From: Martin Reindl <martin@catai.org>
Subject: Re: towards python 3.11 default: math/py-tables, devel/py-lief, www/py-cookies
To: ports@openbsd.org
Date: Thu, 4 Apr 2024 09:03:31 +0200

On Wed, Apr 03, 2024 at 09:54:24PM +0100, Stuart Henderson wrote:
> On 2024/04/03 21:26, Martin Reindl wrote:
> > 
> > graphics/openvdb still requires blosc1. Attached is a port of blosc2, I
> > can update py-tables afterwards.
> 
> Ah great, thanks Martin. Slight tweaks to the CMakeLists in the
> attached ("AND NOT OPENBSD" isn't a thing, but you can do what you
> want and reduce the number of lines touched with 'AND NOT
> CMAKE_SYSTEM_NAME STREQUAL "OpenBSD"'), OK with that.
> 

Looks good, this seems more acceptable to upstream too.

Turns out py-tables still depends on blosc1 AND blosc2, plus py-blosc2 for their
packaging. Or maybe there is a smarter way (py-blosc2 needs py-scikit-build).


Index: Makefile
===================================================================
RCS file: /cvs/ports/math/py-tables/Makefile,v
diff -u -p -u -p -r1.12 Makefile
--- Makefile	25 Nov 2022 19:30:35 -0000	1.12
+++ Makefile	4 Apr 2024 06:54:08 -0000
@@ -1,10 +1,9 @@
 COMMENT=	Python package to manage extremely large amounts of data
 
-MODPY_EGG_VERSION=	3.7.0
+MODPY_EGG_VERSION=	3.9.2
 DISTNAME=		tables-${MODPY_EGG_VERSION}
 PKGNAME=		py-${DISTNAME}
 CATEGORIES=		math
-REVISION=		2
 
 HOMEPAGE=	https://www.pytables.org/
 MAINTAINER=	Martin Reindl <martin@catai.org>
@@ -18,9 +17,11 @@ MODULES=	lang/python
 MODPY_PYBUILD =	setuptools
 MODPY_PI=	Yes
 
-WANTLIB=	pthread ${MODPY_WANTLIB} blosc bz2 hdf5 lzo2
+WANTLIB=	blosc blosc2 bz2 hdf5 lzo2
 
-MODPY_DISTUTILS_BUILDARGS=	--hdf5=${LOCALBASE} \
+MODPY_DISTUTILS_BUILDARGS=	--blosc=${LOCALBASE} \
+				--blosc2=${LOCALBASE} \
+				--hdf5=${LOCALBASE} \
 				--lzo=${LOCALBASE}
 
 CFLAGS+=	-I${LOCALBASE}/include
@@ -29,11 +30,13 @@ LDFLAGS+=	-L${LOCALBASE}/lib
 BUILD_DEPENDS+=	lang/cython${MODPY_FLAVOR} \
 		math/py-numpy${MODPY_FLAVOR} \
 		math/py-oldest-supported-numpy${MODPY_FLAVOR} \
+		sysutils/py-cpuinfo${MODPY_FLAVOR} \
 		sysutils/py-packaging${MODPY_FLAVOR}
 
 LIB_DEPENDS+=	archivers/lzo2 \
 		archivers/bzip2 \
 		archivers/blosc \
+		archivers/blosc2 \
 		math/hdf5
 
 RUN_DEPENDS+=	math/netcdf \
@@ -45,7 +48,7 @@ TEST_DEPENDS=	math/py-numexpr${MODPY_FLA
 FLAVORS =	python3
 FLAVOR =	python3
 
-do-test: fake
+do-test:
 	cd ${WRKDIR} && ${MAKE_ENV} PYTHONPATH=${WRKINST}${MODPY_SITEPKG} \
 		${MODPY_BIN} -c 'import tables ; tables.test()'
 
