fix pytest fixture for 3.11

pcmt on tests

Author: Tieqiong

tests/conftest.py

@@ -3,6 +3,8 @@
 
 import pytest
 
+from pyobjcryst.crystal import create_crystal_from_cif
+
 
 @pytest.fixture
 def user_filesystem(tmp_path):
@@ -17,3 +19,23 @@ def user_filesystem(tmp_path):
         json.dump(home_config_data, f)
 
     yield tmp_path
+
+
+@pytest.fixture
+def datafile():
+    """Fixture to dynamically load any test file."""
+
+    def _load(filename):
+        return "tests/testdata/" + filename
+
+    return _load
+
+
+@pytest.fixture
+def loadcifdata():
+    """Fixture to load CIF data files for testing."""
+
+    def _load(filename):
+        return create_crystal_from_cif("tests/testdata/" + filename)
+
+    return _load

tests/test_cif.py

@@ -17,8 +17,8 @@
 import gc
 import unittest
 
+import pytest
 from numpy import pi
-from utils import datafile, loadcifdata
 
 from pyobjcryst.crystal import CreateCrystalFromCIF
 from pyobjcryst.diffractiondatasinglecrystal import (
@@ -29,33 +29,38 @@
 
 class TestCif(unittest.TestCase):
 
+    @pytest.fixture(autouse=True)
+    def prepare_fixture(self, loadcifdata, datafile):
+        self.loadcifdata = loadcifdata
+        self.datafile = datafile
+
     def test_Ag_silver_cif(self):
         """Check loading of Ag_silver.cif."""
-        c = loadcifdata("Ag_silver.cif")
+        c = self.loadcifdata("Ag_silver.cif")
         self.assertTrue(c is not None)
         return
 
     def test_BaTiO3_cif(self):
         """Check loading of BaTiO3.cif."""
-        c = loadcifdata("BaTiO3.cif")
+        c = self.loadcifdata("BaTiO3.cif")
         self.assertTrue(c is not None)
         return
 
     def test_C_graphite_hex_cif(self):
         """Check loading of C_graphite_hex.cif."""
-        c = loadcifdata("C_graphite_hex.cif")
+        c = self.loadcifdata("C_graphite_hex.cif")
         self.assertTrue(c is not None)
         return
 
     def test_CaF2_fluorite_cif(self):
         """Check loading of CaF2_fluorite.cif."""
-        c = loadcifdata("CaF2_fluorite.cif")
+        c = self.loadcifdata("CaF2_fluorite.cif")
         self.assertTrue(c is not None)
         return
 
     def test_caffeine_cif(self):
         """Check loading of caffeine.cif and the data inside."""
-        c = loadcifdata("caffeine.cif")
+        c = self.loadcifdata("caffeine.cif")
         self.assertTrue(c is not None)
         self.assertEqual(24, c.GetNbScatterer())
         self.assertAlmostEqual(14.9372, c.a, 6)
@@ -103,7 +108,7 @@ def test_caffeine_cif(self):
 
     def test_CaTiO3_cif(self):
         """Check loading of CaTiO3.cif and its ADPs."""
-        c = loadcifdata("CaTiO3.cif")
+        c = self.loadcifdata("CaTiO3.cif")
         self.assertTrue(c is not None)
         s = c.GetScatt(3)
         name = s.GetName()
@@ -125,79 +130,79 @@ def test_CaTiO3_cif(self):
 
     def test_CdSe_cadmoselite_cif(self):
         """Check loading of CdSe_cadmoselite.cif."""
-        c = loadcifdata("CdSe_cadmoselite.cif")
+        c = self.loadcifdata("CdSe_cadmoselite.cif")
         self.assertTrue(c is not None)
         return
 
     def test_CeO2_cif(self):
         """Check loading of CeO2.cif."""
-        c = loadcifdata("CeO2.cif")
+        c = self.loadcifdata("CeO2.cif")
         self.assertTrue(c is not None)
         return
 
     def test_lidocainementhol_cif(self):
         """Check loading of lidocainementhol.cif."""
-        c = loadcifdata("lidocainementhol.cif")
+        c = self.loadcifdata("lidocainementhol.cif")
         self.assertTrue(c is not None)
         return
 
