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.

5 files changed, 51 insertions, 46 deletions

diff --git a/math/py-pytables/Makefile b/math/py-pytables/Makefile
index 2941b962b73..0b2d3f320b7 100644
--- a/math/py-pytables/Makefile
+++ b/math/py-pytables/Makefile
@@ -1,15 +1,19 @@
-# $NetBSD: Makefile,v 1.32 2016/07/15 07:24:06 wiz Exp $
+# $NetBSD: Makefile,v 1.33 2016/08/16 02:42:48 maya Exp $
 
-DISTNAME=		tables-3.1.1
+DISTNAME=		tables-3.2.3
 PKGNAME=		${PYPKGPREFIX}-py${DISTNAME}
 CATEGORIES=		math python
-MASTER_SITES=		${MASTER_SITE_SOURCEFORGE:=pytables/}
+MASTER_SITES=		${MASTER_SITE_GITHUB:=PyTables/}
+GITHUB_PROJECT=		PyTables
+GITHUB_TAG=		v.${PKGVERSION_NOREV}
 
 MAINTAINER=		pkgsrc-users@NetBSD.org
 HOMEPAGE=		http://www.pytables.org/
 COMMENT=		Database package for large amounts of data
 LICENSE=		modified-bsd
 
+WRKSRC=			${WRKDIR}/${GITHUB_PROJECT}-${GITHUB_TAG}
+
 PYSETUPBUILDARGS+=	--hdf5=${BUILDLINK_PREFIX.hdf5}
 PYSETUPINSTALLARGS=	${PYSETUPBUILDARGS}
 PLIST_SUBST+=		PYVERSSUFFIX=${PYVERSSUFFIX:Q}
@@ -34,6 +38,6 @@ do-test:
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../archivers/bzip2/buildlink3.mk"
 .include "../../math/py-numpy/buildlink3.mk"
-BUILDLINK_API_DEPENDS.pycython+=	${PYPKGPREFIX}-cython>=0.13
+BUILDLINK_API_DEPENDS.pycython+=	${PYPKGPREFIX}-cython>=0.21
 .include "../../devel/py-cython/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/math/py-pytables/PLIST b/math/py-pytables/PLIST
index 28246b2d027..7ce13580a80 100644
--- a/math/py-pytables/PLIST
+++ b/math/py-pytables/PLIST
@@ -1,8 +1,15 @@
-@comment $NetBSD: PLIST,v 1.11 2014/01/21 16:32:42 wiz Exp $
-bin/pt2to3${PYVERSSUFFIX}
-bin/ptdump${PYVERSSUFFIX}
-bin/ptrepack${PYVERSSUFFIX}
-${PYSITELIB}/${EGG_FILE}
+@comment $NetBSD: PLIST,v 1.12 2016/08/16 02:42:48 maya Exp $
+bin/pt2to32.7
+bin/ptdump2.7
+bin/ptrepack2.7
+bin/pttree
+${PYSITELIB}/${EGG_FILE}/PKG-INFO
+${PYSITELIB}/${EGG_FILE}/SOURCES.txt
+${PYSITELIB}/${EGG_FILE}/dependency_links.txt
+${PYSITELIB}/${EGG_FILE}/entry_points.txt
+${PYSITELIB}/${EGG_FILE}/not-zip-safe
+${PYSITELIB}/${EGG_FILE}/requires.txt
+${PYSITELIB}/${EGG_FILE}/top_level.txt
 ${PYSITELIB}/tables/__init__.py
 ${PYSITELIB}/tables/__init__.pyc
 ${PYSITELIB}/tables/__init__.pyo
@@ -132,6 +139,9 @@ ${PYSITELIB}/tables/scripts/ptdump.pyo
 ${PYSITELIB}/tables/scripts/ptrepack.py
 ${PYSITELIB}/tables/scripts/ptrepack.pyc
 ${PYSITELIB}/tables/scripts/ptrepack.pyo
+${PYSITELIB}/tables/scripts/pttree.py
+${PYSITELIB}/tables/scripts/pttree.pyc
+${PYSITELIB}/tables/scripts/pttree.pyo
 ${PYSITELIB}/tables/table.py
 ${PYSITELIB}/tables/table.pyc
 ${PYSITELIB}/tables/table.pyo
@@ -150,6 +160,7 @@ ${PYSITELIB}/tables/tests/__init__.pyo
 ${PYSITELIB}/tables/tests/array_mdatom.h5
 ${PYSITELIB}/tables/tests/attr-u16.h5
 ${PYSITELIB}/tables/tests/blosc_bigendian.h5
+${PYSITELIB}/tables/tests/bug-idx.h5
 ${PYSITELIB}/tables/tests/check_leaks.py
 ${PYSITELIB}/tables/tests/check_leaks.pyc
 ${PYSITELIB}/tables/tests/check_leaks.pyo
@@ -167,6 +178,8 @@ ${PYSITELIB}/tables/tests/float.h5
 ${PYSITELIB}/tables/tests/idx-std-1.x.h5
 ${PYSITELIB}/tables/tests/indexes_2_0.h5
 ${PYSITELIB}/tables/tests/indexes_2_1.h5
+${PYSITELIB}/tables/tests/issue_368.h5
+${PYSITELIB}/tables/tests/issue_560.h5
 ${PYSITELIB}/tables/tests/matlab_file.mat
 ${PYSITELIB}/tables/tests/nested-type-with-gaps.h5
 ${PYSITELIB}/tables/tests/non-chunked-table.h5
@@ -194,6 +207,9 @@ ${PYSITELIB}/tables/tests/test_array.pyo
 ${PYSITELIB}/tables/tests/test_attributes.py
 ${PYSITELIB}/tables/tests/test_attributes.pyc
 ${PYSITELIB}/tables/tests/test_attributes.pyo
+${PYSITELIB}/tables/tests/test_aux.py
+${PYSITELIB}/tables/tests/test_aux.pyc
+${PYSITELIB}/tables/tests/test_aux.pyo
 ${PYSITELIB}/tables/tests/test_backcompat.py
 ${PYSITELIB}/tables/tests/test_backcompat.pyc
 ${PYSITELIB}/tables/tests/test_backcompat.pyo
diff --git a/math/py-pytables/distinfo b/math/py-pytables/distinfo
index 0e46318350f..9bbf1ea8453 100644
--- a/math/py-pytables/distinfo
+++ b/math/py-pytables/distinfo
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.13 2015/11/03 23:33:42 agc Exp $
+$NetBSD: distinfo,v 1.14 2016/08/16 02:42:48 maya Exp $
 
