Update stan source and include paths

Author: ariddell

.travis.yml

@@ -1,6 +1,7 @@
 # language is set to c to work around travis ci bug
 # https://github.com/travis-ci/travis-ci/issues/2312
 language: c
+dist: trusty
 sudo: false
 os:
   - linux

MANIFEST.in

@@ -16,9 +16,9 @@ prune pystan/stan/src/python
 prune pystan/stan/src/test
 
 # unused parts of the stan math source
-prune pystan/stan/lib/stan_math*/doc
-prune pystan/stan/lib/stan_math*/doxygen
-prune pystan/stan/lib/stan_math*/lib/cpplint_*
-prune pystan/stan/lib/stan_math*/lib/gtest_*
-prune pystan/stan/lib/stan_math*/make
-prune pystan/stan/lib/stan_math*/test
+prune pystan/stan/lib/stan_math/doc
+prune pystan/stan/lib/stan_math/doxygen
+prune pystan/stan/lib/stan_math/lib/cpplint_*
+prune pystan/stan/lib/stan_math/lib/gtest_*
+prune pystan/stan/lib/stan_math/make
+prune pystan/stan/lib/stan_math/test

pystan/model.py

@@ -249,10 +249,10 @@ def __init__(self, file=None, charset='utf-8', model_name="anon_model",
             lib_dir,
             pystan_dir,
             os.path.join(pystan_dir, "stan", "src"),
-            os.path.join(pystan_dir, "stan", "lib", "stan_math_2.15.0"),
-            os.path.join(pystan_dir, "stan", "lib", "stan_math_2.15.0", "lib", "eigen_3.2.9"),
-            os.path.join(pystan_dir, "stan", "lib", "stan_math_2.15.0", "lib", "boost_1.62.0"),
-            os.path.join(pystan_dir, "stan", "lib", "stan_math_2.15.0", "lib", "cvodes_2.9.0", "include"),
+            os.path.join(pystan_dir, "stan", "lib", "stan_math"),
+            os.path.join(pystan_dir, "stan", "lib", "stan_math", "lib", "eigen_3.3.3"),
+            os.path.join(pystan_dir, "stan", "lib", "stan_math", "lib", "boost_1.62.0"),
+            os.path.join(pystan_dir, "stan", "lib", "stan_math", "lib", "cvodes_2.9.0", "include"),
             np.get_include(),
         ]
 

pystan/stan

@@ -99,10 +99,10 @@ def find_version(*parts):
 from distutils.extension import Extension
 
 stan_include_dirs = ['pystan/stan/src',
-                     'pystan/stan/lib/stan_math_2.15.0/',
-                     'pystan/stan/lib/stan_math_2.15.0/lib/eigen_3.2.9',
-                     'pystan/stan/lib/stan_math_2.15.0/lib/boost_1.62.0',
-                     'pystan/stan/lib/stan_math_2.15.0/lib/cvodes_2.9.0/include']
+                     'pystan/stan/lib/stan_math/',
+                     'pystan/stan/lib/stan_math/lib/eigen_3.3.3',
+                     'pystan/stan/lib/stan_math/lib/boost_1.62.0',
+                     'pystan/stan/lib/stan_math/lib/cvodes_2.9.0/include']
 stan_macros = [
     ('BOOST_RESULT_OF_USE_TR1', None),
     ('BOOST_NO_DECLTYPE', None),