update to 2.1.2

this is a major update, too much to list here

4 files changed, 283 insertions, 105 deletions

diff --git a/math/py-pytables/Makefile b/math/py-pytables/Makefile
index 5a10c57316d..1923e6596bf 100644
--- a/math/py-pytables/Makefile
+++ b/math/py-pytables/Makefile
@@ -1,19 +1,19 @@
-# $NetBSD: Makefile,v 1.16 2008/06/12 02:14:37 joerg Exp $
+# $NetBSD: Makefile,v 1.17 2009/11/15 15:56:55 drochner Exp $
 #
 
-DISTNAME=		pytables-1.3.3
-PKGNAME=		${PYPKGPREFIX}-pytables-1.3.3
+DISTNAME=		tables-2.1.2
+PKGNAME=		${PYPKGPREFIX}-pytables-2.1.2
 CATEGORIES=		math python
-MASTER_SITES=		${MASTER_SITE_SOURCEFORGE:=pytables/}
+MASTER_SITES=		http://www.pytables.org/download/pytables-2.1.2/
 
 MAINTAINER=		pkgsrc-users@NetBSD.org
-HOMEPAGE=		http://pytables.sourceforge.net/
+HOMEPAGE=		http://www.pytables.org/
 COMMENT=		Database package for large amounts of data
 
 PKG_DESTDIR_SUPPORT=	user-destdir
 
 PKG_OPTIONS_VAR=	PKG_OPTIONS.pytables
-PKG_SUPPORTED_OPTIONS=	lzo ucl
+PKG_SUPPORTED_OPTIONS=	lzo
 PKG_SUGGESTED_OPTIONS=
 .include "../../mk/bsd.options.mk"
 
@@ -23,10 +23,6 @@ PYSETUPBUILDARGS=	--hdf5=${BUILDLINK_PREFIX.hdf5}
 PYSETUPBUILDARGS+=	--lzo=${BUILDLINK_PREFIX.lzo}
 .include "../../archivers/lzo/buildlink3.mk"
 .endif
-.if !empty(PKG_OPTIONS:Mucl)
-PYSETUPBUILDARGS+=	--ucl=${BUILDLINK_PREFIX.ucl}
-.include "../../devel/ucl/buildlink3.mk"
-.endif
 PYSETUPINSTALLARGS=	${PYSETUPBUILDARGS}
 PLIST_SUBST+=		PYVERSSUFFIX=${PYVERSSUFFIX:Q}
 
