sci-chemistry/ccpn: Add patch to allow lxml as xml provider

(Portage version: 2.2.10/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

3 files changed, 251 insertions, 1 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index e2de4b10da3e..d4505fcbb405 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.137 2014/04/25 14:31:13 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.138 2014/04/28 16:39:07 jlec Exp $
+
+*ccpn-2.4.0_p140425-r1 (28 Apr 2014)
+
+  28 Apr 2014; Justin Lecher <jlec@gentoo.org> +ccpn-2.4.0_p140425-r1.ebuild,
+  +files/ccpn-2.4.0_p140425-lxml.patch:
+  Add patch to allow lxml as xml provider
 
 *ccpn-2.4.0_p140425 (25 Apr 2014)
 *ccpn-2.3.1_p140425 (25 Apr 2014)
diff --git a/sci-chemistry/ccpn/ccpn-2.4.0_p140425-r1.ebuild b/sci-chemistry/ccpn/ccpn-2.4.0_p140425-r1.ebuild
new file mode 100644
index 000000000000..2ba72f48e672
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.4.0_p140425-r1.ebuild
@@ -0,0 +1,166 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.4.0_p140425-r1.ebuild,v 1.1 2014/04/28 16:39:07 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+PYTHON_REQ_USE="ssl,tk"
+
+inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
+
+PATCHSET="${PV##*_p}"
+MY_PN="${PN}mr"
+MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
+MY_MAJOR="$(get_version_component_range 1-3)"
+
+DESCRIPTION="The Collaborative Computing Project for NMR"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+[[ -n ${PATCHSET} ]] \
+	&& SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+opengl"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	dev-lang/tk[threads]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-tcltk/tix
+	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
+	sci-biology/psipred
+	x11-libs/libXext
+	x11-libs/libX11
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet[${PYTHON_USEDEP}] )"
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2)
+
+src_prepare() {
+	[[ -n ${PATCHSET} ]] && \
+		EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
+
+	epatch "${FILESDIR}"/2.3.1-parallel.patch "${FILESDIR}"/${P}-lxml.patch
+
+	append-lfs-flags
+
+	sed \
+		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
+		-e "s:weights_s:weights:g" \
+		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
+
+	if use opengl; then
+		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
+		IGNORE_GL_FLAG=""
+		GL_FLAG="-DUSE_GL_TRUE"
+		GL_DIR="${EPREFIX}/usr"
+		GL_LIB="-lglut -lGLU -lGL"
+		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
+		GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
+
+	else
+		IGNORE_GL_FLAG="-DIGNORE_GL"
+		GL_FLAG="-DUSE_GL_FALSE"
+	fi
+
+	GLUT_NOT_IN_GL=""
+	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
+
+	rm -rf data model doc license || die
+
+	sed \
+		-e "s|/usr|${EPREFIX}/usr|g" \
+		-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
+		-e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \
+		-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
+		-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
+		-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
+		-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
+		-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
+		-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
+		-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
+		-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
+		-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
+		-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(TK_LIB =\).*|\1 -ltk|g" \
+		-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \
+		-e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \
+		c/environment_default.txt > c/environment.txt || die
+
+	sed \
+		-e 's:ln -s:cp -f:g' \
+		-i $(find python -name linkSharedObjs) || die
+}
+
+src_compile() {
+	emake -C c all
+	emake -C c links
+}
+
+src_install() {
+	local libdir
+	local tkver
+	local _wrapper
+
+	find . -name "*.pyc" -type f -delete || die
+
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
+	for wrapper in ${_wrapper}; do
+		sed \
+			-e "s|gentoo_sitedir|$(python_get_sitedir)|g" \
+		   -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+			-e "s|gentoopython|${EPYTHON}|g" \
+			-e "s|gentoousr|${EPREFIX}/usr|g" \
