numpy 1.9.2__zip → 1.10.0__zip

numpy-1.10.0.post2/doc/source/user/install.rst

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+*****************************
+Building and installing NumPy
+*****************************
+
+Binary installers
+=================
+
+In most use cases the best way to install NumPy on your system is by using an
+installable binary package for your operating system.
+
+Windows
+-------
+
+Good solutions for Windows are, `Enthought Canopy
+<https://www.enthought.com/products/canopy/>`_, `Anaconda
+<http://continuum.io/downloads.html>`_ (which both provide binary installers
+for Windows, OS X and Linux) and `Python (x, y) <http://www.pythonxy.com>`_.
+Both of these packages include Python, NumPy and many additional packages.
+
+A lightweight alternative is to download the Python
+installer from `www.python.org <http://www.python.org>`_ and the NumPy
+installer for your Python version from the Sourceforge `download site 
+<http://sourceforge.net/projects/numpy/files/NumPy`_.
+
+The NumPy installer includes binaries for different CPU's (without SSE
+instructions, with SSE2 or with SSE3) and installs the correct one
+automatically. If needed, this can be bypassed from the command line with ::
+
+  numpy-<1.y.z>-superpack-win32.exe /arch nosse
+
+or ``sse2`` or ``sse3`` instead of ``nosse``.
+
+Linux
+-----
+
+All major distributions provide packages for NumPy.  These are usually
+reasonably up-to-date, but sometimes lag behind the most recent NumPy release.
+
+Mac OS X
+--------
+
+Universal binary installers for NumPy are available from the `download site
+<http://sourceforge.net/projects/numpy/files/NumPy`_, and wheel packages
+from PyPi.  With a recent version of `pip`<https://pip.pypa.io/en/latest/>`_
+this will give you a binary install (from the wheel packages) compatible with
+at python.org Python, Homebrew and MacPorts::
+
+  pip install numpy
+
+
+.. _building-from-source:
+
+Building from source
+====================
+
+A general overview of building NumPy from source is given here, with detailed
+instructions for specific platforms given seperately.
+
+Prerequisites
+-------------
+
+Building NumPy requires the following software installed:
+
+1) Python 2.6.x, 2.7.x, 3.2.x or newer
+
+   On Debian and derivatives (Ubuntu): python, python-dev (or python3-dev)
+
+   On Windows: the official python installer at
+   `www.python.org <http://www.python.org>`_ is enough
+
+   Make sure that the Python package distutils is installed before
+   continuing. For example, in Debian GNU/Linux, installing python-dev
+   also installs distutils.
+
+   Python must also be compiled with the zlib module enabled. This is
+   practically always the case with pre-packaged Pythons.
+
+2) Compilers
+
+   To build any extension modules for Python, you'll need a C compiler.
+   Various NumPy modules use FORTRAN 77 libraries, so you'll also need a
+   FORTRAN 77 compiler installed.
+
+   Note that NumPy is developed mainly using GNU compilers. Compilers from
+   other vendors such as Intel, Absoft, Sun, NAG, Compaq, Vast, Porland,
+   Lahey, HP, IBM, Microsoft are only supported in the form of community
+   feedback, and may not work out of the box. GCC 4.x (and later) compilers
+   are recommended.
+
+3) Linear Algebra libraries
+
+   NumPy does not require any external linear algebra libraries to be
+   installed. However, if these are available, NumPy's setup script can detect
+   them and use them for building. A number of different LAPACK library setups
+   can be used, including optimized LAPACK libraries such as ATLAS, MKL or the
+   Accelerate/vecLib framework on OS X.
+
+Basic Installation
+------------------
+
+To install NumPy run::
+
+    python setup.py install
+
+To perform an in-place build that can be run from the source folder run::
+
+    python setup.py build_ext --inplace
+
+The NumPy build system uses ``distutils`` and ``numpy.distutils``.
+``setuptools`` is only used when building via ``pip`` or with ``python
+setupegg.py``.  Using ``virtualenv`` should work as expected.
+
+*Note: for build instructions to do development work on NumPy itself, see
+:ref:`development-environment`*.
+
+.. _parallel-builds:
+
+Parallel builds
+~~~~~~~~~~~~~~~
+
+From NumPy 1.10.0 on it's also possible to do a parallel build with::
+
+    python setup.py build -j 4 install --prefix $HOME/.local
+
+This will compile numpy on 4 CPUs and install it into the specified prefix.
+to perform a parallel in-place build, run::
+
+    python setup.py build_ext --inplace -j 4
+
+The number of build jobs can also be specified via the environment variable
+``NPY_NUM_BUILD_JOBS``.
+
+
+FORTRAN ABI mismatch
+--------------------
+
+The two most popular open source fortran compilers are g77 and gfortran.
+Unfortunately, they are not ABI compatible, which means that concretely you
+should avoid mixing libraries built with one with another. In particular, if
+your blas/lapack/atlas is built with g77, you *must* use g77 when building
+numpy and scipy; on the contrary, if your atlas is built with gfortran, you
+*must* build numpy/scipy with gfortran. This applies for most other cases
+where different FORTRAN compilers might have been used.
+
+Choosing the fortran compiler
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+To build with g77::
+
+    python setup.py build --fcompiler=gnu
+
+To build with gfortran::
+
+    python setup.py build --fcompiler=gnu95
+
+For more information see::
+
+    python setup.py build --help-fcompiler
+
+How to check the ABI of blas/lapack/atlas
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+One relatively simple and reliable way to check for the compiler used to build
+a library is to use ldd on the library. If libg2c.so is a dependency, this
+means that g77 has been used. If libgfortran.so is a a dependency, gfortran
+has been used. If both are dependencies, this means both have been used, which
+is almost always a very bad idea.
+
+Disabling ATLAS and other accelerated libraries
+-----------------------------------------------
+
+Usage of ATLAS and other accelerated libraries in Numpy can be disabled
+via::
+
+    BLAS=None LAPACK=None ATLAS=None python setup.py build
+
+
+Supplying additional compiler flags
+-----------------------------------
+
+Additional compiler flags can be supplied by setting the ``OPT``,
+``FOPT`` (for Fortran), and ``CC`` environment variables.
+
+
+Building with ATLAS support
+---------------------------
+
+Ubuntu 
+~~~~~~
+
+You can install the necessary package for optimized ATLAS with this command::
+
+    sudo apt-get install libatlas-base-dev
+

