| 1 |
jlec 12/03/04 09:18:53 |
| 2 |
|
| 3 |
Modified: ccpn-2.1.5_p120109.ebuild ccpn-2.2.1_p120109.ebuild |
| 4 |
ChangeLog ccpn-2.1.3.1_p100806.ebuild |
| 5 |
Added: ccpn-2.2.1_p120304.ebuild ccpn-2.1.5_p120304.ebuild |
| 6 |
Log: |
| 7 |
Today's python patches |
| 8 |
|
| 9 |
(Portage version: 2.2.0_alpha89/cvs/Linux x86_64) |
| 10 |
|
| 11 |
Revision Changes Path |
| 12 |
1.2 sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild |
| 13 |
|
| 14 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild?rev=1.2&view=markup |
| 15 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild?rev=1.2&content-type=text/plain |
| 16 |
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild?r1=1.1&r2=1.2 |
| 17 |
|
| 18 |
Index: ccpn-2.1.5_p120109.ebuild |
| 19 |
=================================================================== |
| 20 |
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild,v |
| 21 |
retrieving revision 1.1 |
| 22 |
retrieving revision 1.2 |
| 23 |
diff -u -r1.1 -r1.2 |
| 24 |
--- ccpn-2.1.5_p120109.ebuild 9 Jan 2012 12:42:11 -0000 1.1 |
| 25 |
+++ ccpn-2.1.5_p120109.ebuild 4 Mar 2012 09:18:53 -0000 1.2 |
| 26 |
@@ -1,6 +1,6 @@ |
| 27 |
# Copyright 1999-2012 Gentoo Foundation |
| 28 |
# Distributed under the terms of the GNU General Public License v2 |
| 29 |
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild,v 1.1 2012/01/09 12:42:11 jlec Exp $ |
| 30 |
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p120109.ebuild,v 1.2 2012/03/04 09:18:53 jlec Exp $ |
| 31 |
|
| 32 |
EAPI="3" |
| 33 |
|
| 34 |
@@ -16,7 +16,7 @@ |
| 35 |
|
| 36 |
DESCRIPTION="The Collaborative Computing Project for NMR" |
| 37 |
HOMEPAGE="http://www.ccpn.ac.uk/ccpn" |
| 38 |
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz" |
| 39 |
+SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" |
| 40 |
[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" |
| 41 |
|
| 42 |
SLOT="0" |
| 43 |
|
| 44 |
|
| 45 |
|
| 46 |
1.2 sci-chemistry/ccpn/ccpn-2.2.1_p120109.ebuild |
| 47 |
|
| 48 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p120109.ebuild?rev=1.2&view=markup |
| 49 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p120109.ebuild?rev=1.2&content-type=text/plain |
| 50 |
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p120109.ebuild?r1=1.1&r2=1.2 |
| 51 |
|
| 52 |
Index: ccpn-2.2.1_p120109.ebuild |
| 53 |
=================================================================== |
| 54 |
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p120109.ebuild,v |
| 55 |
retrieving revision 1.1 |
| 56 |
retrieving revision 1.2 |
| 57 |
diff -u -r1.1 -r1.2 |
| 58 |
--- ccpn-2.2.1_p120109.ebuild 9 Jan 2012 12:42:11 -0000 1.1 |
| 59 |
+++ ccpn-2.2.1_p120109.ebuild 4 Mar 2012 09:18:53 -0000 1.2 |
| 60 |
@@ -1,6 +1,6 @@ |
| 61 |
# Copyright 1999-2012 Gentoo Foundation |
| 62 |
# Distributed under the terms of the GNU General Public License v2 |
| 63 |
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p120109.ebuild,v 1.1 2012/01/09 12:42:11 jlec Exp $ |
| 64 |
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p120109.ebuild,v 1.2 2012/03/04 09:18:53 jlec Exp $ |
| 65 |
|
| 66 |
EAPI="3" |
| 67 |
|
| 68 |
@@ -15,7 +15,7 @@ |
| 69 |
MY_MAJOR="$(get_version_component_range 1-3)" |
| 70 |
|
| 71 |
