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.

5 files changed, 27 insertions, 90 deletions

diff --git a/math/py-pytables/Makefile b/math/py-pytables/Makefile
index ce26dc9255e..89f23e903c6 100644
--- a/math/py-pytables/Makefile
+++ b/math/py-pytables/Makefile
@@ -1,29 +1,25 @@
-# $NetBSD: Makefile,v 1.35 2016/08/28 15:48:33 wiz Exp $
+# $NetBSD: Makefile,v 1.36 2017/05/21 07:52:55 adam Exp $
 
-DISTNAME=		tables-3.2.3
-PKGNAME=		${PYPKGPREFIX}-py${DISTNAME}
-PKGREVISION=		1
-CATEGORIES=		math python
-MASTER_SITES=		${MASTER_SITE_GITHUB:=PyTables/}
-GITHUB_PROJECT=		PyTables
-GITHUB_TAG=		v.${PKGVERSION_NOREV}
+DISTNAME=	tables-3.4.2
+PKGNAME=	${PYPKGPREFIX}-py${DISTNAME}
+CATEGORIES=	math python
+MASTER_SITES=	${MASTER_SITE_PYPI:=t/tables/}
 
-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}
+MAINTAINER=	pkgsrc-users@NetBSD.org
+HOMEPAGE=	http://www.pytables.org/
+COMMENT=	Database package for large amounts of data
+LICENSE=	modified-bsd
 
+PYSETUPBUILDARGS+=	--bzip2=${BUILDLINK_PREFIX.bzip2}
 PYSETUPBUILDARGS+=	--hdf5=${BUILDLINK_PREFIX.hdf5}
+PYSETUPBUILDARGS+=	--lzo=${BUILDLINK_PREFIX.lzo}
 PYSETUPINSTALLARGS=	${PYSETUPBUILDARGS}
 
-DEPENDS+=		${PYPKGPREFIX}-numexpr>=2.0:../../math/py-numexpr
+DEPENDS+=	${PYPKGPREFIX}-cython-[0-9]*:../../devel/py-cython
+DEPENDS+=	${PYPKGPREFIX}-numexpr>=2.0:../../math/py-numexpr
 
 USE_LANGUAGES=		c c++
 
-.include "options.mk"
-
 post-install:
 	cd ${DESTDIR}${PREFIX}/bin && \
 		mv pt2to3 pt2to3${PYVERSSUFFIX} && \
@@ -34,11 +30,10 @@ post-install:
 do-test:
 	(cd ${WRKSRC}/tables/tests && ${PYTHONBIN} test_all.py)
 
