Merge pull request #4924 from nouiz/drop_old_version

.travis.yml

@@ -8,7 +8,7 @@ cache:
 
 language: python
 python:
-  - "2.6"
+  - "2.7"
   - "3.3"
 
 # command to install dependencies
@@ -16,7 +16,7 @@ before_install:
 # Install miniconda to avoid compiling scipy
   - mkdir -p download
   - cd download
-  - wget -c https://repo.continuum.io/miniconda/Miniconda2-3.19.0-Linux-x86_64.sh -O miniconda.sh
+  - wget -c https://repo.continuum.io/miniconda/Miniconda2-4.1.11-Linux-x86_64.sh -O miniconda.sh
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
   - cd ..
@@ -30,11 +30,10 @@ addons:
    - dvipng
 
 install:
-  - if [[ $TRAVIS_PYTHON_VERSION == '2.6' ]]; then conda create --yes -q -n pyenv mkl python=2.6 numpy=1.7.1 scipy=0.11 nose=1.3.0 pip flake8=2.3 six=1.9.0 pep8=1.6.2 pyflakes=0.8.1 sphinx; fi
-  - if [[ $TRAVIS_PYTHON_VERSION == '3.3' ]]; then conda create --yes -q -n pyenv mkl python=3.3 numpy=1.9.1 scipy=0.14.0 nose=1.3.4 pip flake8=2.3 six=1.9.0 pep8=1.6.2 pyflakes=0.8.1 sphinx; fi
+  - if [[ $TRAVIS_PYTHON_VERSION == '2.7' ]]; then conda create --yes -q -n pyenv mkl python=2.7 numpy=1.9.1 scipy=0.14 nose=1.3.0 pip flake8=2.3 six=1.9.0 pep8=1.6.2 pyflakes=0.8.1 sphinx libgfortran=1 mkl-service; fi
+  - if [[ $TRAVIS_PYTHON_VERSION == '3.3' ]]; then conda create --yes -q -n pyenv mkl python=3.3 numpy=1.9.1 scipy=0.14.0 nose=1.3.4 pip flake8=2.3 six=1.9.0 pep8=1.6.2 pyflakes=0.8.1 sphinx mkl-service; fi
   - source activate pyenv
-# pydot 1.2 broke support of python 2.6. They won't try to maintain it.
-  - if [[ $TRAVIS_PYTHON_VERSION == '2.6' ]]; then pip install pydot==1.1.0; else pip install pydot-ng; fi
+  - if [[ $TRAVIS_PYTHON_VERSION == '2.7' ]]; then pip install pydot; else pip install pydot-ng; fi
   - pip install . --no-deps
   - pip install flake8-future-import nose-parameterized==0.5.0
 
@@ -49,7 +48,7 @@ matrix:
   include:
     - python: "3.3"
       env: PART="-e test_flake8.py ." THEANO_FLAGS="mode=FAST_COMPILE"
-    - python: "2.6"
+    - python: "2.7"
       env: PART="-e test_flake8.py ." THEANO_FLAGS="mode=FAST_COMPILE,floatX=float32"
 
 script:

doc/conf.py

@@ -42,10 +42,16 @@ todo_include_todos = True
 napoleon_google_docstring = False
 napoleon_include_special_with_doc = False
 
+# We do it like this to support multiple sphinx version without having warning.
+# Our buildbot consider warning as error.
 try:
+    from sphinx.ext import imgmath
+    extensions.append('sphinx.ext.imgmath')
+except ImportError:
+    try:
         from sphinx.ext import pngmath
         extensions.append('sphinx.ext.pngmath')
-except ImportError:
+    except ImportError:
         pass
 
 

doc/requirements.txt

@@ -8,13 +8,16 @@ Requirements
 .. _BLAS: http://en.wikipedia.org/wiki/Basic_Linear_Algebra_Subprograms
 .. _Python: http://www.python.org/
 
-    Python_ >= 2.6 or >= 3.3
-        The development package (python-dev or python-devel on most Linux distributions) is recommended (see just below). Python 2.4 was supported up to and including the release 0.6. Python 3 is supported past the 3.3 release.
+    Python_ >= 2.7 or >= 3.3 The development package (python-dev or
+        python-devel on most Linux distributions) is recommended (see
+        just below). Python 2.4 was supported up to and including the
+        release 0.6. Python 2.6 was supported up to and including the
+        release 0.8.2. Python 3 is supported past the 3.3 release.
 
