fixed test_sample

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

pyproject.toml

@@ -1,49 +1,49 @@
 [project]
-name = "examplepyapp"
-description = "Example Python repo for neutrons"
-dynamic = ["version"]
-requires-python = ">=3.10"
 dependencies = [
   # list all runtime dependencies here
 ]
-license = { text = "MIT" }
+description = "Example Python repo for neutrons"
+dynamic = ["version"]
+license = {text = "LGPL-3.0"}
+name = "examplepyapp"
+requires-python = ">=3.10"
 
 [project.urls]
-homepage = "https://github.com/neutrons/python_project_template/"  # if no homepage, use repo url
+homepage = "https://github.com/neutrons/python_project_template/" # if no homepage, use repo url
 
 [build-system]
+build-backend = "setuptools.build_meta"
 requires = [
   "setuptools >= 40.6.0",
   "wheel",
   "toml",
-  "versioningit"
+  "versioningit",
 ]
-build-backend = "setuptools.build_meta"
 
 [tool.black]
 line-length = 119
 
 [tool.versioningit.vcs]
-method = "git"
 default-tag = "0.0.1"
+method = "git"
 
 [tool.versioningit.next-version]
 method = "minor"
 
 [tool.versioningit.format]
-distance = "{next_version}.dev{distance}"
 dirty = "{version}+d{build_date:%Y%m%d}"
+distance = "{next_version}.dev{distance}"
 distance-dirty = "{next_version}.dev{distance}+d{build_date:%Y%m%d%H%M}"
 
 [tool.versioningit.write]
 file = "src/packagenamepy/_version.py"
 
 [tool.setuptools.packages.find]
-where = ["src"]
 exclude = ["tests*", "scripts*", "docs*", "notebooks*"]
+where = ["src"]
 
 [tool.setuptools.package-data]
-"*" = ["*.yml","*.yaml","*.ini"]
+"*" = ["*.yml", "*.yaml", "*.ini"]
 
 [project.scripts]
 packagename-cli = "packagenamepy.packagename:main"
@@ -52,17 +52,19 @@ packagename-cli = "packagenamepy.packagename:main"
 packagenamepy = "packagenamepy.packagename:gui"
 
 [tool.pytest.ini_options]
-pythonpath = [
-  ".", "src", "scripts"
+markers = [
+  "mymarker: example markers goes here",
 ]
-testpaths = ["tests"]
-python_files = ["test*.py"]
 norecursedirs = [".git", "tmp*", "_tmp*", "__pycache__", "*dataset*", "*data_set*"]
-markers = [
-    "mymarker: example markers goes here"
+python_files = ["test*.py"]
+pythonpath = [
+  ".",
+  "src",
+  "scripts",
 ]
+testpaths = ["tests"]
 
 [tool.ruff]
 line-length = 120
-select = ["A", "ARG","ASYNC","BLE","C90", "E", "F", "I", "N", "UP032", "W"]
+select = ["A", "ARG", "ASYNC", "BLE", "C90", "E", "F", "I", "N", "UP032", "W"]
 # Add additional 3rd party tool configuration here as needed

tests/test_sample.py

@@ -1,74 +1,66 @@
 import numpy as np
-from tavi.sample.sample import Sample
-from tavi.sample.xtal import Xtal
-
-
-def test_b_matrix(lattice_params, b_matrix):
-
-    sample = Sample(lattice_params=lattice_params)
-    print(sample.b_mat())
-    print(np.allclose(sample.b_mat(), b_matrix, atol=1e-4))
-
-
-def test_ub_matrix_to_uv(lattice_params, ub_matrix):
-
-    xtal = Xtal(lattice_params=lattice_params)
-    (u, v) = xtal.ub_matrix_to_uv(ub_matrix)
-    print(f"u={u}")
-    print(f"v={v}")
-
-
-def test_ub_matrix_to_lattice_params(ub_matrix):
-    sample = Xtal()
-    (a, b, c, alpha, beta, gamma) = sample.ub_matrix_to_lattice_params(ub_matrix)
-    print(f"a={np.round(a,5)}, b={np.round(b,5)},c={np.round(c,5)}")
-    print(f"alpha={np.round(alpha,3)}, beta={np.round(beta,3)}, gamma={np.round(gamma,3)}")
-
-
-def test_uv_to_ub_matrix(u, v, lattice_params):
-    sample = Xtal(lattice_params=lattice_params)
-    ub_matrix = sample.uv_to_ub_matrix(u, v)
-
-    print(f"ub matrix = {ub_matrix}")
+import pytest
 
