./math/py-pytables, Database package for large amounts of data

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Branch: CURRENT, Version: 3.4.2, Package name: py27-pytables-3.4.2, Maintainer: pkgsrc-users

PyTables is a hierarchical database package designed to efficiently
manage very large amounts of data. PyTables is built on top of the
HDF5 library and the numarray package. It features an object-oriented
interface that, combined with natural naming and C-code generated from
Pyrex sources, makes it a fast, yet extremely easy-to-use tool for
interactively saving and retrieving very large amounts of data. It also
provides flexible indexed access on disk to anywhere in the data.


Required to run:
[archivers/lzo] [devel/hdf5] [math/py-numpy] [devel/py-cython] [math/py-numexpr]

Required to build:
[pkgtools/cwrappers]

Master sites:

SHA1: ebc3cb44eac73f6efaf5c16d6c09dfee7249a470
RMD160: bf652291d53a7a2078be2f774f0fe67dda5eb1cc
Filesize: 7415.499 KB

Version history: (Expand)


CVS history: (Expand)


   2017-05-21 09:52:56 by Adam Ciarcinski | Files touched by this commit (5)
Log message:
Changes 3.4.2:

Improvements
------------
 - setup.py detects conda env and uses installed conda (hdf5, bzip2, lzo
   and/or blosc) packages when building from source.

Bugs fixed
----------
 - Linux wheels now built against built-in blosc.
 - Fixed windows absolute paths in ptrepack, ptdump, ptree.
   2016-11-03 01:07:52 by Maya Rashish | Files touched by this commit (2)
Log message:
py-pytables: remove quick hack for netbsds new compiler choice claiming
C11 support without the OS having the rest of it.
   2016-08-28 17:48:37 by Thomas Klausner | Files touched by this commit (112)
Log message:
Remove unnecessary PLIST_SUBST and FILES_SUBST that are now provided
by the infrastructure.

Mark a couple more packages as not ready for python-3.x.
   2016-08-18 22:30:02 by Thomas Klausner | Files touched by this commit (4) | Package updated
Log message:
Add a patch to fix build with python-3.x where cpuinfo does not seem
to provide flags.

Fix parallel installation of different python-versions of this package.

Bump PKGREVISION.
   2016-08-16 16:12:35 by Maya Rashish | Files touched by this commit (1)
Log message:
Use PYPKGVERSION in PLIST
   2016-08-16 04:42:48 by Maya Rashish | Files touched by this commit (5) | Package updated
Log message:
Update py-pytables to 3.2.3

Changes from 3.2.2 to 3.2.3
Improvements

    It is now possible to use HDF5 with the new shared library naming scheme \ 
(>= 1.8.10, hdf5.dll instead of hdf5dll.dll) on Windows (gh-540). Thanks to \ 
Tadeu Manoel.
    Now :program: ptdump sorts output by node name and does not print a \ 
backtrace if file cannot be opened. Thanks to Zbigniew Jędrzejewski-Szmek.

Bugs fixed

    Only run tables.tests.test_basics.UnicodeFilename if the filesystem encoding \ 
is utf-8. Closes gh-485.
    Add lib64 to posix search path. (closes gh-507) Thanks to Mehdi Sadeghi.
    Ensure cache entries are removed if fewer than 10 (closes gh-529). Thanks to \ 
Graham Jones.
    Fix segmentation fault in a number of test cases that use index.Index \ 
(closes gh-532 and gh-533). Thanks to Diane Trout.
    Fixed the evaluation of transcendental functions when numexpr is compiled \ 
with VML support (closes gh-534, PR #536). Thanks to Tom Kooij.
    Make sure that index classes use buffersizes that are a multiple of \ 
chunkshape[0] (closes gh-538, PR #538). Thanks to Tom Kooij.
    Ensure benchmark paths exist before benchmarks are executed (PR #544). \ 
Thanks to rohitjamuar.