-    `NumPy <http://numpy.scipy.org/>`_ >= 1.7.1 < 1.11.1
+    `NumPy <http://numpy.scipy.org/>`_ >= 1.9.1 < 1.11.1
         Earlier versions could work, but we don’t test it.
 
-    `SciPy <http://scipy.org>`_ >= 0.11 < 0.17.1
+    `SciPy <http://scipy.org>`_ >= 0.14 < 0.17.1
         Only currently required for sparse matrix and special functions support, but highly recommended. SciPy >=0.8 could work, but earlier versions have known bugs with sparse matrices.
 
     `BLAS`_ installation (with Level 3 functionality)

setup.py

@@ -31,7 +31,6 @@ Operating System :: POSIX
 Operating System :: Unix
 Operating System :: MacOS
 Programming Language :: Python :: 2
-Programming Language :: Python :: 2.6
 Programming Language :: Python :: 2.7
 Programming Language :: Python :: 3
 Programming Language :: Python :: 3.3
@@ -163,7 +162,7 @@ def do_setup():
           platforms=PLATFORMS,
           packages=find_packages(),
           # 1.7.0 give too much warning related to numpy.diagonal.
-          install_requires=['numpy>=1.7.1', 'scipy>=0.11', 'six>=1.9.0'],
+          install_requires=['numpy>=1.9.1', 'scipy>=0.14', 'six>=1.9.0'],
           # pygments is a dependency for Sphinx code highlight
           extras_require={
               'test': ['nose>=1.3.0', 'nose-parameterized>=0.5.0', 'flake8<3'],

theano/compat/python2x.py

 """
 Helper functions to make theano backwards compatible with python 2.6 - 2.7
+Now mostly there for compatibility as we don't support Python 2.6 anymore.
 """
 from __future__ import absolute_import, print_function, division
 
