[gentoo-commits] proj/sci:master commit in: sci-chemistry/freeon/, sci-chemistry/freeon/files/, sci-chemistry/nwchem/files/, ...

[Honza Macháček]

commit:     baefa0bf89ac382b08e24e32646c176a475b4add
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Thu May 30 13:21:59 2013 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Thu May 30 13:21:59 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=baefa0bf

sci-chemistry/freeon improved, the ebuild of the latest snapshot added. sci-chemistry/nwchem bumped to 6.3, building docs allowed.

---
 sci-chemistry/freeon/ChangeLog                     |   8 ++
 .../files/freeon-2012.05.03-no_internal_libs.patch |  50 +++++++
 .../files/freeon-9999-no_internal_libs.patch       |  47 +++++++
 ...freeon-9999.ebuild => freeon-2012.05.03.ebuild} |  21 ++-
 sci-chemistry/freeon/freeon-9999.ebuild            |   9 ++
 sci-chemistry/nwchem/ChangeLog                     |   6 +
 .../nwchem/files/nwchem-6.3-html_doc.patch         |  82 ++++++++++++
 sci-chemistry/nwchem/nwchem-6.3.ebuild             | 146 +++++++++++++++++++++
 8 files changed, 364 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/freeon/ChangeLog b/sci-chemistry/freeon/ChangeLog
index 25af9d7..4e266de 100644
--- a/sci-chemistry/freeon/ChangeLog
+++ b/sci-chemistry/freeon/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*freeon-2012.05.03 (30 May 2013)
+
+  30 May 2013; Honza Macháček <Hloupy.Honza@×××××××.cz>
+  +freeon-2012.05.03.ebuild, freeon-9999.ebuild,
+  +files/freeon-2012.05.03-no_internal_libs.patch,
+  +files/freeon-9999-no_internal_libs.patch:
+  Internal hdf5 and lapack removed, the ebuild of the latest snapshot added.
+
   22 Feb 2013; Justin Lecher <jlec@g.o> freeon-9999.ebuild,
   metadata.xml:
   Add missing dep on virtual/pkgconfig; bump to eapi=5; use pkg-config to

diff --git a/sci-chemistry/freeon/files/freeon-2012.05.03-no_internal_libs.patch b/sci-chemistry/freeon/files/freeon-2012.05.03-no_internal_libs.patch
new file mode 100644
index 0000000..e37622b
--- /dev/null
+++ b/sci-chemistry/freeon/files/freeon-2012.05.03-no_internal_libs.patch
@@ -0,0 +1,50 @@
+diff -Naurp freeon-beta-2012-05-03.orig/Makefile.am freeon-beta-2012-05-03/Makefile.am
+--- freeon-beta-2012-05-03.orig/Makefile.am	2012-05-04 03:53:04.000000000 +0000
++++ freeon-beta-2012-05-03/Makefile.am	2013-05-29 14:42:07.791473885 +0000
+@@ -5,18 +5,9 @@ ACLOCAL_AMFLAGS = -I m4
+ CPP = @CPP@
+ AM_CPPFLAGS = @AM_CPPFLAGS@
+ 
+-if INTERNAL_LAPACK
+-INTERNAL_LAPACK_DIRS = lapack
+-endif
++SUBDIRS = Modules FreeON SCFeqs OneE QCTC HiCu TwoE ONX PostProcessing BasisSets tests Validate
+ 
+-if INTERNAL_HDF5
+-INTERNAL_HDF5_DIRS = hdf5-1.8.3
+-HDF5_INCLUDES = -I$(srcdir)/hdf5-1.8.3/src -I$(builddir)/hdf5-1.8.3/src
+-endif
+-
+-SUBDIRS = $(INTERNAL_LAPACK_DIRS) $(INTERNAL_HDF5_DIRS) Modules FreeON SCFeqs OneE QCTC HiCu TwoE ONX PostProcessing BasisSets tests Validate
+-
+-DIST_SUBDIRS = $(SUBDIRS) lapack hdf5-1.8.3
++DIST_SUBDIRS = $(SUBDIRS)
+ 
+ EXTRA_DIST = fix_localversion.sh localversion FreeON.bibtex $(top_builddir)/latex/refman.pdf
+ 
+--- freeon-beta-2012-05-03.orig/configure.ac	2012-05-04 04:38:47.000000000 +0000
++++ freeon-beta-2012-05-03/configure.ac	2013-05-29 15:04:02.886109082 +0000
+@@ -855,7 +855,6 @@ AC_MSG_RESULT([${use_internal_hdf5}])
+ 
+ AM_CONDITIONAL(INTERNAL_HDF5, [test "${use_internal_hdf5}" = "yes"])
+ 
+-AC_CONFIG_SUBDIRS([hdf5-1.8.3])
+ 
+ if test "${use_internal_hdf5}" = "yes"; then
+ 
+@@ -1027,15 +1026,6 @@ Makefile
+ documentation/main_page.h
+ FreeON/Makefile
+ Modules/Makefile
+-lapack/Makefile
+-lapack/install/Makefile
+-lapack/blas/Makefile
+-lapack/lapack/Makefile
+-lapack/blas_testing/Makefile
+-lapack/lapack_testing/Makefile
+-lapack/lapack_testing/lin/Makefile
+-lapack/lapack_testing/eig/Makefile
+-lapack/lapack_testing/matgen/Makefile
+ SCFeqs/Makefile
+ OneE/Makefile
+ QCTC/Makefile

