gentoo resync : 18.08.2019

30 files changed, 84 insertions, 433 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index ee310635e5be..0ec00a70e274 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
deleted file mode 100644
index a2b30f0178a3..000000000000
--- a/sci-chemistry/coot/Manifest
+++ /dev/null
@@ -1,8 +0,0 @@
-AUX coot-0.8.2-desktop.patch 544 BLAKE2B f63e4d288387958a83c1981368f0d26445680385febba5609634d41e6ecc97deea615d63551346b8cd20ad0eebc843a23acfef794c7e01974a855d302f51aa9d SHA512 f02b506fe8ba02601e95afa733ea13a24baf0c11a42d6947d4c2cd34c81ef046889a959d76ac66acd0aecf4bd665b656aa8d0138213c3a1e538846a62e53608a
-AUX coot-0.8.2-libguile.patch 776 BLAKE2B 8ea0211d8bd52a96da1b48f378c46c87d94a5b33566e2b9a89839060b0e38787bef6a2b3abe93a2694028e5a405f368c651bf2b286445569eaf519d6d31914a6 SHA512 96536508d2fec0d13014636f2eb1fa314fe764a78a0d7b4c5a411570c19005e673b32dc4a67551330d56d9af66bed3571d1d5de44fd1741a01180f64d262f3e5
-AUX coot-0.8.2-libtool.patch 1450 BLAKE2B 7713f3fd0c03107a1a35b617f6b62b321dcbe1a21be1f777f9214e8c929d4c082c092ce2682598fb5ae63231543258fbde89a97f0cc7dfec8251bd14bcfa7637 SHA512 d524764fa99e3a5200b1dccc4ac33bccfbb2554c0b66e54f5e7be9a9f21b54e903b67c5109db9c179d53a7bb9624ac291769463cfac2051c6445e5de280b81e7
-AUX coot-0.8.2-sandbox-icons.patch 740 BLAKE2B 456b4974b64c3c38f294bb63133e8976f7de6160f813bd180dd2e9ecdb30790493f821062eed73f3bea642ef875e8e79bd7e1e4147e38be91d9592a69eb0532e SHA512 2b45caa89309abe3a4a79ddbcfadf2510b055cbf83e3f8f1ad600db7324562cc9cf8de2bfd25f7ce55c754eb36a08e12bd47a2cb01b769d618a18732dd8d0618
-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
-EBUILD coot-0.8.2-r1.ebuild 4489 BLAKE2B 17fc618a696fb4771f96387595525e66bbe931a499e299f1149d7d2e8fb5be6f81537078cf4d45a4a59235d680bdf7a675867031c6944fe2b2a4d7161b1b9a78 SHA512 b1489c66850da37859142ac0db0172283aef99cb1b00b9b1676457350c3bc594e2490f8c0050fa6deb6e544189046c95ba9eae67e099c8578fd375325f65dc99
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
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 b4fa2b21f7b9..000000000000
--- 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 c264dd5a7628..000000000000
--- 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 cbaccefb2947..000000000000
--- 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 10c43ad55594..000000000000
--- 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 2a9ff2d7177c..000000000000
--- 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 8937bad0b175..000000000000
--- 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@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/gelemental/Manifest b/sci-chemistry/gelemental/Manifest
index 3a0bbfcac8dc..ed8170f6400e 100644
--- a/sci-chemistry/gelemental/Manifest
+++ b/sci-chemistry/gelemental/Manifest
@@ -3,6 +3,8 @@ AUX gelemental-1.2.0-fix-c++14.patch 399 BLAKE2B 4368bf6462a1302eb61654e877e1153
 AUX gelemental-1.2.0-gcc4.3.patch 387 BLAKE2B 6421e171408a7d8cbf3de07ad513804ffea94b4fc57cf3e23adaae65b25b381a49bfcc28991675db74df91d58170380a6a2ccf4024f96d4724e1dabfa2d6e3a2 SHA512 d7b103a533dd3edda30d349b0205b241cd5e23c97a562912cc28bd7fb210c3e6f5c33ce2a3321817fe3748812f655b1295d23058aefd35ae2b2746bee99c35e3
 AUX gelemental-1.2.0-glib-2.32.patch 1235 BLAKE2B 723469d6e300579db349294cc7252aadafd910cd10ede2f325cd20dfc8620c8dd335eb15f62c3e1a2c0908f4d9557c537ee89b4c9c3df5fbe8caa3de3fd60782 SHA512 2e414b8d4f57a6edcdb4322b0bf39b6d89c7be0c67086f2bd2d468aaff36f9f98339f14cb2fe11444113b5395b8b4742ea82461df84094c8c1e4ca7f21ebb1c9
