break out tests into separate files

Author: cadenmyers13

tests/test_generators.py

@@ -0,0 +1,67 @@
+import numpy as np
+import pytest
+
+from diffpy.cmipdf import PDFGenerator
+from diffpy.srreal.pdfcalculator import PDFCalculator
+from diffpy.structure import PDFFitStructure
+
+
+def testGenerator(datafile):
+    qmax = 27.0
+    gen = PDFGenerator()
+    gen.set_scattering_type("N")
+    assert "N" == gen.get_scattering_type()
+    gen.set_qmax(qmax)
+    assert qmax == pytest.approx(gen.get_qmax())
+
+    structure = PDFFitStructure()
+    ciffile = datafile("ni.cif")
+    cif_path = str(ciffile)
+    structure.read(cif_path)
+    for i in range(4):
+        structure[i].Bisoequiv = 1
+    gen.set_structure(structure)
+
+    calc = gen._calc
+    # Test parameters
+    for par in gen.iterate_over_parameters(recurse=False):
+        pname = par.name
+        defval = calc._getDoubleAttr(pname)
+        assert defval == par.getValue()
+        # Test setting values
+        par.set_value(1.0)
+        assert 1.0 == par.getValue()
+        par.set_value(defval)
+        assert defval == par.getValue()
+
+    r = np.arange(0, 10, 0.1)
+    y = gen(r)
+
+    # Now create a reference PDF. Since the calculator is testing its
+    # output, we just have to make sure we can calculate from the
+    # PDFGenerator interface.
+
+    calc = PDFCalculator()
+    calc.rstep = r[1] - r[0]
+    calc.rmin = r[0]
+    calc.rmax = r[-1] + 0.5 * calc.rstep
+    calc.qmax = qmax
+    calc.setScatteringFactorTableByType("N")
+    calc.eval(structure)
+    yref = calc.pdf
+
+    diff = y - yref
+    res = np.dot(diff, diff)
+    assert 0 == pytest.approx(res)
+    return
+
+
+def test_set_qmin():
+    """Verify qmin is propagated to the calculator object."""
+    gen = PDFGenerator()
+    assert 0 == gen.get_qmin()
+    assert 0 == gen._calc.qmin
+    gen.set_qmin(0.93)
+    assert 0.93 == gen.get_qmin()
+    assert 0.93 == gen._calc.qmin
+    return

tests/test_parser.py

@@ -0,0 +1,139 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2025 Simon Billinge.
+# All rights reserved.
+#
+# File coded by: Caden Myers, Simon Billinge, and members of the Billinge
+#                group.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.cmipdf/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+"""Tests for pdf package."""
+
+
+import numpy as np
+import pytest
+
+from diffpy.srfit.fitbase import ProfileParser
+
+# ----------------------------------------------------------------------------
+
+
+# The tests in this file are for ProfileParser which belongs to diffpy.srfit,
+# but since it is used here, we will test it here on test data with modern
+# diffpy format.
+def testParser1(datafile):
+    filename = datafile("ni-q27r100-neutron.gr")
+    parser = ProfileParser()
+    parser.parse_file(filename)
+
+    meta = parser._meta
+
+    assert str(filename) == meta["filename"]
+    assert 1 == meta["nbanks"]
+    assert "N" == meta["stype"]
+    assert 27 == meta["qmax"]
+    assert 300 == meta.get("temperature")
+    assert meta.get("qdamp") is None
+    assert meta.get("qbroad") is None
+    assert meta.get("spdiameter") is None
+    assert meta.get("scale") is None
+    assert meta.get("doping") is None
+
+    x, y, dx, dy = parser.get_data()
+    assert dx.tolist() == len(x) * [0]
+    assert dy.tolist() == len(x) * [0]
+
+    testx = np.linspace(0.01, 100, 10000)
+    diff = testx - x
+    res = np.dot(diff, diff)
+    assert 0 == pytest.approx(res)
+
+    testy = np.array(
+        [
+            1.144,
+            2.258,
+            3.312,
+            4.279,
+            5.135,
+            5.862,
+            6.445,
+            6.875,
+            7.150,
+            7.272,
+        ]
+    )
+    diff = testy - y[:10]
+    res = np.dot(diff, diff)
+    assert 0 == pytest.approx(res)
+
+    return
+
+
+def testParser2(datafile):
+    data = datafile("si-q27r60-xray.gr")
+    parser = ProfileParser()
+    parser.parse_file(data)
+
+    meta = parser._meta
+
+    assert str(data) == meta["filename"]
+    assert 1 == meta["nbanks"]
+    assert "X" == meta["stype"]
+    assert 27 == meta["qmax"]
+    assert 300 == meta.get("temperature")
+    assert meta.get("qdamp") is None
+    assert meta.get("qbroad") is None
+    assert meta.get("spdiameter") is None
+    assert meta.get("scale") is None
+    assert meta.get("doping") is None
+
+    x, y, dx, dy = parser.get_data()
+    testx = np.linspace(0.01, 60, 5999, endpoint=False)
+    diff = testx - x
+    res = np.dot(diff, diff)
+    assert 0 == pytest.approx(res)
+
+    testy = np.array(
+        [
+            0.1105784,
+            0.2199684,
+            0.3270088,
+            0.4305913,
+            0.5296853,
+            0.6233606,
+            0.7108060,
+            0.7913456,
+            0.8644501,
+            0.9297440,
+        ]
+    )
+    diff = testy - y[:10]
+    res = np.dot(diff, diff)
+    assert 0 == pytest.approx(res)
+
+    testdy = np.array(
+        [
+            0.001802192,
+            0.003521449,
+            0.005079115,
+            0.006404892,
+            0.007440527,
+            0.008142955,
+            0.008486813,
+            0.008466340,
+            0.008096858,
+            0.007416456,
+        ]
+    )
+    diff = testdy - dy[:10]
+    res = np.dot(diff, diff)
+    assert 0 == pytest.approx(res)
+
+    assert dx.tolist() == [0] * len(dx)
+    return