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authorJustin Lecher <jlec@gentoo.org>2014-07-07 08:36:37 +0200
committerJustin Lecher <jlec@gentoo.org>2014-07-07 08:36:37 +0200
commit8b089a49addab2d4249ef31e8a4dd6f2d4bfa129 (patch)
tree0ee390c2a51f3d9d4ca6d18801e460858dd3ce1f
parentsci-chemistry/nmrpipe: Fix emul-linux deps for modern multilib (diff)
parentMerge pull request #236 from olifre/master (diff)
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Merge remote-tracking branch 'github/master'
* github/master: dev-python/bokeh: dev-python/bokeh: New version with python3 support for bug #516052 dev-python/bokeh: dev-python/bokeh: Copy latest ebuild from portage Add subslot dependency on clhep, we need to rebuild for each clhep subslot change. New live ebuild for VGM, adapting to fixes for cmake install paths in upstream (no need to manually install in ebuild anymore). Released VGM-4.00 does not have these fixes yet, I am discussing with upstream whether they can also provide some tarballs of released versions (as sourceforge svn-snapshotting is unusable for us) and delay packaging of VGM-4.00 until then. New live ebuild, using cmake-buildsystem (upstream switches to cmake for next release), add flags for g4root and mtroot. Adapt to upstream's fixes concerning install paths, we don't need to do manually installation anymore. I will skip geant-vmc-3.00b01 from packaging, it does not include those fixes yet.
-rw-r--r--dev-python/bokeh/ChangeLog11
-rw-r--r--dev-python/bokeh/Manifest1
-rw-r--r--dev-python/bokeh/bokeh-0.4.4.ebuild98
-rw-r--r--dev-python/bokeh/files/bokeh-0.4.4-fix_test_object.patch32
-rw-r--r--dev-python/bokeh/metadata.xml15
-rw-r--r--sci-physics/geant-vmc/ChangeLog8
-rw-r--r--sci-physics/geant-vmc/geant-vmc-9999.ebuild79
-rw-r--r--sci-physics/geant-vmc/metadata.xml3
-rw-r--r--sci-physics/vgm/ChangeLog10
-rw-r--r--sci-physics/vgm/vgm-3.06.ebuild2
-rw-r--r--sci-physics/vgm/vgm-9999.ebuild68
11 files changed, 326 insertions, 1 deletions
diff --git a/dev-python/bokeh/ChangeLog b/dev-python/bokeh/ChangeLog
new file mode 100644
index 000000000..0dac60237
--- /dev/null
+++ b/dev-python/bokeh/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for dev-python/bokeh
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bokeh-0.4.4 (07 Jul 2014)
+
+ 07 Jul 2014; Witold Pilat (fau) <witold.pilat@gmail.com> +bokeh-0.4.4.ebuild,
+ +files/bokeh-0.4.4-fix_test_object.patch, -ChangeLog, -Manifest,
+ -bokeh-0.4.2.ebuild, metadata.xml:
+ dev-python/bokeh: dev-python/bokeh: New version with python3 support for bug
+ #516052
diff --git a/dev-python/bokeh/Manifest b/dev-python/bokeh/Manifest
new file mode 100644
index 000000000..2c752eaeb
--- /dev/null
+++ b/dev-python/bokeh/Manifest
@@ -0,0 +1 @@
+DIST bokeh-0.4.4.tar.gz 40315677 SHA256 ca989c9d554d07bface516ad9eccda39cf999c244c85ca52881b10fea0466417 SHA512 46dfe615a53996158b9e17e1f5cb46b401d017e18638457905f283cb3bb1d734207b370f3b3d78850e8e75ccfbe47736beba8b5730296f5db2677d5eb92423e9 WHIRLPOOL b0c56b43091d171b7b85ccec66f0986bf747479f8fbb20a4758a9e788533f34578c5ce6f87f704c34e27030a58890733003bee23ad85d9cf6ac8a68e6d80bf2c