Other changes

    Minimum Cython version is now v0.21

Changes from 3.2.1.1 to 3.2.2
Bug fixed

    Fix AssertionError in Row.__init_loop. See gh-477.
    Fix issues with Cython 0.23. See gh-481.
    Only run tables.tests.test_basics.UnicodeFilename if the filesystem encoding \ 
is utf-8. Closes gh-485.
    Fix missing missing PyErr_Clear. See gh-#486.
    Fix the C type of some numpy attributes. See gh-494.
    Cast selection indices to integer. See gh-496.
    Fix indexesextension._keysort_string. Closes gh-497 and gh-498.

Changes from 3.2.1 to 3.2.1.1

    Fix permission on distributed source distribution

Other changes

    Minimum Cython version is now v0.21

Changes from 3.2.0 to 3.2.1
Bug fixed

    Fix indexesextension._keysort. Fixes gh-455. Thanks to Andrew Lin.

Changes from 3.1.1 to 3.2.0
Improvements

    The nrowsinbuf is better computed now for EArray/CArray having a small \ 
chunkshape in the main dimension. Fixes #285.

    PyTables should be installable very friendly via pip, including NumPy being \ 
installed automatically in the unlikely case it is not yet installed in the \ 
system. Thanks to Andrea Bedini.

    setup.py has been largely simplified and now it requires setuptools. \ 
Although we think this is a good step, please keep us informed this is breaking \ 
some installation in a very bad manner.

    setup.py now is able to used pkg-config, if available, to locate required \ 
libraries (hdf5, bzip2, etc.). The use of pkg-config can be controlled via \ 
setup.py command line flags or via environment variables. Please refer to the \ 
installation guide (in the User Manual) for details. Closes gh-442.

    It is now possible to create a new node whose parent is a softlink to \ 
another group (see gh-422). Thanks to Alistair Muldal.

    link.SoftLink objects no longer need to be explicitly dereferenced. Methods \ 
and attributes of the linked object are now automatically accessed when the user \ 
acts on a soft-link (see gh-399). Thanks to Alistair Muldal.

    Now ptrepack recognizes hardlinks and replicates them in the output \ 
(repacked) file. This saves disk space and makes repacked files more conformal \ 
to the original one. Closes gh-380.

    New pttree script for printing HDF5 file contents as a pretty ASCII tree \ 
(closes gh-400). Thanks to Alistair Muldal.

    The internal Blosc library has been downgraded to version 1.4.4. This is in \ 
order to still allow using multiple threads inside Blosc, even on multithreaded \ 
applications (see gh-411, gh-412, gh-437 and gh-448).

    The print_versions() function now also reports the version of compression \ 
libraries used by Blosc.

    Now the setup.py tries to use the ‘-march=native’ C flag by default. In \ 
falls back on ‘-msse2’ if ‘-march=native’ is not supported by the \ 
compiler. Closes gh-379.

    Fixed a spurious unicode comparison warning (closes gh-372 and gh-373).

    Improved handling of empty string attributes. In previous versions of \ 
PyTables empty string were stored as scalar HDF5 attributes having size 1 and \ 
value ‘0’ (an empty null terminated string). Now empty string are stored as \ 
HDF5 attributes having zero size

    Added a new cookbook recipe and a couple of examples for simple threading \ 
with PyTables.

    The redundant utilsextension.get_indices() function has been eliminated \ 
(replaced by slice.indices()). Closes gh-195.

    Allow negative indices in point selection (closes gh-360)

    Index wasn’t being used if it claimed there were no results. Closes gh-351 \ 
(see also gh-353)

    Atoms and Col types are no longer generated dynamically so now it is easier \ 
for IDEs and static analysis tool to handle them (closes gh-345)

    The keysort functions in idx-opt.c have been cythonised using fused types. \ 
The perfomance is mostly unchanged, but the code is much more simpler now. \ 
Thanks to Andrea Bedini.

