commit: 17b7393607ac3b08735d76bce6287d31d4d5f27f Author: Sam James <sam <AT> gentoo <DOT> org> AuthorDate: Mon Apr 3 01:27:48 2023 +0000 Commit: Sam James <sam <AT> gentoo <DOT> org> CommitDate: Mon Apr 3 01:30:33 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=17b73936
dev-python/pytables: make cpuinfo optional py-cpuinfo needs explicit porting to a platform and it's only lightly used in pytables. Apply a patch which I've sent upstream to make it optional and restore keywords accordingly. We add a USE=cpudetection for arches where pytables is known to work. Closes: https://bugs.gentoo.org/894078 Signed-off-by: Sam James <sam <AT> gentoo.org> .../files/pytables-3.8.0-optional-cpuinfo.patch | 66 +++++++++++++++++ dev-python/pytables/metadata.xml | 3 + dev-python/pytables/pytables-3.8.0-r2.ebuild | 82 ++++++++++++++++++++++ profiles/arch/amd64/package.use.mask | 4 ++ profiles/arch/base/package.use.mask | 5 ++ 5 files changed, 160 insertions(+) diff --git a/dev-python/pytables/files/pytables-3.8.0-optional-cpuinfo.patch b/dev-python/pytables/files/pytables-3.8.0-optional-cpuinfo.patch new file mode 100644 index 000000000000..f56854b05289 --- /dev/null +++ b/dev-python/pytables/files/pytables-3.8.0-optional-cpuinfo.patch @@ -0,0 +1,66 @@ +https://github.com/PyTables/PyTables/pull/1013 + +From 557f8c22b772506bfbb9e7eb4d60c0cf2125998b Mon Sep 17 00:00:00 2001 +From: Sam James <s...@gentoo.org> +Date: Mon, 3 Apr 2023 02:07:47 +0100 +Subject: [PATCH] Handle py-cpuinfo not being installed + +Fallback gracefully if py-cpuinfo isn't installed. We already handle this in +setup.py but we need to avoid calling it in leaf.py too. + +py-cpuinfo isn't available on all platforms and PyTables is needed to run +the test suite for some software, so we need to be able to run PyTables +in places where py-cpuinfo isn't yet ported. + +Signed-off-by: Sam James <s...@gentoo.org> +--- a/tables/leaf.py ++++ b/tables/leaf.py +@@ -4,7 +4,10 @@ + import math + + import numpy as np +-import cpuinfo ++try: ++ import cpuinfo ++except ImportError: ++ missing_cpuinfo = True + + from .flavor import (check_flavor, internal_flavor, toarray, + alias_map as flavor_alias_map) +@@ -336,20 +339,21 @@ def _calc_chunkshape(self, expectedrows, rowsize, itemsize): + # Use a decent default value for chunksize + chunksize *= 16 + # Now, go explore the L3 size and try to find a smarter chunksize +- cpu_info = cpuinfo.get_cpu_info() +- if 'l3_cache_size' in cpu_info: +- # In general, is a good idea to set the chunksize equal to L3 +- l3_cache_size = cpu_info['l3_cache_size'] +- # cpuinfo sometimes returns cache sizes as strings (like, +- # "4096 KB"), so refuse the temptation to guess and use the +- # value only when it is an actual int. +- # Also, sometimes cpuinfo does not return a correct L3 size; +- # so in general, enforcing L3 > L2 is a good sanity check. +- l2_cache_size = cpu_info.get('l2_cache_size', "Not found") +- if (type(l3_cache_size) is int and +- type(l2_cache_size) is int and +- l3_cache_size > l2_cache_size): +- chunksize = l3_cache_size ++ if not missing_cpuinfo: ++ cpu_info = cpuinfo.get_cpu_info() ++ if 'l3_cache_size' in cpu_info: ++ # In general, is a good idea to set the chunksize equal to L3 ++ l3_cache_size = cpu_info['l3_cache_size'] ++ # cpuinfo sometimes returns cache sizes as strings (like, ++ # "4096 KB"), so refuse the temptation to guess and use the ++ # value only when it is an actual int. ++ # Also, sometimes cpuinfo does not return a correct L3 size; ++ # so in general, enforcing L3 > L2 is a good sanity check. ++ l2_cache_size = cpu_info.get('l2_cache_size', "Not found") ++ if (type(l3_cache_size) is int and ++ type(l2_cache_size) is int and ++ l3_cache_size > l2_cache_size): ++ chunksize = l3_cache_size + # In Blosc2, the chunksize cannot be larger than 