@@ -43,5 +39,5 @@ do-test:
 .include "../../devel/hdf5/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../archivers/bzip2/buildlink3.mk"
-.include "../../math/py-numarray/buildlink3.mk"
+.include "../../math/py-numpy/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/math/py-pytables/PLIST b/math/py-pytables/PLIST
index 9e859076407..c7c58bcd744 100644
--- a/math/py-pytables/PLIST
+++ b/math/py-pytables/PLIST
@@ -1,112 +1,294 @@
-@comment $NetBSD: PLIST,v 1.5 2009/06/14 18:05:48 joerg Exp $
-bin/nctoh5${PYVERSSUFFIX}
-bin/ptdump${PYVERSSUFFIX}
-bin/ptrepack${PYVERSSUFFIX}
-${PYSITELIB}/tables/Array.py
-${PYSITELIB}/tables/Array.pyc
-${PYSITELIB}/tables/Array.pyo
-${PYSITELIB}/tables/Atom.py
-${PYSITELIB}/tables/Atom.pyc
-${PYSITELIB}/tables/Atom.pyo
-${PYSITELIB}/tables/AttributeSet.py
-${PYSITELIB}/tables/AttributeSet.pyc
-${PYSITELIB}/tables/AttributeSet.pyo
-${PYSITELIB}/tables/CArray.py
-${PYSITELIB}/tables/CArray.pyc
-${PYSITELIB}/tables/CArray.pyo
-${PYSITELIB}/tables/EArray.py
-${PYSITELIB}/tables/EArray.pyc
-${PYSITELIB}/tables/EArray.pyo
-${PYSITELIB}/tables/File.py
-${PYSITELIB}/tables/File.pyc
-${PYSITELIB}/tables/File.pyo
-${PYSITELIB}/tables/Group.py
-${PYSITELIB}/tables/Group.pyc
-${PYSITELIB}/tables/Group.pyo
-${PYSITELIB}/tables/Index.py
-${PYSITELIB}/tables/Index.pyc
-${PYSITELIB}/tables/Index.pyo
-${PYSITELIB}/tables/IndexArray.py
-${PYSITELIB}/tables/IndexArray.pyc
-${PYSITELIB}/tables/IndexArray.pyo
-${PYSITELIB}/tables/IsDescription.py
-${PYSITELIB}/tables/IsDescription.pyc
-${PYSITELIB}/tables/IsDescription.pyo
-${PYSITELIB}/tables/Leaf.py
-${PYSITELIB}/tables/Leaf.pyc
-${PYSITELIB}/tables/Leaf.pyo
-${PYSITELIB}/tables/NetCDF.py
-${PYSITELIB}/tables/NetCDF.pyc
-${PYSITELIB}/tables/NetCDF.pyo
-${PYSITELIB}/tables/Node.py
-${PYSITELIB}/tables/Node.pyc
-${PYSITELIB}/tables/Node.pyo
-${PYSITELIB}/tables/Table.py
-${PYSITELIB}/tables/Table.pyc
-${PYSITELIB}/tables/Table.pyo
-${PYSITELIB}/tables/TableExtension.so
-${PYSITELIB}/tables/UnImplemented.py
-${PYSITELIB}/tables/UnImplemented.pyc
-${PYSITELIB}/tables/UnImplemented.pyo
-${PYSITELIB}/tables/VLArray.py
-${PYSITELIB}/tables/VLArray.pyc
-${PYSITELIB}/tables/VLArray.pyo
+@comment $NetBSD: PLIST,v 1.6 2009/11/15 15:56:55 drochner Exp $
+bin/nctoh52.5
+bin/ptdump2.5
+bin/ptrepack2.5
 ${PYSITELIB}/tables/__init__.py
 ${PYSITELIB}/tables/__init__.pyc
 ${PYSITELIB}/tables/__init__.pyo
 ${PYSITELIB}/tables/_comp_bzip2.so
 ${PYSITELIB}/tables/_comp_lzo.so
-${PYSITELIB}/tables/_comp_ucl.so
-${PYSITELIB}/tables/attributeaccess.py
-${PYSITELIB}/tables/attributeaccess.pyc
-${PYSITELIB}/tables/attributeaccess.pyo
-${PYSITELIB}/tables/constants.py
-${PYSITELIB}/tables/constants.pyc
-${PYSITELIB}/tables/constants.pyo
-${PYSITELIB}/tables/enum.py
-${PYSITELIB}/tables/enum.pyc
-${PYSITELIB}/tables/enum.pyo
+${PYSITELIB}/tables/_conditions_common.py
+${PYSITELIB}/tables/_conditions_common.pyc
+${PYSITELIB}/tables/_conditions_common.pyo
+${PYSITELIB}/tables/_parameters_common.py
+${PYSITELIB}/tables/_parameters_common.pyc
+${PYSITELIB}/tables/_parameters_common.pyo
+${PYSITELIB}/tables/_table_common.py
+${PYSITELIB}/tables/_table_common.pyc
+${PYSITELIB}/tables/_table_common.pyo
+${PYSITELIB}/tables/array.py
+${PYSITELIB}/tables/array.pyc