Index: distinfo
===================================================================
RCS file: /cvs/ports/math/py-tables/distinfo,v
diff -u -p -u -p -r1.2 distinfo
--- distinfo	12 Mar 2022 10:36:06 -0000	1.2
+++ distinfo	4 Apr 2024 06:54:08 -0000
@@ -1,2 +1,2 @@
-SHA256 (tables-3.7.0.tar.gz) = 6SqIetbyqYPlZKaZAt5KdkXDAGn8AavTU+xdolXF4f4=
-SIZE (tables-3.7.0.tar.gz) = 8227955
+SHA256 (tables-3.9.2.tar.gz) = 1HAmPC5QxLfIY1oNmawf8vnnBMJNceX6M8RSnn0K2cM=
+SIZE (tables-3.9.2.tar.gz) = 4683437
Index: patches/patch-pyproject_toml
===================================================================
RCS file: patches/patch-pyproject_toml
diff -N patches/patch-pyproject_toml
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ patches/patch-pyproject_toml	4 Apr 2024 06:54:08 -0000
@@ -0,0 +1,14 @@
+Index: pyproject.toml
+--- pyproject.toml.orig
++++ pyproject.toml
+@@ -9,10 +9,6 @@ requires = [
+     "packaging",
+     "py-cpuinfo",
+     "Cython >=0.29.32",
+-    # Included here for seamless wheel builds.
+-    # Packagers can choose to replace it by externally provided
+-    # c-blosc2 library and headers
+-    "blosc2 >=2.3.0",
+ ]
+ build-backend = "setuptools.build_meta"
+ # build-backend = "mesonpy"  # and replace ``setuptools`` above
Index: patches/patch-requirements_txt
===================================================================
RCS file: patches/patch-requirements_txt
diff -N patches/patch-requirements_txt
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ patches/patch-requirements_txt	4 Apr 2024 06:54:08 -0000
@@ -0,0 +1,8 @@
+Index: requirements.txt
+--- requirements.txt.orig
++++ requirements.txt
+@@ -4,4 +4,3 @@ numpy>=1.19.0
+ numexpr>=2.6.2
+ packaging
+ py-cpuinfo
+-blosc2>=2.3.0
Index: pkg/PLIST
===================================================================
RCS file: /cvs/ports/math/py-tables/pkg/PLIST,v
diff -u -p -u -p -r1.6 PLIST
--- pkg/PLIST	25 Nov 2022 19:30:35 -0000	1.6
+++ pkg/PLIST	4 Apr 2024 06:54:08 -0000
@@ -15,6 +15,8 @@ lib/python${MODPY_VERSION}/site-packages
 ${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/tables/${MODPY_PYCACHE}/
 lib/python${MODPY_VERSION}/site-packages/tables/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/tables/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/tables/${MODPY_PYCACHE}_version.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
+lib/python${MODPY_VERSION}/site-packages/tables/${MODPY_PYCACHE}_version.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/tables/${MODPY_PYCACHE}array.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/tables/${MODPY_PYCACHE}array.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/tables/${MODPY_PYCACHE}atom.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
@@ -71,12 +73,11 @@ lib/python${MODPY_VERSION}/site-packages
 lib/python${MODPY_VERSION}/site-packages/tables/${MODPY_PYCACHE}utils.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/tables/${MODPY_PYCACHE}vlarray.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/tables/${MODPY_PYCACHE}vlarray.${MODPY_PYC_MAGIC_TAG}pyc
-lib/python${MODPY_VERSION}/site-packages/tables/_comp_bzip2.c
 @so lib/python${MODPY_VERSION}/site-packages/tables/_comp_bzip2.${MODPY_PYC_MAGIC_TAG}so
 lib/python${MODPY_VERSION}/site-packages/tables/_comp_bzip2.pyx
-lib/python${MODPY_VERSION}/site-packages/tables/_comp_lzo.c
 @so lib/python${MODPY_VERSION}/site-packages/tables/_comp_lzo.${MODPY_PYC_MAGIC_TAG}so
 lib/python${MODPY_VERSION}/site-packages/tables/_comp_lzo.pyx
+lib/python${MODPY_VERSION}/site-packages/tables/_version.py
 lib/python${MODPY_VERSION}/site-packages/tables/array.py
 lib/python${MODPY_VERSION}/site-packages/tables/atom.py
 lib/python${MODPY_VERSION}/site-packages/tables/attributeset.py
@@ -91,22 +92,18 @@ lib/python${MODPY_VERSION}/site-packages
 lib/python${MODPY_VERSION}/site-packages/tables/filters.py
 lib/python${MODPY_VERSION}/site-packages/tables/flavor.py
 lib/python${MODPY_VERSION}/site-packages/tables/group.py
-lib/python${MODPY_VERSION}/site-packages/tables/hdf5extension.c
 @so lib/python${MODPY_VERSION}/site-packages/tables/hdf5extension.${MODPY_PYC_MAGIC_TAG}so
 lib/python${MODPY_VERSION}/site-packages/tables/hdf5extension.pxd
 lib/python${MODPY_VERSION}/site-packages/tables/hdf5extension.pyx
 lib/python${MODPY_VERSION}/site-packages/tables/idxutils.py
 lib/python${MODPY_VERSION}/site-packages/tables/index.py
 lib/python${MODPY_VERSION}/site-packages/tables/indexes.py