diff --git a/dev-python/bokeh/bokeh-0.4.4.ebuild b/dev-python/bokeh/bokeh-0.4.4.ebuild
new file mode 100644
index 000000000..22d38c588
--- /dev/null
+++ b/dev-python/bokeh/bokeh-0.4.4.ebuild
@@ -0,0 +1,98 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_7,3_3,3_4} )
+
+inherit distutils-r1
+
+DESCRIPTION="Statistical and interactive HTML plots for Python"
+HOMEPAGE="http://bokeh.pydata.org/"
+SRC_URI="https://github.com/ContinuumIO/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples test chaco"
+# docs require napoleon sphinx extension which will be included in next sphinx release
+
+RDEPEND="
+ >=dev-python/flask-0.10.1[${PYTHON_USEDEP}]
+ >=dev-python/greenlet-0.4.1[${PYTHON_USEDEP}]
+ >=dev-python/itsdangerous-0.23[${PYTHON_USEDEP}]
+ >=dev-python/jinja-2.7[${PYTHON_USEDEP}]
+ >=dev-python/markdown-2.3.1[${PYTHON_USEDEP}]
+ >=dev-python/markupsafe-0.18[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.7.1[${PYTHON_USEDEP}]
+ >=dev-python/pandas-0.11[${PYTHON_USEDEP}]
+ >=dev-python/pygments-1.6[${PYTHON_USEDEP}]
+ >=dev-python/python-dateutil-2.1[${PYTHON_USEDEP}]
+ >=dev-python/pystache-0.5.3[${PYTHON_USEDEP}]
+ >=dev-python/pytz-2013b[${PYTHON_USEDEP}]
+ >=dev-python/pyyaml-3.10[${PYTHON_USEDEP}]
+ >=dev-python/redis-py-2.7.6[${PYTHON_USEDEP}]
+ >=dev-python/requests-1.2.3[${PYTHON_USEDEP}]
+ >=dev-python/six-1.5.2[${PYTHON_USEDEP}]
+ >=dev-python/werkzeug-0.9.1[${PYTHON_USEDEP}]
+ $(python_gen_cond_dep '>=dev-python/gevent-1.0[${PYTHON_USEDEP}]' python2_7)
+ $(python_gen_cond_dep '>=dev-python/gevent-websocket-0.9.2[${PYTHON_USEDEP}]' python2_7)
+ chaco? (
+ $(python_gen_cond_dep '>=dev-python/traits-4.4[${PYTHON_USEDEP}]' python2_7)
+ $(python_gen_cond_dep '>=dev-python/chaco-4.4[${PYTHON_USEDEP}]' python2_7)
+ )
+
+"
+# testing server: needs websocket not in portage yet
+# >=dev-python/websocket[${PYTHON_USEDEP}]
+# hdf5 backend: needs arraymanagement not in portage yet
+DEPEND="
+ test? (
+ ${RDEPEND}
+ >=dev-python/nose-1.3.0[${PYTHON_USEDEP}]
+ >=dev-python/mock-1.0.1[${PYTHON_USEDEP}]
+ >=dev-python/colorama-0.2.7[${PYTHON_USEDEP}]
+ )
+"
+DOCS=( CHANGELOG QUICKSTART.md README.md )
+
+python_prepare_all() {
+ # Fix test_references_by_ref_by_value from test_object.py
+ local PATCHES=( "${FILESDIR}"/${P}-fix_test_object.patch )
+ # Remove broken test case
+ sed -i -e "s:MetaTest:_&:" bokeh/tests/test_bokeh_init.py || die
+
+ if ! use chaco; then
+ sed -i -e "/'bokeh.chaco_gg'/d" setup.py || die
+ fi
+
+ distutils-r1_python_prepare_all
+}
+
+python_install_all() {
+ use examples && local EXAMPLES=( examples/. )
+
+ distutils-r1_python_install_all
+}
+
+python_test() {
+ cd "${BUILD_DIR}"/lib || die
+ # exclude server tests for now
+ nosetests -v \
+ -e multiuser_auth_test \
+ -e usermodel_test \
+ || die
+}
+
+pkg_postinst() {
