Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  [app-vim/vim-gromacs] Fix typo
  [app-vim/vim-gromacs] Update vim syntax repo uri
  initial commit (thx to Torsten Stuehn)
  package.mask: added sci-physics/espresso++
  sync with gx86

* github.com:gentoo-science/sci:
  [app-vim/vim-gromacs] Fix typo
  [app-vim/vim-gromacs] Update vim syntax repo uri
  initial commit (thx to Torsten Stuehn)
  package.mask: added sci-physics/espresso++
  sync with gx86

9 files changed, 112 insertions, 15 deletions

diff --git a/app-vim/vim-gromacs/ChangeLog b/app-vim/vim-gromacs/ChangeLog
new file mode 100644
index 000000000..f360e2199
--- /dev/null
+++ b/app-vim/vim-gromacs/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for app-vim/vim-gromacs
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  09 Oct 2012; Alexey Shvetsov <alexxy@gentoo.org> vim-gromacs-9999.ebuild:
+  [app-vim/vim-gromacs] Fix typo
+
+  09 Oct 2012; Alexey Shvetsov <alexxy@gentoo.org> +metadata.xml,
+  vim-gromacs-9999.ebuild:
+  [app-vim/vim-gromacs] Update vim syntax repo uri
diff --git a/app-vim/vim-gromacs/metadata.xml b/app-vim/vim-gromacs/metadata.xml
new file mode 100644
index 000000000..02f0be7fb
--- /dev/null
+++ b/app-vim/vim-gromacs/metadata.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<longdescription lang="en">
+	VIM syntax plugin which provides syntax highlighting for the gromacs files.
+</longdescription>
+</pkgmetadata>
diff --git a/app-vim/vim-gromacs/vim-gromacs-9999.ebuild b/app-vim/vim-gromacs/vim-gromacs-9999.ebuild
index d2bc4c658..465c9db1e 100644
--- a/app-vim/vim-gromacs/vim-gromacs-9999.ebuild
+++ b/app-vim/vim-gromacs/vim-gromacs-9999.ebuild
@@ -8,8 +8,11 @@ inherit git-2 vim-plugin
 
 DESCRIPTION="vim plugin: Gromacs file syntax highlighting and some macros"
 HOMEPAGE="https://github.com/HubLot/vim-gromacs"
-#EGIT_REPO_URI="git://github.com/HubLot/${PN}.git"
-EGIT_REPO_URI="git://github.com/Reinis/${PN}.git"
+#EGIT_REPO_URI="git://github.com/Reinis/${PN}.git"
+EGIT_REPO_URI="
+	https://github.com/HubLot/${PN}.git
+	git://github.com/HubLot/${PN}.git
+	git://github.com/Reinis/${PN}.git"
 SRC_URI=""
 
 LICENSE="GPL-3"
@@ -20,6 +23,6 @@ VIM_PLUGIN_MESSAGES="filetype"
 
 pkg_preinst () {
 	# Remove git files
-	rm ${D}/usr/share/vim/vimfiles/.gitignore
-	rm -r ${D}/usr/share/vim/vimfiles/.git
+	rm "${D}/usr/share/vim/vimfiles/.gitignore"
+	rm -r "${D}/usr/share/vim/vimfiles/.git"
 }
diff --git a/profiles/package.mask b/profiles/package.mask
index b1714bcb0..9953a7d9c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -122,6 +122,7 @@ sci-visualization/vtkPOFFReader
 # Christoph Junghans <ottxor@gentoo.org> (20 Apr 2011)
 # mask live ebuild
 =sci-physics/espresso-9999
+=sci-physics/espresso++-9999
 