 DIST gelemental-1.2.0.tar.bz2 460757 BLAKE2B 53fd40cdc37909495cd9051c83418ace482fdf17930df2a94d8cb7f44a8eff2a5e7c37e54dac4e72810b1420d0bf2722eca47eb8c375fc05ecf26b753beb4e9d SHA512 2e6ef2c22b389cff69728b01e1eb397578974362356f5132098f29a9e01a64be228a24686738bd84ea575cee5aef068d9ab3d6c20233f995ccc5f1a1cb5d5673
+DIST gelemental-2.0.0.tar.gz 779052 BLAKE2B 86f98a97acaf84c2bd6e03e991e226f19e65ed9c06fc43c809278d5e6d8b93645aa64ac4983166fad6b6b9b3d0ad5bba7a7cbfe2dccbbe2ea093deaaa8bdfabd SHA512 86b0f59a3508560e3882f40b820d7b24b780bb4d1619df94f3410b0832255deec8e55d11c5ad960f96fc3e16d8a624279bf53bf178bf1dacdfe80a72181e48d6
 DIST gelemental_1.2.0-8.debian.tar.gz 29877 BLAKE2B a19c853cd426e1abdf73b48a21d1d7c830a613dc5802b1478d699d21b3211060b150c25bd525414147d02972dd9ac0940468a2f873aad03f9b7c522e862f29a7 SHA512 83c236e3b91af304c96f28c0f12577821ee2f47c9e01fb1f3664228afb002dc19b1a71e6dcd6040d09ea991d131b147ea5b36283d8ead290d50014c15e69878c
-EBUILD gelemental-1.2.0-r1.ebuild 1842 BLAKE2B 22c740f9b5d9b1811aa592e83751e3533da850af177ff07f27505768f05904d0c016401a7b5713a723078a9f4d49f50d52b23d496b937aad19007eda1613b1d8 SHA512 e34da62f56231fcf5c93040397c2af02b689ee630afbdf658e3bcdcddca3822b216c669b7a247714504dcc925572f60054c2684fca5bc299a4a76c8c87895dde
-MISC metadata.xml 342 BLAKE2B 1d03f804c9a6527a4e6671ed1310591bf964751259435951a609f93693bc80dd8c1b7250cc1eefa030277b859ac333483a5e151e29fd8761de9eda89fe1d04ae SHA512 bb9f0244e85513e0c85bcd55d4f9466ae8a9ab09bebac17713b192ee1b346a31c476bc67e54cdb650a234e696f0783dc493e54df63de379f3fecac00e2ecbc3b
+EBUILD gelemental-1.2.0-r1.ebuild 1836 BLAKE2B 1906739810fa9aac25abc1610ce00d5e60e628b492d54d26e44f3266d97e622279f293017ad1ce7f92901f4a807f3090e25b105ef260d39ea08a4a7883bfa917 SHA512 850d7a1d37b4fcc0b7a65b9aae431e302d86b453c95a0a0cbe4d3380f6ba3b8477c7a18b729b088bba2c9e4428b8a415f8d4240cc38f94e58453e4af55a689ff
+EBUILD gelemental-2.0.0.ebuild 1022 BLAKE2B 4f87649dee59d080728deba62ffca7edbac581a17df4806063ae918b173b3864cffda3427805a277e85538fb8e93c017eaf0264c2b10e4cf376f326ee6555294 SHA512 4ceb393e3cedca8268dbeee698187a5a8a854f992a51831157785be5c96228d55ab5d961cde3c62363736b275f7d3b72b3b4bc5290fc51a359cc0b29921a4c97
+MISC metadata.xml 455 BLAKE2B 7db9d6b4a8896df6385ae2c8c2b8c771c1a6ae82a1072f6d3f9b27fbd7c4d0f3546a03ced3350331d25f48e5631855fc9653a808d49631803f2d526db75b3ac7 SHA512 815bcad86f574f7cb2dfef3205e2a6398f5fd2512395c0c016733d4cb001f70c0003f494a69bc9bc66d675a9eaa89c203ace13f17f4a9f2c6805a34fcf5125d8
diff --git a/sci-chemistry/gelemental/gelemental-1.2.0-r1.ebuild b/sci-chemistry/gelemental/gelemental-1.2.0-r1.ebuild
index 3aa417510233..27588692bfbf 100644
--- a/sci-chemistry/gelemental/gelemental-1.2.0-r1.ebuild
+++ b/sci-chemistry/gelemental/gelemental-1.2.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -6,7 +6,7 @@ EAPI=5
 inherit autotools-utils fdo-mime flag-o-matic gnome2-utils eutils
 
 DESCRIPTION="Periodic table viewer with detailed information on the chemical elements"
-HOMEPAGE="http://freecode.com/projects/gelemental/"
+HOMEPAGE="https://github.com/ginggs/gelemental/"
 SRC_URI="
 	http://www.kdau.com/files/${P}.tar.bz2
 	mirror://debian/pool/main/g/${PN}/${PN}_${PV}-8.debian.tar.gz"
diff --git a/sci-chemistry/gelemental/gelemental-2.0.0.ebuild b/sci-chemistry/gelemental/gelemental-2.0.0.ebuild
new file mode 100644
index 000000000000..7a482363201c
--- /dev/null
+++ b/sci-chemistry/gelemental/gelemental-2.0.0.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools fdo-mime flag-o-matic gnome2-utils eutils
