isf(
         distance = (displacements**2).sum(axis=1) ** 0.5
         return np.sinc(distance * q / np.pi).mean()
     elif axis == "xy" or axis == "yx":
-        distance = (displacements[:, [0, 1]] ** 2).sum(axis=1) ** 0.5
+        distance = (displacements[:, [0, 1]]**2).sum(axis=1) ** 0.5
         return np.real(jn(0, distance * q)).mean()
     elif axis == "xz" or axis == "zx":
-        distance = (displacements[:, [0, 2]] ** 2).sum(axis=1) ** 0.5
+        distance = (displacements[:, [0, 2]]**2).sum(axis=1) ** 0.5
         return np.real(jn(0, distance * q)).mean()
     elif axis == "yz" or axis == "zy":
-        distance = (displacements[:, [1, 2]] ** 2).sum(axis=1) ** 0.5
+        distance = (displacements[:, [1, 2]]**2).sum(axis=1) ** 0.5
         return np.real(jn(0, distance * q)).mean()
     elif axis == "x":
         distance = np.abs(displacements[:, 0])
@@ -349,11 +278,11 @@ def van_hove_self(
     if axis == "all":
         delta_r = (vectors**2).sum(axis=1) ** 0.5
     elif axis == "xy" or axis == "yx":
-        delta_r = (vectors[:, [0, 1]] ** 2).sum(axis=1) ** 0.5
+        delta_r = (vectors[:, [0, 1]]**2).sum(axis=1) ** 0.5
     elif axis == "xz" or axis == "zx":
-        delta_r = (vectors[:, [0, 2]] ** 2).sum(axis=1) ** 0.5
+        delta_r = (vectors[:, [0, 2]]**2).sum(axis=1) ** 0.5
     elif axis == "yz" or axis == "zy":
-        delta_r = (vectors[:, [1, 2]] ** 2).sum(axis=1) ** 0.5
+        delta_r = (vectors[:, [1, 2]]**2).sum(axis=1) ** 0.5
     elif axis == "x":
         delta_r = np.abs(vectors[:, 0])
     elif axis == "y":
@@ -502,9 +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
     """
@@ -516,13 +445,13 @@ def non_gaussian_parameter(
         r = (vectors**2).sum(axis=1)
         dimensions = 3
     elif axis == "xy" or axis == "yx":
-        r = (vectors[:, [0, 1]] ** 2).sum(axis=1)
+        r = (vectors[:, [0, 1]]**2).sum(axis=1)
         dimensions = 2
     elif axis == "xz" or axis == "zx":
-        r = (vectors[:, [0, 2]] ** 2).sum(axis=1)
+        r = (vectors[:, [0, 2]]**2).sum(axis=1)
         dimensions = 2
     elif axis == "yz" or axis == "zy":
-        r = (vectors[:, [1, 2]] ** 2).sum(axis=1)
+        r = (vectors[:, [1, 2]]**2).sum(axis=1)
         dimensions = 2
     elif axis == "x":
         r = vectors[:, 0] ** 2

src/mdevaluate/distribution.py

@@ -182,10 +182,10 @@ def tetrahedral_order(
     )
 
     # Connection vectors
-    neighbors_1 -= atoms
-    neighbors_2 -= atoms
-    neighbors_3 -= atoms
-    neighbors_4 -= atoms
+    neighbors_1 = pbc_diff(neighbors_1, atoms, box=atoms.box)
+    neighbors_2 = pbc_diff(neighbors_2, atoms, box=atoms.box)
+    neighbors_3 = pbc_diff(neighbors_3, atoms, box=atoms.box)
+    neighbors_4 = pbc_diff(neighbors_4, atoms, box=atoms.box)
 
     # Normed Connection vectors
     neighbors_1 /= np.linalg.norm(neighbors_1, axis=-1).reshape(-1, 1)

src/mdevaluate/pbc.py

@@ -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

src/mdevaluate/reader.py

@@ -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):

src/mdevaluate/utils.py

@@ -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
 
 
@@ -177,7 +177,7 @@ def coherent_sum(
     func: Callable[[ArrayLike, ArrayLike], float],
     coord_a: ArrayLike,
     coord_b: ArrayLike,
-) -> NDArray:
+) -> float:
     """
     Perform a coherent sum over two arrays :math:`A, B`.
 

test/test_correlation.py

@@ -1,57 +0,0 @@
-import os
-import pytest
-
-import mdevaluate
-from mdevaluate import correlation
-import numpy as np
-
-
-@pytest.fixture
-def trajectory(request):
-    return mdevaluate.open(os.path.join(os.path.dirname(__file__), "data/water"))
-
-
-def test_shifted_correlation(trajectory):
-    test_array = np.array([100, 82, 65, 49, 39, 29, 20, 13, 7])
-    OW = trajectory.subset(atom_name="OW")
-    t, result = correlation.shifted_correlation(
-        correlation.isf, OW, segments=10, skip=0.1, points=10
-    )
-    assert (np.array(result * 100, dtype=int) == test_array).all()
-
-
-def test_shifted_correlation_no_average(trajectory):
-    t, result = correlation.shifted_correlation(
-        correlation.isf, trajectory, segments=10, skip=0.1, points=5, average=False
-    )
-    assert result.shape == (10, 5)
-
-
-def test_shifted_correlation_selector(trajectory):
-    test_array = np.array([100, 82, 64, 48, 37, 28, 19, 11, 5])
-
-    def selector(frame):
-        index = np.argwhere((frame[:, 0] >= 0) * (frame[:, 0] < 1))
-        return index.flatten()
-
-    OW = trajectory.subset(atom_name="OW")
-    t, result = correlation.shifted_correlation(
-        correlation.isf, OW, segments=10, skip=0.1, points=10, selector=selector
-    )
-    assert (np.array(result * 100, dtype=int) == test_array).all()
-
-
-def test_shifted_correlation_multi_selector(trajectory):
-    def selector(frame):
-        indices = []
-        for i in range(3):
-            x = frame[:, 0].flatten()
-            index = np.argwhere((x >= i) * (x < i + 1))
-            indices.append(index.flatten())
-        return indices
-
-    OW = trajectory.subset(atom_name="OW")
-    t, result = correlation.shifted_correlation(
-        correlation.isf, OW, segments=10, skip=0.1, points=10, selector=selector
-    )
-    assert result.shape == (3, 9)