gentoo resync : 18.08.2019

80 files changed, 1380 insertions, 1782 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index ba723163916e..ef8473b676e3 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/cantera/Manifest b/sci-libs/cantera/Manifest
index 0de1aac66598..5d9f62c911d3 100644
--- a/sci-libs/cantera/Manifest
+++ b/sci-libs/cantera/Manifest
@@ -1,4 +1,4 @@
 AUX cantera_2.4.0_env.patch 3559 BLAKE2B 07af1b751b653b1c92288286b9c82ef230ea0df7d9ea4036d23ac24338a221cc45c8e74f137fcf741bb9bb7148e7f3339f54234e9a92ac939956ba7c0ca8e157 SHA512 f2574c3de42d1666a2b64914c66d97045a2a3598f63678b3b60a701d111d7bfc9bd71031dd665a64e6791c9f311fb9514b1a0462a5713763a1b5f87fcd72e528
 DIST cantera-2.4.0.tar.gz 2321316 BLAKE2B 40750e3864afa3d35817e6f5777a6ac235261e9d134ef749966dbd738a2af5efec2882e6dcc719851f88656b41469e2159d3bff3df32f6abdf57db3b0a2afcae SHA512 8bb0fee34fa5bc9ec78e6f21a100eaa77bdd966bd0b7f0fa27d452e4f122c69e61648beef847178490f5c5d56267a96f6081cac9ccd03cea153c32814e0e84e9
-EBUILD cantera-2.4.0-r1.ebuild 2845 BLAKE2B b3761011ca55477721c6611d0f808bc4b9c95e62518c4c1cbe69f1bc27ec37ea03955a7995699634d0c6aae1fe35cc9781e7e694d255fde018e590c9519628e6 SHA512 92f3cc1d2e71d02474fec596f1787536c4246f8f4d2902e57c38f25f737efe3b3bc085c61869939148f7be2fa3321b92a30f742471c44b89b5b7fca9f9e824d3
-MISC metadata.xml 792 BLAKE2B 8f5617f3f6d8047a15e0fcd14a2e11647fc2a7442759434fb98ce2492b962edf38ba662570bfa627c7db10ef00cf945d73029ade83a5c34d8e21adadaae26454 SHA512 0bc11e72add5ab1e31e0ac5ec7b2c85be2757c0cc4d56d0df16e9a7afdea89f5ec6fd2f46a730d4caf25eeba66de0405631acf64fe271272f2348f3fdeaf7515
+EBUILD cantera-2.4.0-r1.ebuild 2828 BLAKE2B 2b41354065b3ce34ddb7c8535fe8e44d14ddb2bc2afb919f72c91ad92f2915895c9a17461d7575e238a719d0043a826eeb5ebd657edc341e289a669f06a5f3cf SHA512 77fdcddcb93927d08976a11828d82f82c4798b2b85795a230a095af4698c4747d4b2241f89d6933d3c5f6b852edc4626557e5ee67eb2243b0bbf40e24c8a8760
+MISC metadata.xml 794 BLAKE2B 4a92fb553aad7d87d4b7a8d77974dbd67d593b4010783f96324979d9c01067bccc60d2faedf604bd8d44a8ac4316356879301899af8bc08d0fcd548df6d3762d SHA512 a9e6f4e161519d0b3618fe8da7065195bc760ba889fa4356358d4047ea1970eb5fd78bdc5fbeb7c660f1bee48a68ab20ced636514e6f12848e88f6f4dabc9705
diff --git a/sci-libs/cantera/cantera-2.4.0-r1.ebuild b/sci-libs/cantera/cantera-2.4.0-r1.ebuild
index 15cb1776f092..c277d8d01c6e 100644
--- a/sci-libs/cantera/cantera-2.4.0-r1.ebuild
+++ b/sci-libs/cantera/cantera-2.4.0-r1.ebuild
@@ -21,11 +21,11 @@ IUSE="+cti fortran pch +python test"
 
 REQUIRED_USE="
 	python? ( cti )
-	cti? ( ${PYTHON_REQUIRED_USE} )
 	${PYTHON_REQUIRED_USE}
 	"
 
 RDEPEND="
+	${PYTHON_DEPS}
 	python? (
 		dev-python/numpy[${PYTHON_USEDEP}]
 	)
diff --git a/sci-libs/cantera/metadata.xml b/sci-libs/cantera/metadata.xml
index a57df7829d2d..47bc86a96301 100644
--- a/sci-libs/cantera/metadata.xml
+++ b/sci-libs/cantera/metadata.xml
@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
   <maintainer type="person">
-    <email>torokhov_s_a@mail.ru</email>
+    <email>torokhov-s-a@yandex.ru</email>
     <name>Sergey Torokhov</name>
   </maintainer>
   <maintainer type="project">
diff --git a/sci-libs/cctbx/Manifest b/sci-libs/cctbx/Manifest
deleted file mode 100644
index 449f448e8e8a..000000000000
--- a/sci-libs/cctbx/Manifest
+++ /dev/null
@@ -1,11 +0,0 @@