+
+DESCRIPTION="Periodic table viewer with detailed information on the chemical elements"
+HOMEPAGE="https://github.com/ginggs/gelemental/"
+SRC_URI="https://github.com/ginggs/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3 MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc"
+
+RDEPEND="
+	dev-cpp/gtkmm:2.4
+	dev-cpp/glibmm:2"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig
+	sys-devel/gettext
+	dev-util/intltool
+	doc? ( app-doc/doxygen )"
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	append-cxxflags -std=c++11 #566450
+	local myeconfargs=( $(use_enable doc api-docs) )
+
+	default
+}
+
+# src_install() {
+#     de
+#     autotools-utils_src_install apidir="/usr/share/doc/${PF}/html"
+# }
+
+pkg_postinst() {
+	gnome2_icon_cache_update
+	fdo-mime_desktop_database_update
+}
+
+pkg_postrm() {
+	gnome2_icon_cache_update
+	fdo-mime_desktop_database_update
+}
diff --git a/sci-chemistry/gelemental/metadata.xml b/sci-chemistry/gelemental/metadata.xml
index eb677830c9f8..091878c90ab5 100644
--- a/sci-chemistry/gelemental/metadata.xml
+++ b/sci-chemistry/gelemental/metadata.xml
@@ -1,11 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
+	<maintainer type="person">
+		<email>tamiko@gentoo.org</email>
+		<name>Matthias Maier</name>
+	</maintainer>
 	<maintainer type="project">
 		<email>sci-chemistry@gentoo.org</email>
 		<name>Gentoo Chemistry Project</name>
 	</maintainer>
 	<upstream>
-		<remote-id type="freecode">gelemental</remote-id>
+		<remote-id type="github">ginggs/gelemental</remote-id>
 	</upstream>
 </pkgmetadata>
diff --git a/sci-chemistry/gmxapi/Manifest b/sci-chemistry/gmxapi/Manifest
index c099618e92b0..ce2771c016a4 100644
--- a/sci-chemistry/gmxapi/Manifest
+++ b/sci-chemistry/gmxapi/Manifest
@@ -1,3 +1,3 @@
 DIST gmxapi-0.0.7.1.tar.gz 671400 BLAKE2B 5db024bceaed262fc1bd2ef35c0c24a31eff12abde7766ba0eea9d5aabe04c435cdf3c79c04d7932f2110de837a0d06e1f66239f22ba6f313410ed8c9d899788 SHA512 4103d67be3c869907613ec74fc46f14b15242ad93a973fc984dbb25e79bb0bb697d9d2ad9b67a8da2500e5a89b8f78ea1ef1632455af29830e11c2bf1f11bc44
-EBUILD gmxapi-0.0.7.1.ebuild 1237 BLAKE2B e516ec4e3d975635f9dfd13830b41694ab4d09ec2c14305617237587865086c4159ba860aa76228ee61d98ffe556e911555f887d8f83253012d502cf25da2410 SHA512 8e18895c146f44aa2daf125564667b654faacf7566d66b8b3bf41430232d1772fe5bca8008e76eefeac223fbe98e71c01b6545f6c34d76cfeaa5735929a196ab
+EBUILD gmxapi-0.0.7.1.ebuild 1239 BLAKE2B d8d75f403f2bc68f98d5e72713de382c91bbbe341a83bb4705dba7aeb70fad389435b0fd46838a0bf23fe158721e290dee9a67421f37cd1a427bba172bf687c7 SHA512 e2a0406f92983e40cabbc40bed27ba44de8218573dbda11c6087141bd5f1ccc0e1b90fdfcebbcbeae12c5bbdbe51b3f9f15a50830fcb50c23b7052b5ef92c195
 MISC metadata.xml 374 BLAKE2B d93e2ad2f09971909382ad65fc5f5033487979b0694f9dc656439573973f55ce1865e5a30584e55e1c48fdd93898601ac2b11e269fb2b1c5adc3ff8dde66f35d SHA512 1c61c58e1cfbbb42342f7a87625e0044e51523f7a2f7270ecfea537c622965e64195fc88eb8f70fac648a0154a19f4a852b88383de1dcd6e17ff0ac0dc6e22d8
diff --git a/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild b/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild
index ab2e052e7dd5..f27d423c9d24 100644
--- a/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild
+++ b/sci-chemistry/gmxapi/gmxapi-0.0.7.1.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 MAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python2_7 python3_{5,6} )
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
 