diff --git a/sci-chemistry/freeon/files/freeon-9999-no_internal_libs.patch b/sci-chemistry/freeon/files/freeon-9999-no_internal_libs.patch
new file mode 100644
index 0000000..a908aa7
--- /dev/null
+++ b/sci-chemistry/freeon/files/freeon-9999-no_internal_libs.patch
@@ -0,0 +1,47 @@
+diff -Naurp freeon-9999.orig/Modules/Makefile.am freeon-9999/Modules/Makefile.am
+--- freeon-9999.orig/Modules/Makefile.am	2013-05-28 08:09:39.000000000 +0000
++++ freeon-9999/Modules/Makefile.am	2013-05-29 14:32:24.879721200 +0000
+@@ -1,17 +1,5 @@
+ include $(top_srcdir)/make.inc
+ 
+-if INTERNAL_LAPACK
+-INTERNAL_LAPACK_DIRS = lapack
+-endif
+-
+-if INTERNAL_HDF5
+-INTERNAL_HDF5_DIRS = hdf5-1.8.3
+-HDF5_INCLUDES = -I$(srcdir)/hdf5-1.8.3/src -I$(builddir)/hdf5-1.8.3/src
+-endif
+-
+-DIST_SUBDIRS = lapack hdf5-1.8.3
+-SUBDIRS      = $(INTERNAL_HDF5_DIRS) $(INTERNAL_LAPACK_DIRS)
+-
+ if USE_DYNAMIC_LINKING
+ lib_LTLIBRARIES = libfreeonmodules.la
+ else
+--- freeon-9999.orig/configure.ac	2013-05-29 15:34:16.000000000 +0000
++++ freeon-9999/configure.ac	2013-05-29 15:36:22.000063299 +0000
+@@ -870,7 +870,6 @@ AM_CONDITIONAL(INTERNAL_HDF5, [test "${u
+ if test "${use_internal_hdf5}" = "yes"; then
+ 
+   AC_DEFINE(HAVE_INTERNAL_HDF5, 1, [Use the inernal hdf5 library.])
+-  AC_CONFIG_SUBDIRS([Modules/hdf5-1.8.3])
+ 
+ else
+ 
+@@ -1069,15 +1068,6 @@ config_localversion.h
+ Makefile
+ FreeON/Makefile
+ Modules/Makefile
+-Modules/lapack/Makefile
+-Modules/lapack/install/Makefile
+-Modules/lapack/blas/Makefile
+-Modules/lapack/lapack/Makefile
+-Modules/lapack/blas_testing/Makefile
+-Modules/lapack/lapack_testing/Makefile
+-Modules/lapack/lapack_testing/lin/Makefile
+-Modules/lapack/lapack_testing/eig/Makefile
+-Modules/lapack/lapack_testing/matgen/Makefile
+ SCFeqs/Makefile
+ OneE/Makefile
+ QCTC/Makefile

diff --git a/sci-chemistry/freeon/freeon-9999.ebuild b/sci-chemistry/freeon/freeon-2012.05.03.ebuild
similarity index 64%
copy from sci-chemistry/freeon/freeon-9999.ebuild
copy to sci-chemistry/freeon/freeon-2012.05.03.ebuild
index 2fe44e9..99805e0 100644
--- a/sci-chemistry/freeon/freeon-9999.ebuild
+++ b/sci-chemistry/freeon/freeon-2012.05.03.ebuild
@@ -8,14 +8,14 @@ AUTOTOOLS_AUTORECONF=1
 