+			-e "s|//|/|g" \
+			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+		dobin "${T}"/${wrapper}
+	done
+
+	local in_path=$(python_get_sitedir)/${PN}
+	local files
+	local pydocs
+
+	pydocs="$(find python -name doc -type d)"
+	rm -rf ${pydocs} || die
+
+	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
+	sed \
+		-e 's|#from __future__|from __future__|g' \
+		-i ${i} || die
+	done
+
+	dodir ${in_path#${EPREFIX}}/c
+
+	ebegin "Installing main files"
+		python_moduleinto ${PN}
+		python_domodule python
+	eend
+
+	ebegin "Adjusting permissions"
+	for _file in $(find "${ED}" -type f -name "*so"); do
+		chmod 755 ${_file}
+	done
+	eend
+	python_optimize
+}
diff --git a/sci-chemistry/ccpn/files/ccpn-2.4.0_p140425-lxml.patch b/sci-chemistry/ccpn/files/ccpn-2.4.0_p140425-lxml.patch
new file mode 100644
index 000000000000..a476e98dfc8b
--- /dev/null
+++ b/sci-chemistry/ccpn/files/ccpn-2.4.0_p140425-lxml.patch
@@ -0,0 +1,78 @@
+ ccpnmr2.4/python/ccpnmr/format/general/Conversion.py |  2 +-
+ ccpnmr2.4/python/memops/metamodel/XmlModelIo.py      |  3 +++
+ ccpnmr2.4/python/memops/universal/ElementTree.py     | 16 +++++++++++-----
+ ccpnmr2.4/python/pdbe/xml/Util.py                    |  5 +----
+ 4 files changed, 16 insertions(+), 10 deletions(-)
+
+diff --git a/ccpnmr2.4/python/ccpnmr/format/general/Conversion.py b/ccpnmr2.4/python/ccpnmr/format/general/Conversion.py
+index 4e9a13c..66f72d3 100644
+--- a/ccpnmr2.4/python/ccpnmr/format/general/Conversion.py
++++ b/ccpnmr2.4/python/ccpnmr/format/general/Conversion.py
+@@ -1969,7 +1969,7 @@ class FormatConversion(object):
+ 
+   def runFromXml(self,xmlFileName,allowedFormats=None):
+   
+-    import xml.etree.ElementTree as ET
++    from memops.universal.ElementTree import ElementTree as ET
+    
+     root = ET.ElementTree(file=xmlFileName)
+     
+diff --git a/ccpnmr2.4/python/memops/metamodel/XmlModelIo.py b/ccpnmr2.4/python/memops/metamodel/XmlModelIo.py
+index e09a873..05a77a1 100644
+--- a/ccpnmr2.4/python/memops/metamodel/XmlModelIo.py
++++ b/ccpnmr2.4/python/memops/metamodel/XmlModelIo.py
+@@ -329,6 +329,9 @@ class XmlModelRead(TextWriter_py_2_1.TextWriter_py_2_1):
+       # handle contained elements
+       for elem in modelElem:
+         tag = elem.tag
++        # lxml also provides comments in addition to normal content
++        if tag is ElementTree.Comment:
++          continue
+         if classNameMapping.get(tag) is None:
+           # Element content - handle directly
+         
+diff --git a/ccpnmr2.4/python/memops/universal/ElementTree.py b/ccpnmr2.4/python/memops/universal/ElementTree.py
+index 2452217..c53afde 100644
+--- a/ccpnmr2.4/python/memops/universal/ElementTree.py
++++ b/ccpnmr2.4/python/memops/universal/ElementTree.py
+@@ -3,14 +3,20 @@ dependent on Python version
+ """
+ 
+ try:
+-  import xml.etree.cElementTree as ElementTree # in python >=2.5
++  from lxml import etree as ElementTree
+ except ImportError:
+   try:
+-    from  xml.etree import ElementTree # in python >=2.5
++    import xml.etree.cElementTree as ElementTree # in python >=2.5
+   except ImportError:
+-    from elementtree import ElementTree # effbot's pure Python module
++    try:
++      from  xml.etree import ElementTree # in python >=2.5
++    except ImportError:
++      from elementtree import ElementTree # effbot's pure Python module
+ 
+ try:
+-  from  xml.etree import ElementInclude # in python >=2.5
++  from lxml import ElementInclude
+ except ImportError:
+-  from elementtree import ElementInclude # effbot's pure Python module
++  try:
++    from  xml.etree import ElementInclude # in python >=2.5
++  except ImportError:
++    from elementtree import ElementInclude # effbot's pure Python module
+diff --git a/ccpnmr2.4/python/pdbe/xml/Util.py b/ccpnmr2.4/python/pdbe/xml/Util.py
+index eb36031..bc82b01 100644
+--- a/ccpnmr2.4/python/pdbe/xml/Util.py
++++ b/ccpnmr2.4/python/pdbe/xml/Util.py
+@@ -1,9 +1,6 @@
+ import sys, codecs
+ 
+-from xml.etree.ElementTree import ElementTree
+-#from xml.etree import ElementTree # Use this on flynn
+-#import xml.etree.ElementTree as ET
+-#import elementtree.ElementTree as ET
++from memops.universal.ElementTree import ElementTree
+ 
+ #
+ # Generic class to loop through elements/values of an XML ElementTree