Finish off Analysis folder

.github/workflows/tests.yml

@@ -31,6 +31,6 @@ jobs:
         run: (cd MDANSE && python -m pip install .)
 
       - name: run unit tests
+        working-directory: ./MDANSE/
         run: |
-          cd MDANSE/Tests/UnitTests
-          python -m pytest
+          pytest

MDANSE/Tests/CommonFunctions/test_helpers/compare_mdt.py

@@ -39,9 +39,10 @@ def compare_mdt(result_path: Path, benchmark_path: Path,
             if normalised:
                 np.testing.assert_array_almost_equal(
                     result[f"/{key}"] * result[f"/{key}"].attrs["scaling_factor"],
-                    benchmark[f"/{key}"][subset],
+                    benchmark[f"/{key}"][subset], err_msg=f"Failure in key {key!r}.",
                 )
             else:
                 np.testing.assert_array_almost_equal(
                     result[f"/{key}"], benchmark[f"/{key}"][subset],
+                    err_msg=f"Failure in key {key!r}.",
                 )

MDANSE/Tests/UnitTests/Analysis/test_dynamics.py

@@ -132,7 +132,6 @@ def test_dynamics_analysis(
     job = IJob.create(job_type)
     job.run(parameters, status=True)
 
-
     if output_format == "MDAFormat":
         out_file = temp_name.with_suffix(".mda")
         result_file = RESULTS_DIR / f"dynamics_analysis_{traj_info[0]}_{job_type}.mda"

MDANSE/Tests/UnitTests/Analysis/test_resolutions.py

@@ -1,124 +1,104 @@
-import tempfile
-import os
-from os import path
-
-import h5py
-import numpy as np
 import pytest
-
-from MDANSE.Framework.InputData.HDFTrajectoryInputData import HDFTrajectoryInputData
-from MDANSE.Framework.InstrumentResolutions.IInstrumentResolution import (
-    IInstrumentResolution,
-)
+from MDANSE.Framework.InputData.HDFTrajectoryInputData import \
+    HDFTrajectoryInputData
+from MDANSE.Framework.InstrumentResolutions.IInstrumentResolution import \
+    IInstrumentResolution
 from MDANSE.Framework.Jobs.IJob import IJob
+from test_helpers.compare_mdt import compare_mdt
+from test_helpers.paths import CONV_DIR, RESULTS_DIR
 
-
-short_traj = os.path.join(
-    os.path.dirname(os.path.realpath(__file__)),
-    "..",
-    "Converted",
-    "short_trajectory_after_changes.mdt",
-)
-result_dir = os.path.join(
-    os.path.dirname(os.path.realpath(__file__)),
-    "..",
-    "Results",
-)
+short_traj = CONV_DIR / "short_trajectory_after_changes.mdt"
 
 
 @pytest.fixture(scope="module")
 def trajectory():
     trajectory = HDFTrajectoryInputData(short_traj)
     yield trajectory
 
+@pytest.mark.parametrize("resolution_generator", IInstrumentResolution.subclasses())
+def test_disf(tmp_path, trajectory, resolution_generator):
+    temp_name = tmp_path / "output"
+    out_file = temp_name.with_suffix(".mda")
+    log_file = temp_name.with_suffix(".log")
+
+    parameters = {
+        "atom_selection": None,
+        "atom_transmutation": None,
+        "frames": (0, 10, 1, 5),
+        "instrument_resolution": ("Ideal", {}),
+        "q_vectors": (
+            "SphericalLatticeQVectors",
+            {"seed": 0, "shells": (5.0, 36, 10.0), "n_vectors": 10, "width": 9.0},
+        ),
+        "running_mode": ("single-core",),
+        "trajectory": short_traj,
+        "weights": "b_incoherent2",
+    }
+
+    parameters["output_files"] = (temp_name, ("MDAFormat",), "INFO")
+    instance = IInstrumentResolution.create(resolution_generator)
+    resolution_defaults = {
+        name: value[1]["default"] for name, value in instance.settings.items()
+    }
+
+    print(resolution_generator)
+    print(resolution_defaults)
 
