Update pyccc req to fix unicode bug, test tweaks

deployment/codeship_runtests.sh

@@ -5,7 +5,7 @@
 set -e
 
 VERSION="${TESTENV}.py${PYVERSION}"
-PYTESTFLAGS="-n 6 --durations=20 --junit-xml=/opt/reports/junit.${VERSION}.xml --timeout=1800"
+PYTESTFLAGS="-n 5 --durations=20 --junit-xml=/opt/reports/junit.${VERSION}.xml --timeout=1800 --tb=short"
 if [ "${VERSION}" == "complete.py3" ]; then
        PYTESTFLAGS="--cov moldesign ${PYTESTFLAGS}"
 fi

moldesign/_tests/test_tools.py

@@ -50,6 +50,20 @@ def test_ammonium_formal_charge(objkey, request):
             assert atom.formal_charge == 0 * u.q_e
 
 
+def test_set_hybridization_and_saturate():
+    # Creates just the carbons of ethylene, expects the routine to figure out the rest
+    atom1 = mdt.Atom(6)
+    atom2 = mdt.Atom(6)
+    atom2.x = 1.35 * u.angstrom
+    atom1.bond_to(atom2, 1)
+    mol = mdt.Molecule([atom1, atom2])
+    newmol = mdt.set_hybridization_and_saturate(mol)
+    pytest.xfail('This is apparently broken')
+    assert newmol.num_atoms == 6
+    assert newmol.atoms[0].bond_graph[atom1] == 2
+    assert len(newmol.get_atoms(atnum=1)) == 4
+
+
 @pytest.fixture
 def c2_no_hydrogen_from_smiles():
     mymol = mdt.from_smiles('[CH0][CH0]')

moldesign/fileio.py

@@ -324,6 +324,13 @@ def read_xyz(f):
     return mdt.Molecule(tempmol.atoms)
 
 
+def write_xyz(mol, fileobj):
+    fileobj.write("   %d\n%s\n" % (mol.num_atoms, mol.name))
+    for atom in mol.atoms:
+        x, y, z = atom.position.value_in(mdt.units.angstrom)
+        fileobj.write("%s   %24.14f   %24.14f   %24.14f\n" % (atom.element, x, y, z))
+
+
 @utils.exports
 def from_pdb(pdbcode, usecif=False):
     """ Import the given molecular geometry from PDB.org
@@ -442,7 +449,8 @@ def _get_format(filename, format):
            'xyz': read_xyz}
 
 WRITERS = {'pdb': write_pdb,
-           'mmcif': write_mmcif}
+           'mmcif': write_mmcif,
+           'xyz': write_xyz}
 
 if PY2:
     bzopener = bz2.BZ2File

pytest.ini

@@ -0,0 +1,6 @@
+[pytest]
+testpaths = moldesign/_tests
+
+markers =
+   base: tests data structures, molecule construction
+   slow: heavy duty simulation and numerical tests

requirements.txt

@@ -7,7 +7,7 @@ numpy >= 1.12
 pathlib2 ; python_version < '3.3'
 parmed >= 2.7.3
 pint >= 0.8
-pyccc >= 0.7.7
+pyccc >= 0.7.9
 pyyaml
 requests
 scipy