reinit the tree, so we can have metadata

5 files changed, 198 insertions, 0 deletions

diff --git a/sci-chemistry/viewmol/Manifest b/sci-chemistry/viewmol/Manifest
new file mode 100644
index 000000000000..732b77c48906
--- /dev/null
+++ b/sci-chemistry/viewmol/Manifest
@@ -0,0 +1,7 @@
+AUX 2.4.1-change-default-paths.patch 2745 SHA256 a351262fc6c90eb50dd603ee8447eae756e4014b184d3603d540e09bb77cc2ac SHA512 9dda6e39f43706f9868eb02402137573d58e90b14940ad5d10ede6088e49d2ebd8a114ffda3cf4a69bee5874cc0a16b83bb4ea86281203765c5d861cb8dac6dd WHIRLPOOL d500116a4e8e0880470f35097e604f957e4ba918f7279bb4078d5054d338db00f52bedac4cee1cd369d6b446ceefdbc49c399416bf34560eaec0ed36a1c98783
+AUX 2.4.1-remove-icc-check.patch 1020 SHA256 123063ddb68f905580e37a0a83060150cc359499d5b17418bf9b6e5a53d95ea1 SHA512 ea2a1a58730561fcf2bc05a0f23dc2108cf2fd97d228a7a6305d3323abda5ce3510793dbebf2253cef9e6d60326889079bc6a9639228b1b2bfd9d9a3b8c03ebb WHIRLPOOL 9c360865c816bbb61b581729ead42d0c90e31428412f2911c8f87e3ee1af43cab70b5e21f44a519f2c791c909c6d4550d07c17110dc4118629947b6b33612e71
+DIST viewmol-2.4.1.src.tgz 2229379 SHA256 dfed3eed6441d89c4bf2be1c13cbe263341c8880edf1742d446fc0f8f4a99e19 SHA512 42701d570d97e77b84597950a9068dfdf48faf4e551957383c8eea38f082c1ad136c17b7cbd3903673478506116d6fc08d1288842e74d6a9776526c685083584 WHIRLPOOL 0e8703cb763d15543de54b626a3be072d3ca36da04b3728e2d19d11436282ed4f7947017bf03016da3ba3ce3cacbdb7cfa2bcf68dbdfea81040403e8dde90d93
+EBUILD viewmol-2.4.1-r3.ebuild 2244 SHA256 22241c85ce536357c956c5981072098f526dcfad9d5ac3018e82cfed44e24566 SHA512 883277f1919a18c6ef5c0086a7d6e71f2555e8fce2b51c38133ad654e693fa73c0507a81dbb5487f7c921196638da7f9a677fd401ed74c2495aa85f2475c603f WHIRLPOOL 6c4683bdb08397ed22711a8caa1716cade92e0295ab1e9e675d608a90c25380e67002a0be52466c048a7db9ab858ffce6081400c09c0b3094f874b73dcb7c751
+MISC ChangeLog 2670 SHA256 31a74d4c3ebc9da90788bbafece6e83649aabd25abb049abce2a33f3a70c1371 SHA512 9f84f35b254e5d9786c347799f508724a28272161e9c07bca830ce5892e3b10b070e07c61194cb62c72de857e0659075aa9ef93e053a32bdeadfea5f684d80eb WHIRLPOOL 739eb2e5734097b128fe41e626f7cd30bb4906def8dfbef45c54d25b6db696769ccdfe498a9902b53f85d4bc6fc1a024a2aa29cc89979912c5d16adea27339b1
+MISC ChangeLog-2015 2592 SHA256 4453862c6e856a1d30a3ac1e6d7680f2e22c88f7c6fa72558fe84418834efc90 SHA512 9ccfd4c565cc9065ad20a9b6c128745acc05da6bbc6cfdfdd321b6e7b74d9a175967923ea186bbe186f14e7e266201889dbcf7b04d7710c221363bca3a9f5117 WHIRLPOOL 76b9d75e25058fff7ed9a67552a38f89b8850017d02312c98e9d7f9d3ecc7af72dcbb29d1345a06d6da938e962205b4fa73fbb01cf6e11de6a6170c8e392da43
+MISC metadata.xml 342 SHA256 a1ab56cabcebc0343826a7c079fe48f75af51a6b6b7231a0e085a8fc72a9a2b0 SHA512 f77c63597bc5df26ba6dd136ee943f78562c5d99fefc1b435633c602a6eb3433600976884085ea8aa8f87f2f79fd495e9b51f918290bc1751e66d7515fe4e039 WHIRLPOOL ff49efd1ab9dced97e3fa4d3152811ef9d83407d41c34141b03f29ab0757a35e0492744ce63fa1f2d8fa51e2ca1fa4b24da9de362174df87ad24f54d94761cec
diff --git a/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch b/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch
new file mode 100644
index 000000000000..4b1edef7ef8b
--- /dev/null
+++ b/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch
@@ -0,0 +1,68 @@
+diff --git a/source/getrc.c b/source/getrc.c
+index a39b436..c130096 100644
+--- a/getrc.c
++++ b/getrc.c
+@@ -87,7 +87,7 @@ extern XtAppContext app;
