Merge pull request #125 from xsuite/release/0.19.4

Apply fixes and relax some tolerances after scipy.constant changes

tests/test_basics.py

@@ -14,43 +14,43 @@
 
 def _check_consistency_energy_variables(particles):
     # Check consistency between beta0 and gamma0
-    assert np.allclose(particles.gamma0, 1/np.sqrt(1 - particles.beta0**2),
+    xo.assert_allclose(particles.gamma0, 1/np.sqrt(1 - particles.beta0**2),
                        rtol=1e-14, atol=1e-14)
 
     # Assert consistency of p0c
-    assert np.allclose(particles.p0c,
+    xo.assert_allclose(particles.p0c,
                        particles.mass0 * particles.beta0 * particles.gamma0,
                        rtol=1e-14, atol=1e-14)
 
     # Check energy0 property (consistency of p0c and gamma0)
-    assert np.allclose(particles.energy0, particles.mass0 * particles.gamma0,
+    xo.assert_allclose(particles.energy0, particles.mass0 * particles.gamma0,
                        atol=1e-14, rtol=1e-14)
 
     # Check consistency of rpp and delta
-    assert np.allclose(particles.rpp, 1./(particles.delta + 1),
+    xo.assert_allclose(particles.rpp, 1./(particles.delta + 1),
                        rtol=1e-14, atol=1e-14)
 
     beta = particles.beta0 * particles.rvv
     gamma = 1/np.sqrt(1 - beta**2)
     pc = particles.mass0 * gamma * beta
 
     # Check consistency of delta with rvv
-    assert np.allclose(particles.delta, (pc-particles.p0c)/(particles.p0c),
+    xo.assert_allclose(particles.delta, (pc-particles.p0c)/(particles.p0c),
                        rtol=1e-14, atol=1e-14)
 
     # Check consistency of ptau with rvv
     energy = particles.mass0 * gamma
-    assert np.allclose(particles.ptau, (energy - particles.energy0)/particles.p0c,
+    xo.assert_allclose(particles.ptau, (energy - particles.energy0)/particles.p0c,
                        rtol=1e-14, atol=1e-14)
 
     # Check consistency of pzeta
     energy = particles.mass0 * gamma
-    assert np.allclose(particles.pzeta, (energy - particles.energy0)/(particles.beta0 * particles.p0c),
+    xo.assert_allclose(particles.pzeta, (energy - particles.energy0)/(particles.beta0 * particles.p0c),
                        rtol=1e-14, atol=1e-14)
 
 
     # Check energy property
-    assert np.allclose(particles.energy, energy, rtol=1e-14, atol=1e-14)
+    xo.assert_allclose(particles.energy, energy, rtol=1e-14, atol=1e-14)
 
 
 @for_all_test_contexts
@@ -182,8 +182,8 @@ def test_particles_update_p0c_and_energy_deviations(test_context):
 
     part.move(_context=xo.ContextCpu())
     part.sort(interleave_lost_particles = True)
-    assert np.allclose(part.p0c, [2e12, 3e12, 2e12], rtol=0, atol=1e-14)
-    assert np.allclose(part.delta, [-0.5, 0.1, 0], rtol=0, atol=1e-14)
+    xo.assert_allclose(part.p0c, [2e12, 3e12, 2e12], rtol=0, atol=1e-14)
+    xo.assert_allclose(part.delta, [-0.5, 0.1, 0], rtol=0, atol=1e-14)
 
 
 def test_sort():
@@ -286,7 +286,7 @@ def test_python_add_to_energy(test_context):
 
     expected_energy = energy_before + 3e6
     particles.move(_context=xo.ContextCpu())
-    assert np.allclose(particles.energy, expected_energy,
+    xo.assert_allclose(particles.energy, expected_energy,
                        atol=1e-14, rtol=1e-14)
 
     _check_consistency_energy_variables(particles)
@@ -308,7 +308,7 @@ def test_python_delta_setter(test_context):
     particles.delta = -2e-3
 
     particles.move(_context=xo.ContextCpu())
-    assert np.allclose(particles.delta, -2e-3, atol=1e-14, rtol=1e-14)
+    xo.assert_allclose(particles.delta, -2e-3, atol=1e-14, rtol=1e-14)
 
