fep.Gsolv automatically converts EDR to XVG

- completely resolves #82
- test added
- CHANGES updated

CHANGES

@@ -20,6 +20,9 @@ orbeckst, iorga, ianmkenney, rhheilma
 * FEP failed with IndexError when lambdas where presented as a list
   (#78)
 * EDR files are now output by default instead of XVG (#75)
+* fep.Gsolv.analyze() automatically converts EDR to XVG.bz2 if
+  necessary and can process the XVG/MBAR format of Gromacs 5.x
+  for TI (issue #82)
 * deprecated mdpow-ghyd script (issue #14)
 
 

mdpow/fep.py

@@ -896,7 +896,15 @@ def analyze(self, force=False, stride=None, autosave=True, ncorrel=25000):
         stride = stride or self.stride
 
         if force or not self.has_dVdl():
-            self.collect(stride=stride, autosave=False)
+            try:
+                self.collect(stride=stride, autosave=False)
+            except IOError as err:
+                if err.errno == errno.ENOENT:
+                    self.convert_edr()
+                    self.collect(stride=stride, autosave=False)
+                else:
+                    logger.exception()
+                    raise
         else:
             logger.info("Analyzing stored data.")
 

mdpow/tests/test_analysis.py

@@ -52,32 +52,24 @@ def fix_manifest(topdir):
 
 # session scope if read-only use
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope="function")
 def fep_benzene_directory(tmpdir_factory):
     topdir = tmpdir_factory.mktemp('analysis')
     m = pybol.Manifest(fix_manifest(topdir).strpath)
     m.assemble('FEP', topdir.strpath)
     return topdir.join("benzene")
 
 class TestAnalyze(object):
-    def test_TI(self, fep_benzene_directory):
-        gsolv = fep_benzene_directory.join("FEP", "water", "Gsolv.fep")
+    def get_Gsolv(self, pth):
+        gsolv = pth.join("FEP", "water", "Gsolv.fep")
         G = pickle.load(gsolv.open())
         # patch paths
-        G.basedir = fep_benzene_directory.strpath
+        G.basedir = pth.strpath
         G.filename = gsolv.strpath
+        return G
 
-        # convert EDR to XVG.bz2; if the fixture is session scoped then other
-        # workers will pick up these files. Make sure that only one runs convert because
-        # there is no file locking, if in doubt, make fep_benzene_directory locally scoped
-        G.convert_edr()
-
-        try:
-            G.analyze(force=True, autosave=False)
-        except IOError as err:
-            raise AssertionError("Failed to convert edr to xvg: {0}: {1}".format(
-                err.strerror, err.filename))
-
+    @staticmethod
+    def assert_DeltaA(G):
         DeltaA = G.results.DeltaA
         assert_array_almost_equal(DeltaA.Gibbs.astuple(),
                                   (-3.7217472974883794, 2.3144288928034911),
@@ -89,3 +81,28 @@ def test_TI(self, fep_benzene_directory):
                                   (-4.6128782195215781, 2.1942144688960972),
                                   decimal=6)
 
+
+    def test_convert_edr(self, fep_benzene_directory):
+        G = self.get_Gsolv(fep_benzene_directory)
+        try:
+            G.analyze(force=True, autosave=False)
+        except IOError as err:
+            raise AssertionError("Failed to auto-convert edr to xvg: {0}: {1}".format(
+                err.strerror, err.filename))
+        self.assert_DeltaA(G)
+
+
+    def test_TI(self, fep_benzene_directory):
+        G = self.get_Gsolv(fep_benzene_directory)
+        # ensure conversion EDR to XVG.bz2; if the fixture is session scoped
+        # then other workers will pick up these files. Make sure that only one
+        # runs convert because there is no file locking, if in doubt, make
+        # fep_benzene_directory locally scoped
+        G.convert_edr()
+        try:
+            G.analyze(force=True, autosave=False)
+        except IOError as err:
+            raise AssertionError("Failed to convert edr to xvg: {0}: {1}".format(
+                err.strerror, err.filename))
+        self.assert_DeltaA(G)
+