sci-chemistry/ccpn version bump to 2.0.6

8 files changed, 229 insertions, 1 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index dab52f69e..7e5fc5310 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  28 Jan 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +sci-chemistry/ccpn/files/analysis, +sci-chemistry/ccpn/files/dangle,
+  +sci-chemistry/ccpn/files/dataShifter,
+  +sci-chemistry/ccpn/files/formatConverter,
+  +sci-chemistry/ccpn/files/pipe2azara:
+  version bump to 2.0.6
+
   26 Jan 2009; justin Lecher (jlec) <jlec@j-schmitz.net> +licenses/AZARA,
   +sci-chemistry/azara/files/help-makefile.patch,
   +sci-chemistry/azara/metadata.xml,
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index f9853bd03..791d5c02c 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -1,5 +1,12 @@
+AUX analysis 313 RMD160 2fcb8ae4654397b8591994004dae037ce2334ed1 SHA1 6bdac52dcc29987535f4ed4a61aaebb67855495d SHA256 3f9e9c56af2a6f690184660d230460f553d2dd930bc59b6fb92c1a62ee5e6903
+AUX dangle 309 RMD160 b832aba9c613a7d5c60d15787873240da071f8d5 SHA1 e5168bbb2acc287baeb39e9255984794c6ced6f0 SHA256 25eee00940645823dff98e1bcc3b3866963c6b86569012ebd4192164d6afb354
+AUX dataShifter 312 RMD160 ff8aeea7ddbbe57a7a0ca74d7cc1dfb604ae63f7 SHA1 579e090f345b45a4f1dc331610c89ea2c78aa271 SHA256 fe1f39f6f462aa82cf74890e74de9229f1b5521ebbbaf099291d4e4dd8980bca
+AUX formatConverter 316 RMD160 546b9e62215c746d746b37b21a995a3c52d2c99f SHA1 fd4b20aafa0c903611691c57b1fcec5c0082550d SHA256 8564f541f23197a89edda08233a299f6c8652717438900847b5d91dba2eb344c
 AUX missing-link.patch 560 RMD160 17eec66581c4c120306464cd89486283fd1bfc89 SHA1 82198fdc32e22c488a679656c3cc6ac18c7e76ad SHA256 db5518683e254304f8de1420b102bfe08051839666a9edf2529d3235946ecd88
+AUX pipe2azara 320 RMD160 c407146718b918e071724b6c3574139e485b9b28 SHA1 a338d566fff16c9ab465017fd4d32c3da3cfaa42 SHA256 1004b4546bf047956f5b8a9bd0f1383c93821dc901d276ef30ebfcbaa92be20d
 DIST analysis2.0.5.tar.gz 17200055 RMD160 9c6429c00711385462cd753a7c9cd103f9b2cbb4 SHA1 4240c2be876e86b894d2958c218d85976f9f581c SHA256 9b91d4fffbc8fee3449f24af5fc49ca9e633cbafd8f049d8c274dfd30f5acea9
+DIST analysis2.0.6.tar.gz 17351891 RMD160 16d66a2cad36aa65a354ae1524af50f7c6576910 SHA1 cedc7a55a17a9e904a1d575850dc5f6c4fb06e85 SHA256 bfe1aec93f8fe80fc7c6914854239defddde498ffb10a692b7f7445a0563a10f
 EBUILD ccpn-2.0.5.ebuild 4113 RMD160 02e2606ef351199d81c200eff30bc0f5193aab35 SHA1 1f62259120069a075c32a7936f3bb206b89b53ee SHA256 a6e8d8b0eb25c4b9d298c90d2d6db863358b30669dfbc90e5887a32eee80180f
-MISC ChangeLog 411 RMD160 a7adaa8701e7129036893fbe30c410a21b2de5e3 SHA1 79643abe4ac7d8782f834790b30e27f6cb63bca1 SHA256 f8c6b74f0af4d7667bd59eb45d95b8f79026f67a2739b03a191a45fdc4334db0
+EBUILD ccpn-2.0.6.ebuild 4140 RMD160 ec68710f4c97f53b27f970eb69a84f7ac0b862f7 SHA1 1f7fe4021e392ae66c344d2123db25f5a8bc8f8e SHA256 331a4c921209383f8f5eee6af9eac5d88a1437517e5b9fe2271ddf4d360cb33b
+MISC ChangeLog 691 RMD160 fd06dc86569f5548be413a2d7d5538e021951220 SHA1 15f1729cadaa1fba27e9459c0a80bcbe32623f8a SHA256 bb3927ec44096935a28a4cd6ab31b52c45791d2499724f41f1786f25a69c1d41
 MISC metadata.xml 330 RMD160 13bb0be56708a39aabbc10873f8a29ebda9c65b9 SHA1 a6f303065d778f1749afb87ce259dabc1fa46e9d SHA256 8da72694da743462406853a0c8922dac0aebf17c8345df3a19daafcd105dcc04
diff --git a/sci-chemistry/ccpn/ccpn-2.0.6.ebuild b/sci-chemistry/ccpn/ccpn-2.0.6.ebuild
new file mode 100644
index 000000000..d19c110ae
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.0.6.ebuild