+ 
+ static char viewmolpath[MAXLENLINE];
+ 
+-#define DEFAULTPATH "/usr/local/lib/viewmol"
++#define DEFAULTPATH "@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR/viewmol"
+ 
+ int getrc(void)
+ {
+diff --git a/source/install b/source/install
+index 580865b..f136af3 100755
+--- a/install
++++ b/install
+@@ -54,24 +54,27 @@ fi
+ cp $dirorig/viewmol $ROOT/bin
+ chmod 711 $ROOT/bin/viewmol
+ 
+-# install other files needed in $ROOT/lib/viewmol
+-if [ ! -d $ROOT/lib/viewmol/$dir ]
++# install other files needed in $ROOT/GENTOOLIBDIR/viewmol
++if [ ! -d $ROOT/GENTOOLIBDIR/viewmol/$dir ]
+ then
+-  mkdir -p $ROOT/lib/viewmol/$dir
+-  chmod 755 $ROOT/lib/viewmol/$dir
++  mkdir -p $ROOT/GENTOOLIBDIR/viewmol/$dir
++  chmod 755 $ROOT/GENTOOLIBDIR/viewmol/$dir
+ fi
+ cd $dirorig
+-cp tm bio readgamess readgauss readmopac readpdb $ROOT/lib/viewmol/$dir
+-chmod 711 $ROOT/lib/viewmol/$dir/*
++cp tm bio readgamess readgauss readmopac readpdb $ROOT/GENTOOLIBDIR/viewmol/$dir
++chmod 711 $ROOT/GENTOOLIBDIR/viewmol/$dir/*
+ cd ../..
+-cp readdmol readdmol.awk readgulp readpqs writecar writegauss.py writemol writetm $ROOT/lib/viewmol
+-chmod 755 $ROOT/lib/viewmol/*
+-cp -r doc examples locale scripts tests $ROOT/lib/viewmol
+-find $ROOT/lib/viewmol -type f -exec chmod a+r {} \;
+-find $ROOT/lib/viewmol -type d -exec chmod a+rx {} \;
+-sed 's/\/source//g' viewmolrc > $ROOT/lib/viewmol/viewmolrc
+-chmod -R 644 $ROOT/lib/viewmol/viewmolrc
+-if [ -d /usr/X11R6/lib/X11/app-defaults ]
++cp readdmol readdmol.awk readgulp readpqs writecar writegauss.py writemol writetm $ROOT/GENTOOLIBDIR/viewmol
++chmod 755 $ROOT/GENTOOLIBDIR/viewmol/*
++mkdir -p $ROOT/usr/share/viewmol $ROOT/usr/share/doc/GENTOODOCDIR/ $ROOT/GENTOOLIBDIR/viewmol/
++cp -r examples scripts tests $ROOT/usr/share/viewmol
++cp -r locale $ROOT/GENTOOLIBDIR/viewmol/
++cp -r doc/* examples scripts tests $ROOT/usr/share/doc/GENTOODOCDIR/
++find $ROOT/GENTOOLIBDIR/viewmol -type f -exec chmod a+r {} \;
++find $ROOT/GENTOOLIBDIR/viewmol -type d -exec chmod a+rx {} \;
++sed 's/\/source//g' viewmolrc > $ROOT/GENTOOLIBDIR/viewmol/viewmolrc
++chmod -R 644 $ROOT/GENTOOLIBDIR/viewmol/viewmolrc
++if [ -d $ROOT/X11R6/GENTOOLIBDIR/X11/app-defaults ]
+ then
+   locale=`echo $LANG | cut -c1-2`
+   if [ "$locale" = "en" ]
+@@ -82,6 +85,6 @@ then
+     # The C locale is defined by default for rpm builds, overwrite it
+     locale="en_US"
+   fi
+-  cp locale/${locale}/Viewmol /usr/X11R6/lib/X11/app-defaults
+-  chmod a+r /usr/X11R6/lib/X11/app-defaults/Viewmol
++  cp locale/${locale}/Viewmol ${ROOT}/X11R6/GENTOOLIBDIR/X11/app-defaults
++  chmod a+r ${ROOT}/X11R6/GENTOOLIBDIR/X11/app-defaults/Viewmol
+ fi
diff --git a/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch b/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch
new file mode 100644
index 000000000000..fd91e0a5a434
--- /dev/null
+++ b/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch
@@ -0,0 +1,22 @@
+--- a/getmachine
++++ b/getmachine
+@@ -269,19 +269,11 @@
+            makedir
+            cat ../.config.$os > makefile
+            use_icc=`type icc 2> /dev/null`
+-           if [ "$use_icc" = "" ]
+-           then
+ 	     findProcessor
+ 	     echo 'COMPILER=gcc' >> makefile
+              echo "OPT=-O6 -mcpu=$processor -fomit-frame-pointer -ffast-math -malign-double" >> makefile