-.include "../../lang/python/distutils.mk"
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../archivers/lzo/buildlink3.mk"
 .include "../../devel/hdf5/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
-.include "../../archivers/bzip2/buildlink3.mk"
 .include "../../math/py-numpy/buildlink3.mk"
-BUILDLINK_API_DEPENDS.pycython+=	${PYPKGPREFIX}-cython>=0.21
-.include "../../devel/py-cython/buildlink3.mk"
+.include "../../lang/python/distutils.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/math/py-pytables/PLIST b/math/py-pytables/PLIST
index 84a79a5fd15..c2322100da1 100644
--- a/math/py-pytables/PLIST
+++ b/math/py-pytables/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.14 2016/08/18 20:30:02 wiz Exp $
+@comment $NetBSD: PLIST,v 1.15 2017/05/21 07:52:55 adam Exp $
 bin/pt2to3${PYVERSSUFFIX}
 bin/ptdump${PYVERSSUFFIX}
 bin/ptrepack${PYVERSSUFFIX}
@@ -15,9 +15,6 @@ ${PYSITELIB}/tables/__init__.pyc
 ${PYSITELIB}/tables/__init__.pyo
 ${PYSITELIB}/tables/_comp_bzip2.so
 ${PYSITELIB}/tables/_comp_lzo.so
-${PYSITELIB}/tables/_past.py
-${PYSITELIB}/tables/_past.pyc
-${PYSITELIB}/tables/_past.pyo
 ${PYSITELIB}/tables/array.py
 ${PYSITELIB}/tables/array.pyc
 ${PYSITELIB}/tables/array.pyo
@@ -57,9 +54,6 @@ ${PYSITELIB}/tables/flavor.pyo
 ${PYSITELIB}/tables/group.py
 ${PYSITELIB}/tables/group.pyc
 ${PYSITELIB}/tables/group.pyo
-${PYSITELIB}/tables/hdf5Extension.py
-${PYSITELIB}/tables/hdf5Extension.pyc
-${PYSITELIB}/tables/hdf5Extension.pyo
 ${PYSITELIB}/tables/hdf5extension.so
 ${PYSITELIB}/tables/idxutils.py
 ${PYSITELIB}/tables/idxutils.pyc
@@ -70,9 +64,6 @@ ${PYSITELIB}/tables/index.pyo
 ${PYSITELIB}/tables/indexes.py
 ${PYSITELIB}/tables/indexes.pyc
 ${PYSITELIB}/tables/indexes.pyo
-${PYSITELIB}/tables/indexesExtension.py
-${PYSITELIB}/tables/indexesExtension.pyc
-${PYSITELIB}/tables/indexesExtension.pyo
 ${PYSITELIB}/tables/indexesextension.so
 ${PYSITELIB}/tables/leaf.py
 ${PYSITELIB}/tables/leaf.pyc
@@ -80,13 +71,7 @@ ${PYSITELIB}/tables/leaf.pyo
 ${PYSITELIB}/tables/link.py
 ${PYSITELIB}/tables/link.pyc
 ${PYSITELIB}/tables/link.pyo
-${PYSITELIB}/tables/linkExtension.py
-${PYSITELIB}/tables/linkExtension.pyc
-${PYSITELIB}/tables/linkExtension.pyo
 ${PYSITELIB}/tables/linkextension.so
-${PYSITELIB}/tables/lrucacheExtension.py
-${PYSITELIB}/tables/lrucacheExtension.pyc
-${PYSITELIB}/tables/lrucacheExtension.pyo
 ${PYSITELIB}/tables/lrucacheextension.so
 ${PYSITELIB}/tables/misc/__init__.py
 ${PYSITELIB}/tables/misc/__init__.pyc
@@ -145,9 +130,6 @@ ${PYSITELIB}/tables/scripts/pttree.pyo
 ${PYSITELIB}/tables/table.py
 ${PYSITELIB}/tables/table.pyc
 ${PYSITELIB}/tables/table.pyo
-${PYSITELIB}/tables/tableExtension.py
-${PYSITELIB}/tables/tableExtension.pyc
-${PYSITELIB}/tables/tableExtension.pyo
 ${PYSITELIB}/tables/tableextension.so
 ${PYSITELIB}/tables/tests/Table2_1_lzo_nrv2e_shuffle.h5
 ${PYSITELIB}/tables/tests/Tables_lzo1.h5
@@ -264,6 +246,8 @@ ${PYSITELIB}/tables/tests/test_numpy.pyo
 ${PYSITELIB}/tables/tests/test_queries.py
 ${PYSITELIB}/tables/tests/test_queries.pyc
 ${PYSITELIB}/tables/tests/test_queries.pyo
+${PYSITELIB}/tables/tests/test_ref_array1.mat
+${PYSITELIB}/tables/tests/test_ref_array2.mat
 ${PYSITELIB}/tables/tests/test_szip.h5
 ${PYSITELIB}/tables/tests/test_tables.py
 ${PYSITELIB}/tables/tests/test_tables.pyc
@@ -280,6 +264,9 @@ ${PYSITELIB}/tables/tests/test_tree.pyo
 ${PYSITELIB}/tables/tests/test_types.py
 ${PYSITELIB}/tables/tests/test_types.pyc
 ${PYSITELIB}/tables/tests/test_types.pyo
+${PYSITELIB}/tables/tests/test_utils.py
+${PYSITELIB}/tables/tests/test_utils.pyc
+${PYSITELIB}/tables/tests/test_utils.pyo
 ${PYSITELIB}/tables/tests/test_vlarray.py
 ${PYSITELIB}/tables/tests/test_vlarray.pyc
 ${PYSITELIB}/tables/tests/test_vlarray.pyo
@@ -298,9 +285,6 @@ ${PYSITELIB}/tables/unimplemented.pyo
 ${PYSITELIB}/tables/utils.py
 ${PYSITELIB}/tables/utils.pyc
 ${PYSITELIB}/tables/utils.pyo
-${PYSITELIB}/tables/utilsExtension.py
-${PYSITELIB}/tables/utilsExtension.pyc
-${PYSITELIB}/tables/utilsExtension.pyo
 ${PYSITELIB}/tables/utilsextension.so
 ${PYSITELIB}/tables/vlarray.py
 ${PYSITELIB}/tables/vlarray.pyc
diff --git a/math/py-pytables/distinfo b/math/py-pytables/distinfo
index 9a4bbddb349..3e9f5b4d0e6 100644
--- a/math/py-pytables/distinfo
+++ b/math/py-pytables/distinfo
@@ -1,7 +1,6 @@
-$NetBSD: distinfo,v 1.16 2016/11/03 00:07:52 maya Exp $
+$NetBSD: distinfo,v 1.17 2017/05/21 07:52:55 adam Exp $
 
