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

[Matt Turner]

commit:     c399a8bb15acd06ffef54b9c1b7f0e9c36f77c86
Author:     Matt Turner <mattst88 <AT> gentoo <DOT> org>
AuthorDate: Sat Aug 10 04:03:09 2019 +0000
Commit:     Matt Turner <mattst88 <AT> gentoo <DOT> org>
CommitDate: Sat Aug 10 04:05:33 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c399a8bb

sci-chemistry/coot: Remove

Closes: https://bugs.gentoo.org/639760
Signed-off-by: Matt Turner <mattst88 <AT> gentoo.org>

 sci-chemistry/coot/Manifest                        |   2 -
 sci-chemistry/coot/coot-0.8.2-r1.ebuild            | 181 ---------------------
 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 --
 sci-chemistry/coot/metadata.xml                    |   8 -
 7 files changed, 296 deletions(-)

diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
deleted file mode 100644
index 0ef426fb410..00000000000
--- a/sci-chemistry/coot/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST coot-0.8.2-greg-data.tar.gz 8677037 BLAKE2B bb2eac183598fed429c4977f9512e90335ccb988f154a3a29985668e6d3a90a19cb77ec61e0453e7294243b8dffd9b5ef6bb318bac2280b26eab37e2de25a18a SHA512 28396a5fa64af61e8932b565c6593ed27c4708e6a59158d62c94005bea9fa8c46562b6caba97011209a40705e5ec6711b949138dd8a23bb954df2ab4dfa9bb33
-DIST coot-0.8.2.tar.gz 15772937 BLAKE2B 8ee8fb827ef4ec6470f17eea4a91db8c57699c8c3a3d7cce3388c53389ba15c90a7610d8f2592320acdaee0b6c09fe8e9452cd45857659d71d363abc3322bf6f SHA512 a323608df7b63f22eb2d1ac679fc047bba9fe23fe6366ae1d6ae29ca00a567aafb3d29840878e8c5123421037e26b6463f0bb845ef28dcbb4f3647cda2f74575

diff --git a/sci-chemistry/coot/coot-0.8.2-r1.ebuild b/sci-chemistry/coot/coot-0.8.2-r1.ebuild
deleted file mode 100644
index b4fa2b21f7b..00000000000
--- a/sci-chemistry/coot/coot-0.8.2-r1.ebuild
+++ /dev/null
@@ -1,181 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-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"
-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/${MY_P}.tar.gz
-	test? ( https://dev.gentoo.org/~jlec/distfiles/${P}-greg-data.tar.gz )"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-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/guile-2
-	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 '/export LD_LIBRARY/s:^:#:g' \
-		-i src/coot.in || die
-
-	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
deleted file mode 100644
index c264dd5a762..00000000000
--- a/sci-chemistry/coot/files/coot-0.8.2-desktop.patch
+++ /dev/null
@@ -1,21 +0,0 @@
- 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
deleted file mode 100644
index cbaccefb294..00000000000
--- a/sci-chemistry/coot/files/coot-0.8.2-libguile.patch
+++ /dev/null
@@ -1,29 +0,0 @@
- 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
deleted file mode 100644
index 10c43ad5559..00000000000
--- a/sci-chemistry/coot/files/coot-0.8.2-libtool.patch
+++ /dev/null
@@ -1,39 +0,0 @@
- 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
deleted file mode 100644
index 2a9ff2d7177..00000000000
--- a/sci-chemistry/coot/files/coot-0.8.2-sandbox-icons.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- 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;

diff --git a/sci-chemistry/coot/metadata.xml b/sci-chemistry/coot/metadata.xml
deleted file mode 100644
index 8937bad0b17..00000000000
--- a/sci-chemistry/coot/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@g.o</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>