updated allclose to deal with zeros and update all traj conversion files

ISISNeutronMuon · Mar 3, 2025 · 6ea49cd · 6ea49cd
1 parent 17c6560
commit 6ea49cd
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Showing 40 changed files with 58 additions and 48 deletions.
diff --git a/MDANSE/Tests/UnitTests/Analysis/test_dynamics.py b/MDANSE/Tests/UnitTests/Analysis/test_dynamics.py
@@ -71,11 +71,11 @@ def test_vacf(interp_order, normalise):
             if normalise:
                 np.testing.assert_allclose(
                     actual[f"/{key}"] * actual[f"/{key}"].attrs["scaling_factor"],
-                    desired[f"/{key}"],
+                    desired[f"/{key}"], atol=1e-8
                 )
             else:
                 np.testing.assert_allclose(
-                    actual[f"/{key}"], desired[f"/{key}"],
+                    actual[f"/{key}"], desired[f"/{key}"], atol=1e-8
                 )
 
     os.remove(temp_name + ".mda")
@@ -111,7 +111,7 @@ def test_pps():
         ]:
             np.testing.assert_allclose(
                 actual[f"/{key}"] * actual[f"/{key}"].attrs["scaling_factor"],
-                desired[f"/{key}"],
+                desired[f"/{key}"], atol=1e-8
             )
 
     os.remove(temp_name + ".mda")
@@ -201,11 +201,11 @@ def test_dynamics_analysis(
                 if job_info[2]:
                     np.testing.assert_allclose(
                         actual[f"/{key}"] * actual[f"/{key}"].attrs["scaling_factor"],
-                        desired[f"/{key}"],
+                        desired[f"/{key}"], atol=1e-8
                     )
                 else:
                     np.testing.assert_allclose(
-                        actual[f"/{key}"], desired[f"/{key}"],
+                        actual[f"/{key}"], desired[f"/{key}"], atol=1e-8
                     )
 
         os.remove(temp_name + ".mda")

diff --git a/MDANSE/Tests/UnitTests/Analysis/test_infrared.py b/MDANSE/Tests/UnitTests/Analysis/test_infrared.py
@@ -51,7 +51,8 @@ def test_dacf_analysis():
 
     with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
         np.testing.assert_allclose(
-            actual["/dacf"] * actual["/dacf"].attrs["scaling_factor"], desired["/dacf"]
+            actual["/dacf"] * actual["/dacf"].attrs["scaling_factor"],
+            desired["/dacf"], atol=1e-8
         )
 
     os.remove(temp_name + ".mda")
@@ -94,10 +95,11 @@ def test_ir_analysis():
     with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
         np.testing.assert_allclose(
             actual["/ddacf"] * actual["/ddacf"].attrs["scaling_factor"],
-            desired["/ddacf"],
+            desired["/ddacf"], atol=1e-8
         )
         np.testing.assert_allclose(
-            actual["/ir"] * actual["/ir"].attrs["scaling_factor"], desired["/ir"]
+            actual["/ir"] * actual["/ir"].attrs["scaling_factor"],
+            desired["/ir"], atol=1e-8
         )
 
     os.remove(temp_name + ".mda")

diff --git a/MDANSE/Tests/UnitTests/Analysis/test_mdmc_h5md.py b/MDANSE/Tests/UnitTests/Analysis/test_mdmc_h5md.py
@@ -46,16 +46,16 @@ def test_h5md_temperature(trajectory, interp_order):
 
     with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
         np.testing.assert_allclose(
-            actual["/kinetic_energy"], desired["/kinetic_energy"]
+            actual["/kinetic_energy"], desired["/kinetic_energy"], atol=1e-8
         )
         np.testing.assert_allclose(
-            actual["/temperature"], desired["/temperature"]
+            actual["/temperature"], desired["/temperature"], atol=1e-8
         )
         np.testing.assert_allclose(
-            actual["/avg_kinetic_energy"], desired["/avg_kinetic_energy"]
+            actual["/avg_kinetic_energy"], desired["/avg_kinetic_energy"], atol=1e-8
         )
         np.testing.assert_allclose(
-            actual["/avg_temperature"], desired["/avg_temperature"]
+            actual["/avg_temperature"], desired["/avg_temperature"], atol=1e-8
         )
 