numpy-1.10.0.post2/doc/sphinxext/.git

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+gitdir: ../../.git/modules/doc/sphinxext

numpy-1.10.0.post2/numpy/__init__.py

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+"""
+NumPy
+=====
+
+Provides
+  1. An array object of arbitrary homogeneous items
+  2. Fast mathematical operations over arrays
+  3. Linear Algebra, Fourier Transforms, Random Number Generation
+
+How to use the documentation
+----------------------------
+Documentation is available in two forms: docstrings provided
+with the code, and a loose standing reference guide, available from
+`the NumPy homepage <http://www.scipy.org>`_.
+
+We recommend exploring the docstrings using
+`IPython <http://ipython.scipy.org>`_, an advanced Python shell with
+TAB-completion and introspection capabilities.  See below for further
+instructions.
+
+The docstring examples assume that `numpy` has been imported as `np`::
+
+  >>> import numpy as np
+
+Code snippets are indicated by three greater-than signs::
+
+  >>> x = 42
+  >>> x = x + 1
+
+Use the built-in ``help`` function to view a function's docstring::
+
+  >>> help(np.sort)
+  ... # doctest: +SKIP
+
+For some objects, ``np.info(obj)`` may provide additional help.  This is
+particularly true if you see the line "Help on ufunc object:" at the top
+of the help() page.  Ufuncs are implemented in C, not Python, for speed.
+The native Python help() does not know how to view their help, but our
+np.info() function does.
+
+To search for documents containing a keyword, do::
+
+  >>> np.lookfor('keyword')
+  ... # doctest: +SKIP
+
+General-purpose documents like a glossary and help on the basic concepts
+of numpy are available under the ``doc`` sub-module::
+
+  >>> from numpy import doc
+  >>> help(doc)
+  ... # doctest: +SKIP
+
+Available subpackages
+---------------------
+doc
+    Topical documentation on broadcasting, indexing, etc.
+lib
+    Basic functions used by several sub-packages.
+random
+    Core Random Tools
+linalg
+    Core Linear Algebra Tools
+fft
+    Core FFT routines
+polynomial
+    Polynomial tools
+testing
+    Numpy testing tools
+f2py
+    Fortran to Python Interface Generator.
+distutils
+    Enhancements to distutils with support for
+    Fortran compilers support and more.
+
+Utilities
+---------
+test
+    Run numpy unittests
+show_config
+    Show numpy build configuration
+dual
+    Overwrite certain functions with high-performance Scipy tools
+matlib
+    Make everything matrices.
+__version__
+    Numpy version string
+
+Viewing documentation using IPython
+-----------------------------------
+Start IPython with the NumPy profile (``ipython -p numpy``), which will
+import `numpy` under the alias `np`.  Then, use the ``cpaste`` command to
+paste examples into the shell.  To see which functions are available in
+`numpy`, type ``np.<TAB>`` (where ``<TAB>`` refers to the TAB key), or use
+``np.*cos*?<ENTER>`` (where ``<ENTER>`` refers to the ENTER key) to narrow
+down the list.  To view the docstring for a function, use
+``np.cos?<ENTER>`` (to view the docstring) and ``np.cos??<ENTER>`` (to view
+the source code).
+
+Copies vs. in-place operation
+-----------------------------
+Most of the functions in `numpy` return a copy of the array argument
+(e.g., `np.sort`).  In-place versions of these functions are often
+available as array methods, i.e. ``x = np.array([1,2,3]); x.sort()``.
+Exceptions to this rule are documented.
+
+"""
+from __future__ import division, absolute_import, print_function
+
+import sys
+
+
+class ModuleDeprecationWarning(DeprecationWarning):