 inherit cmake-utils python-r1
 
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 8f598312af23..b54b4bab8d9a 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -9,8 +9,8 @@ DIST regressiontests-2019.3.tar.gz 67640462 BLAKE2B ed6c176a144e0407be66585be5d6
 EBUILD gromacs-2018.3.ebuild 7824 BLAKE2B cc5ec314f5338c269d00bb8ec7af34f38134c59dd7009fc593cfa559cc68e69753f17bd8b77f5156f08999a83980d1e1c5684fd9ed489386af309f1babf850aa SHA512 d47c8c6e1e4c1dc5cd2429e5c77f04af822b5995cdd1f93a1331442dfe95d0192bda5565d3837575100f2fe841f1006cd38698ced727525c716d1925c0e65579
 EBUILD gromacs-2018.7.ebuild 7824 BLAKE2B cc5ec314f5338c269d00bb8ec7af34f38134c59dd7009fc593cfa559cc68e69753f17bd8b77f5156f08999a83980d1e1c5684fd9ed489386af309f1babf850aa SHA512 d47c8c6e1e4c1dc5cd2429e5c77f04af822b5995cdd1f93a1331442dfe95d0192bda5565d3837575100f2fe841f1006cd38698ced727525c716d1925c0e65579
 EBUILD gromacs-2018.9999.ebuild 7827 BLAKE2B 97a2437061a55854dd2799c8bdbec6a342586fc480785ea52de8d6b612c747ace1fba0a1fc3dbec9904cafcb3abdabd363ba0d6285cfc44f60964047c52f5b74 SHA512 975f2bcfdd93df006ec2a8f439a2a90e4c9079c58209ec2828b5647d96c29f7eef7fd0c79da844cc8d4e449b573a75884b19c951649c0028133d3fa87b03934c
-EBUILD gromacs-2019.2.ebuild 9132 BLAKE2B 8b31d76f02760d99d6fe4b83f416d80c8909b41933d34c7a2faf609e682634a18ba1dac0df4e17ee30c501f2cb64ab98d235063e563b4a0a056ed776d389d930 SHA512 9a682f3601b1ef884a2e456f9b60b76a460f9f554fcc6fa93b9cb7154c5a23c697ecaa82fc462b14cded92b4f27c5269a73b27cba9ddfefa6cf106b3238fcb66
-EBUILD gromacs-2019.3.ebuild 9135 BLAKE2B c6e5f760933516bc4ea458205990127f5ff5ec676357af042e6d2fc742b934d601e03f96c8dd0b21f5bbe7f52a8e62f5ee21aed6a7b2bb9116ca359b3d0b6bad SHA512 c6581c0ca79fce6223df229d4077ec821c26e98513be0d2c3d9af3f152f9c852917cf2c0873a576eac4dea17af110770a13a848a6312bbfcb476909cb3693998
-EBUILD gromacs-2019.9999.ebuild 9135 BLAKE2B c6e5f760933516bc4ea458205990127f5ff5ec676357af042e6d2fc742b934d601e03f96c8dd0b21f5bbe7f52a8e62f5ee21aed6a7b2bb9116ca359b3d0b6bad SHA512 c6581c0ca79fce6223df229d4077ec821c26e98513be0d2c3d9af3f152f9c852917cf2c0873a576eac4dea17af110770a13a848a6312bbfcb476909cb3693998
+EBUILD gromacs-2019.2.ebuild 9172 BLAKE2B 9a2abe1f9e081dfa1e64e6571cce6a45815f7aadb0cc2c7e3a85b312855a1955fc66915f1e1c6ab3efc3ab7770ebc94ccbb36e32f91f69e873a66157c4a883aa SHA512 b5e0462d8dfae69545a899ddf7c7bbcfa24de4fa59a4ba7f16ae98fba994c20d715ae300ef3998406fb650b94caac9a99b3250dee8646c90129313c47b1e7479
+EBUILD gromacs-2019.3.ebuild 9175 BLAKE2B 2e26ad73b84fd5d8cce499dc77fa51122f08c6214778f327b142fce6c0790ddf68d624b264ac3b9d8c808951fbc2b9db199402a2a9c29865995df5b8a25112f1 SHA512 ab70cbfd71b180571721de010804cc53241f1888c1845ce11c6b53486a051306dfaa7b7da5bb95bf48e7fd9a7e688dedfe2168345b203e917a3d7a9aeb6caa9e
+EBUILD gromacs-2019.9999.ebuild 9175 BLAKE2B 2e26ad73b84fd5d8cce499dc77fa51122f08c6214778f327b142fce6c0790ddf68d624b264ac3b9d8c808951fbc2b9db199402a2a9c29865995df5b8a25112f1 SHA512 ab70cbfd71b180571721de010804cc53241f1888c1845ce11c6b53486a051306dfaa7b7da5bb95bf48e7fd9a7e688dedfe2168345b203e917a3d7a9aeb6caa9e
 EBUILD gromacs-9999.ebuild 8094 BLAKE2B 932061da2ed5e2e20d1ca0c1ef9000fd946bbe3720cea6d585863e4bf2d7821b7e7b934d4d33d20a4c6040865c58c61c11f5bc8ce98812ad4f946a95b1c1fb83 SHA512 e3987a36622751c20e6a5b3fa88d43c94e24a30cd513eb2e9f9375457413c9ad131ec3f3012ec94e7574d50233c00d9edd357a44413ac0873edb88df82487ba0