     os.remove(temp_name + ".mda")
diff --git a/MDANSE/Tests/UnitTests/Analysis/test_meansquare.py b/MDANSE/Tests/UnitTests/Analysis/test_meansquare.py
@@ -45,11 +45,11 @@ def test_basic_meansquare():
     result_file = os.path.join(result_dir, "basic_meansquare.mda")
 
     with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
-        np.testing.assert_allclose(actual["/msd_Cu"], desired["/msd_Cu"])
-        np.testing.assert_allclose(actual["/msd_S"], desired["/msd_S"])
-        np.testing.assert_allclose(actual["/msd_Sb"], desired["/msd_Sb"])
+        np.testing.assert_allclose(actual["/msd_Cu"], desired["/msd_Cu"], atol=1e-8)
+        np.testing.assert_allclose(actual["/msd_S"], desired["/msd_S"], atol=1e-8)
+        np.testing.assert_allclose(actual["/msd_Sb"], desired["/msd_Sb"], atol=1e-8)
         np.testing.assert_allclose(
-            actual["/msd_total"], desired["/msd_total"]
+            actual["/msd_total"], desired["/msd_total"], atol=1e-8
         )
 
     os.remove(temp_name + ".mda")
@@ -82,7 +82,7 @@ def test_parallel_meansquare():
         for kk in single.keys():
             if not "metadata" in kk:
                 np.testing.assert_allclose(
-                    np.array(single[kk]), np.array(parallel[kk])
+                    np.array(single[kk]), np.array(parallel[kk]), atol=1e-8
                 )
     os.remove(temp_name + ".mda")
     os.remove(temp_name2 + ".mda")
diff --git a/MDANSE/Tests/UnitTests/Analysis/test_mock_dynamics.py b/MDANSE/Tests/UnitTests/Analysis/test_mock_dynamics.py
@@ -55,11 +55,11 @@ def test_vacf(interp_order, normalise):
             if normalise:
                 np.testing.assert_allclose(
                     actual[f"/{key}"] * actual[f"/{key}"].attrs["scaling_factor"],
-                    desired[f"/{key}"],
+                    desired[f"/{key}"], atol=1e-8
                 )
             else:
                 np.testing.assert_allclose(
-                    actual[f"/{key}"], desired[f"/{key}"],
+                    actual[f"/{key}"], desired[f"/{key}"], atol=1e-8
                 )
 
     os.remove(temp_name + ".mda")

diff --git a/MDANSE/Tests/UnitTests/Analysis/test_molecule_names.py b/MDANSE/Tests/UnitTests/Analysis/test_molecule_names.py
@@ -75,7 +75,7 @@ def test_structure_analysis(parameters, job_info):
 
     with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
         for key in job_info[1]:
-            np.testing.assert_allclose(actual[f"/{key}"], desired[f"/{key}"])
+            np.testing.assert_allclose(actual[f"/{key}"], desired[f"/{key}"], atol=1e-8)
 
     os.remove(temp_name + ".mda")
     assert path.exists(temp_name + ".log")

diff --git a/MDANSE/Tests/UnitTests/Analysis/test_resolutions.py b/MDANSE/Tests/UnitTests/Analysis/test_resolutions.py
@@ -112,7 +112,7 @@ def test_dos(trajectory, resolution_generator):
         ]:
             np.testing.assert_allclose(
                 actual[f"/{key}"] * actual[f"/{key}"].attrs["scaling_factor"],
-                desired[f"/{key}"],
+                desired[f"/{key}"], atol=1e-8
             )
 
     os.remove(temp_name + ".mda")

diff --git a/MDANSE/Tests/UnitTests/Analysis/test_scattering.py b/MDANSE/Tests/UnitTests/Analysis/test_scattering.py
@@ -117,6 +117,7 @@ def test_dcsf(traj_info, qvector_grid):
             np.testing.assert_allclose(
                 actual[f"/{key}"] * actual[f"/{key}"].attrs["scaling_factor"],
                 desired[f"/{key}"] * desired[f"/{key}"].attrs["scaling_factor"],
+                atol=1e-8
             )
 
