pcmt on tests

Author: Tieqiong

tests/test_clocks.py

@@ -16,9 +16,10 @@
 
 import unittest
 
-from pyobjcryst.refinableobj import RefinableObjClock
 from utils import makeC60
 
+from pyobjcryst.refinableobj import RefinableObjClock
+
 
 class TestClocks(unittest.TestCase):
 

tests/test_crystal.py

@@ -16,14 +16,15 @@
 
 import unittest
 
-from pyobjcryst.atom import Atom
 from utils import (
     getScatterer,
     makeCrystal,
     makeScatterer,
     makeScattererAnisotropic,
 )
 
+from pyobjcryst.atom import Atom
+
 
 class TestCrystal(unittest.TestCase):
 
@@ -163,10 +164,10 @@ def __init__(self, level1):
     def test_display_list(self):
         """Test the creation of a atoms list for display using 3dmol."""
         c = makeCrystal(*makeScatterer())
-        s = c._display_list()
-        s = c._display_list(full_molecule=True)
-        s = c._display_list(enantiomer=True)
-        s = c._display_list(only_independent_atoms=True)
+        c._display_list()
+        c._display_list(full_molecule=True)
+        c._display_list(enantiomer=True)
+        c._display_list(only_independent_atoms=True)
 
 
 if __name__ == "__main__":

tests/test_globaloptim.py

@@ -11,16 +11,13 @@
 
 import unittest
 
+from utils import loadcifdata
+
 from pyobjcryst import refinableobj
 from pyobjcryst.diffractiondatasinglecrystal import (
     DiffractionDataSingleCrystal,
 )
-from pyobjcryst.globaloptim import (
-    AnnealingSchedule,
-    GlobalOptimType,
-    MonteCarlo,
-)
-from utils import loadcifdata
+from pyobjcryst.globaloptim import AnnealingSchedule, MonteCarlo
 
 
 class TestGlobalOptim(unittest.TestCase):
@@ -54,13 +51,13 @@ def test_mc_llk(self):
         mc = MonteCarlo()
         mc.AddRefinableObj(self.c)
         mc.AddRefinableObj(self.d)
-        junk = mc.GetLogLikelihood()
+        mc.GetLogLikelihood()
 
     def test_mc_fix_use_pars(self):
         mc = MonteCarlo()
         mc.AddRefinableObj(self.c)
         mc.AddRefinableObj(self.d)
-        junk = mc.GetLogLikelihood()
+        mc.GetLogLikelihood()
         mc.FixAllPar()
         mc.SetParIsUsed("Scale factor", False)
         mc.SetParIsUsed("Scale factor", True)
@@ -99,7 +96,8 @@ def test_mc_pt(self):
         mc.RandomizeStartingConfig()
         mc.RunParallelTempering(nb_step=1000)
 
-    # TODO: this is experimental and leads to segfault if testcrystal:testDummyAtom() has been run before (?!)
+    # TODO: this is experimental and leads to segfault if
+    # testcrystal:testDummyAtom() has been run before (?!)
     # def test_mc_lsq(self):
     #     mc = MonteCarlo()
     #     mc.AddRefinableObj(self.c)

tests/test_indexing.py

@@ -14,7 +14,6 @@
 from numpy import pi
 
 from pyobjcryst.indexing import (
-    CellExplorer,
     CrystalCentering,
     CrystalSystem,
     EstimateCellVolume,

tests/test_lsq.py

@@ -11,12 +11,13 @@
 
 import unittest
 
+from utils import loadcifdata
+
 from pyobjcryst import refinableobj
 from pyobjcryst.diffractiondatasinglecrystal import (
     DiffractionDataSingleCrystal,
 )
 from pyobjcryst.lsq import LSQ
-from utils import loadcifdata
 
 
 class TestGlobalOptim(unittest.TestCase):
@@ -40,7 +41,9 @@ def test_lsq_get_obs_calc(self):
         """Check Creating a basic LSQ object & get obs&calc arrays."""
         lsq = LSQ()
         lsq.SetRefinedObj(self.d, 0, True, True)
-        junk = lsq.GetLSQObs(), lsq.GetLSQCalc(), lsq.ChiSquare()
+        lsq.GetLSQObs()
+        lsq.GetLSQCalc()
+        lsq.ChiSquare()
 
     def test_lsq_get_refined_obj(self):
         """Check Creating a basic LSQ object & get obs&calc arrays."""

tests/test_molecule.py

@@ -14,11 +14,11 @@
 ##############################################################################
 """Tests for molecule module."""
 
-import io
 import unittest
 from importlib.resources import files
 
 from numpy import pi
+from utils import makeC60, makeMnO6
 
 from pyobjcryst import ObjCrystException
 from pyobjcryst.crystal import Crystal
@@ -32,7 +32,6 @@
     StretchModeTorsion,
 )
 from pyobjcryst.refinableobj import RefinablePar, RefParType
-from utils import makeC60, makeMnO6
 
 numplaces = 6
 
@@ -117,7 +116,7 @@ def testAtoms(self):
         # First, try the same atom again. This will throw an objcryst error.
         self.assertRaises(ObjCrystException, self.m.RemoveAtom, a)
 