DESCRIPTION="The Collaborative Computing Project for NMR" |
| 72 |
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz" |
| 73 |
+SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" |
| 74 |
[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" |
| 75 |
HOMEPAGE="http://www.ccpn.ac.uk/ccpn" |
| 76 |
|
| 77 |
|
| 78 |
|
| 79 |
|
| 80 |
1.80 sci-chemistry/ccpn/ChangeLog |
| 81 |
|
| 82 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ChangeLog?rev=1.80&view=markup |
| 83 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ChangeLog?rev=1.80&content-type=text/plain |
| 84 |
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ChangeLog?r1=1.79&r2=1.80 |
| 85 |
|
| 86 |
Index: ChangeLog |
| 87 |
=================================================================== |
| 88 |
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v |
| 89 |
retrieving revision 1.79 |
| 90 |
retrieving revision 1.80 |
| 91 |
diff -u -r1.79 -r1.80 |
| 92 |
--- ChangeLog 9 Jan 2012 12:42:11 -0000 1.79 |
| 93 |
+++ ChangeLog 4 Mar 2012 09:18:53 -0000 1.80 |
| 94 |
@@ -1,6 +1,14 @@ |
| 95 |
# ChangeLog for sci-chemistry/ccpn |
| 96 |
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 |
| 97 |
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.79 2012/01/09 12:42:11 jlec Exp $ |
| 98 |
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.80 2012/03/04 09:18:53 jlec Exp $ |
| 99 |
+ |
| 100 |
+*ccpn-2.2.1_p120304 (04 Mar 2012) |
| 101 |
+*ccpn-2.1.5_p120304 (04 Mar 2012) |
| 102 |
+ |
| 103 |
+ 04 Mar 2012; Justin Lecher <jlec@g.o> ccpn-2.1.3.1_p100806.ebuild, |
| 104 |
+ ccpn-2.1.5_p120109.ebuild, +ccpn-2.1.5_p120304.ebuild, |
| 105 |
+ ccpn-2.2.1_p120109.ebuild, +ccpn-2.2.1_p120304.ebuild: |
| 106 |
+ Today's python patches |
| 107 |
|
| 108 |
*ccpn-2.2.1_p120109 (09 Jan 2012) |
| 109 |
*ccpn-2.1.5_p120109 (09 Jan 2012) |
| 110 |
|
| 111 |
|
| 112 |
|
| 113 |
1.5 sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild |
| 114 |
|
| 115 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild?rev=1.5&view=markup |
| 116 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild?rev=1.5&content-type=text/plain |
| 117 |
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild?r1=1.4&r2=1.5 |
| 118 |
|
| 119 |
Index: ccpn-2.1.3.1_p100806.ebuild |
| 120 |
=================================================================== |
| 121 |
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild,v |
| 122 |
retrieving revision 1.4 |
| 123 |
retrieving revision 1.5 |
| 124 |
diff -u -r1.4 -r1.5 |
| 125 |
--- ccpn-2.1.3.1_p100806.ebuild 29 Jun 2011 05:51:28 -0000 1.4 |
| 126 |
+++ ccpn-2.1.3.1_p100806.ebuild 4 Mar 2012 09:18:53 -0000 1.5 |
| 127 |
@@ -1,6 +1,6 @@ |
| 128 |
-# Copyright 1999-2011 Gentoo Foundation |
| 129 |
+# Copyright 1999-2012 Gentoo Foundation |
| 130 |
# Distributed under the terms of the GNU General Public License v2 |
| 131 |
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild,v 1.4 2011/06/29 05:51:28 jlec Exp $ |
| 132 |
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.3.1_p100806.ebuild,v 1.5 2012/03/04 09:18:53 jlec Exp $ |
| 133 |
|
| 134 |
EAPI="3" |
| 135 |
PYTHON_DEPEND="2:2.5" |
| 136 |
@@ -14,7 +14,7 @@ |
| 137 |
MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" |
| 138 |
