Устанавливаем PyTables и получаем проблемы с Pandas и NumPy... Вся сборка под угрозой... Что делать?

Универсальный способ собрать стек - переустановить последние версии. После чтения постов про компиляцию и перекомпиляцию... было найдено универсальное средство - неофициальная библиотека экзешников для установки дополнений. Поскольку на эти грабли я наступил второй раз (использовал эту библиотеку и забыл про это), то публикую этот пост в назидание самому себе.

Вот здесь волшебная палочка Unofficial Windows Binaries for Python Extension Packages
А здесь нет бинарника для amd64 Numerical Python
Кроме Анаконды есть еще с десяток Scientific Python distributions
PyTables

NumPy is a fundamental package needed for scientific computing with Python. Note: these builds are not completely compatible with the official SciPy binaries. Note: the MKL builds are linked statically to Intel's high performance Math Kernel Library Note: the unoptimized builds are less tested and not recommended for general use.

После великих откровений философии Python (предыдущий пост) я начинаю ценить сервисы прочих ползучих гадов. Оказалось, что в моей анаконде все, что нужно для PyTables уже установлено. А ссылку на PyTables я нагуглил после того, как сформулировал запрос "Python Tables "
Там, кстати, выскочила еще библиотека PrettyTable на code.google.com, но она показалась мне слишком простой...

In [5]:

from IPython.display import Image
Image(filename='C:\\Users\\kiss\\Pictures\\for_blogs\\pytables.PNG')

Out[5]:

Начал было читать и устанавливать все подряд в соответствии с инструкцией PyTables на github.com, но оказалось, что все уже стоит (в основном в C:/Users/kiss/Anaconda/Lib/site-packages)

Сначала эта команда прошла, и тест внизу показал, что все должно работать..., но далее выскочила ошибка с pandas, хотя раньше я из нее импортировал что-то для прорисовки таблиц... Я попытался обновить pandas... и после этого все и началось...

In [9]:

import tables

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-9-389ecae14f10> in <module>()
----> 1 import tables

C:\Users\kiss\Anaconda\lib\site-packages\tables\__init__.py in <module>()
     80 
     81 # Necessary imports to get versions stored on the cython extension
---> 82 from tables.utilsextension import (get_pytables_version, get_hdf5_version,
     83     getPyTablesVersion, getHDF5Version)  # Pending Deprecation!
     84 

C:\Users\kiss\Documents\IPython Notebooks\web\oboobs\numpy.pxd in init tables.utilsextension (tables\utilsextension.c:14102)()

ValueError: numpy.dtype has the wrong size, try recompiling

In [2]:

tables.test()

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version:  3.0.0
HDF5 version:      1.8.11
NumPy version:     1.7.1
Numexpr version:   2.2.2 (not using Intel's VML/MKL)
Zlib version:      1.2.3 (in Python interpreter)
LZO version:       2.06 (Aug 12 2011)
BZIP2 version:     1.0.6 (6-Sept-2010)
Blosc version:     1.2.3 (2013-05-17)
Cython version:    0.19.2
Python version:    2.7.5 |Anaconda 1.8.0 (64-bit)| (default, Jul  1 2013, 12:37:52) [MSC v.1500 64 bit (AMD64)]
Byte-ordering:     little
Detected cores:    2
Default encoding:  ascii
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing only a light (yet comprehensive) subset of the test suite.
If you want a more complete test, try passing the --heavy flag to this script
(or set the 'heavy' parameter in case you are using tables.test() call).
The whole suite will take more than 4 hours to complete on a relatively
modern CPU and around 512 MB of main memory.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Out[2]:

0

In [1]:

import pandas

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-1-d6ac987968b6> in <module>()
----> 1 import pandas

C:\Users\kiss\Anaconda\lib\site-packages\pandas\__init__.py in <module>()
      4 
      5 try:
----> 6     from . import hashtable, tslib, lib
      7 except Exception:  # pragma: no cover
      8     import sys

C:\Users\kiss\Documents\IPython Notebooks\web\oboobs\numpy.pxd in init pandas.hashtable (pandas\hashtable.c:19547)()

ValueError: numpy.dtype has the wrong size, try recompiling

numpy.dtype has the wrong size, try recompiling

Я смотрел видео и параллельно хотел обновить pandas из консоли wiindows... А там "само вызвалось" обновление Numpy

In []:

 pip install pandas --upgrade

In [4]:

s=Series([1,2,3,4,5],index=['a','b','c','d','e'])

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-4-f21b25ab6e8f> in <module>()
----> 1 s=Series([1,2,3,4,5],index=['a','b','c','d','e'])

NameError: name 'Series' is not defined

In [3]:

import numpy

In [4]:

help(numpy)

In [7]:

numpy.version.full_version

Out[7]:

'1.6.2'

In [6]:

numpy.

