Merge pull request #243 from leeping/v1.9.2-final

Final changes for v1.9.2 release

bin/ForceBalance.py

@@ -60,7 +60,7 @@ def process(word, color):
     return Answer
 
 def main():
-    printcool("Welcome to ForceBalance version 1.9.1! =D\nForce Field Optimization System\n\nAuthors:\nLee-Ping Wang\nYudong Qiu, Keri A. McKiernan\nJeffrey R. Wagner, Hyesu Jang, Simon Boothroyd\nArthur Vigil, Erik G. Brandt, John Stoppelman\nJohnny Israeli, Matt Thompson", ansi="1", bold=True, minwidth=64)
+    printcool("Welcome to ForceBalance version 1.9.2! =D\nForce Field Optimization System\n\nAuthors:\nLee-Ping Wang\nYudong Qiu, Keri A. McKiernan\nJeffrey R. Wagner, Hyesu Jang, Simon Boothroyd\nArthur Vigil, Erik G. Brandt, John Stoppelman\nJohnny Israeli, Matt Thompson", ansi="1", bold=True, minwidth=64)
     logostr = """
                           ,'+++                                        
                        ,++++++.      .:,,.                              

devtools/conda-recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: forcebalance-dev
-  version: !!str 1.9.1
+  version: !!str 1.9.2
 
 source:
   path: ../..

doc/api_header.tex

@@ -57,7 +57,7 @@
 \vspace*{1cm}
 \begin{center}
 
-{\Large ForceBalance Developer API Guide version 1.9.1}\\
+{\Large ForceBalance Developer API Guide version 1.9.2}\\
 \vspace*{2cm}
 {\large Generated by Doxygen 1.8.11}\\
 \vspace*{2.5 cm}

doc/doxygen.cfg

@@ -32,7 +32,7 @@ PROJECT_NAME           = ForceBalance
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER         = 1.9.1
+PROJECT_NUMBER         = 1.9.2
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer

doc/header.tex

@@ -57,7 +57,7 @@
 \vspace*{1cm}
 \begin{center}
 
-{\Large ForceBalance version 1.9.1}\\
+{\Large ForceBalance version 1.9.2}\\
 \vspace*{2cm}
 {\large Generated by Doxygen 1.8.11}\\
 \vspace*{2.5 cm}

setup.py

@@ -21,7 +21,7 @@
 #| doc/api_header.tex              |#
 #| bin/ForceBalance.py             |#
 #===================================#
-__version__ = "v1.9.1"
+__version__ = "v1.9.2"
 try:
     # use git to find current version
     git_describe = subprocess.check_output(["git", "describe"]).strip()

src/forcefield.py

@@ -518,7 +518,7 @@ def check_dupes(self, pid, ffname, ln, pfld):
                 extranum += 1
             def warn_or_err(*args):
                 if self.duplicate_pnames:
-                    logger.warn(*args)
+                    logger.warning(*args)
                 else:
                     logger.error(*args)
             warn_or_err("Encountered an duplicate parameter ID (%s)\n" % pid_)
@@ -527,7 +527,7 @@ def warn_or_err(*args):
             for dupfnm, dupln, dupfld in zip(dupfnms, duplns, dupflds):
                 warn_or_err("file %s line %i field %i\n" % (dupfnm, dupln+1, dupfld))
             if self.duplicate_pnames:
-                logger.warn("Parameter name has been changed to %s\n" % pid)
+                logger.warning("Parameter name has been changed to %s\n" % pid)
             else:
                 raise RuntimeError
         return pid

src/lipid.py

@@ -192,7 +192,7 @@ def prepare_temp_directory(self):
 
     def read_data(self):
         # Read the 'data.csv' file. The file should contain guidelines.
-        with open(os.path.join(self.tgtdir,'data.csv'),'rU') as f: R0 = list(csv.reader(f))
+        with open(os.path.join(self.tgtdir,'data.csv'),'r') as f: R0 = list(csv.reader(f))
         # All comments are erased.
         R1 = [[sub('#.*$','',word) for word in line] for line in R0 if len(line[0]) > 0 and line[0][0] != "#"]
         # All empty lines are deleted and words are converted to lowercase.

