[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/coot/, sci-chemistry/coot/files/

["Justin Lecher" <jlec@gentoo.org>]

commit:     673d602fa0469af10478c8090c69a00fdfef9b40
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 15 13:47:49 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep 15 14:03:52 2015 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=673d602f

sci-chemistry/coot: Version Bump

Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-chemistry/coot/Manifest                        |   2 +
 sci-chemistry/coot/coot-0.8.2.ebuild               | 176 +++++++++++++++++++++
 sci-chemistry/coot/files/coot-0.8.2-desktop.patch  |  21 +++
 sci-chemistry/coot/files/coot-0.8.2-libguile.patch |  29 ++++
 sci-chemistry/coot/files/coot-0.8.2-libtool.patch  |  39 +++++
 .../coot/files/coot-0.8.2-sandbox-icons.patch      |  16 ++
 6 files changed, 283 insertions(+)

diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index 3b897f1..7942eee 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -1,6 +1,8 @@
 DIST coot-0.7.1.tar.gz 16663581 SHA256 2310d48f7581283ee20eeb355d5fcef90e8d36bc032684b7b47f7c61e89ea0a9 SHA512 dad758b227231543cacd9b34ca00a0bff18bdc208c10529bbf2e504db9f17a3f1bbf610a52c21fe6046e443222667a3703dc962241debff87058ac041bbcec2e WHIRLPOOL 7c57f1161016a74449a9fee1202ada82044d17d957002c67c59f2eb9776f676eb525b605a1973b9bc479e15b40df5478e3b3fad9594433fee73bfc544d5d6b52
 DIST coot-0.7.2.tar.gz 16859099 SHA256 67fbb702559be850f3198c11038fa2c25c692ef8a284e88bbf6a0e941cf3dadd SHA512 84ced967ab661a36ae61a529c1e7fdef121283795fe2300946277c8ba0724724a0190806434257cae01302542efd628cb57d0f35f24968b061cb04faf43daefa WHIRLPOOL ef379156fdfafc275fa953c01b81a06bf75dbf51cc84d6669fa92aef4449e507f45429ad599b455ca3b6b53f9944116adfe42e7ef50e2c56396624f3b5ea5f79
 DIST coot-0.7.tar.gz 16172237 SHA256 e3d61d326ee906eb77081a6f646024cc6c5c92281f9508da3086fb937fb05aa2 SHA512 27fe0485240adcb7f370cf2daf116d8ea1c8e80e297c0975f1b2d2f78d4a5cd9314e06537e680993d465ef551ceba46a2b402c63acfabcbf599cca6bdb8f843f WHIRLPOOL cc919a7ec3731cfd482bb906c7fd9dc98d9ce2ba2f6bbaa91facf5e5195e27b3fe3f0e03e93668a1524bc2b2306ec23951e1db5033315ed1f26456768a5ac2a7