Out[6]:

inf

In [8]:

tables.test()

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-8-fdea071a6cc9> in <module>()
----> 1 tables.test()

NameError: name 'tables' is not defined

In [10]:

!pip help install

Usage:   
  pip install [options] <requirement specifier> ...
  pip install [options] -r <requirements file> ...
  pip install [options] [-e] <vcs project url> ...
  pip install [options] [-e] <local project path> ...
  pip install [options] <archive url/path> ...

Description:
  Install packages from:
  
  - PyPI (and other indexes) using requirement specifiers.
  - VCS project urls.
  - Local project directories.
  - Local or remote source archives.
  
  pip also supports installing from "requirements files", which provide
  an easy way to specify a whole environment to be installed.
  
  See http://www.pip-installer.org for details on VCS url formats and
  requirements files.

Install Options:
  -e, --editable <path/url>   Install a project in editable mode (i.e.
                              setuptools "develop mode") from a local project
                              path or a VCS url.
  -r, --requirement <file>    Install from the given requirements file. This
                              option can be used multiple times.
  -b, --build <dir>           Directory to unpack packages into and build in.
                              The default in a virtualenv is "<venv
                              path>/build". The default for global installs is
                              "<OS temp dir>/pip_build_<username>".
  -t, --target <dir>          Install packages into <dir>.
  -d, --download <dir>        Download packages into <dir> instead of
                              installing them, regardless of what's already
                              installed.
  --download-cache <dir>      Cache downloaded packages in <dir>.
  --src <dir>                 Directory to check out editable projects into.
                              The default in a virtualenv is "<venv
                              path>/src". The default for global installs is
                              "<current dir>/src".
  -U, --upgrade               Upgrade all packages to the newest available
                              version. This process is recursive regardless of
                              whether a dependency is already satisfied.
  --force-reinstall           When upgrading, reinstall all packages even if
                              they are already up-to-date.
  -I, --ignore-installed      Ignore the installed packages (reinstalling
                              instead).
  --no-deps                   Don't install package dependencies.
  --no-install                Download and unpack all packages, but don't
                              actually install them.
  --no-download               Don't download any packages, just install the
                              ones already downloaded (completes an install
                              run with --no-install).
  --install-option <options>  Extra arguments to be supplied to the setup.py
                              install command (use like --install-option
                              ="--install-scripts=/usr/local/bin"). Use
                              multiple --install-option options to pass
                              multiple options to setup.py install. If you are
                              using an option with a directory path, be sure
                              to use absolute path.
  --global-option <options>   Extra global options to be supplied to the
                              setup.py call before the install command.
  --user                      Install using the user scheme.
  --egg                       Install as self contained egg file, like
                              easy_install does.
  --root <dir>                Install everything relative to this alternate
                              root directory.
  --use-wheel                 Find and prefer wheel archives when searching
                              indexes and find-links locations. Default to
                              accepting source archives.
  --pre                       Include pre-release and development versions. By
                              default, pip only finds stable versions.
  --no-clean                  Don't clean up build directories.

Package Index Options:
  -i, --index-url <url>       Base URL of Python Package Index (default
                              https://pypi.python.org/simple/).
  --extra-index-url <url>     Extra URLs of package indexes to use in addition
                              to --index-url.
  --no-index                  Ignore package index (only looking at --find-
                              links URLs instead).
  -f, --find-links <url>      If a url or path to an html file, then parse for
                              links to archives. If a local path or file://
                              url that's a directory, then look for archives
                              in the directory listing.
  -M, --use-mirrors           Use the PyPI mirrors as a fallback in case the
                              main index is down.
  --mirrors <url>             Specific mirror URLs to query when --use-mirrors
                              is used.
  --allow-external <package>  Allow the installation of externally hosted
                              files
  --allow-all-external        Allow the installation of all externally hosted
                              files
  --no-allow-external         Disallow the installation of all externally
                              hosted files
  --allow-insecure <package>  Allow the installation of insecure and
                              unverifiable files
  --no-allow-insecure         Disallow the installation of insecure and
                              unverifiable files

General Options:
  -h, --help                  Show help.
  -v, --verbose               Give more output. Option is additive, and can be
                              used up to 3 times.
  -V, --version               Show version and exit.
  -q, --quiet                 Give less output.
  --log <file>                Log file where a complete (maximum verbosity)
                              record will be kept.
  --proxy <proxy>             Specify a proxy in the form
                              [user:passwd@]proxy.server:port.
  --timeout <sec>             Set the socket timeout (default 15 seconds).
  --exists-action <action>    Default action when a path already exists:
                              (s)witch, (i)gnore, (w)ipe, (b)ackup.
  --cert <path>               Path to alternate CA bundle.

