Merge pull request #179 from Becksteinlab/fix-recent-failures

various fixes due to upstream updates

.travis.yml

@@ -27,8 +27,8 @@ env:
 
   matrix:
     # use ci-helper's PACKAGENAME_VERSION magic to pin the 'gromacs' package
-    - GROMACS_VERSION=4.6.5   PYTHON_VERSION=2.7
-    - GROMACS_VERSION=2019.1  PYTHON_VERSION=2.7
+    - GROMACS_VERSION=4.6.5   PYTHON_VERSION=2.7 NUMPY_VERSION=1.16
+    - GROMACS_VERSION=2019.1  PYTHON_VERSION=2.7 NUMPY_VERSION=1.16
     - GROMACS_VERSION=4.6.5   PYTHON_VERSION=3.6
     - GROMACS_VERSION=2018.6  PYTHON_VERSION=3.6
     - GROMACS_VERSION=2019.1  PYTHON_VERSION=3.6
@@ -46,7 +46,7 @@ matrix:
     - os: osx
       env: GROMACS_VERSION=4.6.5 PYTHON_VERSION=3.6    
     - os: osx
-      env: GROMACS_VERSION=2019.1 PYTHON_VERSION=2.7
+      env: GROMACS_VERSION=2019.1 PYTHON_VERSION=2.7 NUMPY_VERSION=1.16
     - os: osx
       env: GROMACS_VERSION=2019.1 PYTHON_VERSION=3.6
 

CHANGES

@@ -2,6 +2,12 @@
  CHANGELOG for GromacsWrapper
 ==============================
 
+2019-xx-xx     0.8.1
+orbeckst
+
+* fixed: xpm.to_df() used outdated convert_objects()
+* fixed: gw-forcefield.py use print() function for Py 2/3 compatibility
+
 2019-04-30     0.8.0
 richardjgowers, theavey, andrejberg, orbeckst
 

gromacs/fileformats/xpm.py

@@ -154,16 +154,17 @@ def __init__(self, filename=None, **kwargs):
 
 
     def to_df(self):
-        import pandas as _pd
+        import pandas as pd
 
         # Add Time to the data as column
         data = numpy.vstack((self.xvalues, self.array.T)).T
 
         # Column names are resids
-        df = _pd.DataFrame(data, columns=["Time"]+ list(self.yvalues))
+        df = pd.DataFrame(data, columns=["Time"]+ list(self.yvalues))
 
         # Converts Time to a numeric type
-        return df.convert_objects(convert_numeric='force')
+        df['Time'] = pd.to_numeric(df['Time'])
+        return df
 
     @property
     def array(self):

scripts/gw-forcefield.py

@@ -1,3 +1,4 @@
+from __future__ import print_function
 
 from gromacs.fileformats import TOP
 import numpy as np
@@ -50,7 +51,7 @@ def scale_dihedrals(mol, dihedrals):
                                         new_dihedrals[key] = dt
                                 break
 
-        print new_dihedrals
+        print(new_dihedrals)
         return new_dihedrals.values()
 
 
@@ -73,7 +74,7 @@ def scale_impropers(mol, impropers):
                                 for i, imt in enumerate(impropers[key]):
                                         new_impropers[key] = imt
                                 break
-        print new_impropers
+        print(new_impropers)
         return new_impropers.values()
 
 

tests/fileformats/test_xpm.py

@@ -18,6 +18,10 @@ def ssfile():
 def xpm(ssfile):
     return XPM(filename=ssfile)
 
+@pytest.fixture
+def xpm_df(xpm):
+    return xpm.to_df()
+
 class TestXPM(object):
     def _run_tests(self, x):
         assert_equal(x.array.shape, (500, 769))
@@ -36,7 +40,10 @@ def test_read(self, ssfile):
     def test_reversed_by_default(self, xpm):
         assert xpm.reverse
 
-    def test_to_pd(self, xpm):
-        df = xpm.to_df()
-        assert_equal(df.shape, (500, 770))
+    def test_to_pd(self, xpm_df):
+        assert_equal(xpm_df.shape, (500, 770))
 
+    def test_to_pd_types(self, xpm_df):
+        time = xpm_df['Time']
+        assert len(time) == 500
+        assert time.dtype == np.dtype("int64")  # true for this file