Create alchemy subpackage (#721)

* Create alchemy subpackage

* Fix docs dependencies

* Fix alchemy tests imports

devtools/conda-envs/test_env.yaml

@@ -32,3 +32,4 @@ dependencies:
   # docs
   - numpydoc
   - sphinxcontrib-bibtex
+  - sphinx-rtd-theme

openmmtools/alchemy/__init__.py

@@ -0,0 +1,22 @@
+"""
+Alchemical factory for free energy calculations package that operates directly on OpenMM
+System objects.
+
+DESCRIPTION
+
+This package contains enumerative factories for generating alchemically-modified System objects
+usable for the calculation of free energy differences of hydration or ligand binding.
+
+Provided classes include:
+
+- :class:`openmmtools.alchemy.alchemy.AlchemicalFunction`
+- :class:`openmmtools.alchemy.alchemy.AlchemicalState`
+- :class:`openmmtools.alchemy.alchemy.AlchemicalRegion`
+- :class:`openmmtools.alchemy.alchemy.AbsoluteAlchemicalFactory`
+- :class:`openmmtools.alchemy.alchemy.AlchemicalStateError`
+
+"""
+
+# Automatically importing everything from the lower level alchemy module to avoid API breakage
+from .alchemy import AlchemicalState, AlchemicalFunction, AlchemicalStateError, AlchemicalRegion, \
+    AbsoluteAlchemicalFactory

openmmtools/tests/test_alchemy.py

@@ -16,6 +16,8 @@
 
 from __future__ import print_function
 
+import copy
+import logging
 import os
 import sys
 import zlib
@@ -25,11 +27,15 @@
 
 import nose
 import scipy
+import numpy as np
 from nose.plugins.attrib import attr
 
-from openmmtools import testsystems, forces
-from openmmtools.constants import kB
-from openmmtools.alchemy import *
+import openmm
+from openmm import unit
+from openmmtools import forces, forcefactories, states, testsystems, utils
+from openmmtools.constants import kB, ONE_4PI_EPS0
+from openmmtools.alchemy import AlchemicalFunction, AlchemicalState, AbsoluteAlchemicalFactory, \
+    AlchemicalRegion, AlchemicalStateError
 from openmmtools.multistate.pymbar import subsample_correlated_data, detect_equilibration, _pymbar_exp
 
 logger = logging.getLogger(__name__)

openmmtools/tests/test_sampling.py

@@ -26,7 +26,6 @@
 
 import numpy as np
 import yaml
-import unittest
 from nose.plugins.attrib import attr
 from nose.tools import assert_raises
 try:
@@ -1445,8 +1444,6 @@ def test_storage_reporter_and_string(self):
             energies_rep, _, _ = sampler._reporter.read_energies()
             assert np.all(energies_str == energies_rep)
 
-    #@unittest.skip("This test needs to fixed, see https://github.com/choderalab/openmmtools/pull/705")
-    #@unittest.skipIf(os.getenv("RUNNER_OS") == "macOS", "Test doesn't work on OSX on GHA")
     def test_online_analysis_works(self):
         """Test online analysis runs"""
         thermodynamic_states, sampler_states, unsampled_states = copy.deepcopy(self.alanine_test)