proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

dev-python/pytables/Manifest

@@ -0,0 +1,2 @@
+DIST tables-3.1.1.tar.gz 6715786 SHA256 39b9036376f1185599771c19276f13b5b9119d98f9108f58595745ded3fe2da3 SHA512 b5b2052dd81c4748c5e26c1f61f9f92891f48335b0a553f7602ab11c9029dd673d27b91e24cac0da21a81df0c26dbcd9a438214fa58af1ae831c5f04dfa212a6 WHIRLPOOL 86fd6dc9e12503fdbd23013b75f33a41eadbbac0e6dd5ac9a91476d073195077fc6b3d5ad24b1dd4b4c18ae7ed8abc8ea1708262e52240f4c2c3b1153f8c9e91
+DIST tables-3.2.0.tar.gz 7039718 SHA256 60980e44676bfe463cdd2582ecdacc0b0763b259477015e866f8af72b4cdba44 SHA512 6ef7925bafbec04a3f581d13e9cc266b9b68b11dce27cf28c501dbbc538d74ddcfa15cbe97fa69fb793911cc6dbf3112f503b29c6e4e3e7631a6761cc1303253 WHIRLPOOL 412ada055b81fd7409b67288bc2bcf9ed527c9c42dbdd75c52ce7287f53ed12322b8b4423c9fab0aba98e0f12a8764a45316104567c193b469a84fdda3cbfc30

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

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

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)

dev-python/pytables/files/pytables-3.2.0-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:
+             CFLAGS.append(ff)
+             break
+ else:
+-    ADDLIBS += ['blosc']
++    ADDLIBS += ['blosc', 'blosc_filter']
+ 
+ 
+ utilsExtension_libs = LIBS + ADDLIBS

dev-python/pytables/metadata.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>python</herd>
+  <herd>sci</herd>
+  <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>

dev-python/pytables/pytables-3.1.1-r2.ebuild

@@ -0,0 +1,75 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} )
+
+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
+}

dev-python/pytables/pytables-3.2.0.ebuild

@@ -0,0 +1,73 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} )
+
+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}/${MY_P}.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="BSD"
+IUSE="doc examples"
+
+RDEPEND="
+	app-arch/bzip2:0=
+	dev-libs/c-blosc:0=[hdf5]
+	dev-libs/lzo:2=
+	>=dev-python/numpy-1.7.1[${PYTHON_USEDEP}]
+	>=dev-python/numexpr-2.4[${PYTHON_USEDEP}]
+	>=sci-libs/hdf5-1.8.4:0="
+DEPEND="${RDEPEND}
+	>=dev-python/cython-0.14[${PYTHON_USEDEP}]"
+
+S="${WORKDIR}/${MY_P}"
+
+DOCS=( ANNOUNCE.txt RELEASE_NOTES.txt THANKS )
+
+PATCHES=(
+	"${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
+}