     os.remove(temp_name + ".mda")
@@ -157,7 +158,7 @@ def test_ccf(traj_info, qvector_grid):
         for key in keys:
             # reference results were not rescaled
             np.testing.assert_allclose(
-                actual[f"/{key}"], desired[f"/{key}"],
+                actual[f"/{key}"], desired[f"/{key}"], atol=1e-8
             )
 
     os.remove(temp_name + ".mda")
@@ -218,6 +219,7 @@ def test_disf(traj_info, qvector_grid):
             np.testing.assert_allclose(
                 actual[f"/{key}"] * actual[f"/{key}"].attrs["scaling_factor"],
                 desired[f"/{key}"] * desired[f"/{key}"].attrs["scaling_factor"],
+                atol=1e-8
             )
 
     os.remove(temp_name + ".mda")
@@ -255,7 +257,7 @@ def test_eisf(traj_info, qvector_grid):
         for key in keys:
             np.testing.assert_allclose(
                 actual[f"/{key}"] * actual[f"/{key}"].attrs["scaling_factor"],
-                desired[f"/{key}"],
+                desired[f"/{key}"], atol=1e-8
             )
 
     os.remove(temp_name + ".mda")
@@ -297,6 +299,7 @@ def test_gdisf(traj_info):
             np.testing.assert_allclose(
                 actual[f"/{key}"] * actual[f"/{key}"].attrs["scaling_factor"],
                 desired[f"/{key}"] * desired[f"/{key}"].attrs["scaling_factor"],
+                atol=1e-8
             )
 
     os.remove(temp_name + ".mda")
@@ -330,7 +333,7 @@ def test_ndtsf(disf, dcsf, qvector_grid):
         ]
         for key in keys:
             np.testing.assert_allclose(
-                actual[f"/{key}"], desired[f"/{key}"],
+                actual[f"/{key}"], desired[f"/{key}"], atol=1e-8
             )
 
     os.remove(temp_name + ".mda")

diff --git a/MDANSE/Tests/UnitTests/Analysis/test_structure.py b/MDANSE/Tests/UnitTests/Analysis/test_structure.py
@@ -129,7 +129,7 @@ def test_structure_analysis(
             keys = [i for i in desired.keys() if any([j in i for j in job_info[1]])]
             for key in keys:
                 np.testing.assert_allclose(
-                    actual[f"/{key}"], desired[f"/{key}"]
+                    actual[f"/{key}"], desired[f"/{key}"], atol=1e-8
                 )
 
         os.remove(temp_name + ".mda")

diff --git a/MDANSE/Tests/UnitTests/Analysis/test_thermodynamics.py b/MDANSE/Tests/UnitTests/Analysis/test_thermodynamics.py
@@ -64,16 +64,16 @@ def test_temperature(traj_info, interp_order):
 
     with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
         np.testing.assert_allclose(
-            actual["/kinetic_energy"], desired["/kinetic_energy"]
+            actual["/kinetic_energy"], desired["/kinetic_energy"], atol=1e-8
         )
         np.testing.assert_allclose(
-            actual["/temperature"], desired["/temperature"]
+            actual["/temperature"], desired["/temperature"], atol=1e-8
         )
         np.testing.assert_allclose(
-            actual["/avg_kinetic_energy"], desired["/avg_kinetic_energy"]
+            actual["/avg_kinetic_energy"], desired["/avg_kinetic_energy"], atol=1e-8
         )
         np.testing.assert_allclose(
-            actual["/avg_temperature"], desired["/avg_temperature"]
+            actual["/avg_temperature"], desired["/avg_temperature"], atol=1e-8
         )
 
     os.remove(temp_name + ".mda")
@@ -110,16 +110,16 @@ def test_density(traj_info, output_format):
 
         with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
             np.testing.assert_allclose(
-                actual["/atomic_density"], desired["/atomic_density"]
+                actual["/atomic_density"], desired["/atomic_density"], atol=1e-8
             )
             np.testing.assert_allclose(
-                actual["/mass_density"], desired["/mass_density"]
+                actual["/mass_density"], desired["/mass_density"], atol=1e-8
             )
             np.testing.assert_allclose(
-                actual["/avg_atomic_density"], desired["/avg_atomic_density"]
+                actual["/avg_atomic_density"], desired["/avg_atomic_density"], atol=1e-8
             )
             np.testing.assert_allclose(
-                actual["/avg_mass_density"], desired["/avg_mass_density"]
+                actual["/avg_mass_density"], desired["/avg_mass_density"], atol=1e-8
             )
 