-import sys
-
-if sys.version_info[:2] < (2, 7):
-    # The following implementation of OrderedDict compatible with python 2.4
-    # was taken from http://pypi.python.org/pypi/ordereddict/1.1
-    # It is under the MIT license.
-
-    # Copyright (c) 2009 Raymond Hettinger
-    #
-    # Permission is hereby granted, free of charge, to any person
-    # obtaining a copy of this software and associated documentation files
-    # (the "Software"), to deal in the Software without restriction,
-    # including without limitation the rights to use, copy, modify, merge,
-    # publish, distribute, sublicense, and/or sell copies of the Software,
-    # and to permit persons to whom the Software is furnished to do so,
-    # subject to the following conditions:
-    #
-    #     The above copyright notice and this permission notice shall be
-    #     included in all copies or substantial portions of the Software.
-    #
-    #     THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-    #     EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-    #     OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-    #     NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-    #     HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-    #     WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-    #     FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-    #     OTHER DEALINGS IN THE SOFTWARE.
-    from UserDict import DictMixin
-
-    class OrderedDict(dict, DictMixin):
-
-        def __init__(self, *args, **kwds):
-            if len(args) > 1:
-                raise TypeError('expected at most 1 arguments, got %d' %
-                                len(args))
-            try:
-                self.__end
-            except AttributeError:
-                self.clear()
-            self.update(*args, **kwds)
-
-        def clear(self):
-            self.__end = end = []
-            end += [None, end, end]      # sentinel node for doubly linked list
-            self.__map = {}              # key --> [key, prev, next]
-            dict.clear(self)
-
-        def __setitem__(self, key, value):
-            if key not in self:
-                end = self.__end
-                curr = end[1]
-                curr[2] = end[1] = self.__map[key] = [key, curr, end]
-            dict.__setitem__(self, key, value)
-
-        def __delitem__(self, key):
-            dict.__delitem__(self, key)
-            key, prev, next = self.__map.pop(key)
-            prev[2] = next
-            next[1] = prev
-
-        def __iter__(self):
-            end = self.__end
-            curr = end[2]
-            while curr is not end:
-                yield curr[0]
-                curr = curr[2]
-
-        def __reversed__(self):
-            end = self.__end
-            curr = end[1]
-            while curr is not end:
-                yield curr[0]
-                curr = curr[1]
-
-        def popitem(self, last=True):
-            if not self:
-                raise KeyError('dictionary is empty')
-            if last:
-                key = next(reversed(self))
-            else:
-                key = next(iter(self))
-            value = self.pop(key)
-            return key, value
-
-        def __reduce__(self):
-            items = [[k, self[k]] for k in self]
-            tmp = self.__map, self.__end
-            del self.__map, self.__end
-            inst_dict = vars(self).copy()
-            self.__map, self.__end = tmp
-            if inst_dict:
-                return (self.__class__, (items,), inst_dict)
-            return self.__class__, (items,)
-
-        def keys(self):
-            return list(self)
-
-        setdefault = DictMixin.setdefault
-        update = DictMixin.update
-        pop = DictMixin.pop
-        values = DictMixin.values
-        items = DictMixin.items
-        iterkeys = DictMixin.iterkeys
-        itervalues = DictMixin.itervalues
-        iteritems = DictMixin.iteritems
-
-        def __repr__(self):
-            if not self:
-                return '%s()' % (self.__class__.__name__,)
-            return '%s(%r)' % (self.__class__.__name__, list(self.items()))
-
-        def copy(self):
-            return self.__class__(self)
-
-        @classmethod
-        def fromkeys(cls, iterable, value=None):
-            d = cls()
-            for key in iterable:
-                d[key] = value
-            return d
-
-        def __eq__(self, other):
-            if isinstance(other, OrderedDict):
-                if len(self) != len(other):
-                    return False
-                for p, q in zip(self.items(), other.items()):
-                    if p != q:
-                        return False
-                return True
-            return dict.__eq__(self, other)
-
-        def __ne__(self, other):
-            return not self == other
-
-    # The following implementation of Counter compatible with python 2.4
-    # was taken from http://code.activestate.com/recipes/576611/
-    # It is under the MIT license.
-
-    # Copyright (c) 2009 Raymond Hettinger
-    #
-    # Permission is hereby granted, free of charge, to any person
-    # obtaining a copy of this software and associated documentation files
-    # (the "Software"), to deal in the Software without restriction,
-    # including without limitation the rights to use, copy, modify, merge,
-    # publish, distribute, sublicense, and/or sell copies of the Software,
-    # and to permit persons to whom the Software is furnished to do so,
-    # subject to the following conditions:
-    #
-    #     The above copyright notice and this permission notice shall be
-    #     included in all copies or substantial portions of the Software.
-    #
-    #     THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-    #     EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-    #     OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-    #     NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-    #     HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-    #     WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-    #     FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-
-    from operator import itemgetter
-    from heapq import nlargest
-    from itertools import repeat
-    from theano.compat import ifilter
-
-    class Counter(dict):
-        '''Dict subclass for counting hashable objects.
-
-        Sometimes called a bag or multiset.  Elements are stored as
-        dictionary keys and their counts are stored as dictionary
-        values.
-
-        >>> Counter('zyzygy')
-        Counter({'y': 3, 'z': 2, 'g': 1})
-        '''
-
-        def __init__(self, iterable=None, **kwds):
-            '''Create a new, empty Counter object.
-