|
| 139 |
DESCRIPTION="The Collaborative Computing Project for NMR" |
| 140 |
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz" |
| 141 |
+SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" |
| 142 |
[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${PATCHSET}.patch.bz2" |
| 143 |
HOMEPAGE="http://www.ccpn.ac.uk/ccpn" |
| 144 |
|
| 145 |
|
| 146 |
|
| 147 |
|
| 148 |
1.1 sci-chemistry/ccpn/ccpn-2.2.1_p120304.ebuild |
| 149 |
|
| 150 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p120304.ebuild?rev=1.1&view=markup |
| 151 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p120304.ebuild?rev=1.1&content-type=text/plain |
| 152 |
|
| 153 |
Index: ccpn-2.2.1_p120304.ebuild |
| 154 |
=================================================================== |
| 155 |
# Copyright 1999-2012 Gentoo Foundation |
| 156 |
# Distributed under the terms of the GNU General Public License v2 |
| 157 |
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p120304.ebuild,v 1.1 2012/03/04 09:18:53 jlec Exp $ |
| 158 |
|
| 159 |
EAPI="3" |
| 160 |
|
| 161 |
PYTHON_DEPEND="2:2.5" |
| 162 |
PYTHON_USE_WITH="ssl tk" |
| 163 |
|
| 164 |
inherit eutils portability python toolchain-funcs versionator |
| 165 |
|
| 166 |
PATCHSET="${PV##*_p}" |
| 167 |
MY_PN="${PN}mr" |
| 168 |
MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" |
| 169 |
MY_MAJOR="$(get_version_component_range 1-3)" |
| 170 |
|
| 171 |
DESCRIPTION="The Collaborative Computing Project for NMR" |
| 172 |
SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" |
| 173 |
[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" |
| 174 |
HOMEPAGE="http://www.ccpn.ac.uk/ccpn" |
| 175 |
|
| 176 |
SLOT="0" |
| 177 |
LICENSE="|| ( CCPN LGPL-2.1 )" |
| 178 |
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
| 179 |
IUSE="extendnmr +opengl" |
| 180 |
|
| 181 |
RDEPEND=" |
| 182 |
dev-lang/tk[threads] |
| 183 |
>=dev-python/numpy-1.4 |
| 184 |
>=dev-tcltk/tix-8.4.3 |
| 185 |
=sci-libs/ccpn-data-"${MY_MAJOR}"* |
| 186 |
>=sci-libs/ccpn-data-2.2.1_p111011 |
| 187 |
sci-biology/psipred |
| 188 |
x11-libs/libXext |
| 189 |
x11-libs/libX11 |
| 190 |
opengl? ( |
| 191 |
media-libs/freeglut |
| 192 |
dev-python/pyglet )" |
| 193 |
# We need to fix this |
| 194 |
# sci-chemistry/mdd |
| 195 |
DEPEND="${RDEPEND}" |
| 196 |
PDEPEND=" |
| 197 |
extendnmr? ( |
| 198 |
>=sci-chemistry/aria-2.3.2-r1 |
| 199 |
sci-chemistry/prodecomp )" |
| 200 |
|
| 201 |
RESTRICT="mirror" |
| 202 |
|
| 203 |
S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV}) |
| 204 |
|
| 205 |
pkg_setup() { |
| 206 |
python_set_active_version 2 |
| 207 |
} |
| 208 |
|
| 209 |
src_prepare() { |
| 210 |
[[ -n ${PATCHSET} ]] && \ |
| 211 |
epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch |
| 212 |
|
| 213 |
epatch "${FILESDIR}"/${MY_PV}-parallel.patch |
| 214 |
|
| 215 |
sed \ |
| 216 |
-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ |
| 217 |
-e "s:weights_s:weights:g" \ |
| 218 |
-i python/ccpnmr/analysis/wrappers/Psipred.py || die |
| 219 |
|
| 220 |
local tk_ver |
| 221 |
local myconf |
| 222 |
|
| 223 |
tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" |
| 224 |
|
| 225 |
if use opengl; then |
| 226 |
GLUT_NEED_INIT="-DNEED_GLUT_INIT" |
| 227 |
IGNORE_GL_FLAG="" |
