qdiffusivity 0.2.0__tar.gz → 0.2.1__tar.gz

{qdiffusivity-0.2.0 → qdiffusivity-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qdiffusivity
-Version: 0.2.0
+Version: 0.2.1
 Summary: Quantile-based estimation of local diffusivities in molecular dynamics simulations of nanoconfined liquids
 Author-email: Shern Ren Tee <shernren@gmail.com>
 Maintainer-email: Shern Ren Tee <shernren@gmail.com>

{qdiffusivity-0.2.0 → qdiffusivity-0.2.1}/qdiffusivity/density.py

@@ -74,6 +74,9 @@ import numpy as np
 from MDAnalysis.analysis.base import AnalysisBase
 from MDAnalysis.units import constants
 
+# Trapezoidal integration: np.trapezoid (NumPy >= 2.0) or np.trapz (older).
+_trapezoid = getattr(np, "trapezoid", None) or np.trapz
+
 # Epanechnikov kernel constants used by the Sheather-Jones plug-in.
 #   ||K||^2 = int K(u)^2 du = 3/5
 #   mu_2(K) = int u^2 K(u) du = 1/5
@@ -169,7 +172,7 @@ def sheather_jones_bw(z_data, z_lo, z_hi):
     kernel = np.where(np.abs(s) < 1.0, 0.75 * (1.0 - s * s) / h0, 0.0)
     f_pilot = kernel @ f_pilot_raw
 
-    integral = np.trapezoid(f_pilot, z_fine)
+    integral = _trapezoid(f_pilot, z_fine)
     if integral > 0:
         f_pilot = f_pilot / integral
 
@@ -178,7 +181,7 @@ def sheather_jones_bw(z_data, z_lo, z_hi):
     f_pp[0] = f_pp[1]
     f_pp[-1] = f_pp[-2]
 
-    int_fpp_sq = np.trapezoid(f_pp**2, z_fine)
+    int_fpp_sq = _trapezoid(f_pp**2, z_fine)
 
     if int_fpp_sq <= 0 or not np.isfinite(int_fpp_sq):
         return h_silver
@@ -406,8 +409,7 @@ class _TransverseDensityQKDEBase(AnalysisBase):
             "silverman",
         ):
             raise ValueError(
-                f"bandwidth must be 'auto', 'silverman' or "
-                f"a float, got {bandwidth!r}"
+                f"bandwidth must be 'auto', 'silverman' or a float, got {bandwidth!r}"
             )
         self._bandwidth = bandwidth
         self._chunk_size = int(chunk_size)
@@ -416,9 +418,7 @@ class _TransverseDensityQKDEBase(AnalysisBase):
         self._masses = self._ag.masses.astype(np.float64)
         if self._grouping == "residues":
             residx = self._ag.resindices
-            self._res_unique, self._res_inv = np.unique(
-                residx, return_inverse=True
-            )
+            self._res_unique, self._res_inv = np.unique(residx, return_inverse=True)
             self._n_res = self._res_unique.size
             self._res_mass = np.zeros(self._n_res, dtype=np.float64)
             np.add.at(self._res_mass, self._res_inv, self._masses)
@@ -458,10 +458,7 @@ class _TransverseDensityQKDEBase(AnalysisBase):
         z_bot = 0.0 if self._z_bot_user is None else float(self._z_bot_user)
         z_top = L if self._z_top_user is None else float(self._z_top_user)
         if z_top <= z_bot:
-            raise ValueError(
-                f"z_top ({z_top}) must be greater than "
-                f"z_bot ({z_bot})"
-            )
+            raise ValueError(f"z_top ({z_top}) must be greater than z_bot ({z_bot})")
 
         M = self._n_points
         self.z_eval = z_bot + (np.arange(M) + 0.5) * (z_top - z_bot) / M

{qdiffusivity-0.2.0 → qdiffusivity-0.2.1}/qdiffusivity/diffusivity.py

@@ -86,6 +86,9 @@ from MDAnalysis.analysis.base import AnalysisBase
 
 from .density import epanechnikov_kernel
 
+# Trapezoidal integration: np.trapezoid (NumPy >= 2.0) or np.trapz (older).
+_trapezoid = getattr(np, "trapezoid", None) or np.trapz
+
 # Gaussian-kernel constants for the Sheather-Jones plug-in.
 #   ||K||_2^2 = 1 / (2*sqrt(pi)),  mu_2(K) = 1
 _GAU_KERNEL_NORM_SQ = 1.0 / (2.0 * np.sqrt(np.pi))
@@ -131,10 +134,7 @@ def _kernel(name):
             _EPA_KERNEL_NORM_SQ,
             _EPA_KERNEL_MU2_SQ,
         )
-    raise ValueError(
-        f"kernel must be 'gaussian' or 'epanechnikov', "
-        f"got {name!r}"
-    )
+    raise ValueError(f"kernel must be 'gaussian' or 'epanechnikov', got {name!r}")
 
