Update dependency requirements (#457)

* Make foyer an optional dependency

* Split dependencies into required and required for development

* Update developer requirements

* Marked appropriate tests to check if Foyer is installed

* Remove duplicate line

* Remove openbabel and gsd from Appveyor testing

* Attempt to fix coverage dependency issue (#466)

* Attempt to fix coverage dependency issue

Currently, the most recent version of python-coveralls requires
`coverage==4.0.3`, while pytest-cov requires `Coverage>=4.4`.

The current fix seems to be to pin `pytest-cov` to a previous
version. This can be changed once:
z4r/python-coveralls#66

has been resolved.

* Hotfix for MDTraj MOL2 file issues

MDTraj has merged a fix for MOL2 file reading
mdtraj/mdtraj#1378

However, it has not been included in a new release on
`conda` yet.

Pinning to an older version without the MOL2 fixes
currently.

* Forgot to update Appveyor build script

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Fixes issues with packmol input files (#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build`

See ContinuumIO/anaconda-issues#10211 (comment)

* Update changelog

* Re-pin mdtraj and pytest-cov

.travis.yml

@@ -25,7 +25,7 @@ install:
   - conda config --add channels bioconda
   - conda config --add channels conda-forge
   - conda config --add channels mosdef
-  - conda create -n test-environment python=$PYTHON_VERSION --file requirements.txt
+  - conda create -n test-environment python=$PYTHON_VERSION --file requirements-dev.txt
   - source activate test-environment
   - pip install -e .
 

devtools/conda-recipe/meta.yaml

@@ -22,7 +22,6 @@ requirements:
     - oset
     - parmed
     - mdtraj 1.9.1
-    - foyer
 
 test:
   requires:
@@ -32,6 +31,7 @@ test:
     - ipykernel
     - ipyext
     - pytest-ignore-flaky
+    - foyer
 
   source_files:
     - mbuild/examples/*

mbuild/compound.py

@@ -1445,9 +1445,10 @@ def _energy_minimize_openmm(
 
 
         """
-        from foyer import Forcefield
+        foyer = import_('foyer')
+
         to_parmed = self.to_parmed()
-        ff = Forcefield(forcefield_files=forcefield_files, name=forcefield_name)
+        ff = foyer.Forcefield(forcefield_files=forcefield_files, name=forcefield_name)
         to_parmed = ff.apply(to_parmed)
 
         from simtk.openmm.app.simulation import Simulation
@@ -1727,9 +1728,9 @@ def save(self, filename, show_ports=False, forcefield_name=None,
                                    show_ports=show_ports)
         # Apply a force field with foyer if specified
         if forcefield_name or forcefield_files:
-            from foyer import Forcefield
-            ff = Forcefield(forcefield_files=forcefield_files,
-                            name=forcefield_name, debug=forcefield_debug)
+            foyer = import_('foyer')
+            ff = foyer.Forcefield(forcefield_files=forcefield_files,
+                                  name=forcefield_name, debug=forcefield_debug)
             structure = ff.apply(structure, references_file=references_file)
             structure.combining_rule = combining_rule
 

mbuild/tests/test_compound.py

@@ -9,7 +9,7 @@
 import mbuild as mb
 from mbuild.exceptions import MBuildError
 from mbuild.utils.geometry import calc_dihedral
-from mbuild.utils.io import get_fn, has_intermol, has_openbabel
+from mbuild.utils.io import get_fn, has_foyer, has_intermol, has_openbabel
 from mbuild.tests.base_test import BaseTest
 
 class TestCompound(BaseTest):
@@ -52,6 +52,7 @@ def test_save_overwrite(self, ch3):
             with pytest.raises(IOError):
                 ch3.save(filename=outfile, overwrite=False)
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer is not installed")
     def test_save_forcefield(self, methane):
         exts = ['.gsd', '.hoomdxml', '.lammps', '.lmp', '.top', '.gro',
                 '.mol2', '.pdb', '.xyz']
@@ -60,6 +61,7 @@ def test_save_forcefield(self, methane):
                          forcefield_name='oplsaa',
                          overwrite=True)
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer is not installed")
     def test_save_forcefield_with_file(self, methane):
         exts = ['.gsd', '.hoomdxml', '.lammps', '.lmp', '.top', '.gro',
                 '.mol2', '.pdb', '.xyz']
@@ -83,11 +85,13 @@ def test_save_resnames_single(self, c3, n4):
         assert struct.residues[0].number ==  1
         assert struct.residues[1].number ==  2
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer is not installed")
     def test_save_references(self, methane):
         methane.save('methyl.mol2', forcefield_name='oplsaa',
                      references_file='methane.bib')
         assert os.path.isfile('methane.bib')
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer is not installed")
     def test_save_combining_rule(self, methane):
         combining_rules = ['lorentz', 'geometric']
         gmx_rules = {'lorentz': 2, 'geometric': 3}
@@ -668,13 +672,14 @@ def test_energy_minimization_ports(self, octane):
         assert np.array_equal(distances, updated_distances)
         assert np.array_equal(orientations, updated_orientations)
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer is not installed")
     def test_energy_minimize_openmm(self, octane):
         octane.energy_minimize(forcefield='oplsaa')
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer is not installed")
     def test_energy_minimize_openmm_xml(self, octane):
         octane.energy_minimize(forcefield=get_fn('small_oplsaa.xml'))
 
