test: fix pytest warnings being raised

docs/examples/npintensity.py

@@ -493,7 +493,7 @@ def makeData(strufile, q, datname, scale, a, Uiso, sig, bkgc, nl=1):
     S.read(str(strufile))
 
     # Set the lattice parameters
-    S.lattice.setLatPar(a, a, a)
+    S.lattice.set_latt_parms(a, a, a)
 
     # Set a DW factor
     for a in S:

news/fix-warnings.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added: Silence warnings raised during testing and use set_latt_parms in place of the deprecated setLatPar in the tests and npintensity example.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

tests/test_characteristicfunctions.py

@@ -818,7 +818,10 @@ def test_deprecated_functions_forward_non_physical_input(
 ):
     old_function = getattr(cf, old_name)
     new_function = getattr(cf, new_name)
-    expected_characteristic_function = new_function(*new_args)
+    # Catch the RuntimeWarning to prevent warnings when tests run.
+    # This test passes non-phyiscal inputs so this behavior is expected here.
+    with pytest.warns(RuntimeWarning):
+        expected_characteristic_function = new_function(*new_args)
 
     # The oracle call above already consumed the once-per-process
     # RuntimeWarning for this (function, requirement) pair; clear the

tests/test_diffpyparset.py

@@ -82,7 +82,7 @@ def _testLattice():
     a1.xyz[1] = 0.123
     a1.U11 = 0.321
     a1.B32 = 0.111
-    dsstru.lattice.setLatPar(a=3.0, gamma=121)
+    dsstru.lattice.set_latt_parms(a=3.0, gamma=121)
     _testAtoms()
     _testLattice()
 

tests/test_fitrecipe.py

@@ -529,9 +529,13 @@ def test_initialize_recipe_from_results_object(build_recipes_one_contribution):
     assert actual_names_before_init == expected_names_before_init
     recipe2.initialize_recipe_with_results(results1)
     optimize_recipe(recipe2)
+    # Fix extra_var to prevent divide by zero warnings when tests run.
+    recipe2.fix("extra_var")
     results2 = FitResults(recipe2)
-    actual_values = sorted(np.round(results2.varvals, 5).tolist())
-    actual_names = sorted(results2.varnames)
+    actual_values = sorted(
+        np.round(np.append(results2.varvals, results2.fixedvals), 5).tolist()
+    )
+    actual_names = sorted(results2.varnames + results2.fixednames)
 
     # Add the name and value of the new variable to the expected ones.
     expected_names = sorted(expected_names + ["extra_var"])