In [2]:

import tables

In [3]:

import numpy

In [4]:

numpy.version.full_version

Out[4]:

'1.8.0'

In [*]:

tables.test()

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version:  3.0.0
HDF5 version:      1.8.11
NumPy version:     1.8.0
Numexpr version:   2.2.2 (not using Intel's VML/MKL)
Zlib version:      1.2.3 (in Python interpreter)
LZO version:       2.06 (Aug 12 2011)
BZIP2 version:     1.0.6 (6-Sept-2010)
Blosc version:     1.2.3 (2013-05-17)
Cython version:    0.19.2

C:\Users\kiss\Anaconda\lib\site-packages\tables\conditions.py:447: DeprecationWarning: using `oa_ndim == 0` when `op_axes` is NULL is deprecated. Use `oa_ndim == -1` or the MultiNew iterator for NumPy <1.8 compatibility
  return func(*args)
C:\Users\kiss\Anaconda\lib\site-packages\tables\tests\test_array.py:2537: DeprecationWarning: using a boolean instead of an integer will result in an error in the future
  a = nparr[key]
C:\Users\kiss\Anaconda\lib\site-packages\tables\tests\test_array.py:2585: DeprecationWarning: using a boolean instead of an integer will result in an error in the future
  s = nparr[key]
C:\Users\kiss\Anaconda\lib\site-packages\tables\tests\test_array.py:2586: DeprecationWarning: using a boolean instead of an integer will result in an error in the future
  nparr[key] = s * 2
C:\Users\kiss\Anaconda\lib\site-packages\tables\tests\test_array.py:2605: DeprecationWarning: using a boolean instead of an integer will result in an error in the future
  nparr[key] = 2   # broadcast value
C:\Users\kiss\Anaconda\lib\site-packages\numexpr\necompiler.py:742: DeprecationWarning: using `oa_ndim == 0` when `op_axes` is NULL is deprecated. Use `oa_ndim == -1` or the MultiNew iterator for NumPy <1.8 compatibility
  return compiled_ex(*arguments, **kwargs)

А это после переустановки еще и Numexpr и Pandas (до кучи)

In [*]:

tables.test()

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version:  3.0.0
HDF5 version:      1.8.11
NumPy version:     1.8.0
Numexpr version:   2.3 (using VML/MKL 11.1.1)
Zlib version:      1.2.3 (in Python interpreter)
LZO version:       2.06 (Aug 12 2011)
BZIP2 version:     1.0.6 (6-Sept-2010)
Blosc version:     1.2.3 (2013-05-17)
Cython version:    0.19.2

C:\Users\kiss\Anaconda\lib\site-packages\tables\tests\test_array.py:2537: DeprecationWarning: using a boolean instead of an integer will result in an error in the future
  a = nparr[key]
C:\Users\kiss\Anaconda\lib\site-packages\tables\tests\test_array.py:2585: DeprecationWarning: using a boolean instead of an integer will result in an error in the future
  s = nparr[key]
C:\Users\kiss\Anaconda\lib\site-packages\tables\tests\test_array.py:2586: DeprecationWarning: using a boolean instead of an integer will result in an error in the future
  nparr[key] = s * 2
C:\Users\kiss\Anaconda\lib\site-packages\tables\tests\test_array.py:2605: DeprecationWarning: using a boolean instead of an integer will result in an error in the future
  nparr[key] = 2   # broadcast value

now worries, it's just a warning. you upgraded numpy version, as this is numpy 1.8.0 deprecation warning. Explained in this pull request. Continuation in this PR.

In [1]:

import pandas

In [2]:

help(pandas)

Help on package pandas:

NAME
    pandas

FILE
    c:\users\kiss\anaconda\lib\site-packages\pandas\__init__.py

DESCRIPTION
    pandas - a powerful data analysis and manipulation library for Python
    =====================================================================
    
    See http://pandas.sourceforge.net for full documentation. Otherwise, see the
    docstrings of the various objects in the pandas namespace:
    
    Series
    DataFrame
    Panel
    Index
    DatetimeIndex
    HDFStore
    bdate_range
    date_range
    read_csv
    read_fwf
    read_table
    ols

PACKAGE CONTENTS
    _sparse
    _testing
    algos
    compat (package)
    computation (package)
    core (package)
    hashtable
    index
    info
    io (package)
    json
    lib
    msgpack
    parser
    rpy (package)
    sandbox (package)
    sparse (package)
    stats (package)
    tests (package)
    tools (package)
    tseries (package)
    tslib
    util (package)
    version

SUBMODULES
    datetools
    offsets

DATA
    NaT = NaT
    __docformat__ = 'restructuredtext'
    __version__ = '0.13.1'
    __warningregistry__ = {('numpy.ufunc size changed, may indicate binary...
    describe_option = <pandas.core.config.CallableDynamicDoc object>
    get_option = <pandas.core.config.CallableDynamicDoc object>
    options = <pandas.core.config.DictWrapper object>
    plot_params = {'xaxis.compat': False}
    reset_option = <pandas.core.config.CallableDynamicDoc object>
    set_option = <pandas.core.config.CallableDynamicDoc object>

VERSION
    0.13.1

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