+DIST coot-0.8.2.tar.gz 15772937 SHA256 2f5961ded7f2cf06b887560afe964c239aba94f9c4bf8a2a80b3ca4fbc471eee SHA512 a323608df7b63f22eb2d1ac679fc047bba9fe23fe6366ae1d6ae29ca00a567aafb3d29840878e8c5123421037e26b6463f0bb845ef28dcbb4f3647cda2f74575 WHIRLPOOL d84d23aa49404dce63649bd6c5f8149e95ad5776ec4fa6ebdfcf44ebabef56c3a29376da7a1d5f8ee6f8013158a7f5c74f5bd74066036ca750bc3ff7de084791
+DIST coot-greg-data.tar.gz 8677037 SHA256 d936795853406f3c2a3dfd6f37a07a7df677e96b2d023d9302668aa49b7f06cb SHA512 28396a5fa64af61e8932b565c6593ed27c4708e6a59158d62c94005bea9fa8c46562b6caba97011209a40705e5ec6711b949138dd8a23bb954df2ab4dfa9bb33 WHIRLPOOL cb85234ece76314661bcfa424904224ac554c41fc63655857f3ba1bd2f0bf8e457c55dd1f42ffecffb9a8582ff759277b0fb9a40ca2393bf47b6a09fdd04ce1e
 DIST greg-data-0.7.1.tar.gz 8142259 SHA256 6f3e1c1bc540c8355583ce2e1807cc9f6a2f7b466384382a843942f96b1d31a1 SHA512 6ce97b72f3f984c0d2dc1eb4a259412761736bfaec23867eba46919b6c6444698dc0b0e717c1a095aa713b2a4726d4229aed5964d89a74f7c1f2aa058f4891bf WHIRLPOOL 65db8c976f481a765e1301526cc7af6939ceb4c1cc26f3c1d5e628512a9c34bc4a10e8380d10ab4773976def9b3e07cf84b2cdc1da821750118c405b2f8b34d4
 DIST greg-data-0.7.2.tar.gz 8142259 SHA256 6f3e1c1bc540c8355583ce2e1807cc9f6a2f7b466384382a843942f96b1d31a1 SHA512 6ce97b72f3f984c0d2dc1eb4a259412761736bfaec23867eba46919b6c6444698dc0b0e717c1a095aa713b2a4726d4229aed5964d89a74f7c1f2aa058f4891bf WHIRLPOOL 65db8c976f481a765e1301526cc7af6939ceb4c1cc26f3c1d5e628512a9c34bc4a10e8380d10ab4773976def9b3e07cf84b2cdc1da821750118c405b2f8b34d4
 DIST greg-data-0.7.tar.gz 8202091 SHA256 b82743b1d3c2d3acaa4adb4901368d46e0638733364963ad62044f79111f21f7 SHA512 71ab00869df074660103b824130776ceeaad398b1df8bbc30c9fc41660cc08a66998a406c5cfc93f4605cc5052aae414bd79b6e6de2ae46acd9c6997dbd5361b WHIRLPOOL 87deff25e864f55b316f432b9a9b595e23352720d08257e2b69bbe7946bf8ab5d1fcc9d13205354a0edd3fbea89422952df5f6fa0c05f9707167b544494b2c14