| 228 |
GL_FLAG="-DUSE_GL_TRUE" |
| 229 |
GL_DIR="${EPREFIX}/usr" |
| 230 |
GL_LIB="-lglut -lGLU -lGL" |
| 231 |
GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" |
| 232 |
GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)" |
| 233 |
|
| 234 |
else |
| 235 |
IGNORE_GL_FLAG="-DIGNORE_GL" |
| 236 |
GL_FLAG="-DUSE_GL_FALSE" |
| 237 |
fi |
| 238 |
|
| 239 |
GLUT_NOT_IN_GL="" |
| 240 |
GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" |
| 241 |
|
| 242 |
rm -rf data model doc license || die |
| 243 |
|
| 244 |
sed \ |
| 245 |
-e "s|/usr|${EPREFIX}/usr|g" \ |
| 246 |
-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ |
| 247 |
-e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \ |
| 248 |
-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ |
| 249 |
-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ |
| 250 |
-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ |
| 251 |
-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ |
| 252 |
-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ |
| 253 |
-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ |
| 254 |
-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ |
| 255 |
-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ |
| 256 |
-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ |
| 257 |
-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ |
| 258 |
-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ |
| 259 |
-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ |
| 260 |
-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \ |
| 261 |
-e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \ |
| 262 |
c/environment_default.txt > c/environment.txt |
| 263 |
} |
| 264 |
|
| 265 |
src_compile() { |
| 266 |
emake -C c all links || die |
| 267 |
} |
| 268 |
|
| 269 |
src_install() { |
| 270 |
local libdir |
| 271 |
local tkver |
| 272 |
local _wrapper |
| 273 |
|
| 274 |
find . -name "*.pyc" -type d -delete |
| 275 |
|
| 276 |
libdir=$(get_libdir) |
| 277 |
tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) |
| 278 |
|
| 279 |
_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara" |
| 280 |
use extendnmr && _wrapper="${_wrapper} extendNmr" |
| 281 |
for wrapper in ${_wrapper}; do |
| 282 |
sed \ |
| 283 |
-e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \ |
| 284 |
-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ |
| 285 |
-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ |
| 286 |
-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ |
| 287 |
-e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \ |
| 288 |
-e "s|gentoousr|${EPREFIX}/usr|g" \ |
| 289 |
-e "s|//|/|g" \ |
| 290 |
"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" |
| 291 |
dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}" |
| 292 |
done |
| 293 |
|
| 294 |
local in_path |
| 295 |
local files |
| 296 |
local pydocs |
| 297 |
|
| 298 |
pydocs="$(find python -name doc -type d)" |
| 299 |
rm -rf ${pydocs} || die |
| 300 |
|
| 301 |
in_path=$(python_get_sitedir)/${PN} |
| 302 |
|
| 303 |
for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do |
| 304 |
sed \ |
| 305 |
-e 's|#from __future__|from __future__|g' \ |
| 306 |
-i ${i} || die |
| 307 |
done |
| 308 |
|
| 309 |
insinto ${in_path} |