 MISC metadata.xml 1123 BLAKE2B 5e945fdf580821b62aaf40c5b4b3252b366284f2df16f02e7c3cf913e5ad498a6a8548bc2e4275d8b80373f88d9879ab59d401e619595014262dcebfe8660f9f SHA512 bac0c94aee957487d8af8a1e06323cb286c8773cef2070d91aff9fdad63eb1bd55f2678dd58dca21b33d8d3e7110d2526e280abd538e3653aee638f6de72090d
diff --git a/sci-chemistry/gromacs/gromacs-2019.2.ebuild b/sci-chemistry/gromacs/gromacs-2019.2.ebuild
index 84864a620b5f..1e54e37089df 100644
--- a/sci-chemistry/gromacs/gromacs-2019.2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.2.ebuild
@@ -49,6 +49,7 @@ CDEPEND="
 	lmfit? ( sci-libs/lmfit )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
+	${PYTHON_DEPS}
 	"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig
@@ -67,7 +68,8 @@ REQUIRED_USE="
 	|| ( single-precision double-precision )
 	cuda? ( single-precision )
 	cuda? ( !opencl )
-	mkl? ( !blas !fftw !lapack )"
+	mkl? ( !blas !fftw !lapack )
+	${PYTHON_REQUIRED_USE}"
 
 DOCS=( AUTHORS README )
 
diff --git a/sci-chemistry/gromacs/gromacs-2019.3.ebuild b/sci-chemistry/gromacs/gromacs-2019.3.ebuild
index 86219e6146cd..f91506d7e52c 100644
--- a/sci-chemistry/gromacs/gromacs-2019.3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.3.ebuild
@@ -49,6 +49,7 @@ CDEPEND="
 	lmfit? ( sci-libs/lmfit )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
+	${PYTHON_DEPS}
 	"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig
@@ -67,7 +68,8 @@ REQUIRED_USE="
 	|| ( single-precision double-precision )
 	cuda? ( single-precision )
 	cuda? ( !opencl )
-	mkl? ( !blas !fftw !lapack )"
+	mkl? ( !blas !fftw !lapack )
+	${PYTHON_REQUIRED_USE}"
 
 DOCS=( AUTHORS README )
 
diff --git a/sci-chemistry/gromacs/gromacs-2019.9999.ebuild b/sci-chemistry/gromacs/gromacs-2019.9999.ebuild
index 86219e6146cd..f91506d7e52c 100644
--- a/sci-chemistry/gromacs/gromacs-2019.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.9999.ebuild
@@ -49,6 +49,7 @@ CDEPEND="
 	lmfit? ( sci-libs/lmfit )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
+	${PYTHON_DEPS}
 	"
 DEPEND="${CDEPEND}
 	virtual/pkgconfig
@@ -67,7 +68,8 @@ REQUIRED_USE="
 	|| ( single-precision double-precision )
 	cuda? ( single-precision )
 	cuda? ( !opencl )
-	mkl? ( !blas !fftw !lapack )"
+	mkl? ( !blas !fftw !lapack )
+	${PYTHON_REQUIRED_USE}"
 
 DOCS=( AUTHORS README )
 
diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest
index d8afb6a89cc3..98a2d7296786 100644
--- a/sci-chemistry/molmol/Manifest
+++ b/sci-chemistry/molmol/Manifest
@@ -2,5 +2,5 @@ DIST molmol-2k.2.0-doc.tar.gz 1062297 BLAKE2B 082d4eea5544bab52ffc1ff6364c503043
 DIST molmol-2k.2.0-src.tar.gz 1088805 BLAKE2B cd649604f6ee491d3a4485391ecdaa48dc1bc4bcd82865cd4a01ca460a6653f8cbba636050bfab9027b9b95dbefa28a8deeff7065b9b461f518001242af4a849 SHA512 6ab01a6fd3d19752634a2cf22919a20e43d195768bd4bdacd5f0bbe016c3058c94915bad4c7fa64dcd86576be39cad0ae112cb62f5e69ffb10041518101e7a9b
 DIST molmol-patches.tbz2 17528 BLAKE2B b91270a980f290edc169be00639e86b3272281c9fe237750f5778eab1605ed482c09bdaf90660a5edf74bd04b3e31adc755e77e39aea6c75d88b6db9bf47a6d6 SHA512 bd94baf0a378f40f854f396963edd9b9e4afc5c56462ee6f8b68889290afdb4c5d9b10878aa5619d0a70153453fe6ee8e7540064522c6db0291ae9162bba9287
 DIST molmol.png 509 BLAKE2B 981217602d128da2eb3765ca07580ed58164a4aa8c2d3e016cd54d9f5133418a7c87bbf0f8a83bcbd5d60ad568bf4938ce680eea315716166592e37f815b5aab SHA512 233d3be0c2e2759a8b064b4cf3708f96817f34eb2a397d5122b26a902864a0f1dca1762f8bcc6981cd030e2644cbedef9eb20c7756016fcf27565e3ed586c271