diff --git a/sci-chemistry/coot/coot-0.8.2.ebuild b/sci-chemistry/coot/coot-0.8.2.ebuild
new file mode 100644
index 0000000..0c45a43
--- /dev/null
+++ b/sci-chemistry/coot/coot-0.8.2.ebuild
@@ -0,0 +1,176 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+AUTOTOOLS_AUTORECONF="true"
+
+inherit autotools-utils python-single-r1 toolchain-funcs versionator
+
+MY_S2_PV=$(replace_version_separator 2 - ${PV})
+MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
+MY_S_P=${MY_S2_P}-${PR/r/revision-}
+MY_PV=${PV}
+MY_P=${PN}-${MY_PV}
+
+DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
+HOMEPAGE="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/"
+SRC_URI="http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/${MY_P}.tar.gz
+	test? ( https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/data/greg-data.tar.gz -> ${PN}-greg-data.tar.gz )"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS=""
+IUSE="+openmp static-libs test"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+SCIDEPS="
+	sci-libs/libccp4
+	sci-libs/clipper
+	>=sci-libs/coot-data-2
+	>=sci-libs/gsl-1.3
+	sci-libs/fftw:2.1=
+	sci-libs/mmdb:2
+	sci-libs/monomer-db
+	sci-libs/ssm
+	sci-chemistry/reduce
+	sci-chemistry/probe"
+
+XDEPS="
+	gnome-base/libgnomecanvas
+	gnome-base/librsvg:2
+	media-libs/libpng:0=
+	media-libs/freeglut
+	x11-libs/gtk+:2
+	x11-libs/goocanvas:0
+	x11-libs/gtkglext
+	virtual/opengl"
+
+SCHEMEDEPS="
+	dev-scheme/net-http
+	dev-scheme/guile-gui
+	>=dev-scheme/guile-lib-0.1.6
+	dev-scheme/guile-www
+	>=x11-libs/guile-gtk-2.1"
+
+RDEPEND="
+	${SCIDEPS}
+	${XDEPS}
+	${SCHEMEDEPS}
+	${PYTHON_DEPS}
+	dev-db/sqlite:3
+	dev-libs/boost:0=[python,${PYTHON_USEDEP}]
+	dev-libs/glib:2
+	>=dev-libs/gmp-4.2.2-r2:0=
+	dev-python/pygobject:2[${PYTHON_USEDEP}]
+	dev-python/pygtk:2[${PYTHON_USEDEP}]
+	>=net-misc/curl-7.19.6
+	net-dns/libidn
+	sys-libs/readline:0=
+	"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig
+	>=sys-devel/libtool-2.4-r2
+	dev-lang/swig
+	sys-devel/bc
+	test? ( dev-scheme/greg )"
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_setup() {
+	if use openmp; then
+		tc-has-openmp || die "Please use an OPENMP capable compiler"
+	fi
+	python-single-r1_pkg_setup
+}
+
+PATCHES=(
+	"${FILESDIR}"/${P}-desktop.patch
+	"${FILESDIR}"/${P}-sandbox-icons.patch
+	"${FILESDIR}"/${P}-libtool.patch
+	"${FILESDIR}"/${P}-libguile.patch
+)
+
+src_unpack() {
+	default
+	if use test; then
+		cd "${S}" || die
+		ln -sf ../greg-data || die
+	fi
+}
+
+src_prepare() {
+	sed \
+		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
+		-i configure.ac || die
+
+	autotools-utils_src_prepare
+}
+
+src_configure() {
+	# All the --with's are used to activate various parts.
+	# Yes, this is broken behavior.
+	local myeconfargs=(
+		--with-goocanvas-prefix="${EPREFIX}/usr"
+		--with-guile="${EPREFIX}/usr"
+		--with-python="${EPREFIX}/usr"
+		--with-guile-gtk
+		--with-pygtk="${EPREFIX}/usr"
+		--with-sqlite3
+		--with-boost="${EPREFIX}/usr"
+		)
+	autotools-utils_src_configure
+}
+
+src_test() {
+	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
+	mkdir "${T}"/coot_test || die
+
+	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
+	export COOT_SCHEME_DIR="${S}/scheme/"
+	export COOT_RESOURCES_FILE="${S}/cootrc"
+	export COOT_PIXMAPS_DIR="${S}/pixmaps/"
+	export COOT_DATA_DIR="${S}/"
+	export COOT_PYTHON_DIR="${S}/python/"
+	export PYTHONPATH="${COOT_PYTHON_DIR}:${S}/src:${PYTHONPATH}"
+	export PYTHONHOME="${EPREFIX}"/usr/
+	export CCP4_SCR="${T}"/coot_test/
+	export CLIBD_MON="${EPREFIX}/usr/share/data/monomers/"
+	export COOT_REF_STRUCTS="${EPREFIX}/usr/share/data/monomers/"
+	export SYMINFO="${S}/syminfo.lib"
+
+	export COOT_TEST_DATA_DIR="${S}"/greg-data/
+
+	cat > command-line-greg.scm <<- EOF
+	(use-modules (ice-9 greg))
+		(set! greg-tools (list "greg-tests"))
+			(set! greg-debug #t)
+			(set! greg-verbose 5)
+			(let ((r (greg-test-run)))
+				(if r
+				(coot-real-exit 0)
+				(coot-real-exit 1)))
+	EOF
+
+	einfo "Running test with following paths ..."
+	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
+	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
+	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
+	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
+	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
+	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
+	einfo "PYTHONPATH $PYTHONPATH"
+	einfo "PYTHONHOME $PYTHONHOME"
+	einfo "CCP4_SCR ${CCP4_SCR}"
+	einfo "CLIBD_MON ${CLIBD_MON}"
+	einfo "SYMINFO ${SYMINFO}"
+
+	"${S}"/src/coot-bin --no-graphics --script command-line-greg.scm || die
+	"${S}"/src/coot-bin --no-graphics --script python-tests/coot_unittest.py || die
+}