-lib/python${MODPY_VERSION}/site-packages/tables/indexesextension.c
 @so lib/python${MODPY_VERSION}/site-packages/tables/indexesextension.${MODPY_PYC_MAGIC_TAG}so
 lib/python${MODPY_VERSION}/site-packages/tables/indexesextension.pyx
 lib/python${MODPY_VERSION}/site-packages/tables/leaf.py
 lib/python${MODPY_VERSION}/site-packages/tables/link.py
-lib/python${MODPY_VERSION}/site-packages/tables/linkextension.c
 @so lib/python${MODPY_VERSION}/site-packages/tables/linkextension.${MODPY_PYC_MAGIC_TAG}so
 lib/python${MODPY_VERSION}/site-packages/tables/linkextension.pyx
-lib/python${MODPY_VERSION}/site-packages/tables/lrucacheextension.c
 @so lib/python${MODPY_VERSION}/site-packages/tables/lrucacheextension.${MODPY_PYC_MAGIC_TAG}so
 lib/python${MODPY_VERSION}/site-packages/tables/lrucacheextension.pxd
 lib/python${MODPY_VERSION}/site-packages/tables/lrucacheextension.pyx
@@ -163,7 +160,6 @@ lib/python${MODPY_VERSION}/site-packages
 lib/python${MODPY_VERSION}/site-packages/tables/scripts/ptrepack.py
 lib/python${MODPY_VERSION}/site-packages/tables/scripts/pttree.py
 lib/python${MODPY_VERSION}/site-packages/tables/table.py
-lib/python${MODPY_VERSION}/site-packages/tables/tableextension.c
 @so lib/python${MODPY_VERSION}/site-packages/tables/tableextension.${MODPY_PYC_MAGIC_TAG}so
 lib/python${MODPY_VERSION}/site-packages/tables/tableextension.pyx
 lib/python${MODPY_VERSION}/site-packages/tables/tests/
@@ -216,6 +212,8 @@ lib/python${MODPY_VERSION}/site-packages
 lib/python${MODPY_VERSION}/site-packages/tables/tests/${MODPY_PYCACHE}test_indexes.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/tables/tests/${MODPY_PYCACHE}test_indexvalues.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/tables/tests/${MODPY_PYCACHE}test_indexvalues.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/tables/tests/${MODPY_PYCACHE}test_large_tables.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
+lib/python${MODPY_VERSION}/site-packages/tables/tests/${MODPY_PYCACHE}test_large_tables.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/tables/tests/${MODPY_PYCACHE}test_links.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/tables/tests/${MODPY_PYCACHE}test_links.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/tables/tests/${MODPY_PYCACHE}test_lists.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
@@ -246,11 +244,11 @@ lib/python${MODPY_VERSION}/site-packages
 lib/python${MODPY_VERSION}/site-packages/tables/tests/${MODPY_PYCACHE}test_vlarray.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/tables/tests/array_mdatom.h5
 lib/python${MODPY_VERSION}/site-packages/tables/tests/attr-u16.h5
+lib/python${MODPY_VERSION}/site-packages/tables/tests/b2nd-no-chunkshape.h5
 lib/python${MODPY_VERSION}/site-packages/tables/tests/blosc_bigendian.h5
 lib/python${MODPY_VERSION}/site-packages/tables/tests/bug-idx.h5
 lib/python${MODPY_VERSION}/site-packages/tables/tests/check_leaks.py
 lib/python${MODPY_VERSION}/site-packages/tables/tests/common.py
-lib/python${MODPY_VERSION}/site-packages/tables/tests/create-nested-type.c
 lib/python${MODPY_VERSION}/site-packages/tables/tests/create_backcompat_indexes.py
 lib/python${MODPY_VERSION}/site-packages/tables/tests/elink.h5
 lib/python${MODPY_VERSION}/site-packages/tables/tests/elink2.h5
@@ -299,6 +297,7 @@ lib/python${MODPY_VERSION}/site-packages
 lib/python${MODPY_VERSION}/site-packages/tables/tests/test_index_backcompat.py
 lib/python${MODPY_VERSION}/site-packages/tables/tests/test_indexes.py
 lib/python${MODPY_VERSION}/site-packages/tables/tests/test_indexvalues.py
+lib/python${MODPY_VERSION}/site-packages/tables/tests/test_large_tables.py
 lib/python${MODPY_VERSION}/site-packages/tables/tests/test_links.py
 lib/python${MODPY_VERSION}/site-packages/tables/tests/test_lists.py
 lib/python${MODPY_VERSION}/site-packages/tables/tests/test_nestedtypes.py
@@ -325,7 +324,6 @@ lib/python${MODPY_VERSION}/site-packages
 lib/python${MODPY_VERSION}/site-packages/tables/undoredo.py
 lib/python${MODPY_VERSION}/site-packages/tables/unimplemented.py
 lib/python${MODPY_VERSION}/site-packages/tables/utils.py
-lib/python${MODPY_VERSION}/site-packages/tables/utilsextension.c
 @so lib/python${MODPY_VERSION}/site-packages/tables/utilsextension.${MODPY_PYC_MAGIC_TAG}so
 lib/python${MODPY_VERSION}/site-packages/tables/utilsextension.pxd
 lib/python${MODPY_VERSION}/site-packages/tables/utilsextension.pyx