-            And if given, count elements from an input iterable.  Or,
-            initialize the count from another mapping of elements to
-            their counts.
-
-            A new, empty counter:
-            >>> c = Counter()
-
-            A new counter from an iterable
-            >>> c = Counter('gallahad')
-
-            A new counter from a mapping
-            >>> c = Counter({'a': 4, 'b': 2})
-
-            A new counter from keyword args
-            >>> c = Counter(a=4, b=2)
-            '''
-            self.update(iterable, **kwds)
-
-        def __missing__(self, key):
-            return 0
-
-        def most_common(self, n=None):
-            '''List the n most common elements and their counts.
-
-            The list goes from the most common to the least.  If n is
-            None, then list all element counts.
-
-            >>> Counter('abracadabra').most_common(3)
-            [('a', 5), ('r', 2), ('b', 2)]
-            '''
-            if n is None:
-                return sorted(self.iteritems(), key=itemgetter(1),
-                              reverse=True)
-            return nlargest(n, self.iteritems(), key=itemgetter(1))
-
-        def elements(self):
-            '''Iterator over elements.
-
-            It repeats each element as many times as its count.
-
-            >>> c = Counter('ABCABC')
-            >>> sorted(c.elements())
-            ['A', 'A', 'B', 'B', 'C', 'C']
-
-            If an element's count has been set to zero or is a negative
-            number, elements() will ignore it.
-            '''
-            for elem, count in self.iteritems():
-                for _ in repeat(None, count):
-                    yield elem
-
-        # Override dict methods where the meaning changes for Counter objects.
-
-        @classmethod
-        def fromkeys(cls, iterable, v=None):
-            raise NotImplementedError(
-                'Counter.fromkeys() is undefined.  '
-                'Use Counter(iterable) instead.')
-
-        def update(self, iterable=None, **kwds):
-            '''Like dict.update() but add counts instead of replacing them.
-
-            Source can be an iterable, a dictionary, or another Counter
-            instance.
-
-            >>> c = Counter('which')
-            >>> c.update('witch')      # add elements from another iterable
-            >>> d = Counter('watch')
-            >>> c.update(d)            # add elements from another counter
-            >>> c['h']                 # four 'h' in which, witch, and watch
-            4
-            '''
-            if iterable is not None:
-                if hasattr(iterable, 'iteritems'):
-                    if self:
-                        self_get = self.get
-                        for elem, count in iterable.iteritems():
-                            self[elem] = self_get(elem, 0) + count
-                    else:
-                        # fast path when counter is empty
-                        dict.update(self, iterable)
-                else:
-                    self_get = self.get
-                    for elem in iterable:
-                        self[elem] = self_get(elem, 0) + 1
-            if kwds:
-                self.update(kwds)
-
-        def copy(self):
-            '''Like dict.copy() but returns a Counter instance instead
-            of a dict.'''
-            return Counter(self)
-
-        def __delitem__(self, elem):
-            '''Like dict.__delitem__() but does not raise KeyError for
-            missing values.'''
-            if elem in self:
-                dict.__delitem__(self, elem)
-
-        def __repr__(self):
-            if not self:
-                return '%s()' % self.__class__.__name__
-            items = ', '.join(map('%r: %r'.__mod__, self.most_common()))
-            return '%s({%s})' % (self.__class__.__name__, items)
-
-        # Multiset-style mathematical operations discussed in:
-        #       Knuth TAOCP Volume II section 4.6.3 exercise 19
-        #       and at http://en.wikipedia.org/wiki/Multiset
-        #
-        # Outputs guaranteed to only include positive counts.
-        #
-        # To strip negative and zero counts, add-in an empty counter:
-        #       c += Counter()
-
-        def __add__(self, other):
-            '''Add counts from two counters.
-
-            >>> Counter('abbb') + Counter('bcc')
-            Counter({'b': 4, 'c': 2, 'a': 1})
-
-
-            '''
-            if not isinstance(other, Counter):
-                return NotImplemented
-            result = Counter()
-            for elem in set(self) | set(other):
-                newcount = self[elem] + other[elem]
-                if newcount > 0:
-                    result[elem] = newcount
-            return result
-
-        def __sub__(self, other):
-            ''' Subtract count, but keep only results with positive counts.
-
-            >>> Counter('abbbc') - Counter('bccd')
-            Counter({'b': 2, 'a': 1})
-
-            '''
-            if not isinstance(other, Counter):
-                return NotImplemented
-            result = Counter()
-            for elem in set(self) | set(other):
-                newcount = self[elem] - other[elem]
-                if newcount > 0:
-                    result[elem] = newcount
-            return result
-
-        def __or__(self, other):
-            '''Union is the maximum of value in either of the input counters.
-
-            >>> Counter('abbb') | Counter('bcc')
-            Counter({'b': 3, 'c': 2, 'a': 1})
-
-            '''
-            if not isinstance(other, Counter):
-                return NotImplemented
-            _max = max
-            result = Counter()
-            for elem in set(self) | set(other):
-                newcount = _max(self[elem], other[elem])
-                if newcount > 0:
-                    result[elem] = newcount
-            return result
-
-        def __and__(self, other):
-            ''' Intersection is the minimum of corresponding counts.
-
-            >>> Counter('abbb') & Counter('bcc')
-            Counter({'b': 1})
-
-            '''
-            if not isinstance(other, Counter):
-                return NotImplemented
-            _min = min
-            result = Counter()
-            if len(self) < len(other):
-                self, other = other, self
-            for elem in ifilter(self.__contains__, other):
-                newcount = _min(self[elem], other[elem])
-                if newcount > 0:
-                    result[elem] = newcount
-            return result
-
-else:
-    try:
+try:
     from UserDict import DictMixin
-    except ImportError:
+except ImportError:
     from collections import MutableMapping as DictMixin
-    from collections import OrderedDict, Counter
+from collections import OrderedDict, Counter
 