     def test_NaCl_cif(self):
         """Check loading of NaCl.cif."""
-        c = loadcifdata("NaCl.cif")
+        c = self.loadcifdata("NaCl.cif")
         self.assertTrue(c is not None)
         return
 
     def test_Ni_cif(self):
         """Check loading of Ni.cif."""
-        c = loadcifdata("Ni.cif")
+        c = self.loadcifdata("Ni.cif")
         self.assertTrue(c is not None)
         return
 
     def test_paracetamol_cif(self):
         """Check loading of paracetamol.cif."""
-        c = loadcifdata("paracetamol.cif")
+        c = self.loadcifdata("paracetamol.cif")
         self.assertTrue(c is not None)
         return
 
     def test_PbS_galena_cif(self):
         """Check loading of PbS_galena.cif."""
-        c = loadcifdata("PbS_galena.cif")
+        c = self.loadcifdata("PbS_galena.cif")
         self.assertTrue(c is not None)
         return
 
     def test_PbTe_cif(self):
         """Check loading of PbTe.cif."""
-        c = loadcifdata("PbTe.cif")
+        c = self.loadcifdata("PbTe.cif")
         self.assertTrue(c is not None)
         return
 
     def test_Si_cif(self):
         """Check loading of Si.cif."""
-        c = loadcifdata("Si.cif")
+        c = self.loadcifdata("Si.cif")
         self.assertTrue(c is not None)
         return
 
     def test_Si_setting2_cif(self):
         """Check loading of Si_setting2.cif."""
-        c = loadcifdata("Si_setting2.cif")
+        c = self.loadcifdata("Si_setting2.cif")
         self.assertTrue(c is not None)
         return
 
     def test_SrTiO3_tausonite_cif(self):
         """Check loading of SrTiO3_tausonite.cif."""
-        c = loadcifdata("SrTiO3_tausonite.cif")
+        c = self.loadcifdata("SrTiO3_tausonite.cif")
         self.assertTrue(c is not None)
         return
 
     def test_TiO2_anatase_cif(self):
         """Check loading of TiO2_anatase.cif."""
-        c = loadcifdata("TiO2_anatase.cif")
+        c = self.loadcifdata("TiO2_anatase.cif")
         self.assertTrue(c is not None)
         return
 
     def test_TiO2_rutile_cif(self):
         """Check loading of TiO2_rutile.cif and its ADP data."""
-        c = loadcifdata("TiO2_rutile.cif")
+        c = self.loadcifdata("TiO2_rutile.cif")
         self.assertTrue(c is not None)
         s = c.GetScatt(0)
         name = s.GetName()
@@ -210,50 +215,56 @@ def test_TiO2_rutile_cif(self):
 
     def test_Zn_zinc_cif(self):
         """Check loading of Zn_zinc.cif."""
-        c = loadcifdata("Zn_zinc.cif")
+        c = self.loadcifdata("Zn_zinc.cif")
         self.assertTrue(c is not None)
         return
 
     def test_ZnS_sphalerite_cif(self):
         """Check loading of ZnS_sphalerite.cif."""
-        c = loadcifdata("ZnS_sphalerite.cif")
+        c = self.loadcifdata("ZnS_sphalerite.cif")
         self.assertTrue(c is not None)
         return
 
     def test_ZnS_wurtzite_cif(self):
         """Check loading of ZnS_wurtzite.cif."""
-        c = loadcifdata("ZnS_wurtzite.cif")
+        c = self.loadcifdata("ZnS_wurtzite.cif")
         self.assertTrue(c is not None)
         return
 
     def testBadCif(self):
         """Make sure we can read all cif files."""
         from pyobjcryst import ObjCrystException
 