+${PYSITELIB}/tables/array.pyo
+${PYSITELIB}/tables/atom.py
+${PYSITELIB}/tables/atom.pyc
+${PYSITELIB}/tables/atom.pyo
+${PYSITELIB}/tables/attributeset.py
+${PYSITELIB}/tables/attributeset.pyc
+${PYSITELIB}/tables/attributeset.pyo
+${PYSITELIB}/tables/carray.py
+${PYSITELIB}/tables/carray.pyc
+${PYSITELIB}/tables/carray.pyo
+${PYSITELIB}/tables/conditions.py
+${PYSITELIB}/tables/conditions.pyc
+${PYSITELIB}/tables/conditions.pyo
+${PYSITELIB}/tables/description.py
+${PYSITELIB}/tables/description.pyc
+${PYSITELIB}/tables/description.pyo
+${PYSITELIB}/tables/earray.py
+${PYSITELIB}/tables/earray.pyc
+${PYSITELIB}/tables/earray.pyo
 ${PYSITELIB}/tables/exceptions.py
 ${PYSITELIB}/tables/exceptions.pyc
 ${PYSITELIB}/tables/exceptions.pyo
+${PYSITELIB}/tables/file.py
+${PYSITELIB}/tables/file.pyc
+${PYSITELIB}/tables/file.pyo
+${PYSITELIB}/tables/filters.py
+${PYSITELIB}/tables/filters.pyc
+${PYSITELIB}/tables/filters.pyo
+${PYSITELIB}/tables/flavor.py
+${PYSITELIB}/tables/flavor.pyc
+${PYSITELIB}/tables/flavor.pyo
+${PYSITELIB}/tables/group.py
+${PYSITELIB}/tables/group.pyc
+${PYSITELIB}/tables/group.pyo
 ${PYSITELIB}/tables/hdf5Extension.so
-${PYSITELIB}/tables/lrucache.py
-${PYSITELIB}/tables/lrucache.pyc
-${PYSITELIB}/tables/lrucache.pyo
-${PYSITELIB}/tables/nestedrecords.py
-${PYSITELIB}/tables/nestedrecords.pyc
-${PYSITELIB}/tables/nestedrecords.pyo
-${PYSITELIB}/tables/nodes/FileNode.py
-${PYSITELIB}/tables/nodes/FileNode.pyc
-${PYSITELIB}/tables/nodes/FileNode.pyo
+${PYSITELIB}/tables/leaf.py
+${PYSITELIB}/tables/leaf.pyc
+${PYSITELIB}/tables/leaf.pyo
+${PYSITELIB}/tables/misc/__init__.py
+${PYSITELIB}/tables/misc/__init__.pyc
+${PYSITELIB}/tables/misc/__init__.pyo
+${PYSITELIB}/tables/misc/enum.py
+${PYSITELIB}/tables/misc/enum.pyc
+${PYSITELIB}/tables/misc/enum.pyo
+${PYSITELIB}/tables/misc/lrucache.py
+${PYSITELIB}/tables/misc/lrucache.pyc
+${PYSITELIB}/tables/misc/lrucache.pyo
+${PYSITELIB}/tables/misc/proxydict.py
+${PYSITELIB}/tables/misc/proxydict.pyc
+${PYSITELIB}/tables/misc/proxydict.pyo
+${PYSITELIB}/tables/netcdf3/__init__.py
+${PYSITELIB}/tables/netcdf3/__init__.pyc
+${PYSITELIB}/tables/netcdf3/__init__.pyo
+${PYSITELIB}/tables/netcdf3/scripts/__init__.py
+${PYSITELIB}/tables/netcdf3/scripts/__init__.pyc
+${PYSITELIB}/tables/netcdf3/scripts/__init__.pyo
+${PYSITELIB}/tables/netcdf3/scripts/nctoh5.py
+${PYSITELIB}/tables/netcdf3/scripts/nctoh5.pyc
+${PYSITELIB}/tables/netcdf3/scripts/nctoh5.pyo
+${PYSITELIB}/tables/netcdf3/tests/__init__.py
+${PYSITELIB}/tables/netcdf3/tests/__init__.pyc
+${PYSITELIB}/tables/netcdf3/tests/__init__.pyo
+${PYSITELIB}/tables/netcdf3/tests/test_netcdf3.py
+${PYSITELIB}/tables/netcdf3/tests/test_netcdf3.pyc
+${PYSITELIB}/tables/netcdf3/tests/test_netcdf3.pyo
+${PYSITELIB}/tables/node.py
+${PYSITELIB}/tables/node.pyc
+${PYSITELIB}/tables/node.pyo
 ${PYSITELIB}/tables/nodes/__init__.py
 ${PYSITELIB}/tables/nodes/__init__.pyc
 ${PYSITELIB}/tables/nodes/__init__.pyo
-${PYSITELIB}/tables/nriterators.py
-${PYSITELIB}/tables/nriterators.pyc
-${PYSITELIB}/tables/nriterators.pyo
-${PYSITELIB}/tables/proxydict.py
-${PYSITELIB}/tables/proxydict.pyc
-${PYSITELIB}/tables/proxydict.pyo
+${PYSITELIB}/tables/nodes/filenode.py
+${PYSITELIB}/tables/nodes/filenode.pyc