-EBUILD molmol-2k_p2-r5.ebuild 2222 BLAKE2B 701c748446929618b42916e94b2742969d7b66acb055dab37834463bd5420f22e2d0119440dd58685236054a61745a36d8cd385dfd1593217595a48f9978111b SHA512 49dafa2d8a771ec2f8e3ff76f16790d61de84419037f7132581ef5de3f7c2ba12aedaf2ec778139420996d610788aef4c23ee8ac4339a8fe81cba4d36f99ebf8
+EBUILD molmol-2k_p2-r5.ebuild 2233 BLAKE2B d0708456f6d32318841ff23e4801470152a4d3443e89f38e43294b57f815f5c04b0d2cfcfb4eb01d3dfb0ba6d01b881db22148c5e39f4cbe3fb9a71217bb1ff1 SHA512 3491df5f67b017100ff7640a33cb18285b67f527dad141363c5edc09ab5fc5e10d8e11a26ae8b48489a4f559090215214cf692b0509b690acb792ef6ad958b35
 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild
index a09bfe07847b..074130cf13dd 100644
--- a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild
+++ b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild
@@ -29,9 +29,9 @@ IUSE=""
 
 RDEPEND="
 	|| (
-		(	media-libs/mesa
+		(	media-libs/mesa[X(+)]
 			x11-libs/libGLw )
-		media-libs/mesa[motif] )
+		media-libs/mesa[motif,X(+)] )
 	media-libs/libpng:0=
 	media-libs/tiff:0
 	sys-libs/zlib
diff --git a/sci-chemistry/pymol-plugins-promol/Manifest b/sci-chemistry/pymol-plugins-promol/Manifest
index 4306aa15928d..6fe2d8b49dee 100644
--- a/sci-chemistry/pymol-plugins-promol/Manifest
+++ b/sci-chemistry/pymol-plugins-promol/Manifest
@@ -1,3 +1,3 @@
 DIST pymol-plugins-promol-3.0.2.zip 2219295 BLAKE2B 7e81de98ee20f6b22fabeca35b0825250c3b839b9ea51f6c0b51f15062c73810474bd377d0e39d3c2ac0d61f1b5cfb4174c53f1dfc67a11dfcd707eee417a7ed SHA512 e40e9c08e2cb1b223390d751bb1f32069924f1c23aa2b4bdafb6689254e6aa673d4412aca587792f660869f97a389db8a9183033d8b2394c998d0f911104d8d7
-EBUILD pymol-plugins-promol-3.0.2-r1.ebuild 1571 BLAKE2B ef454c92a0308901cd2c49223177f37607a663d73b98a9ef7639cf31478d9b7ec2c1e3eeab37049dfcbe03337c95d09007cf2b9f49df42a42bfeb3d9e1f81ad0 SHA512 c44e71917dc976f39055537ce137ca06c5cbf2f58937a5b54bd5b19463b051b5f0fbfcac320d1fdf01a76e6d32ffdb651b33a2945bb3fc9c143babe79a4bd889
+EBUILD pymol-plugins-promol-3.0.2-r1.ebuild 1557 BLAKE2B bc96ecd8a2762c9909e938e044e7ba0933ab969efee727f91ad2686e347f3724f24b4f40bbbcd05d12667a8c0f94559a9019ebc30599bfdb553cade9e09a2248 SHA512 e34fe733afac21168944cb755a9f8d06d1a56d3b16a83079420d17f881d6d3b8840e22f1534de751496d9bd7d7b7b92c42a2d407d0ebcfc1757f0d0280c080db
 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
index bda6bd694819..1c0b12a6a76e 100644
--- a/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
+++ b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -33,7 +33,7 @@ src_prepare() {
 	preparation() {
 		cd "${BUILD_DIR}" || die
 		sed \
-			-e "s:./modules/pmg_tk/startup:${EPREFIX}/$(python_get_sitedir)/pmg_tk/startup/ProMol:g" \
+			-e "s:./modules/pmg_tk/startup:$(python_get_sitedir)/pmg_tk/startup/ProMol:g" \
 			-i ProMOL_302.py || die
 	}
 	python_foreach_impl preparation
diff --git a/sci-chemistry/reduce/Manifest b/sci-chemistry/reduce/Manifest
deleted file mode 100644
index 411c0992e7a1..000000000000
--- a/sci-chemistry/reduce/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-AUX 3.13.080428-LDFLAGS.patch 230 BLAKE2B 7741ea4ed815ec490f6ad17760520984b03637cc14f910978a6e6bbb959b39cf9075459527e082673a0ca6e4ec9573d2f20e749b3c906de0d2cf0a8d046fd016 SHA512 f7b471998c1fa5bb5c4eba7fd3f0900469b3ce1d90399413a18b736e5d35d93875c2b1666afe307935c9e71c516a7bd2db7eee1fba9640d403a2401a4427a539
-AUX 3.14.080821-CFLAGS.patch 736 BLAKE2B b64f12827243d8e8055aaf4602a60d910ece7bb73893907f278deace5b612cd64ae44ed064ae537d09f43b31053fc4060b0b2ef997acf06670550b4b856373d6 SHA512 f435a889845065374753841a0ba5de64e5be0d73935bd145d2e69980671cb3620441e99ec68bedbd876f45a0d61f406dc1a98f1ed7affaf4c923105d7540530a
