Add Chemfiles as a coordinate reader/writer

.travis.yml

@@ -27,9 +27,9 @@ env:
     - MAIN_CMD="pytest ${PYTEST_LIST}"
     - SETUP_CMD="${PYTEST_FLAGS}"
     - BUILD_CMD="pip install -e package/ && (cd testsuite/ && python setup.py build)"
-    - CONDA_MIN_DEPENDENCIES="mmtf-python mock six biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov chemfiles"
+    - CONDA_MIN_DEPENDENCIES="mmtf-python mock six biopython networkx cython matplotlib scipy griddataformats hypothesis gsd codecov"
     # Cap seaborn to 0.9 since 0.10 drops Python 2 support (temporarily solve #2495)
-    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0,<=0.9 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12"
+    - CONDA_DEPENDENCIES="${CONDA_MIN_DEPENDENCIES} seaborn>=0.7.0,<=0.9 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles"
     - CONDA_CHANNELS='biobuilds conda-forge'
     - CONDA_CHANNEL_PRIORITY=True
     - PIP_DEPENDENCIES="duecredit parmed"

package/MDAnalysis/coordinates/__init__.py

@@ -716,6 +716,7 @@ class can choose an appropriate reader automatically.
 from . import base
 from .core import reader, writer
 from . import chain
+from . import chemfiles
 from . import CRD
 from . import DCD
 from . import DLPoly

package/MDAnalysis/coordinates/chemfiles.py

@@ -47,15 +47,25 @@
 
 from . import base, core
 
-import chemfiles
-from chemfiles import Trajectory, Frame, Atom, UnitCell, Residue, Topology
+try:
+    import chemfiles
+except ImportError:
+    HAS_CHEMFILES = False
+else:
+    HAS_CHEMFILES = True
+
 
 
 MIN_CHEMFILES_VERSION = LooseVersion("0.9")
 MAX_CHEMFILES_VERSION = LooseVersion("0.10")
 
 
 def check_chemfiles_version():
+    if not HAS_CHEMFILES:
+        raise RuntimeError(
+            "No Chemfiles package found.  "
+            "Try installing with 'pip install chemfiles'"
+        )
     version = LooseVersion(chemfiles.__version__)
     if version < MIN_CHEMFILES_VERSION or version >= MAX_CHEMFILES_VERSION:
         raise RuntimeError(
@@ -65,8 +75,7 @@ def check_chemfiles_version():
 
 
 class ChemfilesReader(base.ReaderBase):
-    """
-    Coordinate reader using chemfiles.
+    """Coordinate reader using chemfiles.
 
     The file format to used is guessed based on the file extension. If no
     matching format is found, a ``ChemfilesError`` is raised. It is also
@@ -79,12 +88,13 @@ def __init__(self, filename, chemfiles_format="", **kwargs):
         """
         Parameters
         ----------
-        filename : str
-            trajectory filename
+        filename : chemfiles.Trajectory or str
+            the chemfiles object to read or filename to read
         chemfiles_format : str (optional)
-            use the given format name instead of guessing from the extension.
-            The `list of supported formats <formats>`_ and the associated names
-            is available in chemfiles documentation.
+            if *filename* was a string, use the given format name instead of
+            guessing from the extension. The `list of supported formats
+            <formats>`_ and the associated names is available in chemfiles
+            documentation.
         **kwargs : dict
             General reader arguments.
 
@@ -99,13 +109,21 @@ def __init__(self, filename, chemfiles_format="", **kwargs):
         self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs)
         self.next()
 
+    @staticmethod
+    def _format_hint(thing):
+        """Can this Reader read *thing*"""
+        # nb, filename strings can still get passed through if
+        # format='CHEMFILES' is used
+        return HAS_CHEMFILES and isinstance(thing, chemfiles.Trajectory)
+
     def _open(self):
         self._closed = False
         self._step = 0
         self._frame = -1
-        # Open file last to ensure that all other attributes are set
-        # in case of exception
-        self._file = Trajectory(self.filename, 'r', self._format)
+        if isinstance(self.filename, chemfiles.Trajectory):
+            self._file = self.filename
+        else:
+            self._file = chemfiles.Trajectory(self.filename, 'r', self._format)
 