diff --git a/sci-chemistry/coot/files/coot-0.8.2-desktop.patch b/sci-chemistry/coot/files/coot-0.8.2-desktop.patch
new file mode 100644
index 0000000..c264dd5
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.8.2-desktop.patch
@@ -0,0 +1,21 @@
+ coot.desktop | 7 +++----
+ 1 file changed, 3 insertions(+), 4 deletions(-)
+
+diff --git a/coot.desktop b/coot.desktop
+index 74aecf3..8668018 100644
+--- a/coot.desktop
++++ b/coot.desktop
+@@ -1,10 +1,9 @@
+ [Desktop Entry]
+ Type=Application
+-Encoding=UTF-8
+ Name=Coot
+ Comment=Macromolecular model builder
+ Exec=coot
+-Icon=coot.png
++Icon=coot
+ Terminal=true
+-Categories=Science;Graphics
+-MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile
++Categories=Science;Graphics;
++MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile;

diff --git a/sci-chemistry/coot/files/coot-0.8.2-libguile.patch b/sci-chemistry/coot/files/coot-0.8.2-libguile.patch
new file mode 100644
index 0000000..cbaccef
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.8.2-libguile.patch
@@ -0,0 +1,29 @@
+ src/graphics-info-modelling.cc | 1 +
+ src/graphics-info.cc           | 2 ++
+ 2 files changed, 3 insertions(+)
+
+diff --git a/src/graphics-info-modelling.cc b/src/graphics-info-modelling.cc
+index 05a63ad..4b7d129 100644
+--- a/src/graphics-info-modelling.cc
++++ b/src/graphics-info-modelling.cc
+@@ -102,6 +102,7 @@
+ 
+ #include "utils/coot-utils.hh"
+ 
++#include <libguile.h>
+ 
+ // Idealize the geometry without considering the map.
+ //
+diff --git a/src/graphics-info.cc b/src/graphics-info.cc
+index e2f9d52..76b6769 100644
+--- a/src/graphics-info.cc
++++ b/src/graphics-info.cc
+@@ -92,6 +92,8 @@
+ #include "cc-interface-scripting.hh"
+ #endif
+ 
++#include <libguile.h>
++
+ // A few non-class members - should be somewhere else, I guess.
+ // 
+ void initialize_graphics_molecules() { 

diff --git a/sci-chemistry/coot/files/coot-0.8.2-libtool.patch b/sci-chemistry/coot/files/coot-0.8.2-libtool.patch
new file mode 100644
index 0000000..10c43ad
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.8.2-libtool.patch
@@ -0,0 +1,39 @@
+ configure.ac    |  2 +-
+ lbg/Makefile.am | 11 -----------
+ 2 files changed, 1 insertion(+), 12 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 73d6ed7..b04dcd6 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -69,7 +69,7 @@ AC_LIB_PREPARE_MULTILIB
+ 
+ AC_SUBST(COOT_STDTYPES)
+ 
+-EXPORT_DYNAMIC_FLAG_SPEC=$export_dynamic_flag_spec
++eval EXPORT_DYNAMIC_FLAG_SPEC=\"$export_dynamic_flag_spec\"
+ AC_SUBST(EXPORT_DYNAMIC_FLAG_SPEC)
+ 
+ 
+diff --git a/lbg/Makefile.am b/lbg/Makefile.am
+index 1277afe..a79ebe0 100644
+--- a/lbg/Makefile.am
++++ b/lbg/Makefile.am
+@@ -43,17 +43,6 @@ pkginclude_HEADERS = lbg.hh wmolecule.hh  flev-annotations.hh graphics-c-interfa
+ 	lbg-drag-and-drop.hh qed-interface.hh alerts.hh pi-stacking.hh
+ pkgincludedir = $(includedir)/coot/lbg
+ 
+-# 20140521
+-# lidia_LDFLAGS = -Wl,--export-dynamic
+-# 
+-# Now we use EXPORT_DYNAMIC_FLAG_SPEC which usually evaluates to ${wl}--export-dynamic
+-# (but not for MacOSX, where it Does The Right Thing (hopefully)).
+-# We manually set the value of wl here, but maybe the Right Thing To Do for that is 
+-# run (eval) $($LIBTOOL --config | grep ^wl).  How do I do that here though?  
+-# I don't understand.  Maybe the setting of wl should be done in configure?  But then
+-# I have to force the output of libtool.  Bleugh.  Hmm...
+-# Anyway, thankyou Gary Vaughan.
+-wl=-Wl,
+ lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC)
+ 
+ # res spec output operator means we include libcoot-coord-utils

diff --git a/sci-chemistry/coot/files/coot-0.8.2-sandbox-icons.patch b/sci-chemistry/coot/files/coot-0.8.2-sandbox-icons.patch
new file mode 100644
index 0000000..2a9ff2d
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.8.2-sandbox-icons.patch
@@ -0,0 +1,16 @@
+ pixmaps/icons/Makefile.am | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/pixmaps/icons/Makefile.am b/pixmaps/icons/Makefile.am
+index 0c183ae..dddc11a 100644
+--- a/pixmaps/icons/Makefile.am
++++ b/pixmaps/icons/Makefile.am
+@@ -11,6 +11,6 @@ install-data-local:
+ 		CONTEXT=` echo $$icon | cut -d_ -f2`; \
+ 		SIZE=`    echo $$icon | cut -d_ -f3`; \
+ 		ICONFILE=`echo $$icon | cut -d_ -f4`; \
+-		mkdir -p $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \
+-		$(INSTALL_DATA) $(srcdir)/$$icon $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \
++		mkdir -p $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \
++		$(INSTALL_DATA) $(srcdir)/$$icon $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \
+ 	done;