-AUX reduce-3.16.111118-fix-c++14.patch 565 BLAKE2B dc170d9f3ef4718bae108e83ece1faf3bf8ebe41dc2ff34827f7af54425944babaac54ad70fd6892eb63e5488a77f252b612f5ba674cb441734cd7c25d005739 SHA512 8b38d5cbcc76318bb1309185858000daf8cca15a466ce0d4174126c9a5caa50e79d8198d3e3ff3427aa4629d51d0e50773d96b7bce7d94e16cace4bb80f4eed0
-DIST reduce.3.16.111118.src.zip 20342632 BLAKE2B 8c00e4ca881680404777cb788a0f6b4a5a0683ee33492c0050e503ce765d68117159bafded0f04c76f35ebd2f69fafbe471ff9798bea722be6d1585d128dae61 SHA512 f7b4d8d91f1f57e9e96c91139fa919c570aebd07f3a440faf3df54bf5deb3a05ad998996a24b5fe9aff6280e00329c9914e338cbfe802c047c055f52ce8312a9
-EBUILD reduce-3.16.111118.ebuild 1149 BLAKE2B 801ec29606876173d8194a70367fc217ee3950476fa236a1fffd565d57b59c59cfa5bd21482b69a9b3bd2b4bcf608e0d4815f76529f9bcc696218cd0a678b626 SHA512 18b7e9573b1364de97bc7ed54a7ff4480cc79a80dd2a6b1de551d22ef3bc7c0011ac99cc5d5c98f0a434ae99905d982e6f481e14a5a9cf0f43fa82cc0a522a55
-MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a
diff --git a/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch
deleted file mode 100644
index a615be088b24..000000000000
--- a/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/reduce_src/Makefile
-+++ b/reduce_src/Makefile
-@@ -34,7 +34,7 @@
- all:    reduce
- 
- reduce: $(OBJLIST)
--	$(CXX) -o $@ $(OBJLIST) $(LFLAGS)
-+	$(CXX) $(LDFLAGS) -o $@ $(OBJLIST) $(LFLAGS)
- 
- clean:
- 	@rm -rf *.o *.ckp ii_files
diff --git a/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch b/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch
deleted file mode 100644
index 8294c8ca385d..000000000000
--- a/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/reduce_src/Makefile b/reduce_src/Makefile
-index 598e367..067ace4 100644
---- a/reduce_src/Makefile
-+++ b/reduce_src/Makefile
-@@ -12,7 +12,7 @@ PROG_FLGS   = -DAROMATICS_ACCEPT_HBONDS \
- #              -DDEBUGMOVABLENODE -DDEBUGDOTCOUNTS
- #              -DMINPREDEFINED -DMAXPREDEFINED\
- 
--CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC) $(DICT_LOCOLD)\
-+CXXFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC) $(DICT_LOCOLD)\
-          -I$(PDBHOME) -I$(TOOLHOME) 
- #         -Wall
- 
-@@ -26,7 +26,7 @@ OBJLIST = GraphToHoldScores.o reduce.o CTab.o ElementInfo.o StdResH.o ResBlk.o A
- CXX		= g++
- 
- .cpp.o:
--	$(CXX) -c $*.cpp $(CFLAGS)
-+	$(CXX) -c $*.cpp $(CXXFLAGS)
- 
- OPT             = -O3
- DEBUG           = $(CXXDEBUGFLAGS)
diff --git a/sci-chemistry/reduce/files/reduce-3.16.111118-fix-c++14.patch b/sci-chemistry/reduce/files/reduce-3.16.111118-fix-c++14.patch
deleted file mode 100644
index 5a45b7cef49c..000000000000
--- a/sci-chemistry/reduce/files/reduce-3.16.111118-fix-c++14.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Fix building with C++14, which errors out due to an erroneous std::cerr.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=594202
-
---- a/reduce_src/GraphToHoldScores.cpp
-+++ b/reduce_src/GraphToHoldScores.cpp
-@@ -1150,7 +1150,7 @@
- 		}
- 	}
- 	std::cerr << "CRITICAL ERROR IN whichVertex(" << vertex_index << ") called on edge [" <<
--	std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
-+		vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl;
- 	assert(false);
- 	exit(1);
-         return 0; // to avoid warnings
diff --git a/sci-chemistry/reduce/metadata.xml b/sci-chemistry/reduce/metadata.xml
deleted file mode 100644
