Continue process of generalisation

MDANSE/Tests/CommonFunctions/test_helpers/compare_mdt.py

@@ -0,0 +1,47 @@
+import numpy as np
+from pathlib import Path
+import h5py
+from typing import Sequence
+
+def compare_mdt(result_path: Path, benchmark_path: Path,
+                comparison_keys: Sequence[str], *,
+                startswith=False, normalised=False) -> None:
+    """
+    Compare two h5py files by the keys given in comparison_keys.
+
+    Parameters
+    ----------
+    result_path : Path
+        Path to output file from test run.
+    benchmark_path : Path
+        Path to benchmark results.
+    comparison_keys : Sequence[str]
+        List of keys to be present in outputs to compare.
+    startswith : bool
+        ``comparison_keys`` instead define a prefix of keys in ``result`` to check.
+    normalised : bool
+        Whether data should be normalised.
+    """
+
+    with h5py.File(result_path) as result, h5py.File(benchmark_path) as benchmark:
+
+        if startswith:
+            keys = (key for key in result.keys() if key.startswith(comparison_keys))
+        else:
+            keys = comparison_keys
+
+        for key in keys:
+            if isinstance(key, (tuple, list)):
+                key, subset = key
+            else:
+                subset = slice(None)
+
+            if normalised:
+                np.testing.assert_array_almost_equal(
+                    result[f"/{key}"] * result[f"/{key}"].attrs["scaling_factor"],
+                    benchmark[f"/{key}"][subset],
+                )
+            else:
+                np.testing.assert_array_almost_equal(
+                    result[f"/{key}"], benchmark[f"/{key}"][subset],
+                )

MDANSE/Tests/CommonFunctions/test_helpers/get_deep_attr.py

@@ -0,0 +1,38 @@
+from typing import Any
+
+def get_deep_attr(obj: Any, key: str) -> Any:
+    """Get attribute from nested objects.
+
+    Parameters
+    ----------
+    obj : Any
+        Object to get elements from.
+    key : str
+        "." separated string indexing into object.
+
+        "[x]" and "(x, y)" elements are evaluated.
+
+    Returns
+    -------
+    Any
+        Element at path given by key.
+    """
+
+    parts = key.split(".")
+
+    new = obj
+    for part in parts:
+        part, *method = part.split("(", 1)
+        part, *getter = part.split("[", 1)
+        new = getattr(new, part)
+        if method:
+            args = method[0].strip("()")
+            if args:
+                args = args.split(",")
+            print(args)
+            new = new(*map(eval, args))
+        if getter:
+            args = getter[0].strip("[]")
+            new = new[eval(args)]
+
+    return new

MDANSE/Tests/CommonFunctions/test_helpers/paths.py

@@ -0,0 +1,7 @@
+from pathlib import Path
+
+ROOT_DIR = Path(__file__).parents[1]
+UNIT_TEST_DIR = ROOT_DIR / "UnitTests"
+CONV_DIR = UNIT_TEST_DIR / "Converted"
+DATA_DIR = UNIT_TEST_DIR / "Data"
+RESULTS_DIR = UNIT_TEST_DIR / "Results"

MDANSE/Tests/UnitTests/Analysis/test_average_structure.py

@@ -1,46 +1,30 @@
-import tempfile
-import os
-from os import path
 import pytest
-
-from MDANSE.Framework.InputData.HDFTrajectoryInputData import HDFTrajectoryInputData
+from MDANSE.Framework.InputData.HDFTrajectoryInputData import \
+    HDFTrajectoryInputData
 from MDANSE.Framework.Jobs.IJob import IJob
+from test_helpers.paths import CONV_PATH
 
-
-short_traj = os.path.join(
-    os.path.dirname(os.path.realpath(__file__)),
-    "..",
-    "Converted",
-    "short_trajectory_after_changes.mdt",
-)
+short_traj = CONV_PATH / "short_trajectory_after_changes.mdt"
 
 
 @pytest.fixture(scope="module")
 def trajectory():
     trajectory = HDFTrajectoryInputData(short_traj)
     yield trajectory
 
-
-units = ["Angstrom", "Bohr", "nm", "pm"]
-formats = ["vasp", "xyz", "turbomole", "abinit-in"]
-inputs = []
-for u in units:
-    for f in formats:
-        inputs.append((u, f))
-
-
-@pytest.mark.parametrize("output_unit,output_format", inputs)
-def test_avg_structure(trajectory, output_unit, output_format):
-    temp_name = tempfile.mktemp()
-    parameters = {}
-    parameters["frames"] = (0, 10, 1)
-    parameters["output_units"] = output_unit
-    parameters["fold"] = True
-    parameters["output_files"] = (temp_name, output_format, "INFO")
-    parameters["running_mode"] = ("single-core",)
-    parameters["trajectory"] = short_traj
+@pytest.mark.parametrize("output_unit", ["Angstrom", "Bohr", "nm", "pm"])
+@pytest.mark.parametrize("output_format", ["vasp", "xyz", "turbomole", "abinit-in"])
+def test_avg_structure(tmp_path, trajectory, output_unit, output_format):
+    temp_name = tmp_path / "output"
+    parameters = {
+        "frames": (0, 10, 1),
+        "output_units": output_unit,
+        "fold": True,
+        "output_files": (temp_name, output_format, "INFO"),
+        "running_mode": ("single-core",),
+        "trajectory": short_traj,
+    }
     temp = IJob.create("AverageStructure")
     temp.run(parameters, status=True)
-    assert path.exists(temp_name)
-    assert path.isfile(temp_name)
-    os.remove(temp_name)
+
+    assert temp_name.is_file()