     def close(self):
         """close reader"""
@@ -224,7 +242,7 @@ def __init__(self, filename, n_atoms=0, mode="w", chemfiles_format="", topology=
         self.n_atoms = n_atoms
         if mode != "a" and mode != "w":
             raise IOError("Expected 'a' or 'w' as mode in ChemfilesWriter")
-        self._file = Trajectory(self.filename, mode, chemfiles_format)
+        self._file = chemfiles.Trajectory(self.filename, mode, chemfiles_format)
         self._closed = False
         if topology is not None:
             if isinstance(topology, string_types):
@@ -293,21 +311,22 @@ def _timestep_to_chemfiles(self, ts):
         """
         Convert a Timestep to a chemfiles Frame
         """
-        frame = Frame()
+        # TODO: CONVERTERS?
+        frame = chemfiles.Frame()
         frame.resize(ts.n_atoms)
         if ts.has_positions:
             frame.positions[:] = ts.positions[:]
         if ts.has_velocities:
             frame.add_velocities()
             frame.velocities[:] = ts.velocities[:]
-        frame.cell = UnitCell(*ts.dimensions)
+        frame.cell = chemfiles.UnitCell(*ts.dimensions)
         return frame
 
     def _topology_to_chemfiles(self, obj, n_atoms):
         """
         Convert an AtomGroup or an Universe to a chemfiles Topology
         """
-        topology = Topology()
+        topology = chemfiles.Topology()
         if not hasattr(obj, "atoms"):
             # use an empty topology
             topology.resize(n_atoms)
@@ -318,7 +337,7 @@ def _topology_to_chemfiles(self, obj, n_atoms):
         for atom in obj.atoms:
             name = getattr(atom, 'name', "")
             type = getattr(atom, 'type', name)
-            chemfiles_atom = Atom(name, type)
+            chemfiles_atom = chemfiles.Atom(name, type)
 
             if hasattr(atom, 'altLoc'):
                 chemfiles_atom["altloc"] = str(atom.altLoc)
@@ -332,7 +351,7 @@ def _topology_to_chemfiles(self, obj, n_atoms):
             if hasattr(atom, 'resid'):
                 resname = getattr(atom, 'resname', "")
                 if atom.resid not in residues.keys():
-                    residues[atom.resid] = Residue(resname, atom.resid)
+                    residues[atom.resid] = chemfiles.Residue(resname, atom.resid)
                 residue = residues[atom.resid]
 
                 atom_idx = len(topology.atoms)

package/setup.py

@@ -559,7 +559,6 @@ def dynamic_author_list():
           'matplotlib>=1.5.1',
           'mock',
           'parmed',
-          'chemfiles>=0.9.3',
     ]
     if not os.name == 'nt':
         install_requires.append('gsd>=1.4.0')
@@ -602,7 +601,6 @@ def dynamic_author_list():
                 'scipy (>=1.0.0)',
                 'matplotlib (>=1.5.1)',
                 'parmed',
-                'chemfiles (>=0.9.3)',
             ],
           # all standard requirements are available through PyPi and
           # typically can be installed without difficulties through setuptools

testsuite/MDAnalysisTests/coordinates/test_chemfiles.py

@@ -21,20 +21,39 @@
 #
 from __future__ import absolute_import
 
+import numpy as np
 import pytest
 
 import MDAnalysis as mda
-import numpy as np
-from unittest import TestCase
-
-from chemfiles import ChemfilesError
-
 from MDAnalysis.coordinates.chemfiles import ChemfilesReader, ChemfilesWriter
 
 from MDAnalysisTests import datafiles, tempdir
 from MDAnalysisTests.coordinates.base import (
     MultiframeReaderTest, BaseWriterTest, BaseReference
 )
+from MDAnalysisTests.coordinates.test_xyz import XYZReference
+
+
+chemfiles = pytest.importorskip('chemfiles')
+
+
+class TestChemFileXYZ(MultiframeReaderTest):
+    @staticmethod
+    @pytest.fixture
+    def ref():
+        base = XYZReference()
+        base.writer = ChemfilesWriter
+        base.dimensions = np.array([0, 0, 0, 90, 90, 90], dtype=np.float32)
+
+        return base
+
+    @pytest.fixture
+    def reader(self, ref):
+        reader = ChemfilesReader(ref.trajectory)
+        reader.add_auxiliary('lowf', ref.aux_lowf, dt=ref.aux_lowf_dt, initial_time=0, time_selector=None)
+        reader.add_auxiliary('highf', ref.aux_highf, dt=ref.aux_highf_dt, initial_time=0, time_selector=None)
+        return reader
+
 