index da36ecbfcd6a..000000000000
--- a/sci-chemistry/reduce/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/reduce/reduce-3.16.111118.ebuild b/sci-chemistry/reduce/reduce-3.16.111118.ebuild
deleted file mode 100644
index ef1349e6adef..000000000000
--- a/sci-chemistry/reduce/reduce-3.16.111118.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-MY_P="${PN}.${PV}.src"
-
-DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file"
-HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php"
-SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce31/${MY_P}.zip"
-
-LICENSE="richardson"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-
-S="${WORKDIR}/"
-PATCHES=(
-	"${FILESDIR}"/3.13.080428-LDFLAGS.patch
-	"${FILESDIR}"/3.14.080821-CFLAGS.patch
-	"${FILESDIR}"/${PN}-3.16.111118-fix-c++14.patch
-)
-
-src_compile() {
-	DICT_DIR="/usr/share/reduce"
-	DICT_FOLD="reduce_het_dict.txt"
-	DICT_FNEW="reduce_wwPDB_het_dict.txt"
-
-	emake clean
-	emake \
-		CC="$(tc-getCC)" \
-		CXX="$(tc-getCXX)" \
-		OPT="${CXXFLAGS}" \
-		DICT_HOME="${EPREFIX}/${DICT_DIR}/${DICT_FNEW}" \
-		DICT_OLD="${EPREFIX}/${DICT_DIR}/${DICT_FOLD}"
-}
-
-src_install() {
-	dobin "${S}"/reduce_src/reduce
-	insinto ${DICT_DIR}
-	doins "${S}"/${DICT_FOLD} "${S}"/${DICT_FNEW}
-	dodoc README.usingReduce.txt
-}
diff --git a/sci-chemistry/wxmacmolplt/Manifest b/sci-chemistry/wxmacmolplt/Manifest
index 37feb5debd51..199b55c1a275 100644
--- a/sci-chemistry/wxmacmolplt/Manifest
+++ b/sci-chemistry/wxmacmolplt/Manifest
@@ -1,4 +1,4 @@
 AUX wxmacmolplt-7.5-glew.patch 415 BLAKE2B 733398664fae6fa3a6d11026a085010381998c68b2032958e3c7aa6516eb8578d08656b0ff5fcd2742c52f8b20053241a140b207ca08509396dd7177ed5247b4 SHA512 4d15247fbb5c2d9a60e7427b2c2f91d8a8f82cc457c681687f3046eda8e913125a0e041fd5d28744e0b12fe96b71280432b27bcdea5b7a8af7718b2f2d820d9e
 DIST wxmacmolplt-7.5.tar.gz 1965376 BLAKE2B 01033266ae66a215582a62690e792ca4ae82c8a8885fe277e2e77ee67ff70f02f6a9c10467ea6f3cee15933c6c89ba3c6137c9d29e47322ac4f395a3efd41383 SHA512 a1064d5068136b2a91328c7f912ff57d4741081d6d61437e7b4567fbf732917485b391493d637b8892bdad50b539363cfa9c778bb35407a9c0a2bfed20e42bc0
-EBUILD wxmacmolplt-7.5-r1.ebuild 968 BLAKE2B db5f878bd49063e216e7717125abd01921d67784c342efa61a1d381ee2c10eb7a95c36cdb9a70ad794895dce2f6561ad569d776dd45cc6e6e529f9e90b7ac076 SHA512 a9b24d109de51684443e398ee3841ade82f76c1ae4513480cdfb2e71cbad3bdeebf508db38457bee4a6cc811b4a41c643a027c3d9dcd69a2ff0daa532d9ba51e
+EBUILD wxmacmolplt-7.5-r1.ebuild 974 BLAKE2B f10bac00758060fe92c4bb59e19b8efdbb027093b436e1d4bbe9503a4d37c44ea70cedf3ef2506b9bbc842e573d77ff11c759212c620fa1239c341003fe6ac90 SHA512 bb069e1050052910691be01b9a442a0777e800d1593b75de8ab5b0979d31fc5b3e75310d3b183dce3b1ceff36706e2aa2a3affcb45a7d77e9eed35a5550b6e0e
 MISC metadata.xml 754 BLAKE2B ba9feac2d4de3bd14ab7a0f4101c826dadeb9bfd158006affae81f92e5acb613ffa853213ff47019e319810741d87223ac57387f2eba5ea9c87137cdb9a60ef7 SHA512 b5cd355851122f768fe0670518df7d4dbc2bd0a04c057acd95d25c3beedd8483d40dbd95b3d3090904b4e4d6289153731d8b0aa0c4753ee9614f1d693a409486
diff --git a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild
index 17f69a8387ae..9b08f966da9b 100644
--- a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild
+++ b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild
@@ -18,7 +18,7 @@ IUSE="flash"
 
 RDEPEND="
 	media-libs/glew:0=
-	media-libs/mesa
+	media-libs/mesa[X(+)]
 	x11-libs/wxGTK:${WX_GTK_VER}[X,opengl]
 	flash? ( media-libs/ming )"
 DEPEND="${RDEPEND}