-        fname = datafile("ni.stru")
+        fname = self.datafile("ni.stru")
         infile = open(fname, "rb")
         self.assertRaises(ObjCrystException, CreateCrystalFromCIF, infile)
         infile.close()
         return
 
     def test_paracetamol_monomethanolate(self):
         """Test loading crystal and diffraction data."""
-        c = loadcifdata("paracetamol_monomethanolate.cif")
+        c = self.loadcifdata("paracetamol_monomethanolate.cif")
         d = create_singlecrystaldata_from_cif(
-            datafile("paracetamol_monomethanolate_data_single_crystal.cif"), c
+            self.datafile(
+                "paracetamol_monomethanolate_data_single_crystal.cif"
+            ),
+            c,
         )
         self.assertTrue(d is not None)
 
     def test_paracetamol_monomethanolate_ward(self):
         """Test loading crystal and diffraction data, make sure
         custodian & ward works."""
-        c = loadcifdata("paracetamol_monomethanolate.cif")
+        c = self.loadcifdata("paracetamol_monomethanolate.cif")
         d = create_singlecrystaldata_from_cif(
-            datafile("paracetamol_monomethanolate_data_single_crystal.cif"), c
+            self.datafile(
+                "paracetamol_monomethanolate_data_single_crystal.cif"
+            ),
+            c,
         )
         n = d.GetCrystal().GetName()
         # Replace c by another Crystal object
-        c = loadcifdata("ZnS_sphalerite.cif")
+        c = self.loadcifdata("ZnS_sphalerite.cif")
         gc.collect()
         self.assertTrue(gCrystalRegistry.GetObj(n) is not None)
 

tests/test_clocks.py

@@ -16,7 +16,7 @@
 
 import unittest
 
-from utils import makeC60
+from testutils import makeC60
 
 from pyobjcryst.refinableobj import RefinableObjClock
 

tests/test_crystal.py

@@ -16,7 +16,7 @@
 
 import unittest
 
-from utils import (
+from testutils import (
     getScatterer,
     makeCrystal,
     makeScatterer,

tests/test_globaloptim.py

@@ -11,7 +11,7 @@
 
 import unittest
 
-from utils import loadcifdata
+import pytest
 
 from pyobjcryst import refinableobj
 from pyobjcryst.diffractiondatasinglecrystal import (
@@ -22,8 +22,12 @@
 
 class TestGlobalOptim(unittest.TestCase):
 
+    @pytest.fixture(autouse=True)
+    def prepare_fixture(self, loadcifdata):
+        self.loadcifdata = loadcifdata
+
     def setUp(self):
-        self.c = loadcifdata("caffeine.cif")
+        self.c = self.loadcifdata("caffeine.cif")
         self.d = DiffractionDataSingleCrystal(self.c)
         self.d.GenHKLFullSpace2(0.4, True)
         self.d.SetIobsToIcalc()

tests/test_lsq.py

@@ -11,7 +11,7 @@
 
 import unittest
 
-from utils import loadcifdata
+import pytest
 
 from pyobjcryst import refinableobj
 from pyobjcryst.diffractiondatasinglecrystal import (
@@ -22,8 +22,12 @@
 
 class TestGlobalOptim(unittest.TestCase):
 
+    @pytest.fixture(autouse=True)
+    def prepare_fixture(self, loadcifdata):
+        self.loadcifdata = loadcifdata
+
     def setUp(self):
-        self.c = loadcifdata("caffeine.cif")
+        self.c = self.loadcifdata("caffeine.cif")
         self.d = DiffractionDataSingleCrystal(self.c)
         self.d.GenHKLFullSpace2(0.4, True)
         self.d.SetIobsToIcalc()

tests/test_molecule.py

@@ -15,10 +15,10 @@
 """Tests for molecule module."""
 
 import unittest
-from importlib.resources import files
 
+import pytest
 from numpy import pi
-from utils import makeC60, makeMnO6
+from testutils import makeC60, makeMnO6
 
 from pyobjcryst import ObjCrystException
 from pyobjcryst.crystal import Crystal
@@ -38,6 +38,10 @@
 
 class TestMolecule(unittest.TestCase):
 
+    @pytest.fixture(autouse=True)
+    def prepare_fixture(self, datafile):
+        self.datafile = datafile
+
     def setUp(self):
         self.c = makeC60()
         self.m = self.c.GetScatterer("c60")
@@ -445,7 +449,7 @@ def testManipulation(self):
 
     def testZMatrix(self):
         """Test creating a Molecule from a z-matrix."""
-        fname = str(files(__name__).joinpath("testdata", "cime.fhz"))
+        fname = self.datafile("cime.fhz")
         c = Crystal()
         m = ImportFenskeHallZMatrix(c, fname)
         assert m.GetNbAtoms() == 17