-        ## Try to remove an atom from another molecule
+        # Try to remove an atom from another molecule
         c = makeC60()
         m = c.GetScatterer("c60")
         self.assertRaises(ObjCrystException, self.m.RemoveAtom, m.GetAtom(1))

tests/test_powderpattern.py

@@ -17,14 +17,13 @@
 import unittest
 
 import numpy as np
+from utils import loadcifdata
 
 from pyobjcryst import ObjCrystException
-from pyobjcryst.crystal import *
-from pyobjcryst.indexing import *
+from pyobjcryst.indexing import CrystalCentering, CrystalSystem, quick_index
 from pyobjcryst.powderpattern import PowderPattern, SpaceGroupExplorer
 from pyobjcryst.radiation import RadiationType, WavelengthType
 from pyobjcryst.reflectionprofile import ReflectionProfileType
-from utils import datafile, loadcifdata
 
 # ----------------------------------------------------------------------------
 
@@ -232,7 +231,7 @@ def test_spacegroup_explorer(self):
         spgex = SpaceGroupExplorer(pd)
         spgex.Run("P 1 21/c 1")
         spgex.RunAll(verbose=False)
-        spg = spgex.GetScores()[0]
+        spg = spgex.GetScores()[0]  # noqa F841
         # This fails about XX% of the time (fit not converging well enough ?)
         # self.assertEqual(spg.hermann_mauguin, 'P 1 21/c 1')
         # if True:  #spg.hermann_mauguin != 'P 1 21/c 1':

tests/test_radiation.py

@@ -11,18 +11,14 @@
 
 import unittest
 
-from pyobjcryst.diffractiondatasinglecrystal import (
-    DiffractionDataSingleCrystal,
-)
-from pyobjcryst.powderpattern import PowderPattern
 from pyobjcryst.radiation import Radiation, RadiationType, WavelengthType
 
 
 class TestRadiation(unittest.TestCase):
 
     def testRadiation(self):
         """Test Radiation creation."""
-        r = Radiation()
+        Radiation()
         return
 
     def testWavelength(self):

tests/test_refinableobj.py

@@ -17,6 +17,7 @@
 import unittest
 
 import numpy
+from utils import makeCrystal, makeScatterer
 
 from pyobjcryst import ObjCrystException
 from pyobjcryst.refinableobj import (
@@ -26,7 +27,6 @@
     RefParType,
     Restraint,
 )
-from utils import makeCrystal, makeScatterer
 
 
 class TestRefinableObjClock(unittest.TestCase):
@@ -421,7 +421,7 @@ def testOptimStep(self):
 
     def test_xml(self):
         """Test xml() function."""
-        x = self.r.xml()
+        self.r.xml()
 
 
 if __name__ == "__main__":

tests/test_single_crystal_data.py

@@ -3,43 +3,46 @@
 """Tests for diffractiondatasinglecrystal module."""
 
 import unittest
+
 import numpy as np
 
 from pyobjcryst.crystal import Crystal
-from pyobjcryst.diffractiondatasinglecrystal import DiffractionDataSingleCrystal
+from pyobjcryst.diffractiondatasinglecrystal import (
+    DiffractionDataSingleCrystal,
+)
 
 
 class test_single_crystal_data(unittest.TestCase):
 
     def test_create(self):
-        """Test creating a DiffractionDataSingleCrystal object"""
+        """Test creating a DiffractionDataSingleCrystal object."""
         c = Crystal(3.52, 3.52, 3.52, "225")
-        d = DiffractionDataSingleCrystal(c)
+        DiffractionDataSingleCrystal(c)
 
     def test_create_set_hkliobs(self):
-        """test SetHklIobs, SetIobs and SetSigma"""
+        """Test SetHklIobs, SetIobs and SetSigma."""
         c = Crystal(3.1, 3.2, 3.3, "Pmmm")
         d = DiffractionDataSingleCrystal(c)
         n0 = 5
-        nb = n0 ** 3
+        nb = n0**3
         r = np.arange(1, nb + 1, dtype=np.float64)
         h = r % n0
-        l = r // n0 ** 2
-        k = (r - l * n0 ** 2) // n0
+        l = r // n0**2  # noqa: E741
+        k = (r - l * n0**2) // n0
         iobs = np.random.uniform(0, 100, nb)
         sigma = np.sqrt(iobs)
 
         d.SetHklIobs(h, k, l, iobs, sigma)
 
         # SetHklIobs sorts reflecions by sin(theta)/lambda, so do the same for comparison
-        s = np.sqrt(h ** 2 / 3.1 ** 2 + k ** 2 / 3.2 ** 2 + l ** 2 / 3.3 ** 2) / 2
+        s = np.sqrt(h**2 / 3.1**2 + k**2 / 3.2**2 + l**2 / 3.3**2) / 2
         idx = np.argsort(s)
 
         iobs = np.take(iobs, idx)
         sigma = np.take(sigma, idx)
         h = np.take(h, idx)
         k = np.take(k, idx)
-        l = np.take(l, idx)
+        l = np.take(l, idx)  # noqa: E741
         self.assertTrue(np.all(iobs == d.GetIobs()))
         self.assertTrue(np.all(sigma == d.GetSigma()))
         self.assertTrue(np.all(h == d.GetH()))
@@ -55,5 +58,6 @@ def test_create_set_hkliobs(self):
         d.SetSigma(sigma)
         self.assertTrue(np.all(sigma == d.GetSigma()))
 
+
 if __name__ == "__main__":
     unittest.main()