+ elog "websockets work only with python2_7"
+ local chaco_msg="chaco useflag doesn't affect python targets other than python2_7"
+ if use chaco; then
+ if use python_targets_python2_7; then
+ elog "${chaco_msg}"
+ else
+ ewarn "${chaco_msg}"
+ fi
+ fi
+}
diff --git a/dev-python/bokeh/files/bokeh-0.4.4-fix_test_object.patch b/dev-python/bokeh/files/bokeh-0.4.4-fix_test_object.patch
new file mode 100644
index 000000000..24183d831
--- /dev/null
+++ b/dev-python/bokeh/files/bokeh-0.4.4-fix_test_object.patch
@@ -0,0 +1,32 @@
+commit 9606ae037dbd9ee888f9763a1bd9c6d7fc3b5824
+Author: Bryan Van de Ven <bryanv@continuum.io>
+Date: Sat Apr 19 10:05:35 2014 -0500
+
+ fix #548
+
+diff --git a/bokeh/plotobject.py b/bokeh/plotobject.py
+index 7485d27..92ae2dd 100644
+--- a/bokeh/plotobject.py
++++ b/bokeh/plotobject.py
+@@ -220,7 +220,7 @@ class PlotObject(HasProps):
+
+ def references(self):
+ """Returns all ``PlotObjects`` that this object has references to. """
+- return self.collect_plot_objects(self)
++ return set(self.collect_plot_objects(self))
+
+ #---------------------------------------------------------------------
+ # View Model connection methods
+diff --git a/bokeh/tests/test_objects.py b/bokeh/tests/test_objects.py
+index 1a17f69..75d5678 100644
+--- a/bokeh/tests/test_objects.py
++++ b/bokeh/tests/test_objects.py
+@@ -242,7 +242,7 @@ class TestPlotObject(unittest.TestCase):
+ x2 = X2(y=y, z2=z2)
+
+ # TODO: self.assertEqual(x1.references(), [t1, y, t2, x1])
+- self.assertEqual(x2.references(), [t1, y, t2, z2, x2])
++ self.assertEqual(x2.references(), set([t1, y, t2, z2, x2]))
+
+ if __name__ == "__main__":
+ unittest.main()
diff --git a/dev-python/bokeh/metadata.xml b/dev-python/bokeh/metadata.xml
new file mode 100644
index 000000000..b59e358e7
--- /dev/null
+++ b/dev-python/bokeh/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<longdescription lang="en">
+ Bokeh is a Python interactive visualization library for large
+ datasets that natively uses the latest web technologies. Its goal is
+ to provide elegant, concise construction of novel graphics in the
+ style of Protovis/D3, while delivering high-performance
+ interactivity over large data to thin clients.
+</longdescription>
+<use>
+ <flag name="chaco">Enable interface for implementing qplot and ggplot like functionality using chaco</flag>
+</use>
+</pkgmetadata>
diff --git a/sci-physics/geant-vmc/ChangeLog b/sci-physics/geant-vmc/ChangeLog
index 353b8417e..807b464c9 100644
--- a/sci-physics/geant-vmc/ChangeLog
+++ b/sci-physics/geant-vmc/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*geant-vmc-9999 (06 Jul 2014)
+
+ 06 Jul 2014; Oliver Freyermuth <o.freyermuth@googlemail.com>
+ +geant-vmc-9999.ebuild, metadata.xml:
+ New live ebuild, using cmake-buildsystem (upstream switches to cmake for next
+ release), add flags for g4root and mtroot. Adapt to upstream's fixes
+ concerning install paths, we don't need to do manually installation anymore.