+    """Module deprecation warning.
+
+    The nose tester turns ordinary Deprecation warnings into test failures.
+    That makes it hard to deprecate whole modules, because they get
+    imported by default. So this is a special Deprecation warning that the
+    nose tester will let pass without making tests fail.
+
+    """
+    pass
+
+
+class VisibleDeprecationWarning(UserWarning):
+    """Visible deprecation warning.
+
+    By default, python will not show deprecation warnings, so this class
+    can be used when a very visible warning is helpful, for example because
+    the usage is most likely a user bug.
+
+    """
+    pass
+
+
+class _NoValue:
+    """Special keyword value.
+
+    This class may be used as the default value assigned to a
+    deprecated keyword in order to check if it has been given a user
+    defined value.
+    """
+    pass
+
+
+# oldnumeric and numarray were removed in 1.9. In case some packages import
+# but do not use them, we define them here for backward compatibility.
+oldnumeric = 'removed'
+numarray = 'removed'
+
+
+# We first need to detect if we're being called as part of the numpy setup
+# procedure itself in a reliable manner.
+try:
+    __NUMPY_SETUP__
+except NameError:
+    __NUMPY_SETUP__ = False
+
+
+if __NUMPY_SETUP__:
+    import sys as _sys
+    _sys.stderr.write('Running from numpy source directory.\n')
+    del _sys
+else:
+    try:
+        from numpy.__config__ import show as show_config
+    except ImportError:
+        msg = """Error importing numpy: you should not try to import numpy from
+        its source directory; please exit the numpy source tree, and relaunch
+        your python interpreter from there."""
+        raise ImportError(msg)
+    from .version import git_revision as __git_revision__
+    from .version import version as __version__
+
+    from ._import_tools import PackageLoader
+
+    def pkgload(*packages, **options):
+        loader = PackageLoader(infunc=True)
+        return loader(*packages, **options)
+
+    from . import add_newdocs
+    __all__ = ['add_newdocs',
+               'ModuleDeprecationWarning',
+               'VisibleDeprecationWarning']
+
+    pkgload.__doc__ = PackageLoader.__call__.__doc__
+
+    from .testing import Tester
+    test = Tester().test
+    bench = Tester().bench
+
+    from . import core
+    from .core import *
+    from . import compat
+    from . import lib
+    from .lib import *
+    from . import linalg
+    from . import fft
+    from . import polynomial
+    from . import random
+    from . import ctypeslib
+    from . import ma
+    from . import matrixlib as _mat
+    from .matrixlib import *
+    from .compat import long
+
+    # Make these accessible from numpy name-space
+    #  but not imported in from numpy import *
+    if sys.version_info[0] >= 3:
+        from builtins import bool, int, float, complex, object, str
+        unicode = str
+    else:
+        from __builtin__ import bool, int, float, complex, object, unicode, str
+
+    from .core import round, abs, max, min
+
+    __all__.extend(['__version__', 'pkgload', 'PackageLoader',
+               'show_config'])
+    __all__.extend(core.__all__)
+    __all__.extend(_mat.__all__)
+    __all__.extend(lib.__all__)
+    __all__.extend(['linalg', 'fft', 'random', 'ctypeslib', 'ma'])
+
+    # Filter annoying Cython warnings that serve no good purpose.
+    import warnings
+    warnings.filterwarnings("ignore", message="numpy.dtype size changed")
+    warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
+    warnings.filterwarnings("ignore", message="numpy.ndarray size changed")