 
 class ChemfilesXYZReference(BaseReference):
@@ -69,11 +88,11 @@ def test_no_container(self, ref):
         pass
 
     def test_no_extension_raises(self, ref):
-        with pytest.raises(ChemfilesError):
+        with pytest.raises(chemfiles.ChemfilesError):
             ref.writer('foo')
 
 
-class TestChemfiles(TestCase):
+class TestChemfiles(object):
     def test_read_chemfiles_format(self):
         u = mda.Universe(
             datafiles.LAMMPSdata,
@@ -83,7 +102,7 @@ def test_read_chemfiles_format(self):
         )
 
         for ts in u.trajectory:
-            self.assertEqual(ts.n_atoms, 18364)
+            assert ts.n_atoms == 18364
 
     def test_changing_system_size(self):
         outfile = tempdir.TempDir().name + "chemfiles-changing-size.xyz"
@@ -92,11 +111,11 @@ def test_changing_system_size(self):
 
         u = mda.Universe(outfile, format="chemfiles", topology_format="XYZ")
 
-        with self.assertRaises(IOError):
+        with pytest.raises(IOError):
             u.trajectory._read_next_timestep()
 
     def test_wrong_open_mode(self):
-        with self.assertRaises(IOError):
+        with pytest.raises(IOError):
             _ = ChemfilesWriter("", mode="r")
 
     def check_topology(self, reference, file):
@@ -117,10 +136,10 @@ def check_topology(self, reference, file):
         )
 
         for atom in check.atoms:
-            self.assertIn((atom.name, atom.type, atom.record_type), atoms)
+            assert (atom.name, atom.type, atom.record_type) in atoms
 
         for bond in check.bonds:
-            self.assertIn((bond.atoms[0].ix, bond.atoms[1].ix), bonds)
+            assert (bond.atoms[0].ix, bond.atoms[1].ix) in bonds
 
     def test_write_topology(self):
         u = mda.Universe(datafiles.CONECT)
@@ -174,7 +193,7 @@ def test_write_velocities(self):
 
         with open(outfile) as file:
             content = file.read()
-            self.assertEqual(content, EXPECTED_LAMMPS_DATA)
+            assert content == EXPECTED_LAMMPS_DATA
 
 
 VARYING_XYZ = """2

testsuite/MDAnalysisTests/coordinates/test_xyz.py

@@ -31,8 +31,6 @@
     assert_almost_equal,
 )
 
-from MDAnalysis.coordinates import chemfiles
-
 from MDAnalysis.coordinates.XYZ import XYZWriter
 
 from MDAnalysisTests.datafiles import COORDINATES_XYZ, COORDINATES_XYZ_BZ2
@@ -178,21 +176,3 @@ def test_elements_and_names(self, outfile, attr):
             names = ''.join(l.split()[0].strip() for l in r.readlines()[2:-1])
 
         assert names[:-1].lower() == 'testing'
-
-
-class TestChemFileXYZ(MultiframeReaderTest):
-    @staticmethod
-    @pytest.fixture
-    def ref():
-        base = XYZReference()
-        base.writer = chemfiles.ChemfilesWriter
-        base.dimensions = np.array([0, 0, 0, 90, 90, 90], dtype=np.float32)
-
-        return base
-
-    @pytest.fixture
-    def reader(self, ref):
-        reader = chemfiles.ChemfilesReader(ref.trajectory)
-        reader.add_auxiliary('lowf', ref.aux_lowf, dt=ref.aux_lowf_dt, initial_time=0, time_selector=None)
-        reader.add_auxiliary('highf', ref.aux_highf, dt=ref.aux_highf_dt, initial_time=0, time_selector=None)
-        return reader