-AUX 2010.03.29.2334-boost.patch 18175 BLAKE2B 4722757f0dd77989830588d2bf2a5ec8cc7d586ea5f6034f4000da314de2d518166811685546567afe54ddaf1e214be7f29fa82a8b5757057d37aa8df240fb90 SHA512 e722312a878be229a24269471902bd1febe98c5510bfc50e1ba3a841c1a0228cdb7964e69703083850052e49e91899b229bc3543d90485ba50e79e7eceb11e2e
-AUX 2010.03.29.2334-clipper.patch 2209 BLAKE2B b76a321d4e350026c7b8fe7eff64ae225983b58e331e115cad1405db417e9b303abea557d81194690090f7864d9d8df25b871c1e921d421603c05d08c18ac83d SHA512 cb3fc1f89d9a4008b4add3ef2ecf5b2aa8e875e41e169916859a8e508858bc9548023bb552d4cb3794c46788eaa325c75bb858c7c08799b87f2e31bef57cf69a
-AUX 2010.03.29.2334-flags.patch 3336 BLAKE2B 669460625601f2a76f83cc7565ab5e33b1bf45f47a7cfc6f003bc5e349517a210e7f8f2439bd26e1bffaf2c2fdde0bdf9aaa39d1e8c59b44bc2b09540f89c98e SHA512 63ccefc4303136c9fea854fecdbed39efe9d7f565000bc356addc2b268e042c34815da3416e9960200b9f6ac33b7c4bb7ce705a7b7939cd65ef4f925d56ced41
-AUX 2010.03.29.2334-format-security.patch 4696 BLAKE2B 4d6acb991b6dbad44b9b7e73f77f422ea4ea03fda13109b1cd01114b4724296bf6c610662a2ce3b4187fdea555fc0afc07c61ea4a9d1952e60a166fba4078c56 SHA512 715c3b810c7c89864c8192dc9678cd8e758ba1bbb39782a2077f7ca598ddd2bc01114d4e5b58821c3246f1951d8b53b8ecdc085b3a03e2ebb5082a9dbf46a156
-AUX 2010.03.29.2334-gcc-4.6.patch 1059 BLAKE2B affbce02451ac2b20413047ea44bc2eb86c685a8e22d3fe3f5f003c3cfdff6c05417dd9231f7dc8f0cfab4d4a4d17c0e6cdb3cd7276458061e6a3bcc80bfcd65 SHA512 25ad8471b1108549de6806752f886057e86e875dbcf78ad4f11095a54295d2234bf704b55559bf48ff50f0db64fb3d6a0367bcdc85e517a244abecdbbcabb2c1
-AUX 2010.03.29.2334-gcc-4.7.patch 6747 BLAKE2B 6f5d3be4fef428bb9de081c368fe96036248330ed1684fa0c761f43c1df6d62289761c76196332b99abaa082168aba00ce72777433d71fcde0b45023ffde9611 SHA512 17d557567ed135c3c095f3849f2643121f6c183573f8e5b63e056180c5ca6985cd1fcf482378787fbf37078eb185bd2502dfc42fb163e50fc1567588d7e3ef0e
-AUX 2010.03.29.2334-soname.patch 5177 BLAKE2B e3ad5dc99684ead267f4a44dbc94f6383e5af3b480144b2f78052c235f5bf8d126aeb7c5863b79788f9eaf7b4f280d3029f7e43f0443f3dc364d7fa48fd5d4d3 SHA512 3f62bc52c32c3573fbcd90fc49234498d7c28fc0dc7a68497041af35da46cbd9cb386b9b13ed2269a5728e87526987ac49179e38b2bcb6a355ee4c180e9f7861
-AUX 2010.03.29.2334-tst_server.py.patch 774 BLAKE2B e60f610d0a394b905dd6c1f0960f19c580a9f76de50c31619356069c793e9b191201eba1ffeb2cd74383771df7cbb626b271b731f050bc0760a054d297d4f6fc SHA512 490918c3139355ecb0430d908ccafc6d66cb25ec7df285cedbb983d80f3473425c72d0766262c557c0c783626479edd2528eaf83b1decdeba416dde193472d5a
-DIST cctbx-2010.03.29.2334.tar.gz 15570372 BLAKE2B ad0b98fa27b8b13af7a1f41ee3764ce558afc4d53b8e7605c169ed86a9b0dd0e86ad58a72eec6dc570bdbf6574dcee25ca357633d727a36ed36f00186c9cc503 SHA512 7aafd647db49925fc1df16a9ccb4f8caf040b4d73e9601731eb3da3051467c3005fb2cc95b498501c899cd1bd378e6a6135cffe734cb4f93eccacbc13575b2c8
-EBUILD cctbx-2010.03.29.2334-r7.ebuild 5709 BLAKE2B 76b5b5e9e194db71fa413092c26dedb3f94ea7a78270e0417afd8e107c673c8d8ff53257b6a7ff0505e170446aa09d586d581589114891da502a7fced67e1e7c SHA512 6afbc11e892c871a75303c0d7bf735114a1c60c7deebac2777596fbe9e5178eefca1ad1ab50c08337e826de8ac0f488093b69762fd00e3ae84b4e569fa62289a
-MISC metadata.xml 847 BLAKE2B 30bee6dab45b7f8bcba32cdb316b593cedfd0348e9b552cd47df1c95008ad80320dd49634f25df6fe9d3818df5dfa7b123fef7ac69591f98cfe9c14f7b6b8dd6 SHA512 47a592ad0903af960662fd4c90753864c10bcd904fb2a0ad99a451b5ac95cbf29b71c58cca27078319deef0041d631d3ebe1c6642f4614d9d1660954a6432dd4