-def test_disf(trajectory):
-    parameters = {}
-    parameters["atom_selection"] = None
-    parameters["atom_transmutation"] = None
-    parameters["frames"] = (0, 10, 1, 5)
-    parameters["instrument_resolution"] = ("Ideal", {})
-    parameters["q_vectors"] = (
-        "SphericalLatticeQVectors",
-        {"seed": 0, "shells": (5.0, 36, 10.0), "n_vectors": 10, "width": 9.0},
+    parameters["instrument_resolution"] = (
+        resolution_generator,
+        resolution_defaults,
     )
-    parameters["running_mode"] = ("single-core",)
-    parameters["trajectory"] = short_traj
-    parameters["weights"] = "b_incoherent2"
-    for resolution_generator in IInstrumentResolution.subclasses():
-        temp_name = tempfile.mktemp()
-        parameters["output_files"] = (temp_name, ("MDAFormat",), "INFO")
-        instance = IInstrumentResolution.create(resolution_generator)
-        resolution_defaults = {
-            name: value[1]["default"] for name, value in instance.settings.items()
-        }
-        print(resolution_generator)
-        print(resolution_defaults)
-        parameters["instrument_resolution"] = (
-            resolution_generator,
-            resolution_defaults,
-        )
-        disf = IJob.create("DynamicIncoherentStructureFactor")
-        disf.run(parameters, status=True)
-        assert path.exists(temp_name + ".mda")
-        assert path.isfile(temp_name + ".mda")
-        os.remove(temp_name + ".mda")
-        assert path.exists(temp_name + ".log")
-        assert path.isfile(temp_name + ".log")
-        os.remove(temp_name + ".log")
-
-
-list_of_resolutions = IInstrumentResolution.subclasses()
-
-
-@pytest.mark.parametrize("resolution_generator", list_of_resolutions)
-def test_dos(trajectory, resolution_generator):
-    parameters = {}
-    parameters["atom_selection"] = None
-    parameters["atom_transmutation"] = None
-    parameters["frames"] = (0, 10, 1, 5)
-    parameters["instrument_resolution"] = ("Ideal", {})
-    parameters["running_mode"] = ("single-core",)
-    parameters["trajectory"] = short_traj
-    parameters["weights"] = "b_incoherent2"
-    temp_name = tempfile.mktemp()
+
+    disf = IJob.create("DynamicIncoherentStructureFactor")
+    disf.run(parameters, status=True)
+
+    assert out_file.is_file()
+    assert log_file.is_file()
+
+
+@pytest.mark.parametrize("resolution_generator", IInstrumentResolution.subclasses())
+def test_dos(tmp_path, trajectory, resolution_generator):
+    temp_name = tmp_path / "output"
+    out_file = temp_name.with_suffix(".mda")
+    log_file = temp_name.with_suffix(".log")
+    text_file = tmp_path / "output_text.tar"
+
+    parameters = {
+        "atom_selection": None,
+        "atom_transmutation": None,
+        "frames": (0, 10, 1, 5),
+        "instrument_resolution": ("Ideal", {}),
+        "running_mode": ("single-core",),
+        "trajectory": short_traj,
+        "weights": "b_incoherent2",
+    }
+
     parameters["output_files"] = (temp_name, ("MDAFormat", "TextFormat"), "INFO")
+
     instance = IInstrumentResolution.create(resolution_generator)
     resolution_defaults = {
         name: value[1]["default"] for name, value in instance.settings.items()
     }
+
     print(resolution_generator)
     print(resolution_defaults)
+
     parameters["instrument_resolution"] = (
         resolution_generator,
         resolution_defaults,
     )
+
     disf = IJob.create("DensityOfStates")
     disf.run(parameters, status=True)
-    assert path.exists(temp_name + ".mda")
-    assert path.isfile(temp_name + ".mda")
-    result_file = os.path.join(result_dir, f"dos_{resolution_generator}.mda")
-
-    with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
-        for key in [
-            "dos_Cu",
-            "dos_S",
-            "dos_Sb",
-            "dos_total",
-            "vacf_Cu",
-            "vacf_S",
-            "vacf_Sb",
-            "vacf_total",
-        ]:
-            np.testing.assert_array_almost_equal(
-                actual[f"/{key}"] * actual[f"/{key}"].attrs["scaling_factor"],
-                desired[f"/{key}"],
-            )
-
-    os.remove(temp_name + ".mda")
-    assert path.exists(temp_name + "_text.tar")
-    assert path.isfile(temp_name + "_text.tar")
-    os.remove(temp_name + "_text.tar")
-    assert path.exists(temp_name + ".log")
-    assert path.isfile(temp_name + ".log")
-    os.remove(temp_name + ".log")
+
+    assert out_file.is_file()
+    assert log_file.is_file()
+    assert text_file.is_file()
+
+    result_file = RESULTS_DIR / f"dos_{resolution_generator}.mda"
+
+    keys = [f"{fn}_{elem}"
+            for fn in ("dos", "vacf")
+            for elem in ("Cu", "S", "Sb", "total")]
+
+    compare_mdt(out_file, result_file, keys, normalised=True)