Fix constraint list bugs

deployment/codeship_runtests.sh

@@ -5,7 +5,7 @@ set -e  # fail immediately if any command fails
 
 
 VERSION="${TESTENV}.py${PYVERSION}"
-PYTESTFLAGS="-n 2 --disable-warnings --durations=20 --junit-xml=/opt/reports/junit.${VERSION}.xml --timeout=1800 --tb=short"
+PYTESTFLAGS="-n 2 --spec --disable-warnings --durations=20 --junit-xml=/opt/reports/junit.${VERSION}.xml --timeout=1800 --tb=short"
 if [ "${VERSION}" == "complete.py3" ]; then
        PYTESTFLAGS="--cov moldesign ${PYTESTFLAGS}"
 fi

deployment/requirements.txt

@@ -1,9 +1,11 @@
 # Python dependencies for the build/test environment
 coveralls
 nbformat
-pathlib ; python_version < '3.5'
+pathlib ; python_version < '3.3'
 PyGithub
+pyccc >= 0.7.10
 pytest-cov
 pytest-xdist != 1.17.0
 pytest-timeout
+pytest-spec
 

moldesign/_tests/test_constraints.py

@@ -6,7 +6,7 @@
 
 import moldesign as mdt
 from moldesign import units as u
-
+from .molecule_fixtures import *
 from . import helpers
 
 registered_types = {}
@@ -163,3 +163,29 @@ def test_dihedral_constraint_errors_at_0(four_particle_45_twist):
         constraint.value = angle
         np.testing.assert_allclose(constraint.error().value_in(u.degrees), -angle.magnitude)
 
+
+def test_cannot_add_duplicate_constraints(parameterize_zeros):
+    mol = parameterize_zeros
+    mol.constrain_distance(*mol.atoms[:2])
+    mol.constrain_angle(*mol.atoms[:3])
+    mol.constrain_dihedral(*mol.atoms[:4])
+    mol.constrain_atom(mol.atoms[0])
+    mol.constrain_hbonds()
+
+    # Failure on adding duplicates
+    with pytest.raises(KeyError):
+        mol.constrain_distance(*mol.atoms[:2])
+    with pytest.raises(KeyError):
+        mol.constrain_angle(*mol.atoms[:3])
+    with pytest.raises(KeyError):
+        mol.constrain_dihedral(*mol.atoms[:4])
+    with pytest.raises(KeyError):
+        mol.constrain_atom(mol.atoms[0])
+    with pytest.raises(KeyError):
+        mol.constrain_hbonds()
+
+    # These should be ok
+    mol.constrain_distance(*mol.atoms[1:3])
+    mol.constrain_angle(*mol.atoms[1:4])
+    mol.constrain_dihedral(*mol.atoms[1:5])
+    mol.constrain_atom(mol.atoms[1])

moldesign/_tests/test_copies.py

@@ -35,7 +35,7 @@ def test_copy_breaks_link(h2):
     assert h2.atoms[1].px == 0.0 * u.default.momentum
 
 
-def test_h2_harmonic_copy_loses_simulation(h2_harmonic_copy, h2_harmonic):
+def test_h2_harmonic_copy(h2_harmonic_copy, h2_harmonic):
     mol = h2_harmonic_copy
     assert mol.energy_model is mol.integrator is None
     for name in 'num_atoms num_residues positions momenta'.split():
@@ -196,6 +196,7 @@ def test_constraints_copied_with_molecule(parameterize_zeros):
     mol.constrain_hbonds()
 
     mcpy = mol.copy()
+    assert isinstance(mcpy.constraints, mol.constraints.__class__)
     assert mcpy.constraints[0].desc == 'distance'
     assert mcpy.constraints[1].desc == 'angle'
     assert mcpy.constraints[2].desc == 'dihedral'

moldesign/molecules/molecule.py

@@ -1074,8 +1074,9 @@ def __init__(self, atomcontainer,
         self.name = 'uninitialized molecule'
         self._defres = None
         self._defchain = None
+        self._constraints = None
         self.pdbname = pdbname
-        self.constraints = utils.ExclusiveList(key=utils.methodcaller('_constraintsig'))
+        self.constraints = []
         self.energy_model = None
         self.integrator = None
         self.metadata = metadata
@@ -1133,6 +1134,14 @@ def __repr__(self):
     def __str__(self):
         return 'Molecule: %s' % self.name
 
+    @property
+    def constraints(self):
+        return self._constraints
+
+    @constraints.setter
+    def constraints(self, val):
+        self._constraints = utils.ExclusiveList(val, key=utils.methodcaller('_constraintsig'))
+
     def _repr_markdown_(self):
         """A markdown description of this molecule.