 FORTRAN_STANDARD=90
 
-inherit autotools-utils fortran-2 git-2
+inherit autotools-utils fortran-2
+
+REAL_PN="${PN}-beta"
+REAL_PV="${PV//./-}"
 
 DESCRIPTION="an experimental suite of programs for linear scaling quantum chemistry."
 HOMEPAGE="http://www.freeon.org"
-SRC_URI=""
-
-EGIT_REPO_URI="http://git.savannah.gnu.org/r/freeon.git"
-EGIT_BOOTSTRAP="fix_localversion.sh"
+SRC_URI="http://download.savannah.gnu.org/releases/${PN}/${REAL_PN}-${REAL_PV}.tar.bz2"
 
 LICENSE="GPL-3"
 SLOT="0"
@@ -30,6 +30,17 @@ RDEPEND="
 DEPEND="${DEPEND}
 	virtual/pkgconfig"
 
+S="${WORKDIR}/${REAL_PN}-${REAL_PV}"
+
+src_prepare() {
+	# Get rid of the obsolete internal hdf5
+	rm -r "${S}"/hdf5-1.8.3
+	# as well as of the internal lapack
+	rm -r "${S}"/lapack
+	epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch
+	eautoreconf
+}
+
 src_configure() {
 	local myeconfargs=(
 		--disable-internal-hdf5

diff --git a/sci-chemistry/freeon/freeon-9999.ebuild b/sci-chemistry/freeon/freeon-9999.ebuild
index 2fe44e9..369e063 100644
--- a/sci-chemistry/freeon/freeon-9999.ebuild
+++ b/sci-chemistry/freeon/freeon-9999.ebuild
@@ -30,6 +30,15 @@ RDEPEND="
 DEPEND="${DEPEND}
 	virtual/pkgconfig"
 
+src_prepare() {
+	# Get rid of the obsolete internal hdf5
+	rm -r "${S}"/Modules/hdf5-1.8.3
+	# as well as of the internal lapack
+	rm -r "${S}"/Modules/lapack
+	epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch
+	eautoreconf
+}
+
 src_configure() {
 	local myeconfargs=(
 		--disable-internal-hdf5

diff --git a/sci-chemistry/nwchem/ChangeLog b/sci-chemistry/nwchem/ChangeLog
index b6b85fc..687c7c7 100644
--- a/sci-chemistry/nwchem/ChangeLog
+++ b/sci-chemistry/nwchem/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*nwchem-6.3 (30 May 2013)
+
+  30 May 2013; Honza Macháček <Hloupy.Honza@×××××××.cz> +nwchem-6.3.ebuild,
+  +files/nwchem-6.3-html_doc.patch:
+  Version bumped to 6.3, adding the doc option attempted.
+
   14 Mar 2013; François Bissey <francois.bissey@×××××××××××××.nz>
   nwchem-6.1.1.ebuild:
   Improving mpi linking. It will now work with openmpi as well.

