From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- dev-python/pytables/Manifest | 12 ++++ .../pytables/files/pytables-3.1.1-blosc.patch | 16 +++++ .../files/pytables-3.1.1-cython-backport.patch | 65 ++++++++++++++++++ .../files/pytables-3.1.1-numpy19-backport.patch | 51 +++++++++++++++ dev-python/pytables/metadata.xml | 23 +++++++ dev-python/pytables/pytables-3.1.1-r2.ebuild | 75 +++++++++++++++++++++ dev-python/pytables/pytables-3.3.0.ebuild | 74 +++++++++++++++++++++ dev-python/pytables/pytables-3.4.2.ebuild | 76 ++++++++++++++++++++++ 8 files changed, 392 insertions(+) create mode 100644 dev-python/pytables/Manifest create mode 100644 dev-python/pytables/files/pytables-3.1.1-blosc.patch create mode 100644 dev-python/pytables/files/pytables-3.1.1-cython-backport.patch create mode 100644 dev-python/pytables/files/pytables-3.1.1-numpy19-backport.patch create mode 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88dd752e6014f6f133b5df7db6c2aafce0b9da8cdbc057493916dbfbe1da4bf52e0ed43d570d68035fc8f12302794a381a54f5b07b9726b52601724163bc672c WHIRLPOOL 473a4697f2acaa2421863bb928b724ab6e70b6558c3479eda4d12e903eb78f7c97ad113d5883e070ccf7bdb331b67965969d116f76441b715cbb7dab5136b573 diff --git a/dev-python/pytables/files/pytables-3.1.1-blosc.patch b/dev-python/pytables/files/pytables-3.1.1-blosc.patch new file mode 100644 index 000000000000..3a4ba18e5e73 --- /dev/null +++ b/dev-python/pytables/files/pytables-3.1.1-blosc.patch @@ -0,0 +1,16 @@ + setup.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/setup.py b/setup.py +index 2c0c126..1448eb1 100755 +--- a/setup.py ++++ b/setup.py +@@ -768,7 +768,7 @@ if 'BLOSC' not in optional_libs: + print("Setting compiler flag '-msse2'") + CFLAGS.append("-msse2") + else: +- ADDLIBS += ['blosc'] ++ ADDLIBS += ['blosc', 'blosc_filter'] + + + utilsExtension_libs = LIBS + ADDLIBS diff --git a/dev-python/pytables/files/pytables-3.1.1-cython-backport.patch b/dev-python/pytables/files/pytables-3.1.1-cython-backport.patch new file mode 100644 index 000000000000..7db41d2e1a62 --- /dev/null +++ b/dev-python/pytables/files/pytables-3.1.1-cython-backport.patch @@ -0,0 +1,65 @@ + setup.py | 13 +++++++------ + tables/req_versions.py | 2 +- + 2 files changed, 8 insertions(+), 7 deletions(-) + +diff --git a/setup.py b/setup.py +index 0f2f3f7..52cda49 100755 +--- a/setup.py ++++ b/setup.py +@@ -25,6 +25,7 @@ from distutils.core import Extension + from distutils.dep_util import newer + from distutils.util import convert_path + from distutils.ccompiler import new_compiler ++from distutils.version import LooseVersion + + cmdclass = {} + setuptools_kwargs = {} +@@ -106,7 +107,7 @@ def check_import(pkgname, pkgver): + "You need %(pkgname)s %(pkgver)s or greater to run PyTables!" + % {'pkgname': pkgname, 'pkgver': pkgver}) + else: +- if mod.__version__ < pkgver: ++ if mod.