-
     def test_clone_outside_containment(self, ch2, ch3):
         compound = mb.Compound()
         compound.add(ch2)

mbuild/tests/test_gsd.py

@@ -4,7 +4,7 @@
 import numpy as np
 import pytest
 from mbuild.tests.base_test import BaseTest
-from mbuild.utils.io import has_gsd
+from mbuild.utils.io import has_foyer, has_gsd
 
 
 class TestGSD(BaseTest):
@@ -13,19 +13,23 @@ class TestGSD(BaseTest):
     def test_save(self, ethane):
         ethane.save(filename='ethane.gsd')
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer package not installed")
     @pytest.mark.skipif(not has_gsd, reason="GSD package not installed")
     def test_save_forcefield(self, ethane):
         ethane.save(filename='ethane-opls.gsd', forcefield_name='oplsaa')
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer package not installed")
     @pytest.mark.skipif(not has_gsd, reason="GSD package not installed")
     def test_save_box(self, ethane):
         box = mb.Box(lengths=np.array([2.0,2.0,2.0]))
         ethane.save(filename='ethane-box.gsd', forcefield_name='oplsaa',box=box)
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer package not installed")
     def test_save_triclinic_box_(self, ethane):
         box = mb.Box(lengths=np.array([2.0, 2.0, 2.0]), angles=[60, 70, 80])
         ethane.save(filename='triclinic-box.gsd', forcefield_name='oplsaa', box=box)
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer package not installed")
     @pytest.mark.skipif(not has_gsd, reason="GSD package not installed")
     def test_particles(self, ethane):
         from collections import OrderedDict
@@ -65,6 +69,7 @@ def test_particles(self, ethane):
         assert np.array_equal(types_from_gsd, unique_types)
         assert np.array_equal(typeids_from_gsd, expected_typeids)
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer package not installed")
     @pytest.mark.skipif(not has_gsd, reason="GSD package not installed")
     def test_box(self, ethane):
         import gsd, gsd.pygsd
@@ -99,7 +104,7 @@ def test_box(self, ethane):
         assert np.isclose(np.cos(np.radians(70)), xz / c)
         assert np.isclose(np.cos(np.radians(80)), xy / b)
 
-
+    @pytest.mark.skipif(not has_foyer, reason="Foyer package not installed")
     @pytest.mark.skipif(not has_gsd, reason="GSD package not installed")
     def test_rigid(self, benzene):
         import gsd, gsd.pygsd
@@ -115,6 +120,7 @@ def test_rigid(self, benzene):
         for gsd_body, expected_body in zip(rigid_bodies, expected_bodies):
             assert gsd_body == expected_body
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer package not installed")
     @pytest.mark.skipif(not has_gsd, reason="GSD package not installed")
     def test_bonded(self, ethane):
         from foyer import Forcefield
@@ -190,6 +196,7 @@ def test_bonded(self, ethane):
         assert np.array_equal(dihedral_atoms, expected_dihedral_atoms)
         assert np.array_equal(dihedral_typeids, np.zeros(n_dihedrals))
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer package not installed")
     @pytest.mark.skipif(not has_gsd, reason="GSD package not installed")
     def test_pairs(self, benzene):
         from foyer import Forcefield

mbuild/tests/test_hoomdxml.py

@@ -4,13 +4,15 @@
 
 import mbuild as mb
 from mbuild.tests.base_test import BaseTest
+from mbuild.utils.io import has_foyer
 
 
 class TestHoomdXML(BaseTest):
 
     def test_save(self, ethane):
         ethane.save(filename='ethane.hoomdxml')
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer package not installed")
     def test_save_forcefield(self, ethane):
         ethane.save(filename='ethane-opls.hoomdxml', forcefield_name='oplsaa')
 