+${PYSITELIB}/tables/nodes/filenode.pyo
+${PYSITELIB}/tables/nodes/tests/__init__.py
+${PYSITELIB}/tables/nodes/tests/__init__.pyc
+${PYSITELIB}/tables/nodes/tests/__init__.pyo
+${PYSITELIB}/tables/nodes/tests/test_filenode.dat
+${PYSITELIB}/tables/nodes/tests/test_filenode.py
+${PYSITELIB}/tables/nodes/tests/test_filenode.pyc
+${PYSITELIB}/tables/nodes/tests/test_filenode.pyo
+${PYSITELIB}/tables/nodes/tests/test_filenode.xbm
+${PYSITELIB}/tables/nodes/tests/test_filenode_v1.h5
+${PYSITELIB}/tables/nra/__init__.py
+${PYSITELIB}/tables/nra/__init__.pyc
+${PYSITELIB}/tables/nra/__init__.pyo
+${PYSITELIB}/tables/nra/attributeaccess.py
+${PYSITELIB}/tables/nra/attributeaccess.pyc
+${PYSITELIB}/tables/nra/attributeaccess.pyo
+${PYSITELIB}/tables/nra/nestedrecords.py
+${PYSITELIB}/tables/nra/nestedrecords.pyc
+${PYSITELIB}/tables/nra/nestedrecords.pyo
+${PYSITELIB}/tables/nra/nriterators.py
+${PYSITELIB}/tables/nra/nriterators.pyc
+${PYSITELIB}/tables/nra/nriterators.pyo
+${PYSITELIB}/tables/nra/tests/__init__.py
+${PYSITELIB}/tables/nra/tests/__init__.pyc
+${PYSITELIB}/tables/nra/tests/__init__.pyo
+${PYSITELIB}/tables/nra/tests/test_nestedrecords.py
+${PYSITELIB}/tables/nra/tests/test_nestedrecords.pyc
+${PYSITELIB}/tables/nra/tests/test_nestedrecords.pyo
+${PYSITELIB}/tables/nra/tests/test_nriterators.py
+${PYSITELIB}/tables/nra/tests/test_nriterators.pyc
+${PYSITELIB}/tables/nra/tests/test_nriterators.pyo
+${PYSITELIB}/tables/numexpr/__init__.py
+${PYSITELIB}/tables/numexpr/__init__.pyc
+${PYSITELIB}/tables/numexpr/__init__.pyo
+${PYSITELIB}/tables/numexpr/compiler.py
+${PYSITELIB}/tables/numexpr/compiler.pyc
+${PYSITELIB}/tables/numexpr/compiler.pyo
+${PYSITELIB}/tables/numexpr/expressions.py
+${PYSITELIB}/tables/numexpr/expressions.pyc
+${PYSITELIB}/tables/numexpr/expressions.pyo
+${PYSITELIB}/tables/numexpr/info.py
+${PYSITELIB}/tables/numexpr/info.pyc
+${PYSITELIB}/tables/numexpr/info.pyo
+${PYSITELIB}/tables/numexpr/interpreter.so
+${PYSITELIB}/tables/numexpr/setup.py
+${PYSITELIB}/tables/numexpr/setup.pyc
+${PYSITELIB}/tables/numexpr/setup.pyo
+${PYSITELIB}/tables/numexpr/tests/__init__.py
+${PYSITELIB}/tables/numexpr/tests/__init__.pyc
+${PYSITELIB}/tables/numexpr/tests/__init__.pyo
+${PYSITELIB}/tables/numexpr/tests/test_numexpr.py
+${PYSITELIB}/tables/numexpr/tests/test_numexpr.pyc
+${PYSITELIB}/tables/numexpr/tests/test_numexpr.pyo
+${PYSITELIB}/tables/parameters.py
+${PYSITELIB}/tables/parameters.pyc
+${PYSITELIB}/tables/parameters.pyo
+${PYSITELIB}/tables/path.py
+${PYSITELIB}/tables/path.pyc
+${PYSITELIB}/tables/path.pyo
 ${PYSITELIB}/tables/registry.py
 ${PYSITELIB}/tables/registry.pyc
 ${PYSITELIB}/tables/registry.pyo
 ${PYSITELIB}/tables/scripts/__init__.py
 ${PYSITELIB}/tables/scripts/__init__.pyc
 ${PYSITELIB}/tables/scripts/__init__.pyo
-${PYSITELIB}/tables/scripts/nctoh5.py
-${PYSITELIB}/tables/scripts/nctoh5.pyc
-${PYSITELIB}/tables/scripts/nctoh5.pyo
 ${PYSITELIB}/tables/scripts/ptdump.py
 ${PYSITELIB}/tables/scripts/ptdump.pyc
 ${PYSITELIB}/tables/scripts/ptdump.pyo
 ${PYSITELIB}/tables/scripts/ptrepack.py
 ${PYSITELIB}/tables/scripts/ptrepack.pyc
 ${PYSITELIB}/tables/scripts/ptrepack.pyo
+${PYSITELIB}/tables/table.py
+${PYSITELIB}/tables/table.pyc