+
31 Mar 2014; Oliver Freyermuth <o.freyermuth@googlemail.com>
geant-vmc-3.1.15a.ebuild:
Fix syntax bug in dependency atom
diff --git a/sci-physics/geant-vmc/geant-vmc-9999.ebuild b/sci-physics/geant-vmc/geant-vmc-9999.ebuild
new file mode 100644
index 000000000..fa8fa5592
--- /dev/null
+++ b/sci-physics/geant-vmc/geant-vmc-9999.ebuild
@@ -0,0 +1,79 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils versionator git-r3
+
+if [[ ${PV} == *9999* ]]; then
+ EGIT_REPO_URI=" http://root.cern.ch/git/geant4_vmc.git"
+ KEYWORDS=""
+else
+ MPV=$(get_version_component_range 2-)
+ SRC_URI="ftp://root.cern.ch/root/vmc/geant4_vmc.${MPV}.tar.gz"
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+DESCRIPTION="Virtual Monte Carlo Geant4 implementation"
+HOMEPAGE="http://root.cern.ch/root/vmc/VirtualMC.html"
+
+LICENSE="GPL-2"
+SLOT="4"
+IUSE="doc examples geant3 +g4root +mtroot vgm"
+
+RDEPEND="
+ sci-physics/root:=
+ >=sci-physics/geant-4.9.6[opengl,geant3?]
+ vgm? ( >=sci-physics/vgm-4.00 )"
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen )"
+
+src_configure() {
+ local mycmakeargs=(
+ $(cmake-utils_use vgm Geant4VMC_USE_VGM)
+ $(cmake-utils_use geant3 Geant4VMC_USE_GEANT4_G3TOG4)
+ $(cmake-utils_use g4root Geant4VMC_USE_G4Root)
+ $(cmake-utils_use mtroot Geant4VMC_USE_MTRoot)
+ $(cmake-utils_use examples Geant4VMC_INSTALL_EXAMPLES)
+ )
+ cmake-utils_src_configure
+}
+
+src_compile() {
+ cmake-utils_src_compile
+ local dirs="g4root mtroot source"
+ use g4root && dirs+=" g4root "
+ use mtroot && dirs+=" mtroot "
+ use examples && dirs+=" examples "
+ local d
+ for d in ${dirs}; do
+ pushd ${d} > /dev/null || die
+ if use doc; then
+ doxygen || die
+ fi
+ popd > /dev/null
+ done
+}
+
+src_test() {
+ cd examples || die
+ local origDir=${CMAKE_USE_DIR}
+ CMAKE_USE_DIR=${CMAKE_USE_DIR}/examples
+ CMAKE_IN_SOURCE_BUILD=1
+ CMAKE_MODULE_PATH=../cmake
+ local mycmakeargs=(
+ -DCMAKE_MODULE_PATH=${origDir}/cmake
+ )
+ cmake-utils_src_configure
+ cmake-utils_src_compile
+ ./run_suite.sh || die
+ CMAKE_IN_SOURCE_BUILD=0
+ CMAKE_USE_DIR=$origDir
+}
+
+src_install() {
+ cmake-utils_src_install
+ dodoc README history version_number
+ use doc && dohtml -r Geant4VMC.html doc/*
+}
diff --git a/sci-physics/geant-vmc/metadata.xml b/sci-physics/geant-vmc/metadata.xml
index 1bbc127a3..828e0454c 100644
--- a/sci-physics/geant-vmc/metadata.xml
+++ b/sci-physics/geant-vmc/metadata.xml
@@ -15,5 +15,8 @@
</longdescription>
<use>
<flag name="vgm">Enable the Virtual Geometry Model (<pkg>sci-physics/vgm</pkg>)</flag>
+ <flag name="g4root">Build G4Root (interface for GEANT4 simulation with a ROOT geometry)</flag>
+ <flag name="geant3">Build with Geant4 G3toG4 library</flag>
+ <flag name="mtroot">Build MTRoot (provides ROOT IO manager classes with multi-threading support)</flag>
</use>
</pkgmetadata>
diff --git a/sci-physics/vgm/ChangeLog b/sci-physics/vgm/ChangeLog
index 78f7e21fc..5b5dce520 100644
--- a/sci-physics/vgm/ChangeLog
+++ b/sci-physics/vgm/ChangeLog
@@ -2,6 +2,16 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 06 Jul 2014; Oliver Freyermuth <o.freyermuth@googlemail.com> vgm-3.06.ebuild:
+ Add subslot dependency on clhep, we need to rebuild for each clhep subslot
+ change.