     _check_consistency_energy_variables(particles)
 
@@ -352,7 +352,7 @@ class TestElement(xt.BeamElement):
     telem.track(particles)
 
     particles.move(_context=xo.ContextCpu())
-    assert np.allclose(particles.energy, energy_before + 1e6,
+    xo.assert_allclose(particles.energy, energy_before + 1e6,
                        atol=1e-14, rtol=1e-14)
 
     _check_consistency_energy_variables(particles)
@@ -378,17 +378,17 @@ class TestElement(xt.BeamElement):
     telem.track(particles)
 
     particles.move(_context=xo.ContextCpu())
-    assert np.allclose(particles.energy, energy_before + 1e6,
+    xo.assert_allclose(particles.energy, energy_before + 1e6,
                        atol=1e-14, rtol=1e-14)
 
     _check_consistency_energy_variables(particles)
 
     rpp_after = particles.copy(_context=xo.ContextCpu()).rpp
     assert np.all(particles.gamma0 == gamma0_before)
     assert np.all(particles.zeta == zeta_before)
-    assert np.allclose(particles.px, px_before*rpp_before/rpp_after,
+    xo.assert_allclose(particles.px, px_before*rpp_before/rpp_after,
                        atol=1e-14, rtol=1e-14)
-    assert np.allclose(particles.py, py_before*rpp_before/rpp_after,
+    xo.assert_allclose(particles.py, py_before*rpp_before/rpp_after,
                        atol=1e-14, rtol=1e-14)
 
 
@@ -423,7 +423,7 @@ class TestElement(xt.BeamElement):
     telem.track(particles)
 
     particles.move(_context=xo.ContextCpu())
-    assert np.allclose(particles.delta, -2e-3, atol=1e-14, rtol=1e-14)
+    xo.assert_allclose(particles.delta, -2e-3, atol=1e-14, rtol=1e-14)
 
     _check_consistency_energy_variables(particles)
 
@@ -464,7 +464,7 @@ class TestElement(xt.BeamElement):
     telem.track(particles)
 
     particles.move(_context=xo.ContextCpu())
-    assert np.allclose(particles.ptau, -2e-3, atol=1e-14, rtol=1e-14)
+    xo.assert_allclose(particles.ptau, -2e-3, atol=1e-14, rtol=1e-14)
 
     _check_consistency_energy_variables(particles)
 
@@ -506,7 +506,7 @@ class TestElement(xt.BeamElement):
     telem.track(particles)
 
     particles.move(_context=xo.ContextCpu())
-    assert np.allclose((particles.ptau - ptau_before)/particles.beta0,
+    xo.assert_allclose((particles.ptau - ptau_before)/particles.beta0,
                        -2e-3, atol=1e-14, rtol=1e-14)
 
     _check_consistency_energy_variables(particles)
@@ -538,6 +538,7 @@ class TestElement(xt.BeamElement):
 
     particles = xp.Particles(_context=test_context, p0c=1.4e9, delta=[0, 1e-3],
                              px=[1e-6, -1e-6], py=[2e-6, 0], zeta=0.1)
+
     _check_consistency_energy_variables(
                                 particles.copy(_context=xo.ContextCpu()))
     px_before = particles.copy(_context=xo.ContextCpu()).px
@@ -549,14 +550,14 @@ class TestElement(xt.BeamElement):
     telem.track(particles)
 
     particles.move(_context=xo.ContextCpu())
-    assert np.allclose(particles.p0c, 1.5e9, atol=1e-14, rtol=1e-14)
-    assert np.allclose(particles.energy, energy_before, atol=1e-14, rtol=1e-14)
+    xo.assert_allclose(particles.p0c, 1.5e9, atol=1e-14, rtol=1e-14)
+    xo.assert_allclose(particles.energy, energy_before, atol=1e-14, rtol=1e-14)
 