| 310 |
|
| 311 |
dodir ${in_path}/c |
| 312 |
|
| 313 |
ebegin "Installing main files" |
| 314 |
doins -r python || die "main files installation failed" |
| 315 |
eend |
| 316 |
|
| 317 |
einfo "Adjusting permissions" |
| 318 |
|
| 319 |
files=" |
| 320 |
cambridge/c/BayesPeakSeparator.so |
| 321 |
ccp/c/StructUtil.so |
| 322 |
ccp/c/StructStructure.so |
| 323 |
ccp/c/StructBond.so |
| 324 |
ccp/c/StructAtom.so |
| 325 |
ccpnmr/c/DyAtomCoord.so |
| 326 |
ccpnmr/c/DyDistConstraint.so |
| 327 |
ccpnmr/c/DyDistForce.so |
| 328 |
ccpnmr/c/AtomCoordList.so |
| 329 |
ccpnmr/c/DyAtomCoordList.so |
| 330 |
ccpnmr/c/ContourStyle.so |
| 331 |
ccpnmr/c/ContourLevels.so |
| 332 |
ccpnmr/c/SliceFile.so |
| 333 |
ccpnmr/c/PeakCluster.so |
| 334 |
ccpnmr/c/Dynamics.so |
| 335 |
ccpnmr/c/Bacus.so |
| 336 |
ccpnmr/c/Midge.so |
| 337 |
ccpnmr/c/DyDistConstraintList.so |
| 338 |
ccpnmr/c/WinPeakList.so |
| 339 |
ccpnmr/c/PeakList.so |
| 340 |
ccpnmr/c/DistConstraint.so |
| 341 |
ccpnmr/c/CloudUtil.so |
| 342 |
ccpnmr/c/DistForce.so |
| 343 |
ccpnmr/c/DistConstraintList.so |
| 344 |
ccpnmr/c/AtomCoord.so |
| 345 |
ccpnmr/c/DyDynamics.so |
| 346 |
ccpnmr/c/ContourFile.so |
| 347 |
memops/c/ShapeFile.so |
| 348 |
memops/c/BlockFile.so |
| 349 |
memops/c/PdfHandler.so |
| 350 |
memops/c/MemCache.so |
| 351 |
memops/c/FitMethod.so |
| 352 |
memops/c/PsHandler.so |
| 353 |
memops/c/GlHandler.so |
| 354 |
memops/c/StoreFile.so |
| 355 |
memops/c/StoreHandler.so |
| 356 |
memops/c/TkHandler.so" |
| 357 |
for FILE in ${files}; do |
| 358 |
fperms 755 ${in_path}/python/${FILE} |
| 359 |
done |
| 360 |
} |
| 361 |
|
| 362 |
pkg_postinst() { |
| 363 |
python_mod_optimize ${PN} |
| 364 |
} |
| 365 |
|
| 366 |
pkg_postrm() { |
| 367 |
python_mod_cleanup ${PN} |
| 368 |
} |
| 369 |
|
| 370 |
|
| 371 |
|
| 372 |
1.1 sci-chemistry/ccpn/ccpn-2.1.5_p120304.ebuild |
| 373 |
|
| 374 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p120304.ebuild?rev=1.1&view=markup |
| 375 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p120304.ebuild?rev=1.1&content-type=text/plain |
| 376 |
|
| 377 |
Index: ccpn-2.1.5_p120304.ebuild |
| 378 |
=================================================================== |
| 379 |
# Copyright 1999-2012 Gentoo Foundation |
| 380 |
# Distributed under the terms of the GNU General Public License v2 |
| 381 |
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p120304.ebuild,v 1.1 2012/03/04 09:18:53 jlec Exp $ |
| 382 |
|
| 383 |
EAPI="3" |
| 384 |
|
| 385 |
PYTHON_DEPEND="2:2.5" |
| 386 |
PYTHON_USE_WITH="ssl tk" |
| 387 |
|
| 388 |
inherit eutils portability python toolchain-funcs versionator |
| 389 |
|
| 390 |
PATCHSET="${PV##*_p}" |
| 391 |
MY_PN="${PN}mr" |
| 392 |
MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" |
| 393 |
MY_MAJOR="$(get_version_component_range 1-3)" |
| 394 |
|
| 395 |
DESCRIPTION="The Collaborative Computing Project for NMR" |
| 396 |
HOMEPAGE="http://www.ccpn.ac.uk/ccpn" |
| 397 |
SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" |
| 398 |
[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" |
| 399 |
|
| 400 |
SLOT="0" |
| 401 |
LICENSE="|| ( CCPN LGPL-2.1 )" |
| 402 |
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
| 403 |
IUSE="extendnmr +opengl" |