diff --git a/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild b/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild
deleted file mode 100644
index 5ac1e461f684..000000000000
--- a/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild
+++ /dev/null
@@ -1,189 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils fortran-2 multilib prefix python-single-r1 toolchain-funcs
-
-MY_PV="${PV//./_}"
-
-DESCRIPTION="Computational Crystallography Toolbox"
-HOMEPAGE="http://cctbx.sourceforge.net/"
-SRC_URI="http://cci.lbl.gov/cctbx_build/results/${MY_PV}/${PN}_bundle.tar.gz -> ${P}.tar.gz"
-
-LICENSE="cctbx-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="+minimal openmp threads"
-
-REQUIRED_USE="
-	${PYTHON_REQUIRED_USE}
-	?? ( openmp threads )"
-
-RDEPEND="
-	${PYTHON_DEPS}
-	>=dev-libs/boost-1.48[python,${PYTHON_USEDEP}]
-	sci-libs/clipper
-	sci-libs/fftw:3.0=
-	!minimal? (
-		sci-chemistry/cns
-		sci-chemistry/shelx )"
-DEPEND="${RDEPEND}
-	!prefix? ( >=dev-util/scons-1.2[${PYTHON_USEDEP}] )"
-
-S="${WORKDIR}"
-MY_S="${WORKDIR}"/cctbx_sources
-MY_B="${WORKDIR}"/cctbx_build
-
-pkg_setup() {
-	use openmp && FORTRAN_NEED_OPENMP="1"
-	if use openmp && ! tc-has-openmp; then
-		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 and icc"
-		ewarn "If you want to build ${PN} with OpenMP, abort now,"
-		ewarn "and switch CC to an OpenMP capable compiler"
-		FORTRAN_NEED_OPENMP=1
-	fi
-	fortran-2_pkg_setup
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	local opts
-	local optsld
-
-	epatch \
-		"${FILESDIR}"/${PV}-tst_server.py.patch \
-		"${FILESDIR}"/${PV}-boost.patch \
-		"${FILESDIR}"/${PV}-clipper.patch \
-		"${FILESDIR}"/${PV}-flags.patch \
-		"${FILESDIR}"/${PV}-soname.patch \
-		"${FILESDIR}"/${PV}-gcc-4.6.patch \
-		"${FILESDIR}"/${PV}-gcc-4.7.patch \
-		"${FILESDIR}"/${PV}-format-security.patch
-
-	eprefixify "${MY_S}"/scitbx/libtbx_refresh.py
-
-	rm -rvf "${MY_S}/boost" "${MY_S}/PyCifRW" >> "${T}"/clean.log || die
-	if ! use prefix; then
-		rm -rvf "${MY_S}/scons" >> "${T}"/clean.log || die
-		echo "import os, sys; os.execvp('scons', sys.argv)" > "${MY_S}"/libtbx/command_line/scons.py || die
-	fi
-
-	find "${MY_S}/clipper" -name "*.h" -print -delete >> "${T}"/clean.log || die
-
-	sed \
-		-e "/LIBS/s:boost_python:boost_python-$(echo ${EPYTHON} | sed 's/python//'):g" \
-		-i "${MY_S}"/boost_adaptbx/SConscript "${MY_S}"/scitbx/boost_python/SConscript || die
-}
-
-src_configure() {
-	local compiler
-	local myconf
-
-	myconf="${MY_S}/libtbx/configure.py"
-
-	compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
-	myconf="${myconf} --compiler=${compiler}"
-
-	# Additional USE flag usage
-	myconf="${myconf} --enable-openmp-if-possible=$(usex openmp true false)"
-
-	use threads && USEthreads="--enable-boost-threads"
-
-	myconf="${myconf} ${USE_threads} --scan-boost --use_environment_flags"
-
-	mkdir "${MY_B}" && myconf="${myconf} --current_working_directory=${MY_B}"
-	cd "${MY_B}"
-
-	myconf="${myconf} --build=release fftw3tbx rstbx smtbx mmtbx clipper_adaptbx fable"
-	einfo "configuring with ${python} ${myconf}"
-
-	${EPYTHON} ${myconf} || die "configure failed"
-}
-
-src_compile() {
-	local makeopts_exp
-
-	cd "${MY_B}"
-