src/smirnoff_hack.py

@@ -40,11 +40,11 @@ def hash_molecule_args_and_kwargs(molecule, *args, **kwargs):
 
 
 if _SHOULD_CACHE:
-
-    print(
-        "SMIRNOFF functions will be replaced with cached versions to improve their "
-        "performance."
-    )
+    # Commented out because it is printed even for non-SMIRNOFF calculations.
+    # print(
+    #     "SMIRNOFF functions will be replaced with cached versions to improve their "
+    #     "performance."
+    # )
 
     # time based on total 540s evaluation
     # cache for OE find_smarts_matches (save 300+ s)

src/tests/__init__.py

@@ -27,3 +27,21 @@ def setup_method(self, method):
 
     def teardown_method(self):
         os.chdir(self.start_directory)
+
+def check_for_openmm():
+    try:
+        try:
+            # Try importing openmm using >=7.6 namespace
+            from openmm import app
+            import openmm as mm
+            from openmm import unit
+        except ImportError:
+            # Try importing openmm using <7.6 namespace
+            import simtk.openmm as mm
+            from simtk.openmm import app
+            from simtk import unit
+        return True
+    except ImportError:
+        # If OpenMM classes cannot be imported, then set this flag 
+        # so the testing classes/functions can use to skip.
+        return False

src/tests/test_engine.py

@@ -7,7 +7,7 @@
 from forcebalance.tinkerio import TINKER
 from forcebalance.openmmio import OpenMM
 from collections import OrderedDict
-from .__init__ import ForceBalanceTestCase
+from .__init__ import ForceBalanceTestCase, check_for_openmm
 
 # Set SAVEDATA to True and run the tests in order to save data
 # to a file for future reference. This is easier to use for troubleshooting
@@ -86,12 +86,12 @@ def setup_class(cls):
         if gmxpath != '':
             cls.engines['GMX'] = GMX(coords="all.gro", gmx_top="topol.top", gmx_mdp="shot.mdp", gmxpath=gmxpath, gmxsuffix=gmxsuffix)
         else:
-            logger.warn("GROMACS cannot be found, skipping GMX tests.")
+            logger.warning("GROMACS cannot be found, skipping GMX tests.")
         # Set up TINKER engine
         if tinkerpath != '':
             cls.engines['TINKER'] = TINKER(coords="all.arc", tinker_key="alaglu.key", tinkerpath=tinkerpath)
         else:
-            logger.warn("TINKER cannot be found, skipping TINKER tests.")
+            logger.warning("TINKER cannot be found, skipping TINKER tests.")
         # Set up OpenMM engine
         try:
             try:
@@ -100,7 +100,7 @@ def setup_class(cls):
                 import simtk.openmm
             cls.engines['OpenMM'] = OpenMM(coords="all.gro", pdb="conf.pdb", ffxml="a99sb.xml", platname="Reference", precision="double")
         except:
-            logger.warn("OpenMM cannot be imported, skipping OpenMM tests.")
+            logger.warning("OpenMM cannot be imported, skipping OpenMM tests.")
 
     @classmethod
     def teardown_class(cls):
@@ -351,6 +351,7 @@ class TestAmoebaWater6(ForceBalanceTestCase):
     """
     @classmethod
     def setup_class(cls):
+        if not check_for_openmm(): pytest.skip("No OpenMM modules found.")
         super(TestAmoebaWater6, cls).setup_class()
         #self.logger.debug("\nBuilding options for target...\n")
         cls.cwd = os.path.dirname(os.path.realpath(__file__))

src/tests/test_liquid.py

@@ -7,10 +7,11 @@
 from forcebalance.forcefield import FF
 from forcebalance.objective import Objective
 from forcebalance.optimizer import Optimizer
-from .__init__ import ForceBalanceTestCase
+from .__init__ import ForceBalanceTestCase, check_for_openmm
 
 class TestWaterTutorial(ForceBalanceTestCase):
     def setup_method(self, method):
+        if not check_for_openmm(): pytest.skip("No OpenMM modules found.")
         super(TestWaterTutorial, self).setup_method(method)
         self.cwd = os.path.dirname(os.path.realpath(__file__))
         # copy folder 'files/test_liquid' into a new folder 'files/test_liquid.run'

