Merge pull request #296 from choderalab/replace_scipymisc

Replace scipy.misc
choderalab · Feb 28, 2018 · d4c974a · d4c974a
2 parents a511aad + 837a422
commit d4c974a
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Showing 5 changed files with 8 additions and 8 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -32,7 +32,6 @@ script:
 env:
   matrix:
     - python=2.7  CONDA_PY=27
-    - python=3.4  CONDA_PY=34
     - python=3.5  CONDA_PY=35
     - python=3.6  CONDA_PY=36
 

diff --git a/pymbar/tests/test_covariance.py b/pymbar/tests/test_covariance.py
@@ -1,7 +1,6 @@
 import numpy as np
 import pymbar
 from pymbar.utils_for_testing import eq
-import scipy.misc
 from nose import SkipTest
 
 def load_oscillators(n_states, n_samples):

diff --git a/pymbar/tests/test_mbar_solvers.py b/pymbar/tests/test_mbar_solvers.py
@@ -1,7 +1,6 @@
 import numpy as np
 import pymbar
 from pymbar.utils_for_testing import eq
-import scipy.misc
 from nose import SkipTest
 
 

diff --git a/pymbar/tests/test_utils.py b/pymbar/tests/test_utils.py
@@ -1,16 +1,19 @@
 import numpy as np
 import pymbar
 from pymbar.utils_for_testing import eq
-import scipy.misc
-from nose import SkipTest
+try:
+    from scipy.special import logsumexp
+except ImportError:
+    from scipy.misc import logsumexp
+
 
 def test_logsumexp():
     a = np.random.normal(size=(200, 500, 5))
 
     for axis in range(a.ndim):
         ans_ne = pymbar.utils.logsumexp(a, axis=axis)
         ans_no_ne = pymbar.utils.logsumexp(a, axis=axis, use_numexpr=False)
-        ans_scipy = scipy.misc.logsumexp(a, axis=axis)
+        ans_scipy = logsumexp(a, axis=axis)
         eq(ans_ne, ans_no_ne)
         eq(ans_ne, ans_scipy)
 
@@ -21,7 +24,7 @@ def test_logsumexp_b():
     for axis in range(a.ndim):
         ans_ne = pymbar.utils.logsumexp(a, b=b, axis=axis)
         ans_no_ne = pymbar.utils.logsumexp(a, b=b, axis=axis, use_numexpr=False)
-        ans_scipy = scipy.misc.logsumexp(a, b=b, axis=axis)
+        ans_scipy = logsumexp(a, b=b, axis=axis)
         eq(ans_ne, ans_no_ne)
         eq(ans_ne, ans_scipy)
 

diff --git a/pymbar/utils.py b/pymbar/utils.py
@@ -294,7 +294,7 @@ def logsumexp(a, axis=None, b=None, use_numexpr=True):
 
     See Also
     --------
-    numpy.logaddexp, numpy.logaddexp2, scipy.misc.logsumexp
+    numpy.logaddexp, numpy.logaddexp2, scipy.misc.logsumexp (soon to be replaced with  scipy.special.logsumexp)
 
     Notes
     -----