-SHA1 (tables-3.1.1.tar.gz) = c1ff909112b69b38b744cf81381496173c85c8af
-RMD160 (tables-3.1.1.tar.gz) = f4c4c68c931fe8d3c5817f2619e699bab6fc7f07
-SHA512 (tables-3.1.1.tar.gz) = b5b2052dd81c4748c5e26c1f61f9f92891f48335b0a553f7602ab11c9029dd673d27b91e24cac0da21a81df0c26dbcd9a438214fa58af1ae831c5f04dfa212a6
-Size (tables-3.1.1.tar.gz) = 6715786 bytes
-SHA1 (patch-setup.py) = a343bbf94ab7bcc46c81c5db7ca5a9afa85e306a
+SHA1 (tables-3.2.3.tar.gz) = d7a2965821f436aabcf97e2851fe857c40e71cca
+RMD160 (tables-3.2.3.tar.gz) = b0eaa61390a65d4e23f0499ca64409c20fd23bae
+SHA512 (tables-3.2.3.tar.gz) = 565ae648a81daa6e9eb7d8dfbecef4f0b195122dd2c60a99f89f903f7366515997c302e649441f68b20c13b0f7ccff1e97971cc16b4bd56b579a069d92247e9a
+Size (tables-3.2.3.tar.gz) = 3821258 bytes
+SHA1 (patch-c-blosc_blosc_blosc.c) = 53751c1242e9d2e3057bb1eef0f075f2fdd97c3f
diff --git a/math/py-pytables/patches/patch-c-blosc_blosc_blosc.c b/math/py-pytables/patches/patch-c-blosc_blosc_blosc.c
new file mode 100644
index 00000000000..3e5d241d28b
--- /dev/null
+++ b/math/py-pytables/patches/patch-c-blosc_blosc_blosc.c
@@ -0,0 +1,16 @@
+$NetBSD: patch-c-blosc_blosc_blosc.c,v 1.1 2016/08/16 02:42:48 maya Exp $
+
+Workaround NetBSD-7.99.35 missing C11 includes and having C11 support
+PR standards/51416
+
+--- c-blosc/blosc/blosc.c.orig	2016-07-03 11:46:48.000000000 +0000
++++ c-blosc/blosc/blosc.c
+@@ -59,7 +59,7 @@
+ #endif
+ 
+ /* If C11 is supported, use it's built-in aligned allocation. */
+-#if __STDC_VERSION__ >= 201112L
++#if 0
+   #include <stdalign.h>
+ #endif
+ 
diff --git a/math/py-pytables/patches/patch-setup.py b/math/py-pytables/patches/patch-setup.py
deleted file mode 100644
index 12c61e175f7..00000000000
--- a/math/py-pytables/patches/patch-setup.py
+++ /dev/null
@@ -1,31 +0,0 @@
-$NetBSD: patch-setup.py,v 1.1 2014/09/20 17:56:36 wiz Exp $
-
-Fix build with cython-0.20++.
-
---- setup.py.orig	2014-03-25 20:49:03.000000000 +0000
-+++ setup.py
-@@ -122,21 +122,21 @@ if not has_setuptools:
- 
- # Check if Cython is installed or not (requisite)
- try:
-+    from Cython import __version__ as CythonVersion
-     from Cython.Distutils import build_ext
--    from Cython.Compiler.Main import Version
-     cmdclass['build_ext'] = build_ext
- except ImportError:
-     exit_with_error(
-         "You need %(pkgname)s %(pkgver)s or greater to compile PyTables!"
-         % {'pkgname': 'Cython', 'pkgver': min_cython_version})
- 
--if Version.version < min_cython_version:
-+if CythonVersion < min_cython_version:
-     exit_with_error(
-         "At least Cython %s is needed so as to generate extensions!"
-         % (min_cython_version))
- else:
-     print("* Found %(pkgname)s %(pkgver)s package installed."
--          % {'pkgname': 'Cython', 'pkgver': Version.version})
-+          % {'pkgname': 'Cython', 'pkgver': CythonVersion})
- 
- VERSION = open('VERSION').read().strip()
-