Refactor tests

.gitignore

@@ -43,3 +43,11 @@ build/
 test/data
 test/.coverage
 test/coverage.xml
+examples/data/continuum/traj.h5amep
+examples/data/continuum/#traj.h5amep
+examples/data/continuum/##temp*
+examples/data/trajs/
+examples/data/lammps/traj.h5amep
+examples/data/lammps/#traj.h5amep
+examples/data/lammps/##temp*
+examples/data/invalid

amep/continuum.py

@@ -32,6 +32,7 @@
 # =============================================================================
 # IMPORT MODULES
 # =============================================================================
+from packaging.version import Version
 import numpy as np
 import scipy.fft as fft
 
@@ -782,8 +783,12 @@ def cluster_properties(
         # set all grid points outside the cluster to zero
         y[labels != i] = 0
         # integral
-        N = np.trapz(y, x=X, axis=1)
-        N = np.trapz(N, x=Y[:, 0])
+        if Version(np.__version__)<Version("2.0.0"):
+            N = np.trapz(y, x=X, axis=1)
+            N = np.trapz(N, x=Y[:, 0])
+        else:
+            N = np.trapezoid(y, x=X, axis=1)
+            N = np.trapezoid(N, x=Y[:, 0])
         sizes.append(N)
 
     # calculate the radius of gyration and linear extension

amep/evaluate.py

@@ -31,6 +31,7 @@
 # =============================================================================
 # IMPORT MODULES
 # =============================================================================
+from packaging.version import Version
 import warnings
 import numpy as np
 
@@ -1840,16 +1841,22 @@ def __compute(self):
                                               (self.__k0[i][0]*np.cos(self.__theta) +\
                                               self.__k0[i][1]*np.sin(self.__theta)))
 
-            ck += np.trapz(integrand, x=self.__theta, axis=1)
-
+            if Version(np.__version__) < Version("2.0.0"):
+                ck += np.trapz(integrand, x=self.__theta, axis=1)
+            else:
+                ck += np.trapezoid(integrand, x=self.__theta, axis=1)
+
         ck = np.abs(ck/len(self.__k0))
 
         # normalization
-        norm = np.trapz(self.__grt, x=self.__theta, axis=1)
+        if Version(np.__version__) < Version("2.0.0"):
+            norm = np.trapz(self.__grt, x=self.__theta, axis=1)
+        else:
+            norm = np.trapezoid(self.__grt, x=self.__theta, axis=1)
 
         return ck/norm
-    
-    
+
+
     def __getk(self):
         r'''
         Calculates the k vectors corresponding to the first peaks of 
@@ -3191,15 +3198,26 @@ def __init__(
             if self.__xmax is None:
                 if self.__use_density:
                     # integrated density
-                    val_total_x = np.trapz(
-                        self.__traj[-1].data(self.__ftype),
-                        x = self.__traj[-1].grid[0],
-                        axis=1
-                    )
-                    val_total = np.trapz(
-                        val_total_x,
-                        x = self.__traj[-1].grid[1][:, 0]
-                    )
+                    if Version(np.__version) < Version("2.0.0"):
+                        val_total_x = np.trapz(
+                            self.__traj[-1].data(self.__ftype),
+                            x=self.__traj[-1].grid[0],
+                            axis=1
+                        )
+                        val_total = np.trapz(
+                            val_total_x,
+                            x=self.__traj[-1].grid[1][:, 0]
+                        )
+                    else:
+                        val_total_x = np.trapezoid(
+                            self.__traj[-1].data(self.__ftype),
+                            x=self.__traj[-1].grid[0],
+                            axis=1
+                        )
+                        val_total = np.trapezoid(
+                            val_total_x,
+                            x=self.__traj[-1].grid[1][:, 0]
+                        )
                     self.__xmax = val_total
                 else:
                     # total number of grid points

amep/utils.py

@@ -31,6 +31,7 @@
 # =============================================================================
 import os
 import time
+from packaging.version import Version
 
 import numpy as np
 
@@ -1188,10 +1189,14 @@ def sq_from_gr(
     '''
     if twod:
         ydata = ((gr - 1) * r).reshape(-1, 1) * special.jv(0, r.reshape(-1, 1) * q.reshape(1, -1))
-        return np.trapz(x=r, y=ydata, axis=0) * (2 * np.pi * rho) + 1
+        if Version(np.__version__) < Version("2.0.0"):
+            return np.trapz(x=r, y=ydata, axis=0) * (2 * np.pi * rho) + 1
+        return np.trapezoid(x=r, y=ydata, axis=0) * (2 * np.pi * rho) + 1
     else:
         ydata = ((gr - 1) * r).reshape(-1, 1) * np.sin(r.reshape(-1, 1) * q.reshape(1, -1))
-        return np.trapz(x=r, y=ydata, axis=0) * (4 * np.pi * rho / q) + 1    
+        if Version(np.__version__) < Version("2.0.0"):
+            return np.trapz(x=r, y=ydata, axis=0) * (4 * np.pi * rho / q) + 1
+        return np.trapezoid(x=r, y=ydata, axis=0) * (4 * np.pi * rho / q) + 1
 
 
 def sq_from_sf2d(
@@ -1273,7 +1278,10 @@ def msd_from_vacf(vacf, times):
         Time values as 1D array.
 
     '''
-    msd = 2*np.array([np.trapz((times[i]-times[:i+1])*vacf[:i+1], x=times[:i+1]) for i in range(len(times))])
+    if Version(np.__version__) < Version("2.0.0"):
+        msd = 2*np.array([np.trapz((times[i]-times[:i+1])*vacf[:i+1], x=times[:i+1]) for i in range(len(times))])
+    else:
+        msd = 2*np.array([np.trapezoid((times[i]-times[:i+1])*vacf[:i+1], x=times[:i+1]) for i in range(len(times))])
     return msd, times
 
 
@@ -1385,7 +1393,9 @@ def domain_length(
         s_fac = s_fac[q<=qmax]
         q = q[q<=qmax]
 
-    return 2*np.pi*(np.trapz(s_fac, x=q)/np.trapz(s_fac*q, x=q))
+    if Version(np.__version__) < Version("2.0.0"):
+        return 2*np.pi*(np.trapz(s_fac, x=q)/np.trapz(s_fac*q, x=q))
+    return 2*np.pi*(np.trapezoid(s_fac, x=q)/np.trapezoid(s_fac*q, x=q))
 
 
 # =============================================================================

pyproject.toml

@@ -33,7 +33,7 @@ dependencies = [
     "h5py >= 3.7.0",
     "matplotlib >= 3.6.2",
     "numba >= 0.56.4",
-    "numpy >= 1.21.6",
+    "numpy >= 1.26.6",
     "scipy >= 1.10.0",
     "scikit-image >= 0.20.0",
     "tqdm >= 4.65.0"