+              echo 'CFLAGS=-Wall -I/usr/X11R6/include -DLINUX -Wno-strict-aliasing' >> makefile
+              echo "LDFLAGS=$LINKFORSHARED" >> makefile
+-           else
+-	     echo 'COMPILER=icc' >> makefile
+-             echo 'OPT=-O2 -ipo' >> makefile
+-             echo 'CFLAGS=-I/opt/intel/compiler50/ia32/include -I/usr/X11R6/include -DLINUX' >> makefile
+-             echo "LDFLAGS=$LINKFORSHARED -ipo" >> makefile
+-           fi
+            echo 'SCANDIR=' >> makefile
+            echo 'INCLUDE=$(TIFFINCLUDE) -I$(PNGINCLUDE) -I$(PYTHONINCLUDE)' >> makefile
+            echo 'LIBRARY=$(LIBTIFF) $(LIBPNG) -L$(LIBPYTHON)' >> makefile
diff --git a/sci-chemistry/viewmol/metadata.xml b/sci-chemistry/viewmol/metadata.xml
new file mode 100644
index 000000000000..335c7edd503b
--- /dev/null
+++ b/sci-chemistry/viewmol/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="sourceforge">viewmol</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-chemistry/viewmol/viewmol-2.4.1-r3.ebuild b/sci-chemistry/viewmol/viewmol-2.4.1-r3.ebuild
new file mode 100644
index 000000000000..7881b3a708c3
--- /dev/null
+++ b/sci-chemistry/viewmol/viewmol-2.4.1-r3.ebuild
@@ -0,0 +1,90 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk(-)"
+
+inherit prefix python-single-r1 toolchain-funcs
+
+DESCRIPTION="Open-source graphical front end for computational chemistry programs"
+HOMEPAGE="http://viewmol.sourceforge.net/"
+SRC_URI="mirror://sourceforge/viewmol/${P}.src.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+	media-libs/libpng:0=
+	media-libs/tiff:0
+	virtual/glu
+	virtual/opengl
+	x11-libs/libX11
+	x11-libs/libXi
+	x11-libs/libXmu
+	x11-libs/libXt
+	x11-libs/motif:0
+	${PYTHON_DEPS}"
+DEPEND="${RDEPEND}
+	x11-proto/inputproto
+	x11-proto/xproto"
+
+S="${WORKDIR}/${P}/source"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-remove-icc-check.patch
+	"${FILESDIR}"/${PV}-change-default-paths.patch
+)
+
+src_prepare() {
+	default
+
+	eprefixify getrc.c
+	sed "s:GENTOOLIBDIR:$(get_libdir):g" -i install getrc.c || die
+	sed "s:GENTOODOCDIR:${PF}:g" -i install || die
+
+	mkdir "$(uname -s)" || die
+	cd "$(uname -s)" || die
+
+	cat >> ".config.$(uname -s)" <<- EOF || die
+		LIBTIFF = -L"${EPREFIX}/usr/$(get_libdir)"
+		TIFFINCLUDE = "${EPREFIX}/usr/include"
+
+		LIBPNG = -L"${EPREFIX}/usr/$(get_libdir)"
+		PNGINCLUDE = "${EPREFIX}/usr/include"
+
+		PYTHONVERSION = ${EPYTHON}
+		PYTHONINCLUDE = $(python_get_CFLAGS)
+		PYTHONLIB = $(python_get_LIBS)
+
+		COMPILER = $(tc-getCC)
+		CFLAGS = ${CFLAGS} -DLINUX
+		LDFLAGS = ${LDFLAGS}
+		SCANDIR=
+		INCLUDE=\$(TIFFINCLUDE) -I\$(PNGINCLUDE) \$(PYTHONINCLUDE)
+		LIBRARY=\$(LIBTIFF) \$(LIBPNG) \$(PYTHONLIB)
+		LIBS=-L"${EPREFIX}/usr/$(get_libdir)" -ltiff -lpng -lz -lGLU -lGL -L"${EPREFIX}/usr/X11R6/lib" -lXm -lXmu -lXp -lXi -lXext -lXt -lX11 -lpthread -lutil -ldl -lm
+	EOF
+
+	cp .config.$(uname -s) makefile || die
+	cat ../Makefile >> makefile || die
+}
+
+src_compile() {
+	emake -C "$(uname -s)" viewmol_ tm_ bio_ readgamess_ readgauss_ readmopac_ readpdb_
+	"${EPREFIX}"/bin/bash makeTranslations || die
+}
+
+src_install() {
+	./install "${ED%/}"/usr || die
+
+	# fix broken layout
+	mv "${ED%/}"/usr/{usr/share,} || die
+	rm -rf "${ED%/}"/usr/usr || die
+	mv "${ED%/}"/usr/{$(get_libdir)/${PN}/locale,share} || die
+	mv "${ED%/}"/usr/{$(get_libdir),libexec} || die
+}