__version__ < LooseVersion(pkgver): + exit_with_error( + "You need %(pkgname)s %(pkgver)s or greater to run PyTables!" + % {'pkgname': pkgname, 'pkgver': pkgver}) +@@ -122,21 +123,21 @@ if not has_setuptools: + + # Check if Cython is installed or not (requisite) + try: ++ from Cython import __version__ as cython_version + from Cython.Distutils import build_ext +- from Cython.Compiler.Main import Version + cmdclass['build_ext'] = build_ext + except ImportError: + exit_with_error( + "You need %(pkgname)s %(pkgver)s or greater to compile PyTables!" + % {'pkgname': 'Cython', 'pkgver': min_cython_version}) + +-if Version.version < min_cython_version: ++if LooseVersion(cython_version) < min_cython_version: + exit_with_error( +- "At least Cython %s is needed so as to generate extensions!" +- % (min_cython_version)) ++ "You need %(pkgname)s %(pkgver)s or greater to run PyTables!" ++ % {'pkgname': 'Cython', 'pkgver': min_cython_version}) + else: + print("* Found %(pkgname)s %(pkgver)s package installed." +- % {'pkgname': 'Cython', 'pkgver': Version.version}) ++ % {'pkgname': 'Cython', 'pkgver': cython_version}) + + VERSION = open('VERSION').read().strip() + +diff --git a/tables/req_versions.py b/tables/req_versions.py +index 2c9ca01..bd498c3 100644 +--- a/tables/req_versions.py ++++ b/tables/req_versions.py +@@ -17,7 +17,7 @@ + # Minimum recommended versions for mandatory packages + min_numpy_version = '1.4.1' + min_numexpr_version = '2.0.0' +-min_cython_version = '0.13' ++min_cython_version = '0.14' + + # The THG team has decided to fix an API inconsistency in the definition + # of the H5Z_class_t structure in version 1.8.3 diff --git a/dev-python/pytables/files/pytables-3.1.1-numpy19-backport.patch b/dev-python/pytables/files/pytables-3.1.1-numpy19-backport.patch new file mode 100644 index 000000000000..c2f0c2280f01 --- /dev/null +++ b/dev-python/pytables/files/pytables-3.1.1-numpy19-backport.patch @@ -0,0 +1,51 @@ +From 854d5798ca9fd78c00e18710de2e93202f675f3e Mon Sep 17 00:00:00 2001 +From: Antonio Valentino +Date: Sun, 6 Jul 2014 21:21:39 +0200 +Subject: [PATCH] Fix a compatibility problem with numpy 1.9 (close: #362) + +--- + RELEASE_NOTES.txt | 6 ++++++ + tables/table.py | 6 +++++- + 2 files changed, 11 insertions(+), 1 deletion(-) + +diff --git a/RELEASE_NOTES.txt b/RELEASE_NOTES.txt +index f219eb3..1da20e2 100644 +--- a/RELEASE_NOTES.txt ++++ b/RELEASE_NOTES.txt +@@ -19,6 +19,12 @@ Improvements + requiring strict access alignment. + + ++Bugs fixed ++---------- ++ ++- Fixed compatibitily problems with numpy 1.9 (closes :issue:`362`) ++ ++ + Changes from 3.1.0 to 3.1.1 + =========================== + +diff --git a/tables/table.py b/tables/table.py +index 235f599..ffe8fd6 100644 +--- a/tables/table.py ++++ b/tables/table.py +@@ -3406,6 +3406,10 @@ def _getindex(self): + associated with this column (None if the column is not + indexed).""") + ++ @lazyattr ++ def _itemtype(self): ++ return self.descr._v_dtypes[self.name] ++ + def _getshape(self): + return (self.table.nrows,) + self.descr._v_dtypes[self.name].shape + +@@ -3529,7 +3533,7 @@ def __iter__(self): + table = self.table + itemsize = self.dtype.itemsize + nrowsinbuf = table._v_file.params['IO_BUFFER_SIZE'] // itemsize +- buf = numpy.empty((nrowsinbuf, ), self.dtype) ++ buf = numpy.empty((nrowsinbuf, ), self._itemtype) + max_row = len(self) + for start_row in xrange(0, len(self), nrowsinbuf): + end_row = min(start_row + nrowsinbuf, max_row) diff --git a/dev-python/pytables/metadata.xml b/dev-python/pytables/metadata.xml new file mode 100644 index 000000000000..7eafceceedf5 --- /dev/null +++ b/dev-python/pytables/metadata.xml @@ -0,0 +1,23 @@ + + + + + python@gentoo.org + Python + + + sci@gentoo.org + Gentoo Science Project + + + PyTables is a hierarchical database package designed to efficently + manage very large amounts of data. PyTables is built on top of the + HDF5 library and the NumPy package. It features an object-oriented + interface that, combined with natural naming and C-code generated + from Pyrex sources, makes it a fast, yet extremely easy to use tool + for interactively save and retrieve large amounts of data. + + + tables + + diff --git a/dev-python/pytables/pytables-3.1.1-r2.ebuild b/dev-python/pytables/pytables-3.1.1-r2.ebuild new file mode 100644 index 000000000000..f22a4f0c61e9 --- /dev/null +++ b/dev-python/pytables/pytables-3.1.1-r2.ebuild @@ -0,0 +1,75 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) +PYTHON_REQ_USE="threads(+)" + +MY_PN=tables +MY_P=${MY_PN}-${PV} + +inherit distutils-r1 + +DESCRIPTION="Hierarchical datasets for Python" +HOMEPAGE="http://www.pytables.org/" +SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz" + +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +LICENSE="BSD" +IUSE="doc examples" + +RDEPEND=" + app-arch/bzip2:0= + dev-libs/c-blosc:0=[hdf5] + dev-libs/lzo:2= + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/numexpr[${PYTHON_USEDEP}] + sci-libs/hdf5:0=" +DEPEND="${RDEPEND} + >=dev-python/cython-0.14[${PYTHON_USEDEP}]" + +S="${WORKDIR}/${MY_P}" + +DOCS=( ANNOUNCE.txt RELEASE_NOTES.txt THANKS ) + +PATCHES=( + "${FILESDIR}"/${P}-cython-backport.patch + "${FILESDIR}"/${P}-numpy19-backport.patch + "${FILESDIR}"/${P}-blosc.patch + ) + +python_prepare_all() { + export HDF5_DIR="${EPREFIX}"/usr + sed \ + -e "s:/usr:${EPREFIX}/usr:g" \ + -e 's:"c-blosc/hdf5/blosc_filter.c"::g' \ + -i setup.py || die + rm -r c-blosc/{blosc,hdf5,internal-complibs} || die + distutils-r1_python_prepare_all +} + +python_compile() { + python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing" + distutils-r1_python_compile +} + +python_test() { + cd "${BUILD_DIR}"/lib* || die + ${EPYTHON} tables/tests/test_all.py || die +} + +python_install_all() { + if use doc; then + HTML_DOCS=( doc/html/. ) + DOCS+=( doc/scripts ) + fi + distutils-r1_python_install_all + + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + doins -r contrib + fi +} diff --git a/dev-python/pytables/pytables-3.3.0.ebuild b/dev-python/pytables/pytables-3.3.0.ebuild new file mode 100644 index 000000000000..cb23edbefc05 --- /dev/null +++ b/dev-python/pytables/pytables-3.3.0.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) +PYTHON_REQ_USE="threads(+)" + +MY_PN=tables +MY_P=${MY_PN}-${PV} + +inherit distutils-r1 + +DESCRIPTION="Hierarchical datasets for Python" +HOMEPAGE="http://www.pytables.org/" +SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz" + +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +LICENSE="BSD" +IUSE="doc examples" + +RDEPEND=" + app-arch/bzip2:0= + app-arch/lz4:0= + >=app-arch/zstd-1.0.0 + >=dev-libs/c-blosc-1.11.1:0= + dev-libs/lzo:2= + >=dev-python/numpy-1.8.1[${PYTHON_USEDEP}] + >=dev-python/numexpr-2.5.2[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + >=sci-libs/hdf5-1.8.15:0= +