@@ -38,6 +40,7 @@ def test_rigid(self, benzene):
             assert rigid_bodies.count(body_id) == 6
         assert rigid_bodies.count(-1) == n_benzenes * 6
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer package not installed")
     def test_number_in_each_section(self, box_of_benzenes):
         box_of_benzenes.save(filename='benzene.hoomdxml', forcefield_name='oplsaa')
         xml_file = xml.etree.ElementTree.parse('benzene.hoomdxml').getroot()

mbuild/tests/test_lammpsdata.py

@@ -3,16 +3,19 @@
 
 import mbuild as mb
 from mbuild.tests.base_test import BaseTest
+from mbuild.utils.io import has_foyer
 
 
 class TestLammpsData(BaseTest):
 
     def test_save(self, ethane):
         ethane.save(filename='ethane.lammps')
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer package not installed")
     def test_save_forcefield(self, ethane):
         ethane.save(filename='ethane-opls.lammps', forcefield_name='oplsaa')
 
+    @pytest.mark.skipif(not has_foyer, reason="Foyer package not installed")
     def test_save_box(self, ethane):
         box = mb.Box(lengths=np.array([2.0, 2.0, 2.0]))
         ethane.save(filename='ethane-box.lammps', forcefield_name='oplsaa', box=box)

mbuild/utils/io.py

@@ -65,6 +65,18 @@ class DelayImportError(ImportError, SkipTest):
 
 MESSAGES['pybel'] = MESSAGES['openbabel']
 
+MESSAGES['foyer'] = '''
+The code at {filename}:{line_number} requires the "foyer" package
+
+foyer can be installed using:
+
+# conda install -c mosdef foyer
+
+or
+
+# pip install foyer
+'''
+
 
 def import_(module):
     """Import a module, and issue a nice message to stderr if the module isn't installed.
@@ -133,6 +145,13 @@ def import_(module):
 except ImportError:
     has_openbabel = False
 
+try:
+    import foyer
+    has_foyer = True
+    del foyer
+except ImportError:
+    has_foyer = False
+
 
 def get_fn(name):
     """Get the full path to one of the reference files shipped for utils.

requirements-dev.txt

@@ -0,0 +1,31 @@
+numpy
+scipy
+packmol=1.0.0
+nglview>=0.6.2.3
+oset
+parmed
+# TODO: Remove pinning of mdtraj version once mol2 reader issues have been resolved.
+#       https://github.com/mdtraj/mdtraj/pull/1378
+#       Once this has been released in a new MDTraj version, this can be removed.
+mdtraj==1.9.1
+foyer
+gsd
+openbabel
+pytest >=3.0
+jupyter
+nbformat
+ipykernel
+ipyext
+python-coveralls
+# TODO: Remove the pinning of the pytest-cov version again once issue
+#       https://github.com/z4r/python-coveralls/issues/66
+#       is resolved.
+#       Background: pytest-cov 2.6.0 has increased the version
+#       requirement for the coverage package from >=3.7.1 to
+#       >=4.4, which is in conflict with the version requirement
+#       defined by the python-coveralls package for coverage==4.0.3.
+# This fix from:
+# https://github.com/pywbem/pywbem/commit/d85a3e73e08d2846073087733b790b5a8864d93f
+pytest-cov>=2.4.0,<2.6
+pytest-faulthandler
+pytest-ignore-flaky

requirements.txt

@@ -8,24 +8,3 @@ parmed
 #       https://github.com/mdtraj/mdtraj/pull/1378
 #       Once this has been released in a new MDTraj version, this can be removed.
 mdtraj==1.9.1
-foyer
-gsd
-openbabel
-pytest >=3.0
-jupyter
-nbformat
-ipykernel
-ipyext
-python-coveralls
-# TODO: Remove the pinning of the pytest-cov version again once issue
-#       https://github.com/z4r/python-coveralls/issues/66
-#       is resolved.
-#       Background: pytest-cov 2.6.0 has increased the version
-#       requirement for the coverage package from >=3.7.1 to
-#       >=4.4, which is in conflict with the version requirement
-#       defined by the python-coveralls package for coverage==4.0.3.
-# This fix from:
-# https://github.com/pywbem/pywbem/commit/d85a3e73e08d2846073087733b790b5a8864d93f
-pytest-cov>=2.4.0,<2.6
-pytest-faulthandler
-pytest-ignore-flaky