 
 def silverman_bw(u_data):
@@ -218,7 +218,7 @@ def sheather_jones_bw(u_data, kernel="gaussian"):
     kernel_vals = kernel_fn(diff, h0)
     f_pilot = kernel_vals @ f_pilot_raw
 
-    integral = np.trapezoid(f_pilot, u_fine)
+    integral = _trapezoid(f_pilot, u_fine)
     if integral > 0:
         f_pilot = f_pilot / integral
 
@@ -227,7 +227,7 @@ def sheather_jones_bw(u_data, kernel="gaussian"):
     f_pp[0] = f_pp[1]
     f_pp[-1] = f_pp[-2]
 
-    int_fpp_sq = np.trapezoid(f_pp**2, u_fine)
+    int_fpp_sq = _trapezoid(f_pp**2, u_fine)
 
     if int_fpp_sq <= 0 or not np.isfinite(int_fpp_sq):
         return h_silver
@@ -340,7 +340,7 @@ def build_cdf(z_pooled):
     kernel /= kernel.sum()
     rho_smooth = np.convolve(rho_padded, kernel, mode="same")[n_pad:-n_pad]
 
-    integral = np.trapezoid(rho_smooth, centers)
+    integral = _trapezoid(rho_smooth, centers)
     if integral > 0:
         rho_smooth = rho_smooth / integral
 
@@ -350,9 +350,7 @@ def build_cdf(z_pooled):
     # precedes the differencing, so the derivative is not dominated by
     # Poisson noise from the histogram bins).
     rho_prime_smooth = np.empty_like(rho_smooth)
-    rho_prime_smooth[1:-1] = (
-        rho_smooth[2:] - rho_smooth[:-2]
-    ) / (2.0 * bin_width)
+    rho_prime_smooth[1:-1] = (rho_smooth[2:] - rho_smooth[:-2]) / (2.0 * bin_width)
     rho_prime_smooth[0] = rho_prime_smooth[1]
     rho_prime_smooth[-1] = rho_prime_smooth[-2]
 
@@ -631,12 +629,9 @@ class LocalDiffusivityQKDE(AnalysisBase):
         self._dim = dim
         self._para_dims = tuple(i for i in (0, 1, 2) if i != dim)
         self._n_points = int(n_points)
-        if isinstance(bandwidth, str) and bandwidth not in (
-            "auto", "silverman"
-        ):
+        if isinstance(bandwidth, str) and bandwidth not in ("auto", "silverman"):
             raise ValueError(
-                f"bandwidth must be 'auto', 'silverman' or a float, "
-                f"got {bandwidth!r}"
+                f"bandwidth must be 'auto', 'silverman' or a float, got {bandwidth!r}"
             )
         self._bandwidth = bandwidth
         if kernel not in ("gaussian", "epanechnikov"):

{qdiffusivity-0.2.0 → qdiffusivity-0.2.1}/qdiffusivity/tests/test_binned.py

@@ -11,6 +11,8 @@ from qdiffusivity.binned import (
     resolve_bins,
 )
 
+_trapezoid = getattr(np, "trapezoid", None) or np.trapz
+
 
 def test_resolve_bins():
     """int, 'quantile', explicit edges (padded/full), and invalid specs."""
@@ -132,12 +134,8 @@ def test_diffusivity_binned(diff_universe, bins, expected_n):
     assert binned.dt == pytest.approx(1.0)
     bulk = (binned.z_centers > 20) & (binned.z_centers < 40)
     valid = binned.n_eff_perp > 5
-    assert np.median(
-        binned.D_perp[bulk & valid]
-    ) == pytest.approx(D_perp_true, rel=0.3)
-    assert np.median(
-        binned.D_para[bulk & valid]
-    ) == pytest.approx(D_para_true, rel=0.3)
+    assert np.median(binned.D_perp[bulk & valid]) == pytest.approx(D_perp_true, rel=0.3)
+    assert np.median(binned.D_para[bulk & valid]) == pytest.approx(D_para_true, rel=0.3)
 