    Small unit tests re-factoring:

        print_versions() and tests.common.print_heavy() functions

            moved to the tests.common module

        always use print_versions() when test modules are called as scripts

        use the unittest2 package in Python 2.6.x

        removed internal machinery used to replicate unittest2 features

        always use tests.common.PyTablesTestCase as base class for all test cases

        code of the old tasts.common.cleanup() function has been moved to \ 
tests.common.PyTablesTestCase.tearDown() method

        new implementation of tests.common.PyTablesTestCase.assertWarns() \ 
compatible with the one provided by the standard unittest module in Python >= \ 
3.2

        use tests.common.PyTablesTestCase.assertWarns() as context manager when \ 
appropriate

        use the unittest.skipIf() decorator when appropriate

        new :class:tests.comon.TestFileMixin: class

Bugs fixed

    Fixed compatibility problems with numpy 1.9 and 1.10-dev (closes gh-362 and \ 
gh-366)
    Fixed compatibility with Cython >= 0.20 (closes gh-386 and gh-387)
    Fixed support for unicode node names in LRU cache (only Python 2 was \ 
affected). Closes gh-367 and gh-369.
    Fixed support for unicode node titles (only Python 2 was affected). Closes \ 
gh-370 and gh-374.
    Fixed a bug that caused the silent truncation of unicode attributes \ 
containing the ‘0’ character. Closes gh-371.
    Fixed descr_from_dtype() to work as expected with complex types. Closes gh-381.
    Fixed the tests.test_basics.ThreadingTestCase test case. Closes gh-359.
    Fix incomplete results when performing the same query twice and exhausting \ 
the second iterator before the first. The first one writes incomplete results to \ 
seqcache (gh-353)
    Fix false results potentially going to seqcache if \ 
tableextension.Row.update() is used during iteration (see gh-353)
    Fix Column.create_csindex() when there’s NaNs
    Fixed handling of unicode file names on windows (closes gh-389)
    No longer not modify sys.argv at import time (closes gh-405)
    Fixed a performance issue on NFS (closes gh-402)
    Fixed a nasty problem affecting results of indexed queries. Closes gh-319 \ 
and probably gh-419 too.
    Fixed another problem affecting results of indexed queries too. Closes gh-441.
    Replaced “len(xrange(start, stop, step))” -> “len(xrange(0, stop - \ 
start, step))” to fix issues with large row counts with Python 2.x. Fixes \ 
#447.

Other changes

    Cython is not a hard dependency anymore (although developers will need it so \ 
as to generated the C extension code).

    The number of threads used by default for numexpr and Blosc operation that \ 
was set to the number of available cores have been reduced to 2. This is a much \ 
more reasonable setting for not creating too much overhead.
   2016-07-15 09:24:06 by Thomas Klausner | Files touched by this commit (2)
Log message:
Do not include py-numexpr/bl3.mk, just DEPEND on it.
   2015-11-04 00:33:46 by Alistair G. Crooks | Files touched by this commit (262)
Log message:
Add SHA512 digests for distfiles for math category

Problems found locating distfiles:
	Package dfftpack: missing distfile dfftpack-20001209.tar.gz
	Package eispack: missing distfile eispack-20001130.tar.gz
	Package fftpack: missing distfile fftpack-20001130.tar.gz
	Package linpack: missing distfile linpack-20010510.tar.gz
	Package minpack: missing distfile minpack-20001130.tar.gz
	Package odepack: missing distfile odepack-20001130.tar.gz
	Package py-networkx: missing distfile networkx-1.10.tar.gz
	Package py-sympy: missing distfile sympy-0.7.6.1.tar.gz
	Package quadpack: missing distfile quadpack-20001130.tar.gz

Otherwise, existing SHA1 digests verified and found to be the same on
the machine holding the existing distfiles (morden).  All existing
SHA1 digests retained for now as an audit trail.