| 404 |
|
| 405 |
RDEPEND=" |
| 406 |
dev-lang/tk[threads] |
| 407 |
>=dev-python/numpy-1.4 |
| 408 |
>=dev-tcltk/tix-8.4.3 |
| 409 |
=sci-libs/ccpn-data-"${MY_MAJOR}"* |
| 410 |
>=sci-libs/ccpn-data-2.1.5_p111011 |
| 411 |
sci-biology/psipred |
| 412 |
x11-libs/libXext |
| 413 |
x11-libs/libX11 |
| 414 |
opengl? ( |
| 415 |
media-libs/freeglut |
| 416 |
dev-python/pyglet )" |
| 417 |
# We need to fix this |
| 418 |
# sci-chemistry/mdd |
| 419 |
DEPEND="${RDEPEND}" |
| 420 |
PDEPEND=" |
| 421 |
extendnmr? ( |
| 422 |
<=sci-chemistry/aria-2.3.2 |
| 423 |
sci-chemistry/prodecomp )" |
| 424 |
|
| 425 |
RESTRICT="mirror" |
| 426 |
|
| 427 |
S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV}) |
| 428 |
|
| 429 |
pkg_setup() { |
| 430 |
python_set_active_version 2 |
| 431 |
} |
| 432 |
|
| 433 |
src_prepare() { |
| 434 |
[[ -n ${PATCHSET} ]] && \ |
| 435 |
epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch |
| 436 |
|
| 437 |
epatch "${FILESDIR}"/${MY_PV}-parallel.patch |
| 438 |
|
| 439 |
sed \ |
| 440 |
-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ |
| 441 |
-e "s:weights_s:weights:g" \ |
| 442 |
-i python/ccpnmr/analysis/wrappers/Psipred.py || die |
| 443 |
|
| 444 |
local tk_ver |
| 445 |
local myconf |
| 446 |
|
| 447 |
tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" |
| 448 |
|
| 449 |
if use opengl; then |
| 450 |
GLUT_NEED_INIT="-DNEED_GLUT_INIT" |
| 451 |
IGNORE_GL_FLAG="" |
| 452 |
GL_FLAG="-DUSE_GL_TRUE" |
| 453 |
GL_DIR="${EPREFIX}/usr" |
| 454 |
GL_LIB="-lglut -lGLU -lGL" |
| 455 |
GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" |
| 456 |
GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)" |
| 457 |
|
| 458 |
else |
| 459 |
IGNORE_GL_FLAG="-DIGNORE_GL" |
| 460 |
GL_FLAG="-DUSE_GL_FALSE" |
| 461 |
fi |
| 462 |
|
| 463 |
GLUT_NOT_IN_GL="" |
| 464 |
GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" |
| 465 |
|
| 466 |
rm -rf data model doc license || die |
| 467 |
|
| 468 |
sed \ |
| 469 |
-e "s|/usr|${EPREFIX}/usr|g" \ |
| 470 |
-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ |
| 471 |
-e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \ |
| 472 |
-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ |
| 473 |
-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ |
| 474 |
-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ |
| 475 |
-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ |
| 476 |
-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ |
| 477 |
-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ |
| 478 |
-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ |
| 479 |
-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ |
| 480 |
-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ |
| 481 |
-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ |
| 482 |
-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ |
| 483 |
-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ |
| 484 |
-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \ |
| 485 |
-e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \ |
| 486 |
c/environment_default.txt > c/environment.txt |
| 487 |
} |
| 488 |
|
| 489 |
src_compile() { |
| 490 |
emake -C c all links || die |
| 491 |
} |
| 492 |
|
| 493 |
src_install() { |
| 494 |