diff --git a/sci-chemistry/nwchem/files/nwchem-6.3-html_doc.patch b/sci-chemistry/nwchem/files/nwchem-6.3-html_doc.patch
new file mode 100644
index 0000000..fa0e8fa
--- /dev/null
+++ b/sci-chemistry/nwchem/files/nwchem-6.3-html_doc.patch
@@ -0,0 +1,82 @@
+diff -Naurp old/doc/update_www new/doc/update_www
+--- doc/update_www	2013-05-18 00:40:51.000000000 +0000
++++ doc/update_www	2013-05-22 12:15:27.543414281 +0000
+@@ -16,7 +16,8 @@ set document = $argv[1]
+ echo Updating WWW pages for $document.tex
+ #...............   public 
+ #foreach WWWDIR (/msrc/www/pub/docs/nwchem/doc)
+-foreach WWWDIR (/msrc/emslweb/docs/nwchem/doc)
++#foreach WWWDIR (/msrc/emslweb/docs/nwchem/doc)
++foreach WWWDIR ("${NWCHEM_TOP}"/html)
+ #
+ # Now copy the revised source into the EMSL public WWW tree
+   echo "update_www: Public pages .. "
+diff -Naurp old/user/geometry.tex new/user/geometry.tex
+--- user/geometry.tex	2013-05-18 00:40:51.000000000 +0000
++++ user/geometry.tex	2013-05-23 13:00:44.234316049 +0000
+@@ -472,11 +472,11 @@ and angles.
+ \ifx\pdfoutput\undefined
+ \includegraphics[angle=270,width=6in]{zmat1.eps}
+ \else
+-\includegraphics[angle=0,width=6in]{zmat1.pdf}
++\includegraphics[angle=0,width=6in,bburx=509,bbury=201]{zmat1.pdf}
+ \fi
+ \end{latexonly}
+ \begin{htmlonly}
+-\psfig{figure=zmat1.eps,angle=270,width=6in}
++\epsfig{figure=zmat1.eps,angle=270,width=6in}
+ \end{htmlonly}
+ \caption{\label{fig:zmat1} Relationships between the centers, bond angle
+ and dihedral angle in Z-matrix input.}
+@@ -488,11 +488,11 @@ and dihedral angle in Z-matrix input.}
+ \ifx\pdfoutput\undefined
+ \includegraphics[angle=270,width=6in]{zmat2.eps}
+ \else
+-\includegraphics[angle=270,width=6in]{zmat2.pdf}
++\includegraphics[angle=270,width=6in,bburx=266,bbury=485]{zmat2.pdf}
+ \fi
+ \end{latexonly}
+ \begin{htmlonly}
+-\psfig{figure=zmat2.eps,angle=270,width=6in}
++\epsfig{figure=zmat2.eps,angle=270,width=6in}
+ \end{htmlonly}
+ 
+ \caption{\label{fig:zmat2} Relationships between the centers and two
+@@ -505,11 +505,11 @@ and dihedral angle in Z-matrix input.}
+ \ifx\pdfoutput\undefined
+ \includegraphics[angle=270,width=6in]{zmat3.eps}
+ \else
+-\includegraphics[angle=270,width=6in]{zmat3.pdf}
++\includegraphics[angle=270,width=6in,bburx=266,bbury=482]{zmat3.pdf}
+ \fi
+ \end{latexonly}
+ \begin{htmlonly}
+-\psfig{figure=zmat3.eps,angle=270,width=6in}
++\epsfig{figure=zmat3.eps,angle=270,width=6in}
+ \end{htmlonly}
+ \caption{\label{fig:zmat3} Relationships between the centers and two
+   bond angles in Z-matrix input with optional parameter specified as $-1$.}
+diff -Naurp old/user/titlepage.tex new/user/titlepage.tex
+--- user/titlepage.tex	2013-05-18 00:40:51.000000000 +0000
++++ user/titlepage.tex	2013-05-23 13:01:07.304152791 +0000
+@@ -19,7 +19,7 @@
+ {\bf\Large \nwchemmonth \ \nwchemyear}\\[1.0in]
+ 
+ 
+-%\psfig{figure=zsm.major.ps,height=4in,width=4in}
++%\epsfig{figure=zsm.major.ps,height=4in,width=4in}
+ 
+ 
+ \end{centering}
+diff -Naurp old/user/user.tex new/user/user.tex
+--- user/user.tex	2013-05-18 00:40:51.000000000 +0000
++++ user/user.tex	2013-05-23 13:00:04.961296411 +0000
+@@ -2,7 +2,7 @@
+ \input{top}
+ \usepackage[dvips]{graphicx}
+ \begin{htmlonly}
+-\usepackage{psfig}
++\usepackage{epsfig}
+ \end{htmlonly}
+ 
+ 