+${PYSITELIB}/tables/table.pyo
+${PYSITELIB}/tables/tableExtension.so
+${PYSITELIB}/tables/tests/Table2_1_lzo_nrv2e_shuffle.h5
+${PYSITELIB}/tables/tests/Tables_lzo1.h5
+${PYSITELIB}/tables/tests/Tables_lzo1_shuffle.h5
+${PYSITELIB}/tables/tests/Tables_lzo2.h5
+${PYSITELIB}/tables/tests/Tables_lzo2_shuffle.h5
+${PYSITELIB}/tables/tests/__init__.py
+${PYSITELIB}/tables/tests/__init__.pyc
+${PYSITELIB}/tables/tests/__init__.pyo
+${PYSITELIB}/tables/tests/attr-u16.h5
+${PYSITELIB}/tables/tests/check_leaks.py
+${PYSITELIB}/tables/tests/check_leaks.pyc
+${PYSITELIB}/tables/tests/check_leaks.pyo
+${PYSITELIB}/tables/tests/common.py
+${PYSITELIB}/tables/tests/common.pyc
+${PYSITELIB}/tables/tests/common.pyo
+${PYSITELIB}/tables/tests/ex-noattr.h5
+${PYSITELIB}/tables/tests/flavored_vlarrays-format1.6.h5
+${PYSITELIB}/tables/tests/idx-std-1.x.h5
+${PYSITELIB}/tables/tests/indexes_2_0.h5
+${PYSITELIB}/tables/tests/nested-type-with-gaps.h5
+${PYSITELIB}/tables/tests/non-chunked-table.h5
+${PYSITELIB}/tables/tests/old-flavors.h5
+${PYSITELIB}/tables/tests/smpl_SDSextendible.h5
+${PYSITELIB}/tables/tests/smpl_compound_chunked.h5
+${PYSITELIB}/tables/tests/smpl_enum.h5
+${PYSITELIB}/tables/tests/smpl_f64be.h5
+${PYSITELIB}/tables/tests/smpl_f64le.h5
+${PYSITELIB}/tables/tests/smpl_i32be.h5
+${PYSITELIB}/tables/tests/smpl_i32le.h5
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+${PYSITELIB}/tables/tests/smpl_i64le.h5
+${PYSITELIB}/tables/tests/smpl_unsupptype.h5
+${PYSITELIB}/tables/tests/test_Numeric.py
+${PYSITELIB}/tables/tests/test_Numeric.pyc
+${PYSITELIB}/tables/tests/test_Numeric.pyo
+${PYSITELIB}/tables/tests/test_all.py
+${PYSITELIB}/tables/tests/test_all.pyc
+${PYSITELIB}/tables/tests/test_all.pyo
+${PYSITELIB}/tables/tests/test_array.py
+${PYSITELIB}/tables/tests/test_array.pyc
+${PYSITELIB}/tables/tests/test_array.pyo
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+${PYSITELIB}/tables/tests/test_tree.py
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+${PYSITELIB}/tables/tests/test_types.py
+${PYSITELIB}/tables/tests/test_types.pyc
+${PYSITELIB}/tables/tests/test_types.pyo
+${PYSITELIB}/tables/tests/test_vlarray.py
+${PYSITELIB}/tables/tests/test_vlarray.pyc
+${PYSITELIB}/tables/tests/test_vlarray.pyo
+${PYSITELIB}/tables/tests/time-table-vlarray-1_x.h5
+${PYSITELIB}/tables/tests/times-nested-be.h5
+${PYSITELIB}/tables/tests/vlunicode_endian.h5
+${PYSITELIB}/tables/tests/zerodim-attrs-1.3.h5
+${PYSITELIB}/tables/tests/zerodim-attrs-1.4.h5
 ${PYSITELIB}/tables/undoredo.py
 ${PYSITELIB}/tables/undoredo.pyc
 ${PYSITELIB}/tables/undoredo.pyo
+${PYSITELIB}/tables/unimplemented.py
+${PYSITELIB}/tables/unimplemented.pyc
+${PYSITELIB}/tables/unimplemented.pyo
 ${PYSITELIB}/tables/utils.py
 ${PYSITELIB}/tables/utils.pyc
 ${PYSITELIB}/tables/utils.pyo
 ${PYSITELIB}/tables/utilsExtension.so
+${PYSITELIB}/tables/vlarray.py
+${PYSITELIB}/tables/vlarray.pyc
+${PYSITELIB}/tables/vlarray.pyo
diff --git a/math/py-pytables/distinfo b/math/py-pytables/distinfo
index 31aa178c81f..a4d562ef0e9 100644
--- a/math/py-pytables/distinfo
+++ b/math/py-pytables/distinfo
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.6 2006/10/17 14:32:32 drochner Exp $
+$NetBSD: distinfo,v 1.7 2009/11/15 15:56:55 drochner Exp $
 