-	makeopts_exp=${MAKEOPTS/j/j }
-	makeopts_exp=${makeopts_exp%-l[0-9]*}
-
-	source setpaths_all.sh
-
-	einfo "compiling with libtbx.scons ${makeopts_exp}"
-	libtbx.scons ${makeopts_exp} .|| die "make failed"
-}
-
-src_test(){
-	source "${MY_B}"/setpaths_all.sh
-	libtbx.python $(libtbx.show_dist_paths boost_adaptbx)/tests/tst_rational.py && \
-	libtbx.python ${SCITBX_DIST}/run_tests.py ${MAKEOPTS_EXP} && \
-	libtbx.python ${CCTBX_DIST}/run_tests.py  ${MAKEOPTS_EXP} \
-	|| die "test failed"
-}
-
-src_install(){
-	local lib baselib
-#	find cctbx_build/ -type f \( -name "*.py" -o -name "*sh" \) -exec \
-#	sed -e "s:${MY_S}:${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_sources:g" \
-#	    -e "s:${MY_B}:${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build:g"  \
-#	    -i '{}' \; || die "Fail to correct path"
-
-	sed \
-		-e "s:${MY_B}:${EPREFIX}/usr:g" \
-		-e "s:${MY_S}:${EPREFIX}/$(python_get_sitedir):g" \
-		-i "${MY_B}/libtbx_env" || die
-
-	insinto /usr/share/cctbx
-	doins "${MY_B}/libtbx_env" || die
-
-	ebegin "removing unnessary files"
-		rm -r "${S}"/cctbx_sources/{clipper,ccp4io,ucs-fonts,TAG} || die "failed to remove uneeded scons"
-		find -O3 "${S}" -type f \
-			\( -name "*conftest*" -o -name "*.o" -o -name "*.c" -o -name "*.f" -o -name "*.cpp" -o \
-			-name "*.pyc" -o -name "SCons*" -o -name "Makefile" -o -name "config.log" \) -delete \
-			-print >> "${T}"/clean.log || die
-		find "${S}" -type d -empty -delete -print >> "${T}"/clean.log || die
-		find "${MY_B}" -maxdepth 1 -type f -delete -print >> "${T}"/clean.log || die
-	eend
-
-	dobin "${MY_B}"/bin/*
-	rm -vrf "${MY_B}/bin" >> "${T}"/clean.log || die
-	dolib.so "${MY_B}"/lib/lib*
-	mv "${ED}"/usr/$(get_libdir)/libscitbx_min{,i}pack.so || die
-	rm -vf "${MY_B}"/lib/lib* >> "${T}"/clean.log || die
-
-	for lib in "${ED}"/usr/$(get_libdir)/*.so; do
-		baselib=$(basename ${lib})
-		mv ${lib}{,.0.0} || die
-		dosym ${baselib}.0.0 /usr/$(get_libdir)/${baselib}
-	done
-
-	insinto /usr/include
-	doins -r "${MY_B}"/include/* || die
-	rm -rvf "${MY_B}/include" >> "${T}"/clean.log || die
-
-	insinto /usr/libexec/${PN}
-	doins -r "${MY_B}"/* || die
-	find "${ED}"/usr/libexec/${PN} -type f -exec chmod 755 '{}' \;
-
-	cd "${MY_S}"
-	python_domodule * "${MY_B}"/lib/*
-	rm -rvf "${MY_B}/lib" >> "${T}"/clean.log || die
-
-	sed \
-		-e "/PYTHONPATH/s:${MY_S}:$(python_get_sitedir):g" \
-		-e "/PYTHONPATH/s:${MY_B}:$(python_get_sitedir):g" \
-		-e "/LD_LIBRARY_PATH/s:${MY_B}/lib:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "/PATH/s:${MY_B}/bin:${EPREFIX}/usr/bin:g" \
-		-e "/PATH/s:${MY_B}/exe:${EPREFIX}/usr/bin:g" \
-		-e "/exec/s:${MY_S}:$(python_get_sitedir):g" \
-		-e "/LIBTBX_BUILD/s:${MY_B}:${EPREFIX}/usr/share/cctbx:g" \
-		-e "s:${MY_B}/exe_dev/:${EPREFIX}/usr/libexec/${PN}/exe_dev/:g" \
-		-i "${ED}"/usr/bin/* || die
-
-	python_optimize
-}
diff --git a/sci-libs/cctbx/files/2010.03.29.2334-boost.patch b/sci-libs/cctbx/files/2010.03.29.2334-boost.patch
deleted file mode 100644
index 5b4439ee6780..000000000000
--- a/sci-libs/cctbx/files/2010.03.29.2334-boost.patch
+++ /dev/null
@@ -1,516 +0,0 @@
-From 7e77ff8694b87e95efe56ed961fbc8dd30d8c238 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <gentoo@mgorny.alt.pl>
-Date: Sun, 4 Jul 2010 12:21:10 +0200
-Subject: [PATCH] Unbundle boost.