     _check_consistency_energy_variables(particles)
 
-    assert np.all(particles.zeta == zeta_before*particles.beta0/beta0_before)
-    assert np.all(particles.px == px_before*p0c_before/particles.p0c)
-    assert np.all(particles.py == py_before*p0c_before/particles.p0c)
+    xo.assert_allclose(particles.zeta, zeta_before*particles.beta0/beta0_before, atol=1e-14)
+    xo.assert_allclose(particles.px, px_before*p0c_before/particles.p0c, atol=1e-14)
+    xo.assert_allclose(particles.py, py_before*p0c_before/particles.p0c, atol=1e-14)
 
 
 
@@ -617,8 +618,8 @@ class KickAng(xt.BeamElement):
                              px=[1.0e-3, -1.0e-3], py=[2.0e-3, -1.2e-3], zeta=0.1)
     line.track(particles)
     particles.move(_context=xo.ContextCpu())
-    assert np.allclose(particles.px, [24.0e-3, 18.021e-3], atol=1e-14, rtol=1e-14)
-    assert np.allclose(particles.py, [-1.82e-3, -4.73564e-3], atol=1e-14, rtol=1e-14)
+    xo.assert_allclose(particles.px, [24.0e-3, 18.021e-3], atol=1e-14, rtol=1e-14)
+    xo.assert_allclose(particles.py, [-1.82e-3, -4.73564e-3], atol=1e-14, rtol=1e-14)
 
     class ScaleAngExact(xt.BeamElement):
         _xofields={
@@ -675,5 +676,5 @@ class KickAngExact(xt.BeamElement):
                              px=[1.0e-3, -1.0e-3], py=[2.0e-3, -1.2e-3], zeta=0.1)
     line.track(particles)
     particles.move(_context=xo.ContextCpu())
-    assert np.allclose(particles.px, [23.99302e-3, 18.01805e-3], atol=1e-14)
-    assert np.allclose(particles.py, [-1.81976e-3, -4.73529e-3], atol=1e-14)
+    xo.assert_allclose(particles.px, [23.99302e-3, 18.01805e-3], atol=1e-14)
+    xo.assert_allclose(particles.py, [-1.81976e-3, -4.73529e-3], atol=1e-14, rtol=5e-7)

tests/test_build_particles_normalized.py

@@ -38,7 +38,7 @@ def test_build_particles_normalized(test_context):
                                        nemitt_x=3e-6, nemitt_y=3e-6)
 
         dct = particles.to_dict() # transfers it to cpu
-        assert np.allclose(dct['x'], [-0.0003883 , -0.0006076 , -0.00082689],
+        xo.assert_allclose(dct['x'], [-0.0003883 , -0.0006076 , -0.00082689],
                            rtol=0, atol=1e-7)
         assert np.isclose(dct['ptau'][1], 1e-3, rtol=0, atol=1e-9)
         assert np.isclose(1/(dct['rpp'][1]) - 1, 1e-3, rtol=0, atol=1e-10)
@@ -56,7 +56,7 @@ def test_build_particles_normalized(test_context):
                                        px_norm=[0, 1, 0],  # in sigmas
                                        nemitt_x=3e-6, nemitt_y=3e-6)
         dct = particles.to_dict() # transfers it to cpu
-        assert np.allclose(dct['x'], [-0.0003883, -0.0006076, -0.00082689],
+        xo.assert_allclose(dct['x'], [-0.0003883, -0.0006076, -0.00082689],
                            rtol=0, atol=1e-7)
         assert np.isclose(dct['ptau'][1], 1e-3, rtol=0, atol=1e-9)
         assert np.isclose(1/(dct['rpp'][1]) - 1, 1e-3, rtol=0, atol=1e-10)
@@ -76,7 +76,7 @@ def test_build_particles_normalized(test_context):
                                        nemitt_x=3e-6, nemitt_y=3e-6)
 