@@ -0,0 +1,174 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+NEED_PYTHON=2.4
+PYTHON_MODNAME="ccpn"
+
+inherit python toolchain-funcs portability distutils eutils
+
+MY_PN="${PN}mr"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~x86"
+DESCRIPTION="The Collaborative Computing Project for NMR"
+SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${PV}.tar.gz"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+IUSE="doc numpy opengl"
+RESTRICT="mirror"
+RDEPEND="${DEPEND}"
+DEPEND="virtual/glut
+	 dev-tcltk/tix
+	 dev-python/numpy"
+
+S="${WORKDIR}"/${MY_PN}
+
+pkg_setup() {
+	python_tkinter_exists
+	python_version
+}
+
+src_unpack() {
+	unpack ${A}
+
+#	epatch "${FILESDIR}"/missing-link.patch
+
+	echo "" > "${S}"/ccpnmr2.0/c/environment.txt || die "failed to kill environment.txt"
+}
+
+src_compile() {
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
+
+	if use opengl; then
+
+	if has_version media-libs/freeglut; then
+		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
+	else
+		GLUT_NEED_INIT=""
+	fi
+
+		IGNORE_GL_FLAG=""
+		GL_FLAG="-DUSE_GL_FALSE"
+		GLUT_NOT_IN_GL=""
+		GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
+		GL_DIR="/usr"
+		GL_LIB="-lglut -lGLU -lGL"
+		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
+		GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
+
+	else
+		IGNORE_GL_FLAG="-DIGNORE_GL"
+		GL_FLAG="-DUSE_GL_FALSE"
+		GLUT_NOT_IN_GL=""
+		GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
+	fi
+
+	cd ccpnmr2.0/c
+
+	emake \
+		CC="$(tc-getCC)" \
+		LDFLAGS="${LDFLAGGS}" \
+		MALLOC_FLAG= \
+		FPIC_FLAG="-fPIC" \
+		SHARED_FLAGS="-shared" \
+		MATH_LIB="-lm" \
+		X11_DIR="/usr" \
+		X11_LIB="-lX11 -lXext" \
+		X11_INCLUDE_FLAGS="-I\$(X11_DIR)/include" \
+		X11_LIB_FLAGS="-L\$(X11_DIR)/lib" \
+		TCL_DIR="/usr" \
+		TCL_LIB="-ltcl${tk_ver}" \
+		TCL_INCLUDE_FLAGS="-I\$(TCL_DIR)/include" \
+		TCL_LIB_FLAGS="-L\$(TCL_DIR)/$(get_libdir)" \
+		TK_DIR="/usr" \
+		TK_LIB="-ltk${tk_ver}" \
+		TK_INCLUDE_FLAGS="-I\$(TK_DIR)/include" \
+		TK_LIB_FLAGS="-L\$(TK_DIR)/$(get_libdir)" \
+		PYTHON_DIR="/usr" \
+		PYTHON_INCLUDE_FLAGS="-I\$(PYTHON_DIR)/include/python${PYVER}" \
+		CFLAGS="${CFLAGS} \$(MALLOC_FLAG) \$(FPIC_FLAG)" \
+		GLUT_NEED_INIT="${GLUT_NEED_INIT}" \
+		IGNORE_GL_FLAG="${IGNORE_GL_FLAG}" \
+		GL_FLAG="${GL_FLAG}" \
+		GLUT_NOT_IN_GL="${GLUT_NOT_IN_GL}" \
+		GLUT_FLAG="${GLUT_FLAG}" \
+		GL_DIR="${GL_DIR}" \
+		GL_LIB="${GL_LIB}" \
+		GL_INCLUDE_FLAGS="${GL_INCLUDE_FLAGS}" \
+		GL_LIB_FLAGS="${GL_LIB_FLAGS}" \
+	all links || \
+	die "failed to compile"
+
+}
+
+src_install() {
+
+	local IN_PATH
+	local GENTOO_SITEDIR
+	local LIBDIR
+	local FILES
+
+	IN_PATH=$(python_get_sitedir)/${PN}
+	GENTOO_SITEDIR=$(python_get_sitedir)
+	LIBDIR=$(get_libdir)
+
+	for wrapper in analysis dangle dataShifter formatConverter pipe2azara; do
+		sed -e "s:GENTOO_SITEDIR:${GENTOO_SITEDIR}:g" \
+		    -e "s:LIBDIR:${LIBDIR}:g" \
+		    "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+		dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
+	done
+
+	use doc && treecopy $(find . -name doc) "${D}"usr/share/doc/${PF}/html/
+
+	ebegin "Removing unneeded docs"
+	find . -name doc -exec rm -rf '{}' \; 2> /dev/null
+	eend
+
+	insinto ${IN_PATH}
+
+	ebegin "Installing main files"
+	doins -r ccpnmr2.0/{data,model,python} || die "main files installation failed"
+	eend
+
+	einfo "Adjusting permissions"
+
+	FILES="ccpnmr/c/ContourFile.so
+		ccpnmr/c/ContourLevels.so
+		ccpnmr/c/ContourStyle.so
+		ccpnmr/c/PeakList.so
+		ccpnmr/c/SliceFile.so