 __all__ = ['DictMixin', 'OrderedDict', 'Counter']

theano/configdefaults.py

@@ -1253,7 +1253,7 @@ def default_blas_ldflags():
                                           "mk2_rt"]])
 
         # Anaconda
-        if "Anaconda" in sys.version and sys.platform == "win32":
+        if "Anaconda" in sys.version or "Continuum" in sys.version:
             # If the "mkl-service" conda package (available
             # through Python package "mkl") is installed and
             # importable, then the libraries (installed by conda
@@ -1266,14 +1266,23 @@ def default_blas_ldflags():
                 _logger.info('Conda mkl is not available: %s', e)
             else:
                 # This branch is executed if no exception was raised
+                if sys.platform == "win32":
                     lib_path = os.path.join(sys.prefix, 'DLLs')
                     flags = ['-L"%s"' % lib_path]
+                else:
+                    lib_path = blas_info.get('library_dirs', [])[0]
+                    flags = ['-L%s' % lib_path]
                 flags += ['-l%s' % l for l in ["mkl_core",
                                                "mkl_intel_thread",
                                                "mkl_rt"]]
                 res = try_blas_flag(flags)
                 if res:
                     return res
+                flags.extend(['-Wl,-rpath,' + l for l in
+                              blas_info.get('library_dirs', [])])
+                res = try_blas_flag(flags)
+                if res:
+                    return res
 
         # to support path that includes spaces, we need to wrap it with double quotes on Windows
         path_wrapper = "\"" if os.name == 'nt' else ""
@@ -1344,7 +1353,7 @@ def try_blas_flag(flags):
             return 0;
         }
         """)
-    cflags = flags
+    cflags = list(flags)
     # to support path that includes spaces, we need to wrap it with double quotes on Windows
     path_wrapper = "\"" if os.name == 'nt' else ""
     cflags.extend(['-L%s%s%s' % (path_wrapper, d, path_wrapper) for d in theano.gof.cmodule.std_lib_dirs()])

theano/printing.py

@@ -47,6 +47,9 @@ except ImportError:
         # tests should not fail on optional dependency
         pydot_imported_msg = ("Install the python package pydot or pydot-ng."
                               " Install graphviz.")
+    except Exception as e:
+        pydot_imported_msg = "An error happened while importing/trying pydot: "
+        pydot_imported_msg += str(e.args)
 
 
 _logger = logging.getLogger("theano.printing")