-
----
- work/cctbx_sources/boost_adaptbx/SConscript   |  260 -------------------------
- work/cctbx_sources/cbflib_adaptbx/SConscript  |    1 -
- work/cctbx_sources/cctbx/SConscript           |    1 -
- work/cctbx_sources/clipper_adaptbx/SConscript |    1 -
- work/cctbx_sources/fable/SConscript           |    1 -
- work/cctbx_sources/fable/libtbx_config        |    2 +-
- work/cctbx_sources/fftw3tbx/SConscript        |    1 -
- work/cctbx_sources/gltbx/SConscript           |    1 -
- work/cctbx_sources/iotbx/SConscript           |    2 -
- work/cctbx_sources/mmtbx/SConscript           |    1 -
- work/cctbx_sources/omptbx/libtbx_config       |    2 +-
- work/cctbx_sources/rstbx/SConscript           |    1 -
- work/cctbx_sources/scitbx/SConscript          |    1 -
- work/cctbx_sources/scitbx/libtbx_config       |    2 +-
- work/cctbx_sources/scitbx/libtbx_refresh.py   |    3 +-
- work/cctbx_sources/smtbx/SConscript           |    1 -
- work/cctbx_sources/spotfinder/SConscript      |    1 -
- work/cctbx_sources/tntbx/SConscript           |    1 -
- 18 files changed, 4 insertions(+), 279 deletions(-)
-
-diff --git a/work/cctbx_sources/boost_adaptbx/SConscript b/work/cctbx_sources/boost_adaptbx/SConscript
-index 0701816..9f8cbf9 100644
---- a/work/cctbx_sources/boost_adaptbx/SConscript
-+++ b/work/cctbx_sources/boost_adaptbx/SConscript
-@@ -8,39 +8,9 @@ import string
- import sys, os
- op = os.path
- Import("env_base", "env_etc")
--env_etc.boost_dist = libtbx.env.dist_path("boost")
--env_etc.boost_include = env_etc.boost_dist
- env_etc.boost_adaptbx_dist = libtbx.env.dist_path("boost_adaptbx")
- env_etc.boost_adaptbx_include = os.path.dirname(env_etc.boost_adaptbx_dist)
- 
--def build_boost_thread():
--  if (not libtbx.env.build_options.enable_boost_threads):
--    return
--  if (sys.platform == "win32"): s = "win32"
--  else:                         s = "pthread"
--  join = os.path.join
--  src = join("libs", "thread", "src", s)
--  prefix = "#" + join(os.path.basename(env_etc.boost_dist), src)
--  source = []
--  for node in sorted(os.listdir(join(env_etc.boost_dist, src))):
--    if (not node.lower().endswith(".cpp")): continue
--    source.append(join(prefix, node))
--  env = env_base.Clone(
--    SHLINKFLAGS=env_etc.shlinkflags)
--  env.Append(SHCXXFLAGS=["-DBOOST_THREAD_BUILD_DLL"])
--  env_etc.include_registry.append(
--    env=env,
--    paths=[env_etc.boost_include])
--  darwin_shlinkcom(env_etc, env,
--                   lo="boost/libs/thread/src/libboost_thread.lo",
--                   dylib="lib/libboost_thread.dylib")
--  env.Repository(os.path.dirname(env_etc.boost_dist))
--  env.SharedLibrary(
--    target='#lib/boost_thread',
--    source=source)
--
--build_boost_thread()
--
- if (not env_etc.no_boost_python):
-   env_etc.cxxflags_bpl_defines_base = [
-     "-DBOOST_PYTHON_MAX_BASES=2"]
-@@ -64,12 +34,10 @@ if (not env_etc.no_boost_python):
-         ' /manifest ${TARGET}.manifest'])
-   Export("env_no_includes_boost_python_ext")
-   env_pure_boost_python_ext = env_no_includes_boost_python_ext.Clone()
--  env_etc.include_registry.set_boost_dir_name(env_etc.boost_dist)
-   env_etc.include_registry.append(
-     env=env_pure_boost_python_ext,
-     paths=[
-       "#include",
--      env_etc.boost_include,
-       env_etc.python_include])
-   env_boost_python_ext = env_pure_boost_python_ext.Clone()
-   env_etc.include_registry.prepend(
-@@ -113,234 +81,6 @@ if (not env_etc.no_boost_python):
-     target="tests/tst_optional_copy",
-     source="tests/tst_optional_copy.cpp")
- 
--  import os, os.path
--  env = env_base.Clone(LIBS=env_etc.libs_python)
--  env.Append(LIBPATH=env_etc.libpath_python)
--  env.Append(SHCXXFLAGS=env_etc.cxxflags_bpl_defines_base)
--  env.Append(SHCXXFLAGS=["-DBOOST_PYTHON_SOURCE"])
--  if (libtbx.env.build_options.boost_python_bool_int_strict):
--    env.Append(SHCXXFLAGS=["-DBOOST_PYTHON_BOOL_INT_STRICT"])