+		ccpnmr/c/WinPeakList.so
+		ccpnmr/c/AtomCoordList.so
+		ccpnmr/c/AtomCoord.so
+		ccpnmr/c/Bacus.so
+		ccpnmr/c/CloudUtil.so
+		ccpnmr/c/DistConstraintList.so
+		ccpnmr/c/DistConstraint.so
+		ccpnmr/c/DistForce.so
+		ccpnmr/c/Dynamics.so
+		ccpnmr/c/Midge.so
+		ccp/c/StructAtom.so
+		ccp/c/StructBond.so
+		ccp/c/StructStructure.so
+		ccp/c/StructUtil.so
+		memops/c/BlockFile.so
+		memops/c/FitMethod.so
+		memops/c/GlHandler.so
+		memops/c/MemCache.so
+		memops/c/PdfHandler.so
+		memops/c/PsHandler.so
+		memops/c/ShapeFile.so
+		memops/c/StoreFile.so
+		memops/c/StoreHandler.so
+		memops/c/TkHandler.so"
+
+	for FILE in ${FILES}; do
+		fperms 755 ${IN_PATH}/python/${FILE}
+	done
+}
diff --git a/sci-chemistry/ccpn/files/analysis b/sci-chemistry/ccpn/files/analysis
new file mode 100644
index 000000000..dbdd44dcc
--- /dev/null
+++ b/sci-chemistry/ccpn/files/analysis
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+export CCPNMR_TOP_DIR=GENTOO_SITEDIR
+export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
+export LD_LIBRARY_PATH=/usr/LIBDIR
+export TCL_LIBRARY=/usr/LIBDIR/tcl8.4
+export TK_LIBRARY=/usr/LIBDIR/tk8.4
+/usr/bin/python2.5 -i -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/analysis/AnalysisGui.py $1 $2 $3 $4 $5 $6
diff --git a/sci-chemistry/ccpn/files/dangle b/sci-chemistry/ccpn/files/dangle
new file mode 100644
index 000000000..4013139fe
--- /dev/null
+++ b/sci-chemistry/ccpn/files/dangle
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+export CCPNMR_TOP_DIR=GENTOO_SITEDIR
+export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
+export LD_LIBRARY_PATH=/usr/LIBDIR
+export TCL_LIBRARY=/usr/LIBDIR/tcl8.4
+export TK_LIBRARY=/usr/LIBDIR/tk8.4
+/usr/bin/python2.5 -O ${CCPNMR_TOP_DIR}/ccpn/python/cambridge/dangle/DangleGui.py $1 $2 $3 $4 $5 $6
diff --git a/sci-chemistry/ccpn/files/dataShifter b/sci-chemistry/ccpn/files/dataShifter
new file mode 100644
index 000000000..7e29ad0c1
--- /dev/null
+++ b/sci-chemistry/ccpn/files/dataShifter
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+export CCPNMR_TOP_DIR=GENTOO_SITEDIR
+export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
+export LD_LIBRARY_PATH=/usr/LIBDIR
+export TCL_LIBRARY=/usr/LIBDIR/tcl8.4
+export TK_LIBRARY=/usr/LIBDIR/tk8.4
+/usr/bin/python2.5 -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/DataShifter.py $1 $2 $3 $4 $5 $6
diff --git a/sci-chemistry/ccpn/files/formatConverter b/sci-chemistry/ccpn/files/formatConverter
new file mode 100644
index 000000000..d5f5beb22
--- /dev/null
+++ b/sci-chemistry/ccpn/files/formatConverter
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+export CCPNMR_TOP_DIR=GENTOO_SITEDIR
+export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
+export LD_LIBRARY_PATH=/usr/LIBDIR
+export TCL_LIBRARY=/usr/LIBDIR/tcl8.4
+export TK_LIBRARY=/usr/LIBDIR/tk8.4
+/usr/bin/python2.5 -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/FormatConverter.py $1 $2 $3 $4 $5 $6
diff --git a/sci-chemistry/ccpn/files/pipe2azara b/sci-chemistry/ccpn/files/pipe2azara
new file mode 100644
index 000000000..bedef4dc4
--- /dev/null
+++ b/sci-chemistry/ccpn/files/pipe2azara
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+export CCPNMR_TOP_DIR=GENTOO_SITEDIR
+export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
+export LD_LIBRARY_PATH=/usr/LIBDIR
+export TCL_LIBRARY=/usr/LIBDIR/tcl8.4
+export TK_LIBRARY=/usr/LIBDIR/tk8.4
+/usr/bin/python2.5 -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/NmrPipeData.py $1 $2 $3 $4 $5 $6