-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-setup.py) = 51e92744674fbc8b64e3dc150fcf9927efebc821
+SHA1 (tables-3.4.2.tar.gz) = ebc3cb44eac73f6efaf5c16d6c09dfee7249a470
+RMD160 (tables-3.4.2.tar.gz) = bf652291d53a7a2078be2f774f0fe67dda5eb1cc
+SHA512 (tables-3.4.2.tar.gz) = 8c3bb9113e5082f8b44866b04728a04dae37fbd576c3259309fc305fd4cc0c4f74925557e74f6bd1bd1fc5150d8091648139c4c702e5ed9f53e0ace11c2ac58b
+Size (tables-3.4.2.tar.gz) = 7593471 bytes
diff --git a/math/py-pytables/options.mk b/math/py-pytables/options.mk
deleted file mode 100644
index 5d88d4f7a0a..00000000000
--- a/math/py-pytables/options.mk
+++ /dev/null
@@ -1,13 +0,0 @@
-# $NetBSD: options.mk,v 1.1 2014/01/21 16:32:42 wiz Exp $
-
-PKG_OPTIONS_VAR=	PKG_OPTIONS.pytables
-PKG_SUPPORTED_OPTIONS=	lzo
-
-.include "../../mk/bsd.options.mk"
-
-.if !empty(PKG_OPTIONS:Mlzo)
-PYSETUPBUILDARGS+=	--lzo=${BUILDLINK_PREFIX.lzo}
-.include "../../archivers/lzo/buildlink3.mk"
-.else
-PYSETUPBUILDARGS+=	--lzo=XXX
-.endif
diff --git a/math/py-pytables/patches/patch-setup.py b/math/py-pytables/patches/patch-setup.py
deleted file mode 100644
index 03702b9f8ec..00000000000
--- a/math/py-pytables/patches/patch-setup.py
+++ /dev/null
@@ -1,28 +0,0 @@
-$NetBSD: patch-setup.py,v 1.3 2016/08/18 20:30:02 wiz Exp $
-
---- setup.py.orig	2016-07-03 11:46:48.000000000 +0000
-+++ setup.py
-@@ -793,23 +793,6 @@ if 'BLOSC' not in optional_libs:
-         finally:
-             os.remove(fd.name)
- 
--    # Detection code for SSE2/AVX2 only works for gcc/clang, not for MSVC yet
--    # SSE2
--    if ('sse2' in cpu_info['flags'] and
--        compiler_has_flags(compiler, ["-msse2"])):
--        print('SSE2 detected')
--        CFLAGS.append('-DSHUFFLE_SSE2_ENABLED')
--        CFLAGS.append('-msse2')
--        blosc_sources += [f for f in glob.glob('c-blosc/blosc/*.c')
--                          if 'sse2' in f]
--    # AVX2
--    if ('avx2' in cpu_info['flags'] and
--        compiler_has_flags(compiler, ["-mavx2"])):
--        print('AVX2 detected')
--        CFLAGS.append('-DSHUFFLE_AVX2_ENABLED')
--        CFLAGS.append('-mavx2')
--        blosc_sources += [f for f in glob.glob('c-blosc/blosc/*.c')
--                          if 'avx2' in f]
- else:
-     ADDLIBS += ['blosc']
-