Deploy 0.8.0beta2

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

deployment/send_test_status.py

@@ -8,7 +8,15 @@
 
 import github
 
-status = {'0':'success', 'na':'pending'}.get(sys.argv[1], 'failure')
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument('exitcode', type=str)
+parser.add_argument('msg', type=str)
+parser.add_argument('--deployed', action='store_true')
+args = parser.parse_args()
+
+status = {'0':'success', 'na':'pending'}.get(args.exitcode, 'failure')
 
 missing_env = []
 for key in 'CI_COMMIT_ID TESTENV GITHUB_REPO_TOKEN CI_PROJECT_ID CI_BUILD_ID PYVERSION'.split():
@@ -28,15 +36,22 @@
 data = dict(state=status,
             target_url='https://app.codeship.com/projects/%s/builds/%s' %
                        (projid, buildid),
-            description=" ".join(sys.argv[2:]).replace("=","").strip(),
+            description=args.msg.replace("=","").strip(),
             context='%s/py%s' % (testenv, pyversion))
 
 
 if missing_env:
     print("Not sending status update b/c of missing env vars: %s" % ','.join(missing_env))
     print(data)
+    sys.exit(0)
+
+
+g = github.Github(ghtoken)
+repo = g.get_repo('autodesk/molecular-design-toolkit')
+commit = repo.get_commit(sha)
+
+if args.deployed:
+    raise NotImplementedError
 else:
-    g = github.Github(ghtoken)
-    repo = g.get_repo('autodesk/molecular-design-toolkit')
-    commit = repo.get_commit(sha)
     commit.create_status(**data)
+

moldesign/_tests/helpers.py

@@ -62,7 +62,6 @@ def native_str_buffer(*args, **kwargs):
         return io.StringIO(*args, **kwargs)
 
 
-
 class ZeroEnergy(mdt.models.base.EnergyModelBase):
     """ All 0, all the time
     """
@@ -84,10 +83,46 @@ def _internet(host="8.8.8.8", port=53, timeout=3):
     """
     try:
         socket.setdefaulttimeout(timeout)
-        socket.socket(socket.AF_INET, socket.SOCK_STREAM).connect((host, port))
+        try:
+            socket.socket(socket.AF_INET, socket.SOCK_STREAM).connect((host, port))
+        except OSError:
+            return False
         return True
     except Exception as ex:
         print(ex.message)
         return False
 
 INTERNET_ON = _internet()
+
+
+def assert_something_resembling_minimization_happened(p0, e0, traj, mol):
+    """ Raises assertion error if results do not correspond to a successful optimization
+
+    Args:
+        p0 (Array[length]): initial position array
+        e0 (Scalar[energy]): initial energy
+        traj (moldesign.Trajectory): trajectory created from minimization
+        mol (moldesign.Molecule): state of molecule AFTER minimization
+
+    Returns:
+
+    """
+    import scipy.optimize.optimize
+
+    assert traj.num_frames > 1
+
+    assert traj.potential_energy[0] == e0
+    assert traj.potential_energy[-1] < e0
+    assert traj.potential_energy[-1] == mol.potential_energy
+
+    assert (traj.positions[0] == p0).all()
+    assert (traj.positions[-1] != p0).any()
+    assert (traj.positions[-1] == mol.positions).all()
+
+    scipyresult = getattr(traj, 'info', None)
+    if isinstance(scipyresult, scipy.optimize.optimize.OptimizeResult):
+        np.testing.assert_allclose(scipyresult.x,
+                                   mol.positions.defunits_value().flat)
+        np.testing.assert_almost_equal(scipyresult.fun,
+                                       mol.potential_energy.defunits_value())
+

moldesign/_tests/molecule_fixtures.py

@@ -47,6 +47,13 @@ def ligand3aid(ligand_residue_3aid):
     return newmol
 
 
+@typedfixture('molecule')
+def ethylene_waterbox_2na_2cl():
+    mol = mdt.from_smiles('C=C')
+    solvated = mdt.add_water(mol, padding=15.0*u.angstrom, ion_concentration=0.6*u.molar)
+    return solvated
+
+
 @pytest.fixture
 def random_atoms_from_3aid(pdb3aid):
     atoms = mdt.molecules.atomcollections.AtomList(random.sample(pdb3aid.atoms, 10))

moldesign/_tests/test_atom_containers.py

@@ -9,6 +9,7 @@
 from moldesign import units as u
 
 from . import helpers
+from .molecule_fixtures import pdb3aid, ethylene_waterbox_2na_2cl
 
 
 registered_types = {}
@@ -234,3 +235,46 @@ def test_get_atoms(protein):
         assert (atom.name == 'CA' and atom.residue.resname == 'GLY') == (
             atom in gly_alpha_carbons)
 
+
+def test_get_atoms_keywords(ethylene_waterbox_2na_2cl):
+    mol = ethylene_waterbox_2na_2cl
+    with pytest.raises(ValueError):
+        mol.get_atoms('arglebargle')
+
+    with pytest.raises(ValueError):
+        mol.get_atoms('ions')  # it's "ion" only (for now)
+
+    ions = mol.get_atoms('ion')
+    assert ions.num_atoms == 4
+    for ion in ions:
+        assert ion.residue.resname in ('NA','CL') and ion.name in ('Na','Cl')
+
+    waters = mol.get_atoms('water')
+    for w in waters:
+        assert w.residue.resname == 'HOH'
+
+    solute = mol.get_atoms('unknown')
+    assert len(solute) == 6
+
+    assert len(waters) + len(ions) + len(solute) == mol.num_atoms
+
+
+def test_get_residues_in_molecule(pdb3aid):
+    mol = pdb3aid
+    waters = mol.get_residues(type='water')
+    assert set(waters) == set(res for res in mol.residues if res.resname == 'HOH')
+
+
+def test_get_residues_in_chain(pdb3aid):
+    mol = pdb3aid
+    chain = mol.chains['A']
+    waters = chain.get_residues(type='water')
+    assert set(waters) == set(res for res in mol.chains['A'].residues if res.resname == 'HOH')
+
+
+def test_get_residues_two_parameters(pdb3aid):
+    mol = pdb3aid
+    alas = mol.chains['B'].get_residues(resname='ALA')
+    assert set(alas) == set(res for res in mol.chains['B'].residues if res.resname == 'ALA')
+    ala2 = mol.get_residues(resname='ALA', chain='B')
+    assert set(ala2) == set(alas)

moldesign/_tests/test_biopython_xface.py

@@ -0,0 +1,21 @@
+
+import pytest
+import Bio.PDB
+import moldesign as mdt
+
+from .helpers import get_data_path
+from .molecule_fixtures import pdb3aid
+
+
+@pytest.fixture
+def biopy_3aid():
+    parser = Bio.PDB.PDBParser()
+    structure = parser.get_structure('3aid', get_data_path('3aid.pdb'))
+    return structure
+
+
+def test_biopy_to_mdt(biopy_3aid, pdb3aid):
+    mol = mdt.interfaces.biopython_to_mol(biopy_3aid)
+    assert mol.num_atoms == pdb3aid.num_atoms
+    assert mol.num_residues == pdb3aid.num_residues
+    assert mol.numchains == pdb3aid.num_chains

moldesign/_tests/test_imports.py

@@ -2,6 +2,7 @@
 import sys
 
 
+@pytest.mark.tryfirst
 def test_lazy_imports():
     import moldesign