         dct = particles.to_dict() # transfers it to cpu
-        assert np.allclose(dct['x'], [-0.00038813 , -0.00060738 , -0.00082664],
+        xo.assert_allclose(dct['x'], [-0.00038813 , -0.00060738 , -0.00082664],
                            rtol=0, atol=1e-7)
         assert np.isclose(dct['ptau'][1], 1e-3, rtol=0, atol=1e-9)
         assert np.isclose(1/(dct['rpp'][1]) - 1, 1e-3, rtol=0, atol=1e-10)
@@ -102,11 +102,11 @@ def test_build_particles_normalized_ions(test_context):
                                        nemitt_x=3e-6, nemitt_y=3e-6)
 
         dct = particles.to_dict() # transfers it to cpu
-        assert np.allclose(dct['x'], [6.5404e-3, 1.21e-5, -6.5163e-3],
+        xo.assert_allclose(dct['x'], [6.5404e-3, 1.21e-5, -6.5163e-3],
                            rtol=0, atol=1e-7)
         assert np.isclose(dct['ptau'][1], 9.906e-6, rtol=0, atol=1e-9)
         assert np.isclose(1/(dct['rpp'][1]) - 1, 1e-5, rtol=0, atol=1e-10)
-        assert np.allclose(dct['p0c'], 1.4024063e+12, rtol=0, atol=1e3)
+        xo.assert_allclose(dct['p0c'], 1.4024063e+12, rtol=0, atol=1e3)
 
 
 @for_all_test_contexts
@@ -140,7 +140,7 @@ def test_build_particles_normalized_closed_orbit(test_context):
         dct_co = particle_on_co.to_dict()
 
         for nn in 'x px y py zeta delta ptau rvv rpp gamma0 beta0 p0c'.split():
-            assert np.allclose(dct[nn], dct_co[nn], atol=1e-15, rtol=0)
+            xo.assert_allclose(dct[nn], dct_co[nn], atol=1e-15, rtol=0)
 
 
 @for_all_test_contexts
@@ -195,7 +195,7 @@ def test_build_particles_normalized_match_at_s(test_context):
         particles.move(_context=xo.context_default)
         assert (np.unique(particles.at_element[particles.state>0])[0]
                          == line.element_names.index('match_at_s'))
-        assert np.allclose(particles.x, 0.02, atol=1e-20)
+        xo.assert_allclose(particles.x, 0.02, atol=1e-20)
 
 
 @for_all_test_contexts
@@ -221,14 +221,14 @@ def test_build_perticles_dispersion(test_context):
                                     particles, nemitt_x=3e-6, nemitt_y=3e-6)
     particles.move(_context=xo.ContextCpu())
 
-    assert np.allclose(particles.x, [1e-3, -1e-3], atol=1e-10, rtol=0)
-    assert np.allclose((particles.x-tw.x[0])/particles.delta, tw.dx[0],
+    xo.assert_allclose(particles.x, [1e-3, -1e-3], atol=1e-10, rtol=0)
+    xo.assert_allclose((particles.x-tw.x[0])/particles.delta, tw.dx[0],
                        atol=5e-3, rtol=0)
 
-    assert np.allclose(norm_coords['x_norm'], 0, 1e-12)
-    assert np.allclose(norm_coords['px_norm'], 0, 1e-12)
-    assert np.allclose(norm_coords['y_norm'], 0, 1e-12)
-    assert np.allclose(norm_coords['py_norm'], 0, 1e-12)
+    xo.assert_allclose(norm_coords['x_norm'], 0, 1e-12)
+    xo.assert_allclose(norm_coords['px_norm'], 0, 1e-12)
+    xo.assert_allclose(norm_coords['y_norm'], 0, 1e-12)
+    xo.assert_allclose(norm_coords['py_norm'], 0, 1e-12)
 
     particles = line.build_particles(nemitt_x=3e-6, nemitt_y=3e-6,
                     x=[1e-3, -1e-3], x_norm=[0.3, 0.4], px_norm=[0.5, 0.6],
@@ -239,9 +239,9 @@ def test_build_perticles_dispersion(test_context):
                                     particles, nemitt_x=3e-6, nemitt_y=3e-6)
     particles.move(_context=xo.ContextCpu())
 
