reinit the tree, so we can have metadata

8 files changed, 392 insertions, 0 deletions

diff --git a/dev-python/pytables/Manifest b/dev-python/pytables/Manifest
new file mode 100644
index 000000000000..3de284b85b74
--- /dev/null
+++ b/dev-python/pytables/Manifest
@@ -0,0 +1,12 @@
+AUX pytables-3.1.1-blosc.patch 418 SHA256 b91909a1e9f2e91b62e24e2afa3d7d686212f39747aa3f84b0cef623a92a75d7 SHA512 fa60a3a5c60faa07b64fa5f0241e8d81a4c86287b86808cd39a5a861f5de91d6c83da7d774c25643e2591e8a04731f10c6b188a6854a9bf4c0bea7a94d51ac35 WHIRLPOOL 2bb4c45564cf91595cc8c8cb8ef131af9d01323dea147b21bb06099a5c197d4532e9928b55d78e20355795f35db67383859dfadb316f510f9645641a8fa601a6
+AUX pytables-3.1.1-cython-backport.patch 2472 SHA256 3c7441ef6cbe36e5cc4e4947af832a9d591db027819b4f2745e932d58bd70511 SHA512 c8f235ab3765410e4c0e488e30e00050d6bbc0f8b6874d4e794fc5edf69ad1877c4290a35c111d44a5626c567bc4fff35213ee6b3005a6bb25d5879489c49a63 WHIRLPOOL 1d5f9eb91af30a1b5e09eb023d3869b37bf983b5a8e1e499559da75a5af55f0ae166f92df4d4966365d1510ad67edd5e6b06a8454ae75d41cad405c7d679696d
+AUX pytables-3.1.1-numpy19-backport.patch 1636 SHA256 9b18bf3ceae99ec4dada2842cb4fc31cfa3dc345103315a6aba233bb8fbe3e36 SHA512 6553229186b6007b67f79c63cf4bcb168f7fe77c62478fcfa29bb27402decb30ec36a2df4f0794bab19d7fb7d77dcd5072caaa88ae2a7aa4025608f610efde75 WHIRLPOOL 73dd5745049571cf4c515feda70f1602fbe6d98b658bc6b6eca030a165be0d3bbd89ca3cb8a8789e8ca0c603b8ff6c8f9a45f75a8c18e70c30e3961ad54f267b
+DIST tables-3.1.1.tar.gz 6715786 SHA256 39b9036376f1185599771c19276f13b5b9119d98f9108f58595745ded3fe2da3 SHA512 b5b2052dd81c4748c5e26c1f61f9f92891f48335b0a553f7602ab11c9029dd673d27b91e24cac0da21a81df0c26dbcd9a438214fa58af1ae831c5f04dfa212a6 WHIRLPOOL 86fd6dc9e12503fdbd23013b75f33a41eadbbac0e6dd5ac9a91476d073195077fc6b3d5ad24b1dd4b4c18ae7ed8abc8ea1708262e52240f4c2c3b1153f8c9e91
+DIST tables-3.3.0.tar.gz 7004337 SHA256 8383ccf02e041a5d55494a09fc5514140b4653055a2732c981b5fd0f7408822c SHA512 e19445f0f5f2530d49ce55f258931babb7b05df2366637ddbc306323a1f75b7f7dcf91d70a8cc1f41b182d4cdd9c83872873168592bdcce7bd5acae9f3274f36 WHIRLPOOL f270f741d6886775cc730fbcb79de215fbbe2d9b7b2b6efc6b5b3fa7d141046e7c69daad140ad7cc533b439bfae801ea0e1567939dc4258e5c3b6a88f27cd86c
+DIST tables-3.4.2.tar.gz 7593471 SHA256 fdbbea4edb6bad0ac0e53fc7bc6970e78e12eef4944aa4146bcdcb573201676c SHA512 8c3bb9113e5082f8b44866b04728a04dae37fbd576c3259309fc305fd4cc0c4f74925557e74f6bd1bd1fc5150d8091648139c4c702e5ed9f53e0ace11c2ac58b WHIRLPOOL 392e117a3ad372ee91a02ee66994f3c03e67b4ae7473f5761e13215ce33084fc3ac8e9e371ca9b59f374066523bcd3ebbced01c49faaa84d4af75a26811ee35f
+EBUILD pytables-3.1.1-r2.ebuild 1609 SHA256 1eeae5da5abad2c87b5dc92e7d7154595297871ca99bdc32dc55187b0ead9c43 SHA512 a0cd26ad7a2191ffe573ec9cd6e327264d2d61690eace3955efc90a244f3f7bf594a987a5c34a9aa8d5a5bf2cddde111004613e917100a01a308440a3c18f702 WHIRLPOOL 428bcfd4932acea979832a8c77868933bebe42943dd4d6104cb9954fdf1df0cf743e52da09fdd46cba7021c9c6c3661bd46a2cce2621cac3ab99e8b2782ba01d