+
+*vgm-9999 (06 Jul 2014)
+
+ 06 Jul 2014; Oliver Freyermuth <o.freyermuth@googlemail.com> +vgm-9999.ebuild:
+ New live ebuild for VGM, adapting to fixes for cmake install paths in upstream
+ (no need to manually install in ebuild anymore).
+
03 Apr 2014; Oliver Freyermuth <o.freyermuth@googlemail.com> vgm-3.06.ebuild:
Use zip-snapshot mirrored by jlec, sourceforge cannot automatically recreate
them and changes CRC each time
diff --git a/sci-physics/vgm/vgm-3.06.ebuild b/sci-physics/vgm/vgm-3.06.ebuild
index ccdc5a3d2..bd650c6e2 100644
--- a/sci-physics/vgm/vgm-3.06.ebuild
+++ b/sci-physics/vgm/vgm-3.06.ebuild
@@ -24,7 +24,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="doc examples +geant4 +root test xml"
RDEPEND="
- sci-physics/clhep
+ sci-physics/clhep:=
root? ( sci-physics/root:= )
geant4? ( >=sci-physics/geant-4.9.6[examples?] )
xml? ( dev-libs/xerces-c )"
diff --git a/sci-physics/vgm/vgm-9999.ebuild b/sci-physics/vgm/vgm-9999.ebuild
new file mode 100644
index 000000000..ddadd9970
--- /dev/null
+++ b/sci-physics/vgm/vgm-9999.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils versionator subversion
+
+if [[ ${PV} == *9999* ]]; then
+ ESVN_REPO_URI="svn://svn.code.sf.net/p/vgm/code/trunk/vgm"
+ KEYWORDS=""
+else
+ # .zip-snapshot can be recreated by visiting
+ # http://sourceforge.net/p/${PN}/code/${COMMIT}/tarball?path=/tags/v$(replace_all_version_separators '-')
+ TAG_VER="${PN}-code-731-tags-v$(replace_all_version_separators '-')"
+ SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${TAG_VER}.zip"
+ S=${WORKDIR}/${TAG_VER}/${PN}
+ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+DESCRIPTION="Virtual Geometry Model for High Energy Physics Experiments"
+HOMEPAGE="http://ivana.home.cern.ch/ivana/VGM.html"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="doc examples +geant4 +root test xml"
+
+RDEPEND="
+ sci-physics/clhep:=
+ root? ( sci-physics/root:= )
+ geant4? ( >=sci-physics/geant-4.9.6 )
+ xml? ( dev-libs/xerces-c )"
+DEPEND="${RDEPEND}
+ doc? ( app-doc/doxygen[dot] )
+ test? ( geant4? ( xml? ( >=sci-physics/geant-4.9.6[gdml] ) ) )"
+
+src_configure() {
+ local mycmakeargs=(
+ -DCLHEP_DIR="${EROOT}usr"
+ $(cmake-utils_use_with examples)
+ $(cmake-utils_use examples VGM_INSTALL_EXAMPLES)
+ $(cmake-utils_use_with geant4)
+ $(cmake-utils_use_with root)
+ $(cmake-utils_use_with test)
+ $(cmake-utils_use_with xml xercesc)
+ )
+ cmake-utils_src_configure
+}
+
+src_compile() {
+ cmake-utils_src_compile
+ if use doc; then
+ cd packages
+ doxygen || die
+ fi
+}
+
+src_test() {
+ cd "${BUILD_DIR}"/test
+ ./test_suite.sh || die
+}
+
+src_install() {
+ cmake-utils_src_install
+ cd doc || die
+ dodoc README todo.txt VGMhistory.txt VGM.html VGMversions.html
+ use doc && dohtml -r html/*
+}