 
 @pytest.mark.parametrize(
@@ -149,9 +147,7 @@ def test_diffusivity_binned(diff_universe, bins, expected_n):
         (LocalDiffusivityQBinned, {"dim": 5}, True),
     ],
 )
-def test_binned_validation(
-    density_universe, diff_universe, cls, kwargs, use_diff
-):
+def test_binned_validation(density_universe, diff_universe, cls, kwargs, use_diff):
     if use_diff:
         u = diff_universe(n_atoms=10, n_frames=3, Lz=10.0)
     else:
@@ -171,7 +167,9 @@ def test_diffusivity_binned_explicit_dt(diff_universe):
     u = diff_universe(n_atoms=50, n_frames=5, Lz=40.0, seed=68)
     binned = LocalDiffusivityQBinned(
         u.select_atoms("all"),
-        dim=2, bins=10, dt=2.0,
+        dim=2,
+        bins=10,
+        dt=2.0,
     )
     binned.run()
     assert binned.dt == pytest.approx(2.0)
@@ -183,9 +181,7 @@ def test_diffusivity_binned_ito(diff_universe, ito):
     on D_para."""
     u = diff_universe(n_atoms=200, n_frames=20, Lz=60.0, seed=66)
     ag = u.select_atoms("all")
-    binned = LocalDiffusivityQBinned(
-        ag, dim=2, bins=15, ito_correction=ito
-    )
+    binned = LocalDiffusivityQBinned(ag, dim=2, bins=15, ito_correction=ito)
     binned.run()
     if not ito:
         assert binned.ito_bias is None

{qdiffusivity-0.2.0 → qdiffusivity-0.2.1}/qdiffusivity/tests/test_density.py

@@ -12,17 +12,15 @@ from qdiffusivity.density import (
     silverman_bw,
 )
 
+_trapezoid = getattr(np, "trapezoid", None) or np.trapz
+
 
 def test_epanechnikov_kernel():
     """Normalised, compact support, non-negative, peak at zero."""
     x = np.linspace(-3.0, 3.0, 200_001)
-    assert np.trapezoid(epanechnikov_kernel(x, 1.0), x) == pytest.approx(
-        1.0, abs=1e-4
-    )
+    assert _trapezoid(epanechnikov_kernel(x, 1.0), x) == pytest.approx(1.0, abs=1e-4)
     assert epanechnikov_kernel(np.array([1.6]), 1.5)[0] == 0.0
-    assert epanechnikov_kernel(np.array([0.0]), 1.5)[0] == pytest.approx(
-        0.75 / 1.5
-    )
+    assert epanechnikov_kernel(np.array([0.0]), 1.5)[0] == pytest.approx(0.75 / 1.5)
     assert np.all(epanechnikov_kernel(x, 2.0) >= 0.0)
 
 
@@ -49,7 +47,7 @@ def test_kde_1d():
     z = rng.normal(50.0, 5.0, size=20_000)
     z_eval = np.linspace(20.0, 80.0, 2001)
     rho, n_eff = kde_1d(z, z_eval, 0.5, 0.0, 100.0)
-    assert np.trapezoid(rho, z_eval) == pytest.approx(1.0, abs=0.02)
+    assert _trapezoid(rho, z_eval) == pytest.approx(1.0, abs=0.02)
     interior = (z_eval > 40) & (z_eval < 60)
     assert np.all(n_eff[interior] > 0)
     assert np.all(n_eff <= z.size)
@@ -59,9 +57,7 @@ def test_kde_1d():
     assert np.all(rho_e == 0.0) and np.all(n_eff_e == 0.0)
 
 
-@pytest.mark.parametrize(
-    "cls", [TransverseNumDensityQKDE, TransverseMassDensityQKDE]
-)
+@pytest.mark.parametrize("cls", [TransverseNumDensityQKDE, TransverseMassDensityQKDE])
 @pytest.mark.parametrize("grouping", ["atoms", "residues"])
 def test_density_qkde(density_universe, cls, grouping):
     """Run, attributes, density positive, auto bandwidth."""
@@ -142,9 +138,7 @@ def test_density_qkde_auto_boundaries(density_universe):
     assert kde.z_eval[-1] < 40.0
 
 
-@pytest.mark.parametrize(
-    "cls", [TransverseNumDensityQKDE, TransverseMassDensityQKDE]
-)
+@pytest.mark.parametrize("cls", [TransverseNumDensityQKDE, TransverseMassDensityQKDE])
 @pytest.mark.parametrize(
     "kwargs",
     [{"dim": 5}, {"grouping": "molecules"}, {"bandwidth": "bogus"}],
@@ -155,9 +149,7 @@ def test_density_qkde_validation(density_universe, cls, kwargs):
         cls(u.select_atoms("all"), **kwargs)
 