2 GB - BLOSC2_MAX_BUFFERSIZE + if chunksize > 2**31 - 32: + chunksize = 2**31 - 32 + diff --git a/dev-python/pytables/metadata.xml b/dev-python/pytables/metadata.xml index 75a6770d99e4..2fea045e5982 100644 --- a/dev-python/pytables/metadata.xml +++ b/dev-python/pytables/metadata.xml @@ -17,6 +17,9 @@ from Pyrex sources, makes it a fast, yet extremely easy to use tool for interactively save and retrieve large amounts of data. </longdescription> + <use> + <flag name="cpudetection">Enables runtime CPU detection (useful for bindist, compatibility on other CPUs)</flag> + </use> <upstream> <remote-id type="github">PyTables/PyTables</remote-id> <remote-id type="pypi">tables</remote-id> diff --git a/dev-python/pytables/pytables-3.8.0-r2.ebuild b/dev-python/pytables/pytables-3.8.0-r2.ebuild new file mode 100644 index 000000000000..1e479c6bc7d4 --- /dev/null +++ b/dev-python/pytables/pytables-3.8.0-r2.ebuild @@ -0,0 +1,82 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) +PYPI_PN="tables" +PYTHON_REQ_USE="threads(+)" + +inherit distutils-r1 prefix pypi + +DESCRIPTION="Hierarchical datasets for Python" +HOMEPAGE=" + https://www.pytables.org/ + https://github.com/PyTables/PyTables/ + https://pypi.org/project/tables/ +" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~amd64-linux ~x86-linux" +IUSE="+cpudetection examples test" +RESTRICT="!test? ( test )" + +DEPEND=" + app-arch/bzip2:0= + app-arch/lz4:0= + >=app-arch/zstd-1.0.0:= + >=dev-libs/c-blosc-1.11.1:0= + dev-libs/c-blosc2:= + dev-libs/lzo:2= + >=dev-python/numpy-1.19[${PYTHON_USEDEP}] + >=sci-libs/hdf5-1.8.4:= +" +RDEPEND=" + ${DEPEND} + >=dev-python/numexpr-2.6.2[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + cpudetection? ( dev-python/py-cpuinfo[${PYTHON_USEDEP}] ) +" +BDEPEND=" + >=dev-python/cython-0.21[${PYTHON_USEDEP}] + virtual/pkgconfig + cpudetection? ( dev-python/py-cpuinfo[${PYTHON_USEDEP}] ) + test? ( + ${RDEPEND} + ) +" + +python_prepare_all() { + local PATCHES=( + "${FILESDIR}"/${P}-blosc2.patch + "${FILESDIR}"/${P}-optional-cpuinfo.patch + ) + + export PYTABLES_NO_EMBEDDED_LIBS=1 + export USE_PKGCONFIG=TRUE + + rm -r c-blosc/{blosc,internal-complibs} || die + rm tables/libblosc2.so || die + sed -i -e '/blosc2/d' requirements.txt || die + hprefixify -w '/prefixes =/' setup.py + distutils-r1_python_prepare_all +} + +python_compile() { + distutils-r1_python_compile -j1 +} + +python_test() { + cd "${BUILD_DIR}"/lib* || die + "${EPYTHON}" tables/tests/test_all.py -v || die +} + +python_install_all() { + distutils-r1_python_install_all + + if use examples; then + dodoc -r contrib examples + docompress -x /usr/share/doc/${PF}/{contrib,examples} + fi +} diff --git a/profiles/arch/amd64/package.use.mask b/profiles/arch/amd64/package.use.mask index 634a8a2278c5..0e00baae5e9c 100644 --- a/profiles/arch/amd64/package.use.mask +++ b/profiles/arch/amd64/package.use.mask @@ -17,6 +17,10 @@ #--- END OF EXAMPLES --- +# Sam James <s...@gentoo.org> (2023-04-03) +# pytables is available here. +dev-python/pytables -cpudetection + # Yiyang Wu <xgreenlandfor...@gmail.com> (2023-01-27) # AMDGPU enablement depends on dev-libs/rocr-runtime, ~amd64 only # See also: https://bugs.gentoo.org/891499 diff --git a/profiles/arch/base/package.use.mask b/profiles/arch/base/package.use.mask index 228e18bc1d72..9af8d281351a 100644 --- a/profiles/arch/base/package.use.mask +++ b/profiles/arch/base/package.use.mask @@ -1,6 +1,11 @@ # Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 +# Sam James <s...@gentoo.org> (2023-04-03) +# Needs dev-python/py-cpuinfo which is not ported to all of our platforms +# See bug #894078. +dev-python/pytables cpudetection + # Michał Górny <mgo...@gentoo.org> (2023-01-24) # libomptarget is only supported on 64-bit architectures. >=sys-libs/libomp-16.0.0_pre20230124 offload