         os.remove(temp_name + ".mda")

diff --git a/MDANSE/Tests/UnitTests/Converted/ase.mdt b/MDANSE/Tests/UnitTests/Converted/ase.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/ase_xyz.mdt b/MDANSE/Tests/UnitTests/Converted/ase_xyz.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/castep.mdt b/MDANSE/Tests/UnitTests/Converted/castep.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/cp2k.mdt b/MDANSE/Tests/UnitTests/Converted/cp2k.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/cp2k_srtio3.mdt b/MDANSE/Tests/UnitTests/Converted/cp2k_srtio3.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/cp2k_velocity.mdt b/MDANSE/Tests/UnitTests/Converted/cp2k_velocity.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/dftb.mdt b/MDANSE/Tests/UnitTests/Converted/dftb.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/discover.mdt b/MDANSE/Tests/UnitTests/Converted/discover.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/dlp_v2.mdt b/MDANSE/Tests/UnitTests/Converted/dlp_v2.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/dlp_v4.mdt b/MDANSE/Tests/UnitTests/Converted/dlp_v4.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/dlp_with_grad.mdt b/MDANSE/Tests/UnitTests/Converted/dlp_with_grad.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/forcite.mdt b/MDANSE/Tests/UnitTests/Converted/forcite.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/gromacs-nvt.mdt b/MDANSE/Tests/UnitTests/Converted/gromacs-nvt.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/hem_cam.mdt b/MDANSE/Tests/UnitTests/Converted/hem_cam.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/lammps.mdt b/MDANSE/Tests/UnitTests/Converted/lammps.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/lammps_cgs.mdt b/MDANSE/Tests/UnitTests/Converted/lammps_cgs.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/lammps_electron.mdt b/MDANSE/Tests/UnitTests/Converted/lammps_electron.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/lammps_metal.mdt b/MDANSE/Tests/UnitTests/Converted/lammps_metal.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/lammps_micro.mdt b/MDANSE/Tests/UnitTests/Converted/lammps_micro.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/lammps_moly_custom.mdt b/MDANSE/Tests/UnitTests/Converted/lammps_moly_custom.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/lammps_moly_h5md.mdt b/MDANSE/Tests/UnitTests/Converted/lammps_moly_h5md.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/lammps_moly_xyz.mdt b/MDANSE/Tests/UnitTests/Converted/lammps_moly_xyz.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/lammps_nano.mdt b/MDANSE/Tests/UnitTests/Converted/lammps_nano.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/lammps_real.mdt b/MDANSE/Tests/UnitTests/Converted/lammps_real.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/lammps_si.mdt b/MDANSE/Tests/UnitTests/Converted/lammps_si.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/md.mdt b/MDANSE/Tests/UnitTests/Converted/md.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/namd.mdt b/MDANSE/Tests/UnitTests/Converted/namd.mdt
diff --git a/MDANSE/Tests/UnitTests/Converted/vasp.mdt b/MDANSE/Tests/UnitTests/Converted/vasp.mdt
diff --git a/MDANSE/Tests/UnitTests/TrajectoryEditor/test_editor.py b/MDANSE/Tests/UnitTests/TrajectoryEditor/test_editor.py
@@ -68,9 +68,10 @@ def test_editor_null():
 
     with h5py.File(temp_name + ".mdt") as actual, h5py.File(short_traj) as desired:
         np.testing.assert_allclose(
-            actual["/configuration/coordinates"], desired["/configuration/coordinates"]
+            actual["/configuration/coordinates"], desired["/configuration/coordinates"],
+            atol=1e-8
         )
-        np.testing.assert_allclose(actual["/time"], desired["/time"])
+        np.testing.assert_allclose(actual["/time"], desired["/time"], atol=1e-8)
 
