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