numpy-1.10.0.post2/numpy/_build_utils/README

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+=======
+WARNING
+=======
+
+This directory (numpy/_build_utils) is *not* part of the pubic numpy API,
+ - it is internal build support for numpy.
+ - it is only present in source distributions or during an in place build
+ - it is *not* installed with the rest of numpy

numpy-1.10.0.post2/numpy/_build_utils/apple_accelerate.py

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+import os
+import sys
+import re
+
+__all__ = ['uses_accelerate_framework', 'get_sgemv_fix']
+
+def uses_accelerate_framework(info):
+    """ Returns True if Accelerate framework is used for BLAS/LAPACK """
+    if sys.platform != "darwin":
+        return False
+    r_accelerate = re.compile("Accelerate")
+    extra_link_args = info.get('extra_link_args', '')
+    for arg in extra_link_args:
+        if r_accelerate.search(arg):
+            return True
+    return False
+
+def get_sgemv_fix():
+    """ Returns source file needed to correct SGEMV """
+    path = os.path.abspath(os.path.dirname(__file__))
+    return [os.path.join(path, 'src', 'apple_sgemv_fix.c')]

numpy-1.10.0.post2/numpy/_build_utils/common.py

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+from __future__ import division, absolute_import, print_function
+
+import sys
+import copy
+import binascii
+
+LONG_DOUBLE_REPRESENTATION_SRC = r"""
+/* "before" is 16 bytes to ensure there's no padding between it and "x".
+ *    We're not expecting any "long double" bigger than 16 bytes or with
+ *       alignment requirements stricter than 16 bytes.  */
+typedef %(type)s test_type;
+
+struct {
+        char         before[16];
+        test_type    x;
+        char         after[8];
+} foo = {
+        { '\0', '\0', '\0', '\0', '\0', '\0', '\0', '\0',
+          '\001', '\043', '\105', '\147', '\211', '\253', '\315', '\357' },
+        -123456789.0,
+        { '\376', '\334', '\272', '\230', '\166', '\124', '\062', '\020' }
+};
+"""
+
+def pyod(filename):
+    """Python implementation of the od UNIX utility (od -b, more exactly).
+
+    Parameters
+    ----------
+    filename : str
+        name of the file to get the dump from.
+
+    Returns
+    -------
+    out : seq
+        list of lines of od output
+
+    Note
+    ----
+    We only implement enough to get the necessary information for long double
+    representation, this is not intended as a compatible replacement for od.
+    """
+    def _pyod2():
+        out = []
+
+        fid = open(filename, 'r')
+        try:
+            yo = [int(oct(int(binascii.b2a_hex(o), 16))) for o in fid.read()]
+            for i in range(0, len(yo), 16):
+                line = ['%07d' % int(oct(i))]
+                line.extend(['%03d' % c for c in yo[i:i+16]])
+                out.append(" ".join(line))
+            return out
+        finally:
+            fid.close()
+
+    def _pyod3():
+        out = []
+
+        fid = open(filename, 'rb')
+        try:
+            yo2 = [oct(o)[2:] for o in fid.read()]
+            for i in range(0, len(yo2), 16):
+                line = ['%07d' % int(oct(i)[2:])]
+                line.extend(['%03d' % int(c) for c in yo2[i:i+16]])
+                out.append(" ".join(line))
+            return out