 # Christoph Junghans <ottxor@gentoo.org> (23 Jan 2011)
 # mask live ebuild
diff --git a/sci-physics/espresso++/ChangeLog b/sci-physics/espresso++/ChangeLog
new file mode 100644
index 000000000..2602ad68d
--- /dev/null
+++ b/sci-physics/espresso++/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-physics/espresso++
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*espresso++-9999 (09 Oct 2012)
+
+  09 Oct 2012; Christoph Junghans <ottxor@gentoo.org> +espresso++-9999.ebuild,
+  +metadata.xml:
+  initial commit (thx to Torsten Stuehn)
diff --git a/sci-physics/espresso++/espresso++-9999.ebuild b/sci-physics/espresso++/espresso++-9999.ebuild
new file mode 100644
index 000000000..41eda0d61
--- /dev/null
+++ b/sci-physics/espresso++/espresso++-9999.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/espresso/espresso-3.1.0.ebuild,v 1.5 2012/05/06 23:08:00 ottxor Exp $
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+
+inherit cmake-utils python
+
+DESCRIPTION="extensible, flexible, fast and parallel simulation software for soft matter research"
+HOMEPAGE="https://www.espresso-pp.de"
+
+if [[ ${PV} = 9999 ]]; then
+	EHG_REPO_URI="https://hg.berlios.de/repos/espressopp"
+	EHG_REVISION="default"
+	inherit mercurial
+else
+	SRC_URI="https://www.espresso-pp.de/Download/${PN%++}pp_${PV//./_}.tgz"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos"
+IUSE="-system-boost"
+
+RDEPEND="
+	system-boost? ( dev-libs/boost[python,mpi] )
+	virtual/mpi
+	"
+
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${PN%++}pp"
+
+DOCS=( AUTHORS NEWS README )
+
+src_configure() {
+	mycmakeargs=(
+	$(cmake-utils_use system-boost EXTERNAL_BOOST)
+	)
+	cmake-utils_src_configure
+}
diff --git a/sci-physics/espresso++/metadata.xml b/sci-physics/espresso++/metadata.xml
new file mode 100644
index 000000000..14341e73e
--- /dev/null
+++ b/sci-physics/espresso++/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-physics</herd>
+	<maintainer>
+		<email>ottxor@gentoo.org</email>
+		<name>Christoph Junghans</name>
+	</maintainer>
+	<use>
+		<flag name='system-boost'>Use system boost (<pkg>dev-libs/boost</pkg>) instead of bundled one</flag>
+	</use>
+</pkgmetadata>
diff --git a/sci-physics/espresso/ChangeLog b/sci-physics/espresso/ChangeLog
index c273e468f..7264ecad2 100644
--- a/sci-physics/espresso/ChangeLog
+++ b/sci-physics/espresso/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  09 Oct 2012; Christoph Junghans <ottxor@gentoo.org> espresso-9999.ebuild:
+  sync with gx86
+
   06 May 2012; Christoph Junghans <ottxor@gentoo.org> espresso-9999.ebuild:
   sync with gx86
 
@@ -46,4 +49,3 @@
 
   16 May 2009; Christoph Junghans <kleiner_otti@gmx.de> ChangeLog:
   Initial commit. Ebuild written by me. bug #266648
-
diff --git a/sci-physics/espresso/espresso-9999.ebuild b/sci-physics/espresso/espresso-9999.ebuild
index 01f7b5106..18df79b86 100644
--- a/sci-physics/espresso/espresso-9999.ebuild
+++ b/sci-physics/espresso/espresso-9999.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-physics/espresso/espresso-3.0.0.ebuild,v 1.1 2011/04/20 13:03:00 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-physics/espresso/espresso-3.1.0.ebuild,v 1.5 2012/05/06 23:08:00 ottxor Exp $
 
 EAPI=4
 
@@ -46,6 +46,10 @@ src_prepare() {
 	autotools-utils_src_prepare
 	eautoreconf
 	restore_config myconfig.h
+	if [[ ${CHOST} == *-darwin* ]]; then
+		#tclline uses stty, which has different exit code on Darwin
+		sed -i '/source.*tclline/s/^/#/' "scripts/init.tcl" || die
+	fi
 }
 
 src_configure() {
@@ -60,8 +64,8 @@ src_configure() {
 
 src_compile() {
 	autotools-utils_src_compile
-	use doc && autotools-utils_src_compile ug doxygen tutorials
-	[[ ${PV} = 9999 ]] && use doc && autotools-utils_src_compile dg
+	use doc && autotools-utils_src_compile doxygen
+	[[ ${PV} = 9999 ]] && use doc && autotools-utils_src_compile ug dg tutorials
 }
 
 src_install() {
@@ -75,13 +79,19 @@ src_install() {
 	save_config ${AUTOTOOLS_BUILD_DIR}/src/myconfig-final.h
 
 	if use doc; then
-		[[ ${PV} = 9999 ]] && \
-			newdoc ${AUTOTOOLS_BUILD_DIR}/doc/dg/dg.pdf developer_guide.pdf
-		newdoc ${AUTOTOOLS_BUILD_DIR}/doc/ug/ug.pdf user_guide.pdf
-		dohtml -r ${AUTOTOOLS_BUILD_DIR}/doc/doxygen/html/*
-		for i in ${AUTOTOOLS_BUILD_DIR}/doc/tutorials/*/[0-9]*.pdf; do
-			newdoc ${i} tutorial_${i##*/}
-		done
+		if [[ ${PV} = 9999 ]] ; then
+			newdoc "${AUTOTOOLS_BUILD_DIR}"/doc/dg/dg.pdf developer_guide.pdf
+			newdoc "${AUTOTOOLS_BUILD_DIR}"/doc/ug/ug.pdf user_guide.pdf
+			for i in "${AUTOTOOLS_BUILD_DIR}"/doc/tutorials/*/[0-9]*.pdf; do
+				newdoc "${i}" "tutorial_${i##*/}"
+			done
+		else
+			newdoc "${S}"/doc/ug/ug.pdf user_guide.pdf
+			for i in "${S}"/doc/tutorials/*/[0-9]*.pdf; do
+				newdoc "${i}" "tutorial_${i##*/}"
+			done
+		fi
+		dohtml -r "${AUTOTOOLS_BUILD_DIR}"/doc/doxygen/html/*
 	fi
 
 	if use examples; then