--  env.Replace(SHLINKFLAGS=env_etc.shlinkflags)
--  env.Append(CXXFLAGS=env_etc.cxxflags_bpl_defines_base)
--  env.Append(CXXFLAGS="-DBOOST_PYTHON_SOURCE")
--  env.Replace(LINKFLAGS=env_etc.shlinkflags)
--  env_etc.include_registry.append(
--    env=env,
--    paths=[env_etc.boost_include, env_etc.python_include])
--
--  darwin_shlinkcom(env_etc, env,
--                   lo="boost/libs/python/src/libboost_python.lo",
--                   dylib="lib/libboost_python.dylib")
--
--  # fixed list of file names introduced 2009-09-29, due to major changes in
--  # boost/libs/python/build/Jamfile.v2 svn rev. 56305 (new Python 3 support)
--  bpl_dll_sources = """\
--numeric.cpp
--list.cpp
--long.cpp
--dict.cpp
--tuple.cpp
--str.cpp
--slice.cpp
--converter/from_python.cpp
--converter/registry.cpp
--converter/type_id.cpp
--object/enum.cpp
--object/class.cpp
--object/function.cpp
--object/inheritance.cpp
--object/life_support.cpp
--object/pickle_support.cpp
--errors.cpp
--module.cpp
--converter/builtin_converters.cpp
--converter/arg_to_python_base.cpp
--object/iterator.cpp
--object/stl_iterator.cpp
--object_protocol.cpp
--object_operators.cpp
--wrapper.cpp
--import.cpp
--exec.cpp
--object/function_doc_signature.cpp
--""".splitlines()
--  prefix = "#"+os.path.join(
--    os.path.basename(env_etc.boost_dist), "libs", "python", "src")
--  bpl_dll_sources = [os.path.join(prefix, path) for path in bpl_dll_sources]
--  #
--  env.Repository(os.path.dirname(env_etc.boost_dist))
--  if (env_etc.static_bpl):
--    env.StaticLibrary(target="#lib/boost_python", source=bpl_dll_sources)
--  else:
--    env.SharedLibrary(target="#lib/boost_python", source=bpl_dll_sources)
--  if (int(ARGUMENTS.get("boost_python_tests", 0))):
--    warn_if_unexpected_md5_hexdigest(
--      path=libtbx.env.under_dist("boost", "libs/python/test/Jamfile.v2"),
--      expected_md5_hexdigests=[
--        "c7a3dd81bf730635146f5c908ac982eb", # svn revision 39065M
--        "d40aac0029bcd28f6e205ae3b30a1284", # svn revision 40216
--        "b79f016d3ec10cf1625a9e006e605428", # svn revision 40714
--        "f948983d970fd47e83a3a785bb54520a", # svn revision 41550
--        "c3d84006331d534840c42ab956fdfa05", # svn revision 50367M
--        "cedfd061d767a27413ef4a75ee0e446f", # svn revision 56310
--        "e5507482a1937825e4c9f3ffe555fc59", # svn revision 59331
--      ])
--    bpl_tests = Split("""
--staticmethod
--shared_ptr
--enable_shared_from_this
--andreas_beyer
--polymorphism
--polymorphism2
--auto_ptr
--minimal
--args
--numpy
--enum
--exception_translator
--test_pointer_adoption
--operators
--callbacks
--defaults
--object
--list
--long
--dict
--tuple
--str
--virtual_functions
--back_reference
--implicit
--data_members
--ben_scott1
--bienstman1
--bienstman2
--bienstman3
--multi_arg_constructor
--extract
--opaque
--pickle1
--pickle2
--pickle3
--pickle4
--nested
--docstring
--pytype_function
--bienstman4
--bienstman5
--test_builtin_converters,builtin_converters_ext,test_builtin_converters
--cltree,cltree,test_cltree
--m1,m1,newtest
--m2,m2,newtest
--iterator,iterator_ext,iterator
--input_iterator,input_iterator,iterator
--crossmod_exception_a,crossmod_exception_a,crossmod_exception
--crossmod_exception_b,crossmod_exception_b,crossmod_exception
--vector_indexing_suite
--return_arg
--keywords,keywords,keywords_test
--properties
--map_indexing_suite;int_map_indexing_suite;a_map_indexing_suite,map_indexing_suite_ext,map_indexing_suite
--injected
--slice
--const_argument
--raw_ctor
--pointer_vector
--wrapper_held_type
--polymorphism2_auto_ptr
--stl_iterator
--voidptr
--crossmod_opaque_a,crossmod_opaque_a,crossmod_opaque
--crossmod_opaque_b,crossmod_opaque_b,crossmod_opaque
--""")
--# non-portable tests are not included above:
--#   calling_conventions
--#   calling_conventions_mf
--#
--    Import("env_boost_python_ext")
--    test_dir = libtbx.env.under_dist("boost", "libs/python/test")
--    prefix = "#"+os.path.join(