+        finally:
+            fid.close()
+
+    if sys.version_info[0] < 3:
+        return _pyod2()
+    else:
+        return _pyod3()
+
+_BEFORE_SEQ = ['000', '000', '000', '000', '000', '000', '000', '000',
+              '001', '043', '105', '147', '211', '253', '315', '357']
+_AFTER_SEQ = ['376', '334', '272', '230', '166', '124', '062', '020']
+
+_IEEE_DOUBLE_BE = ['301', '235', '157', '064', '124', '000', '000', '000']
+_IEEE_DOUBLE_LE = _IEEE_DOUBLE_BE[::-1]
+_INTEL_EXTENDED_12B = ['000', '000', '000', '000', '240', '242', '171', '353',
+                       '031', '300', '000', '000']
+_INTEL_EXTENDED_16B = ['000', '000', '000', '000', '240', '242', '171', '353',
+                       '031', '300', '000', '000', '000', '000', '000', '000']
+_IEEE_QUAD_PREC_BE = ['300', '031', '326', '363', '105', '100', '000', '000',
+                      '000', '000', '000', '000', '000', '000', '000', '000']
+_IEEE_QUAD_PREC_LE = _IEEE_QUAD_PREC_BE[::-1]
+_DOUBLE_DOUBLE_BE = ['301', '235', '157', '064', '124', '000', '000', '000'] + \
+                    ['000'] * 8
+
+def long_double_representation(lines):
+    """Given a binary dump as given by GNU od -b, look for long double
+    representation."""
+
+    # Read contains a list of 32 items, each item is a byte (in octal
+    # representation, as a string). We 'slide' over the output until read is of
+    # the form before_seq + content + after_sequence, where content is the long double
+    # representation:
+    #  - content is 12 bytes: 80 bits Intel representation
+    #  - content is 16 bytes: 80 bits Intel representation (64 bits) or quad precision
+    #  - content is 8 bytes: same as double (not implemented yet)
+    read = [''] * 32
+    saw = None
+    for line in lines:
+        # we skip the first word, as od -b output an index at the beginning of
+        # each line
+        for w in line.split()[1:]:
+            read.pop(0)
+            read.append(w)
+
+            # If the end of read is equal to the after_sequence, read contains
+            # the long double
+            if read[-8:] == _AFTER_SEQ:
+                saw = copy.copy(read)
+                if read[:12] == _BEFORE_SEQ[4:]:
+                    if read[12:-8] == _INTEL_EXTENDED_12B:
+                        return 'INTEL_EXTENDED_12_BYTES_LE'
+                elif read[:8] == _BEFORE_SEQ[8:]:
+                    if read[8:-8] == _INTEL_EXTENDED_16B:
+                        return 'INTEL_EXTENDED_16_BYTES_LE'
+                    elif read[8:-8] == _IEEE_QUAD_PREC_BE:
+                        return 'IEEE_QUAD_BE'
+                    elif read[8:-8] == _IEEE_QUAD_PREC_LE:
+                        return 'IEEE_QUAD_LE'
+                    elif read[8:-8] == _DOUBLE_DOUBLE_BE:
+                        return 'DOUBLE_DOUBLE_BE'
+                elif read[:16] == _BEFORE_SEQ:
+                    if read[16:-8] == _IEEE_DOUBLE_LE:
+                        return 'IEEE_DOUBLE_LE'
+                    elif read[16:-8] == _IEEE_DOUBLE_BE:
+                        return 'IEEE_DOUBLE_BE'
+
+    if saw is not None:
+        raise ValueError("Unrecognized format (%s)" % saw)
+    else:
+        # We never detected the after_sequence
+        raise ValueError("Could not lock sequences (%s)" % saw)