 
-@pytest.mark.parametrize(
-    "cls", [TransverseNumDensityQKDE, TransverseMassDensityQKDE]
-)
+@pytest.mark.parametrize("cls", [TransverseNumDensityQKDE, TransverseMassDensityQKDE])
 def test_density_qkde_inverted_boundaries(density_universe, cls):
     u = density_universe(n_atoms=10, n_res=2, n_frames=1, Lz=10.0)
     kde = cls(

{qdiffusivity-0.2.0 → qdiffusivity-0.2.1}/qdiffusivity/tests/test_diffusivity.py

@@ -12,13 +12,13 @@ from qdiffusivity.diffusivity import (
     select_diff_bandwidth,
 )
 
+_trapezoid = getattr(np, "trapezoid", None) or np.trapz
+
 
 def test_gaussian_kernel():
     """Normalised, symmetric, peak at zero."""
     x = np.linspace(-10.0, 10.0, 200_001)
-    assert np.trapezoid(
-        gaussian_kernel(x, 1.0), x
-    ) == pytest.approx(1.0, abs=1e-4)
+    assert _trapezoid(gaussian_kernel(x, 1.0), x) == pytest.approx(1.0, abs=1e-4)
     k = gaussian_kernel(np.array([-3, -1, 0, 1, 3.0]), 1.5)
     assert k[0] == pytest.approx(k[-1])
     assert k[2] > k[1] > k[0]
@@ -56,7 +56,7 @@ def test_build_cdf():
     assert np.allclose(z_back, z_grid, atol=0.1)
     rho_vals = rho(z_grid)
     assert np.all(rho_vals >= 0)
-    assert np.trapezoid(rho_vals, z_grid) == pytest.approx(1.0, abs=0.1)
+    assert _trapezoid(rho_vals, z_grid) == pytest.approx(1.0, abs=0.1)
     rho_p = rho_prime(np.array([45.0, 50.0, 55.0]))
     assert rho_p[0] > 0 and rho_p[2] < 0
     assert rho_p[1] == pytest.approx(0.0, abs=2e-3)
@@ -130,12 +130,8 @@ def test_diffusivity_qkde(diff_universe, kernel):
     assert np.all(kde.D_perp >= 0)
     bulk = (kde.z_eval > 20) & (kde.z_eval < 40)
     valid = kde.n_eff_perp > 5
-    assert np.median(
-        kde.D_perp[bulk & valid]
-    ) == pytest.approx(D_perp_true, rel=0.3)
-    assert np.median(
-        kde.D_para[bulk & valid]
-    ) == pytest.approx(D_para_true, rel=0.3)
+    assert np.median(kde.D_perp[bulk & valid]) == pytest.approx(D_perp_true, rel=0.3)
+    assert np.median(kde.D_para[bulk & valid]) == pytest.approx(D_para_true, rel=0.3)
 
 
 @pytest.mark.parametrize(
@@ -151,7 +147,8 @@ def test_diffusivity_qkde_single_frame_raises(diff_universe):
     u = diff_universe(n_atoms=10, n_frames=1, Lz=10.0)
     kde = LocalDiffusivityQKDE(
         u.select_atoms("all"),
-        n_points=10, bandwidth=0.1,
+        n_points=10,
+        bandwidth=0.1,
     )
     with pytest.raises(ValueError):
         kde.run()
@@ -204,9 +201,7 @@ def test_ito_correction(diff_universe, ito):
     kde2.run()
     bulk2 = (kde2.z_eval > 20) & (kde2.z_eval < 40)
     valid2 = kde2.n_eff_perp > 5
-    assert np.median(
-        kde2.D_perp[bulk2 & valid2]
-    ) == pytest.approx(0.05, rel=0.3)
+    assert np.median(kde2.D_perp[bulk2 & valid2]) == pytest.approx(0.05, rel=0.3)
 
 
 def test_package_exports():

{qdiffusivity-0.2.0 → qdiffusivity-0.2.1}/qdiffusivity.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qdiffusivity
-Version: 0.2.0
+Version: 0.2.1
 Summary: Quantile-based estimation of local diffusivities in molecular dynamics simulations of nanoconfined liquids
 Author-email: Shern Ren Tee <shernren@gmail.com>
 Maintainer-email: Shern Ren Tee <shernren@gmail.com>