--      os.path.basename(env_etc.boost_dist), "libs", "python", "test")
--    all_tst = []
--    for bpl_test in bpl_tests:
--      flds = bpl_test.split(",")
--      assert len(flds) in (1,3)
--      if (len(flds) == 1):
--        src = bpl_test
--        pyd = bpl_test + "_ext"
--        tst = bpl_test
--      else:
--        src = flds[0]
--        pyd = flds[1]
--        tst = flds[2]
--      env = env_pure_boost_python_ext.Clone()
--      env.Repository(os.path.dirname(env_etc.boost_dist))
--      ok = True
--      source = []
--      for s in src.split(";"):
--        cpp = "%s.cpp" % s
--        file_name = os.path.join(test_dir, cpp)
--        if (not os.path.isfile(file_name)):
--          print "Warning: source file not available:", show_string(file_name)
--          ok = False
--        else:
--          source.append(os.path.join(prefix, cpp))
--      if (ok):
--        if (not tst in all_tst):
--          all_tst.append(tst)
--        env.SharedLibrary(target="#lib/%s" % pyd, source=source)
--    all_tst = [os.path.join(test_dir, tst+".py") for tst in all_tst]
--    #
--    if (sys.platform == "linux2"):
--      base_lib = libtbx.env.under_build(path="base/lib")
--      if (os.path.isdir(base_lib)):
--        env_prog = env.Clone()
--        env_prog.Append(LIBPATH=[base_lib])
--        env_prog.Append(LIBS=[
--          "-lpython%d.%d" % sys.version_info[:2],
--          "-lpthread",
--          "-lutil",
--          "-ldl"])
--        exe = env_prog.Program(
--          target="boost/libs/python/test/exec_dynamic",
--          source=[os.path.join(prefix, "exec.cpp")])
--        libtbx.env.write_dispatcher_in_bin(
--          source_file=exe[0].get_abspath(),
--          target_file="boost_libs_python_test_exec_dynamic")
--        all_tst.append("$ boost_libs_python_test_exec_dynamic %s"
--          % show_string(os.path.join(test_dir, "exec.py")))
--    #
--    if (os.name != "nt"):
--      env.SharedLibrary(
--        target="#lib/boost_adaptbx_char_array_ext",
--        source=["char_array_ext.cpp"])
--      all_tst.append(
--        libtbx.env.under_dist("boost_adaptbx", "tests/tst_char_array.py"))
--    #
--    if (os.name == "nt"):
--      boost_python_run_tests = \
--        "%s\\boost_python_run_tests.bat" % libtbx.env.build_path
--      f = open(boost_python_run_tests, "w")
--      for tst in all_tst:
--        if (tst.startswith("$ ")):
--          print >> f, 'call %s' % tst[2:]
--        else:
--          print >> f, 'call libtbx.python %s' % show_string(tst)
--      f.close()
--    else:
--      boost_python_run_tests = \
--        "%s/boost_python_run_tests.csh" % libtbx.env.build_path
--      f = open(boost_python_run_tests, "w")
--      print >> f, "#! /bin/csh -f"
--      print >> f, "set verbose"
--      for tst in all_tst:
--        if (tst.startswith("$ ")):
--          print >> f, tst[2:]
--        else:
--          print >> f, 'libtbx.python "%s"' % show_string(tst)
--      f.close()
--      os.chmod(boost_python_run_tests, 0755)
--
-   def write_type_id_eq_h():
-     unsigned_types = [
-       "unsigned short",
-diff --git a/work/cctbx_sources/cbflib_adaptbx/SConscript b/work/cctbx_sources/cbflib_adaptbx/SConscript
-index 78c1297..dffc247 100644
---- a/work/cctbx_sources/cbflib_adaptbx/SConscript
-+++ b/work/cctbx_sources/cbflib_adaptbx/SConscript
-@@ -14,7 +14,6 @@ env_etc.cbflib_common_includes = [
-   env_etc.libtbx_include,
-   env_etc.scitbx_include,
-   env_etc.boost_adaptbx_include,
--  env_etc.boost_include,
-   env_etc.cbflib_dist,    # for the adaptor cpp files
-   env_etc.cbflib_include[0], # for the cbflib c-files
-   env_etc.cbflib_include[1], # for the cbflib c-files
-diff --git a/work/cctbx_sources/cctbx/SConscript b/work/cctbx_sources/cctbx/SConscript
-index 6ec7c93..2dfb442 100644
---- a/work/cctbx_sources/cctbx/SConscript
-+++ b/work/cctbx_sources/cctbx/SConscript
-@@ -10,7 +10,6 @@ env_etc.cctbx_common_includes = [