local libdir |
| 495 |
local tkver |
| 496 |
local _wrapper |
| 497 |
|
| 498 |
find . -name "*.pyc" -type d -delete |
| 499 |
|
| 500 |
libdir=$(get_libdir) |
| 501 |
tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) |
| 502 |
|
| 503 |
_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara" |
| 504 |
use extendnmr && _wrapper="${_wrapper} extendNmr" |
| 505 |
for wrapper in ${_wrapper}; do |
| 506 |
sed \ |
| 507 |
-e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \ |
| 508 |
-e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ |
| 509 |
-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ |
| 510 |
-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ |
| 511 |
-e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \ |
| 512 |
-e "s|gentoousr|${EPREFIX}/usr|g" \ |
| 513 |
-e "s|//|/|g" \ |
| 514 |
"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" |
| 515 |
dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}" |
| 516 |
done |
| 517 |
|
| 518 |
local in_path |
| 519 |
local files |
| 520 |
local pydocs |
| 521 |
|
| 522 |
pydocs="$(find python -name doc -type d)" |
| 523 |
rm -rf ${pydocs} || die |
| 524 |
|
| 525 |
in_path=$(python_get_sitedir)/${PN} |
| 526 |
|
| 527 |
for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do |
| 528 |
sed \ |
| 529 |
-e 's|#from __future__|from __future__|g' \ |
| 530 |
-i ${i} || die |
| 531 |
done |
| 532 |
|
| 533 |
insinto ${in_path} |
| 534 |
|
| 535 |
dodir ${in_path}/c |
| 536 |
|
| 537 |
ebegin "Installing main files" |
| 538 |
doins -r python || die "main files installation failed" |
| 539 |
eend |
| 540 |
|
| 541 |
einfo "Adjusting permissions" |
| 542 |
|
| 543 |
files=" |
| 544 |
cambridge/c/BayesPeakSeparator.so |
| 545 |
ccp/c/StructUtil.so |
| 546 |
ccp/c/StructStructure.so |
| 547 |
ccp/c/StructBond.so |
| 548 |
ccp/c/StructAtom.so |
| 549 |
ccpnmr/c/DyAtomCoord.so |
| 550 |
ccpnmr/c/DyDistConstraint.so |
| 551 |
ccpnmr/c/DyDistForce.so |
| 552 |
ccpnmr/c/AtomCoordList.so |
| 553 |
ccpnmr/c/DyAtomCoordList.so |
| 554 |
ccpnmr/c/ContourStyle.so |
| 555 |
ccpnmr/c/ContourLevels.so |
| 556 |
ccpnmr/c/SliceFile.so |
| 557 |
ccpnmr/c/PeakCluster.so |
| 558 |
ccpnmr/c/Dynamics.so |
| 559 |
ccpnmr/c/Bacus.so |
| 560 |
ccpnmr/c/Midge.so |
| 561 |
ccpnmr/c/DyDistConstraintList.so |
| 562 |
ccpnmr/c/WinPeakList.so |
| 563 |
ccpnmr/c/PeakList.so |
| 564 |
ccpnmr/c/DistConstraint.so |
| 565 |
ccpnmr/c/CloudUtil.so |
| 566 |
ccpnmr/c/DistForce.so |
| 567 |
ccpnmr/c/DistConstraintList.so |
| 568 |
ccpnmr/c/AtomCoord.so |
| 569 |
ccpnmr/c/DyDynamics.so |
| 570 |
ccpnmr/c/ContourFile.so |
| 571 |
memops/c/ShapeFile.so |
| 572 |
memops/c/BlockFile.so |
| 573 |
memops/c/PdfHandler.so |
| 574 |
memops/c/MemCache.so |
| 575 |
memops/c/FitMethod.so |
| 576 |
memops/c/PsHandler.so |
| 577 |
memops/c/GlHandler.so |
| 578 |
memops/c/StoreFile.so |
| 579 |
memops/c/StoreHandler.so |
| 580 |
memops/c/TkHandler.so" |
| 581 |
for FILE in ${files}; do |
| 582 |
fperms 755 ${in_path}/python/${FILE} |
| 583 |
done |
| 584 |
} |
| 585 |
|
| 586 |
pkg_postinst() { |
| 587 |
python_mod_optimize ${PN} |
| 588 |
} |
| 589 |
|
| 590 |
pkg_postrm() { |
| 591 |
python_mod_cleanup ${PN} |
| 592 |
} |
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