src/tests/test_openmmio.py

@@ -5,16 +5,21 @@
 import numpy as np
 
 try:
-    # Try importing openmm using >=7.6 namespace
-    from openmm import app
-    import openmm as mm
-    from openmm import unit
+    try:
+        # Try importing openmm using >=7.6 namespace
+        from openmm import app
+        import openmm as mm
+        from openmm import unit
+    except ImportError:
+        # Try importing openmm using <7.6 namespace
+        import simtk.openmm as mm
+        from simtk.openmm import app
+        from simtk import unit
+    no_openmm = False
 except ImportError:
-    # Try importing openmm using <7.6 namespace
-    import simtk.openmm as mm
-    from simtk.openmm import app
-    from simtk import unit
-
+    # If OpenMM classes cannot be imported, then set this flag 
+    # so the testing classes/functions can use to skip.
+    no_openmm = True
 
 import os
 import shutil
@@ -26,6 +31,7 @@
 
 class TestLiquid_OpenMM(TargetTests):
     def setup_method(self, method):
+        if no_openmm: pytest.skip("No OpenMM modules found.")
         super(TestLiquid_OpenMM, self).setup_method(method)
         self.check_grad_fd = False
         # settings specific to this target
@@ -53,6 +59,7 @@ def teardown_method(self):
 class TestInteraction_OpenMM(TargetTests):
 
     def setup_method(self, method):
+        if no_openmm: pytest.skip("No OpenMM modules found.")
         super(TestInteraction_OpenMM, self).setup_method(method)
         # TargetTests.setup_class(cls)
         # settings specific to this target
@@ -77,9 +84,10 @@ def teardown_method(self):
         shutil.rmtree('temp')
         super(TestInteraction_OpenMM, self).teardown_method()
 
-
+        
 def test_local_coord_sites():
     """Make sure that the internal prep of vs positions matches that given by OpenMM."""
+    if no_openmm: pytest.skip("No OpenMM modules found.")
     # make a system
     mol = app.PDBFile(os.path.join("files", "vs_mol.pdb"))
     modeller = app.Modeller(topology=mol.topology, positions=mol.positions)

src/tests/test_system.py

@@ -3,7 +3,7 @@
 from builtins import str
 import os, shutil
 import tarfile
-from .__init__ import ForceBalanceTestCase
+from .__init__ import ForceBalanceTestCase, check_for_openmm
 from forcebalance.parser import parse_inputs
 from forcebalance.forcefield import FF
 from forcebalance.objective import Objective
@@ -181,7 +181,7 @@ def test_thermo_bromine_study(self):
 
 class TestEvaluatorBromineStudy(ForceBalanceSystemTest):
     def setup_method(self, method):
-        pytest.importorskip("evaluator")
+        pytest.importorskip("openff.evaluator")
         super(TestEvaluatorBromineStudy, self).setup_method(method)
         cwd = os.path.dirname(os.path.realpath(__file__))
         os.chdir(os.path.join(cwd, '..', '..', 'studies', '003d_evaluator_liquid_bromine'))
@@ -213,7 +213,7 @@ def test_bromine_study(self):
         msgX="\nCalculated objective function is outside expected range.\n If this seems reasonable, update EXPECTED_EVALUATOR_BROMINE_OBJECTIVE in test_system.py with these values"
         np.testing.assert_allclose(EXPECTED_EVALUATOR_BROMINE_OBJECTIVE, X, atol=120, err_msg=msgX)
         msgG="\nCalculated gradient is outside expected range.\n If this seems reasonable, update EXPECTED_EVALUATOR_BROMINE_GRADIENT in test_system.py with these values"
-        np.testing.assert_allclose(EXPECTED_EVALUATOR_BROMINE_GRADIENT, G, atol=2000, err_msg=msgG)
+        np.testing.assert_allclose(EXPECTED_EVALUATOR_BROMINE_GRADIENT, G, atol=4000, err_msg=msgG)
 
 class TestLipidStudy(ForceBalanceSystemTest):
     def setup_method(self, method):
@@ -232,6 +232,7 @@ def test_lipid_study(self):
 
 class TestImplicitSolventHFEStudy(ForceBalanceSystemTest):
     def setup_method(self, method):
+        if not check_for_openmm(): pytest.skip("No OpenMM modules found.")
         super(TestImplicitSolventHFEStudy, self).setup_method(method)
         cwd = os.path.dirname(os.path.realpath(__file__))
         os.chdir(os.path.join(cwd, '..', '..', 'studies', '012_implicit_solvent_hfe'))