diff --git a/sci-chemistry/nwchem/nwchem-6.3.ebuild b/sci-chemistry/nwchem/nwchem-6.3.ebuild
new file mode 100644
index 0000000..380de67
--- /dev/null
+++ b/sci-chemistry/nwchem/nwchem-6.3.ebuild
@@ -0,0 +1,146 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+inherit eutils fortran-2 multilib python-single-r1 toolchain-funcs
+
+DATE="2013-05-17"
+
+DESCRIPTION="NWChem: Delivering High-Performance Computational Chemistry to Science"
+HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
+SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV}-src.${DATE}.tar.gz"
+
+LICENSE="ECL-2.0"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="mpi doc examples nwchem-tests python"
+
+RDEPEND="sys-fs/sysfsutils
+	python? ( ${PYTHON_DEPS} )"
+DEPEND="${RDEPEND}
+	virtual/fortran
+	app-shells/tcsh
+	mpi? ( virtual/mpi[fortran] )
+	doc? ( dev-texlive/texlive-latex
+		dev-tex/latex2html )"
+
+S="${WORKDIR}/${P}-src.${DATE}"
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	use python && python-single-r1_pkg_setup
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/nwchem-6.1.1-makefile.patch \
+		"${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch \
+		"${FILESDIR}"/nwchem-6.1.1-adjust-dir-length.patch
+	use python && epatch "${FILESDIR}"/nwchem-6.1.1-python_makefile.patch
+	use doc && epatch "${FILESDIR}"/nwchem-6.3-html_doc.patch
+
+	sed \
+		-e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
+		-i src/basis/MakeFile src/basis/GNUmakefile || die
+	sed \
+		-e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
+		-i src/nwpw/libraryps/GNUmakefile || die
+	sed \
+		-e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \
+		-i src/GNUmakefile src/MakeFile || die
+
+	if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then
+		sed \
+			-e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \
+			-e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \
+			-i src/config/makefile.h || die
+	fi
+}
+
+src_compile() {
+	export USE_SUBGROUPS=yes
+	if use mpi ; then
+		export MSG_COMMS=MPI
+		export USE_MPI=yes
+		export MPI_LOC=/usr
+		export MPI_INCLUDE=$MPI_LOC/include
+		export MPI_LIB=$MPI_LOC/$(get_libdir)
+		export LIBMPI="$(mpif90 -showme:link)"
+	fi
+	if [ "$ARCH" = "amd64" ]; then
+		export NWCHEM_TARGET=LINUX64
+	elif [ "$ARCH" = "ia64" ]; then
+		export NWCHEM_TARGET=LINUX64
+	elif [ "$ARCH" = "x86" ]; then
+		export NWCHEM_TARGET=LINUX
+	elif [ "$ARCH" = "ppc" ]; then
+		export NWCHEM_TARGET=LINUX
+	else
+		die "Unknown architecture"
+	fi
+	if use python ; then
+		if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then
+			export USE_PYTHON64=yes
+		fi
+		export PYTHONHOME=/usr
+		export PYTHONVERSION=$(eselect python show|awk -Fpython '{ print $2 }')
+		export PYTHONPATH="./:${S}/contrib/python/"
+		export NWCHEM_MODULES="all python"
+	else
+		export NWCHEM_MODULES="all"
+	fi
+
+	cd src
+	emake \
+		DIAG=PAR \
+		FC=$(tc-getFC) \
+		CC=$(tc-getCC) \
+		CXX=$(tc-getCXX) \
+		NWCHEM_TOP="${S}" \
+		NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem"
+
+	if use doc; then
+		cd "${S}"/doc
+		emake \
+			DIAG=PAR \
+			NWCHEM_TOP="${S}" \
+			pdf html
+	fi
+}
+
+src_install() {
+	dobin bin/${NWCHEM_TARGET}/nwchem
+
+	insinto /usr/share/NWChem/basis/
+	doins -r src/basis/libraries src/data
+	insinto /usr/share/NWChem/nwpw
+	doins -r src/nwpw/libraryps
+
+	insinto /etc
+	doins nwchemrc
+
+	use examples && \
+		insinto /usr/share/NWChem/ && \
+		doins -r examples
+
+	use nwchem-tests && \
+		insinto /usr/share/NWChem && \
+		doins -r QA/tests
+
+	use doc && \
+		insinto /usr/share/doc/"${P}" && \
+		doins -r doc/nwahtml && \
+		doins -r html
+
+}
+
+pkg_postinst() {
+	echo
+	elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc"
+	elog "or copy it in order to tell NWChem the right position of the"
+	elog "basis library and other necessary data."
+	echo
+}