+EBUILD pytables-3.3.0.ebuild 1576 SHA256 4e9576f26e16efd96269f4931d2044f4162998ec38cfbdfc43a86ad593caf76a SHA512 245b0b83df781420beb759ffcd1e66106739e4a56fdc524f1f9ddb0a65c5c91442b17775e123ec474f55a5ad7d6b26993dc4453c2afb8522507f0ec2f66997f6 WHIRLPOOL 408217e74ab64bc82d7da83ad3fd73e3a2aa6f9b5e32f9e9766a324b384c65a13bc6d6265488065c0a0e7672c2419ea91e4b8e600eddf166b48b18cf4fd39f8c
+EBUILD pytables-3.4.2.ebuild 1645 SHA256 e0224efd367f141c2c5f5a766d7b35dac6748689eb14e8f82f5f3e12503dfda7 SHA512 c6d226ba1c1233e6ab02268109fdb363d43e23df114dc9fec407770fd01026f5964c16f29d5e024ec3de371c32af8622f30d460eade6b7e47ffd033f809ea545 WHIRLPOOL f8841e7c8419d27805f12e12ffafe634f7a6ef947bf81710386669a686ba78f428415af194e1279150ad8811ed16bd921335249fee597316032abf6b3c54a8b7
+MISC ChangeLog 4621 SHA256 8137f3d983910823bb53c274beb325b89833e5b90ed02f9b408bd0fe0d0645cb SHA512 13e3a3a86747cfc579867e0adb1bba83d5b03eb708888533559c1c5f33907982a669f582300d07327fae4a909568e2f8875c3f9cca1dec455df7a34f70727889 WHIRLPOOL 256fdfcbdd1837fe8722e4b6b3b5905c3115f36cb25c0e3da6caac79d1f8abbc219ef5f9d6f180362f3afb27b1c2d086430930d9004aa0fbe5b29d92d0aa933b
+MISC ChangeLog-2015 9449 SHA256 68b24a91f265bd48bf296dfe39ec3ce1039decdc2eddb3cfabd02c67afa80819 SHA512 a12596b2df744a8f0d6f7bbd61bfaad8c5f30add4cde27f39d5207a07c1a0ab0cfc6ba9e2b6925ce043f71175c7b7d9d8baf4af547ae2dc8dd791745ebb958f1 WHIRLPOOL c9f2b581bbc177eeb4292f8f65445cfe81fa09a9bfc26dc092e92e06563a8cddc3fb8852f3005d330b18a4d6af38bb1c8c96d30794ac143649d42db5e54c5177
+MISC metadata.xml 894 SHA256 82374f549ee5cdeaa036501a1c952c5e0286a388d2f3ddbf3cff728e036ab6f1 SHA512 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 <antonio.valentino@tiscali.it>
+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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>python@gentoo.org</email>
+    <name>Python</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <longdescription lang="en">
+  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.
+</longdescription>
+  <upstream>
+    <remote-id type="pypi">tables</remote-id>
+  </upstream>
+</pkgmetadata>
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=
+	<sci-libs/hdf5-1.10
+	"
+DEPEND="${RDEPEND}
+	>=dev-python/cython-0.21[${PYTHON_USEDEP}]"
+
+S="${WORKDIR}/${MY_P}"
+
+DOCS=( ANNOUNCE.txt RELEASE_NOTES.txt THANKS )
+
+python_prepare_all() {
+	export HDF5_DIR="${EPREFIX}"/usr
+	rm tables/*.c || die
+	sed \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		-i setup.py || die
+	rm -r c-blosc/{blosc,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-3.4.2.ebuild b/dev-python/pytables/pytables-3.4.2.ebuild
new file mode 100644
index 000000000000..02d1be95e967
--- /dev/null
+++ b/dev-python/pytables/pytables-3.4.2.ebuild
@@ -0,0 +1,76 @@
+# 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=
+"
+DEPEND="${RDEPEND}
+	>=dev-python/cython-0.21[${PYTHON_USEDEP}]
+"
+
+S="${WORKDIR}/${MY_P}"
+
+DOCS=( ANNOUNCE.txt RELEASE_NOTES.txt THANKS )
+
+python_prepare_all() {
+	export HDF5_DIR="${EPREFIX}"/usr
+	rm tables/*.c || die
+	sed -e "s:/usr:${EPREFIX}/usr:g" \
+		-i setup.py || die
+	rm -r c-blosc/{blosc,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
+		docompress -x /usr/share/doc/${PF}/examples
+		docompress -x /usr/share/doc/${PF}/contrib
+
+	fi
+}