+from tavi.sample.xtal import Xtal
 
-if __name__ == "__main__":
 
+@pytest.fixture
+def xtal_info():
     a = 3.574924
     b = 3.574924
     c = 5.663212
     alpha = 90
     beta = 90
     gamma = 120
+    lattice_params = (a, b, c, alpha, beta, gamma)
+    xtal = Xtal(lattice_params=lattice_params)
 
-    # ub_matrix = np.array(
-    #     [
-    #         [0.053821, 0.107638, 0.166485],
-    #         [0.272815, -0.013290, 0.002566],
-    #         [0.164330, 0.304247, -0.058788],
-    #     ]
-    # )
-    ub_matrix = np.array(
-        [
-            [0.0538, 0.1076, 0.1665],
-            [0.2728, -0.0133, 0.0026],
-            [0.1643, 0.3042, -0.0588],
-        ]
-    )
     b_matrix = np.array(
         [
             [0.3230, 0.1615, 0.0000],
             [0.0000, 0.2797, -0.0000],
             [0.0000, 0.0000, 0.1766],
         ]
     )
+    ub_matrix = np.array(
+        [
+            [0.0538, 0.1076, 0.1665],
+            [0.2728, -0.0133, 0.0026],
+            [0.1643, 0.3042, -0.0588],
+        ]
+    )
 
     u = [0.15623, 2.83819, -1.88465]
     v = [-0.00060, 1.03219, 5.33915]
 
-    lattice_params = (a, b, c, alpha, beta, gamma)
+    return (xtal, b_matrix, ub_matrix, u, v)
+
+
+def test_b_matrix(xtal_info):
+    xtal, b_matrix, ub_matrix, u, v = xtal_info
+    assert np.allclose(xtal.b_mat(), b_matrix, atol=1e-4)
+
+
+def test_ub_matrix_to_uv(xtal_info):
+    xtal, b_matrix, ub_matrix, u, v = xtal_info
+    (u_calc, v_calc) = xtal.ub_matrix_to_uv(ub_matrix)
+    assert np.allclose(u_calc, u, atol=1e-3)
+    assert np.allclose(v_calc, v, atol=1e-3)
+
+
+def test_ub_matrix_to_lattice_params(xtal_info):
+    xtal, b_matrix, ub_matrix, u, v = xtal_info
+    (a, b, c, alpha, beta, gamma) = xtal.ub_matrix_to_lattice_params(ub_matrix)
+    assert np.allclose(a, xtal.a, atol=1e-2)
+    assert np.allclose(b, xtal.b, atol=1e-2)
+    assert np.allclose(c, xtal.c, atol=1e-2)
+    assert np.allclose(alpha, xtal.alpha, atol=1e-2)
+    assert np.allclose(beta, xtal.beta, atol=1e-2)
+    assert np.allclose(gamma, xtal.gamma, atol=1e-2)
+
+
+def test_uv_to_ub_matrix(xtal_info):
+    xtal, b_matrix, ub_matrix, u, v = xtal_info
+    ub_matrix_calc = xtal.uv_to_ub_matrix(u, v)
 
-    # test_b_matrix(lattice_params, b_matrix)
-    test_ub_matrix_to_uv(lattice_params, ub_matrix)
-    # test_ub_matrix_to_lattice_params(ub_matrix)
-    test_uv_to_ub_matrix(u, v, lattice_params)
+    assert np.allclose(ub_matrix_calc, ub_matrix, atol=1e-2)

tests/test_tas.py

@@ -1,8 +1,11 @@
+import pytest
+
 from tavi.instrument.tas import TAS
 from tavi.sample.xtal import Xtal
 from tavi.utilities import *
 
 
+@pytest.fixture
 def instrument_sample_setup(instrument_config, sample_config):
     tax = TAS()
     tax.load_instrument_from_dicts(instrument_config)