-SHA1 (pytables-1.3.3.tar.gz) = 1cc49d342eb0bb7dbe239be07812a2a8d325b7b4
-RMD160 (pytables-1.3.3.tar.gz) = 032e0414df575ed81392e7e8e87979ea1d7dd100
-Size (pytables-1.3.3.tar.gz) = 3841630 bytes
-SHA1 (patch-aa) = 6d8aebeb3c7608c5b69e5259dc8f1491889a6cf1
+SHA1 (tables-2.1.2.tar.gz) = 545cc16491d37e2f6b8ce10bc8bdfa559b174e2e
+RMD160 (tables-2.1.2.tar.gz) = 09bfb73e9252baa34aa40274a0b07f6c6cc60d70
+Size (tables-2.1.2.tar.gz) = 4677233 bytes
+SHA1 (patch-aa) = 3cf2812635aaa12e445398243ca765d209fb9cdf
diff --git a/math/py-pytables/patches/patch-aa b/math/py-pytables/patches/patch-aa
index 567d1670f5c..d9e97d7e16b 100644
--- a/math/py-pytables/patches/patch-aa
+++ b/math/py-pytables/patches/patch-aa
@@ -1,13 +1,13 @@
-$NetBSD: patch-aa,v 1.5 2006/10/17 14:32:32 drochner Exp $
+$NetBSD: patch-aa,v 1.6 2009/11/15 15:56:55 drochner Exp $
 
---- setup.py.orig	2006-07-28 10:42:25.000000000 +0200
+--- setup.py.orig	2009-03-05 18:12:19.000000000 +0100
 +++ setup.py
-@@ -409,7 +409,7 @@ else:
-     setuptools_kwargs['packages'] = [
-         'tables', 'tables.nodes', 'tables.scripts']
+@@ -463,7 +463,7 @@ else:
+         'tables.tests', 'tables.numexpr.tests', 'tables.nodes.tests',
+         'tables.netcdf3.tests', 'tables.nra.tests']
      setuptools_kwargs['scripts'] = [
 -        'utils/ptdump', 'utils/ptrepack', 'utils/nctoh5']
 +        'utils/ptdump' + sys.version[0:3], 'utils/ptrepack' + sys.version[0:3], 'utils/nctoh5' + sys.version[0:3]]
- 
- 
- #Having the Python version included in the package name makes managing a
+ # Copy additional data for packages that need it.
+ setuptools_kwargs['package_data'] = {
+     'tables.tests': ['*.h5'],