-    assert np.allclose(particles.x, [1e-3, -1e-3], atol=1e-10, rtol=0)
+    xo.assert_allclose(particles.x, [1e-3, -1e-3], atol=1e-10, rtol=0)
 
-    assert np.allclose(norm_coords['x_norm'], [0.3, 0.4], 1e-12)
-    assert np.allclose(norm_coords['px_norm'], [0.5, 0.6], 1e-12)
-    assert np.allclose(norm_coords['y_norm'], [0.7, 0.8], 1e-12)
-    assert np.allclose(norm_coords['py_norm'], [0.9, 1.0], 1e-12)
+    xo.assert_allclose(norm_coords['x_norm'], [0.3, 0.4], 1e-12)
+    xo.assert_allclose(norm_coords['px_norm'], [0.5, 0.6], 1e-12)
+    xo.assert_allclose(norm_coords['y_norm'], [0.7, 0.8], 1e-12)
+    xo.assert_allclose(norm_coords['py_norm'], [0.9, 1.0], 1e-12)

tests/test_pdg.py

@@ -39,7 +39,7 @@ def test_lead_208():
     assert _mass_consistent(pdg_id, xp.Pb208_MASS_EV)
     assert xp.pdg.get_element_name_from_Z(82) == 'Pb'
     assert xp.pdg.get_element_full_name_from_Z(82) == 'Lead'
-    assert np.allclose(xp.pdg.get_mass_from_pdg_id(pdg_id), xp.Pb208_MASS_EV,
+    xo.assert_allclose(xp.pdg.get_mass_from_pdg_id(pdg_id), xp.Pb208_MASS_EV,
                        rtol=1e-10, atol=0)
     assert xp.pdg.get_properties_from_pdg_id(pdg_id) == (82., 208, 82, 'Pb208')
 
@@ -52,5 +52,5 @@ def test_build_reference_from_pdg_id(test_context):
     particle_ref_lead = xp.reference_from_pdg_id(pdg_id='Pb208',
                                                  _context=test_context)
     particle_ref_lead.move(_context=xo.context_default)
-    assert np.allclose(particle_ref_lead.q0, 82.)
-    assert np.allclose(particle_ref_lead.mass0, xp.Pb208_MASS_EV)
+    xo.assert_allclose(particle_ref_lead.q0, 82.)
+    xo.assert_allclose(particle_ref_lead.mass0, xp.Pb208_MASS_EV)

tests/test_pencil_with_absolute_cut.py

@@ -114,8 +114,8 @@ def test_pencil_with_absolute_cut(test_context):
             w_norm = getattr(norm_coords, other_plane+'_norm')
             pw_norm = getattr(norm_coords, 'p'+other_plane+'_norm')
 
-            assert np.allclose(w_in_sigmas, w_norm, 1e-12)
-            assert np.allclose(pw_in_sigmas, pw_norm, 1e-12)
+            xo.assert_allclose(w_in_sigmas, w_norm, 1e-12)
+            xo.assert_allclose(pw_in_sigmas, pw_norm, 1e-12)
 
             assert(np.allclose(zeta, particles.zeta, atol=1e-12))
             assert(np.allclose(delta, particles.delta, atol=1e-12))

tests/test_phase_monitor.py

@@ -7,6 +7,7 @@
 
 import numpy as np
 
+import xobjects as xo
 import xpart as xp
 import xtrack as xt
 
@@ -38,8 +39,8 @@ def test_phase_monitor(test_context):
         line.track(particles)
 
     tw = line.twiss()
-    assert np.allclose(phase_monitor.qx[:], np.mod(tw['qx'], 1),
+    xo.assert_allclose(phase_monitor.qx[:], np.mod(tw['qx'], 1),
                        rtol=0, atol=1e-3)
-    assert np.allclose(phase_monitor.qy[:], np.mod(tw['qy'], 1),
+    xo.assert_allclose(phase_monitor.qy[:], np.mod(tw['qy'], 1),
                        rtol=0, atol=1e-3)