     os.remove(temp_name + ".mdt")
     os.remove(temp_name + ".log")
@@ -103,10 +104,10 @@ def test_editor_frames():
     with h5py.File(temp_name + ".mdt") as actual, h5py.File(short_traj) as desired:
         np.testing.assert_allclose(
             actual["/configuration/coordinates"],
-            desired["/configuration/coordinates"][0:501:10],
+            desired["/configuration/coordinates"][0:501:10], atol=1e-8
         )
         np.testing.assert_allclose(
-            actual["/time"], desired["/time"][0:501:10]
+            actual["/time"], desired["/time"][0:501:10], atol=1e-8
         )
 
     os.remove(temp_name + ".mdt")
@@ -141,9 +142,9 @@ def test_editor_atoms():
     with h5py.File(temp_name + ".mdt") as actual, h5py.File(short_traj) as desired:
         np.testing.assert_allclose(
             actual["/configuration/coordinates"],
-            desired["/configuration/coordinates"][:, 6:20, :],
+            desired["/configuration/coordinates"][:, 6:20, :], atol=1e-8
         )
-        np.testing.assert_allclose(actual["/time"], desired["/time"])
+        np.testing.assert_allclose(actual["/time"], desired["/time"], atol=1e-8)
 
     os.remove(temp_name + ".mdt")
     os.remove(temp_name + ".log")
@@ -178,9 +179,10 @@ def test_editor_unit_cell():
 
     with h5py.File(temp_name + ".mdt") as actual, h5py.File(short_traj) as desired:
         np.testing.assert_allclose(
-            actual["/configuration/coordinates"], desired["/configuration/coordinates"]
+            actual["/configuration/coordinates"],
+            desired["/configuration/coordinates"], atol=1e-8
         )
-        np.testing.assert_allclose(actual["/time"], desired["/time"])
+        np.testing.assert_allclose(actual["/time"], desired["/time"], atol=1e-8)
 
     os.remove(temp_name + ".mdt")
     os.remove(temp_name + ".log")
@@ -219,9 +221,10 @@ def test_editor_transmute():
 
     with h5py.File(temp_name + ".mdt") as actual, h5py.File(short_traj) as desired:
         np.testing.assert_allclose(
-            actual["/configuration/coordinates"], desired["/configuration/coordinates"]
+            actual["/configuration/coordinates"],
+            desired["/configuration/coordinates"], atol=1e-8
         )
-        np.testing.assert_allclose(actual["/time"], desired["/time"])
+        np.testing.assert_allclose(actual["/time"], desired["/time"], atol=1e-8)
 
     os.remove(temp_name + ".mdt")
     os.remove(temp_name + ".log")
@@ -253,9 +256,10 @@ def test_editor_set_charges():
 
     with h5py.File(temp_name + ".mdt") as actual, h5py.File(short_traj) as desired:
         np.testing.assert_allclose(
-            actual["/configuration/coordinates"], desired["/configuration/coordinates"]
+            actual["/configuration/coordinates"],
+            desired["/configuration/coordinates"], atol=1e-8
         )
-        np.testing.assert_allclose(actual["/time"], desired["/time"])
+        np.testing.assert_allclose(actual["/time"], desired["/time"], atol=1e-8)
 
     os.remove(temp_name + ".mdt")
     os.remove(temp_name + ".log")
@@ -284,9 +288,10 @@ def test_editor_find_molecules():
 
     with h5py.File(temp_name + ".mdt") as actual, h5py.File(short_traj) as desired:
         np.testing.assert_allclose(
-            actual["/configuration/coordinates"], desired["/configuration/coordinates"]
+            actual["/configuration/coordinates"],
+            desired["/configuration/coordinates"], atol=1e-8
         )
-        np.testing.assert_allclose(actual["/time"], desired["/time"])
+        np.testing.assert_allclose(actual["/time"], desired["/time"], atol=1e-8)
 
     os.remove(temp_name + ".mdt")
     os.remove(temp_name + ".log")
diff --git a/MDANSE/Tests/UnitTests/test_converter.py b/MDANSE/Tests/UnitTests/test_converter.py
@@ -68,7 +68,7 @@ def _converter_test(tmp_path, converter_type, result, compare, parameters, compr
 
     with h5py.File(out_name) as actual, h5py.File(result_name) as desired:
         for prop in compare:
-            np.testing.assert_allclose(actual[prop], desired[prop])
+            np.testing.assert_allclose(actual[prop], desired[prop], atol=1e-8)
 
     assert out_name.is_file()
     assert log_name.is_file()