-   env_etc.scitbx_include,
-   env_etc.chiltbx_include,
-   env_etc.omptbx_include,
--  env_etc.boost_include,
- ]
- 
- env = env_base.Clone(
-diff --git a/work/cctbx_sources/fable/SConscript b/work/cctbx_sources/fable/SConscript
-index bf8e198..b6acccf 100644
---- a/work/cctbx_sources/fable/SConscript
-+++ b/work/cctbx_sources/fable/SConscript
-@@ -13,7 +13,6 @@ if (not env_etc.no_boost_python):
-       env_etc.libtbx_include,
-       env_etc.fable_include,
-       env_etc.boost_adaptbx_include,
--      env_etc.boost_include,
-       env_etc.python_include])
-   env.SharedLibrary(
-     target="#lib/fable_ext",
-diff --git a/work/cctbx_sources/fable/libtbx_config b/work/cctbx_sources/fable/libtbx_config
-index d456588..f00ae86 100644
---- a/work/cctbx_sources/fable/libtbx_config
-+++ b/work/cctbx_sources/fable/libtbx_config
-@@ -1,4 +1,4 @@
- {
--  "modules_required_for_build": ["boost"],
-+  "modules_required_for_build": [],
-   "modules_required_for_use": ["boost_adaptbx"],
- }
-diff --git a/work/cctbx_sources/fftw3tbx/SConscript b/work/cctbx_sources/fftw3tbx/SConscript
-index ecc3a03..4fc1ec1 100755
---- a/work/cctbx_sources/fftw3tbx/SConscript
-+++ b/work/cctbx_sources/fftw3tbx/SConscript
-@@ -8,7 +8,6 @@ env_etc.fftw3tbx_dist = libtbx.env.dist_path("fftw3tbx")
- env_etc.fftw3tbx_common_includes = [
-   env_etc.libtbx_include,
-   env_etc.scitbx_include,
--  env_etc.boost_include,
- ]
- 
- base_include = libtbx.env.under_build("base/include")
-diff --git a/work/cctbx_sources/gltbx/SConscript b/work/cctbx_sources/gltbx/SConscript
-index 56a7115..f6214a4 100644
---- a/work/cctbx_sources/gltbx/SConscript
-+++ b/work/cctbx_sources/gltbx/SConscript
-@@ -7,7 +7,6 @@ env_etc.gltbx_common_includes = [
-   env_etc.libtbx_include,
-   env_etc.gltbx_include,
-   env_etc.scitbx_include,
--  env_etc.boost_include,
- ]
- 
- if (not env_etc.no_boost_python):
-diff --git a/work/cctbx_sources/iotbx/SConscript b/work/cctbx_sources/iotbx/SConscript
-index df17856..c5cf7da 100644
---- a/work/cctbx_sources/iotbx/SConscript
-+++ b/work/cctbx_sources/iotbx/SConscript
-@@ -10,7 +10,6 @@ env_etc.iotbx_common_includes = [
-   env_etc.iotbx_include,
-   env_etc.cctbx_include,
-   env_etc.scitbx_include,
--  env_etc.boost_include,
-   env_etc.boost_adaptbx_include,
- ]
- 
-@@ -37,7 +36,6 @@ if (not env_etc.no_boost_python):
-   env_etc.include_registry.append(
-     env=env,
-     paths=[env_etc.libtbx_include,
--           env_etc.boost_include,
-            env_etc.python_include])
-   env.SharedLibrary(
-     target="#lib/iotbx_wildcard_ext",
-diff --git a/work/cctbx_sources/mmtbx/SConscript b/work/cctbx_sources/mmtbx/SConscript
-index 0532878..9bcaeb2 100755
---- a/work/cctbx_sources/mmtbx/SConscript
-+++ b/work/cctbx_sources/mmtbx/SConscript
-@@ -10,7 +10,6 @@ env_etc.mmtbx_common_includes = [
-   env_etc.mmtbx_include,
-   env_etc.cctbx_include,
-   env_etc.scitbx_include,
--  env_etc.boost_include,
- ]
- 
- if (not env_etc.no_boost_python):
-diff --git a/work/cctbx_sources/omptbx/libtbx_config b/work/cctbx_sources/omptbx/libtbx_config
-index d456588..f00ae86 100644
---- a/work/cctbx_sources/omptbx/libtbx_config
-+++ b/work/cctbx_sources/omptbx/libtbx_config
-@@ -1,4 +1,4 @@
- {
--  "modules_required_for_build": ["boost"],
-+  "modules_required_for_build": [],
-   "modules_required_for_use": ["boost_adaptbx"],
- }
-diff --git a/work/cctbx_sources/rstbx/SConscript b/work/cctbx_sources/rstbx/SConscript
-index 2213c2f..232b5d7 100644
---- a/work/cctbx_sources/rstbx/SConscript
-+++ b/work/cctbx_sources/rstbx/SConscript
-@@ -11,7 +11,6 @@ env_etc.rstbx_common_includes = [
-   env_etc.scitbx_include,
-   env_etc.chiltbx_include,
-   env_etc.omptbx_include,
--  env_etc.boost_include,
- ]
- 
- env = env_base.Clone(SHLINKFLAGS=env_etc.shlinkflags)
-diff --git a/work/cctbx_sources/scitbx/SConscript b/work/cctbx_sources/scitbx/SConscript
-index f30b9db..10e0967 100644
---- a/work/cctbx_sources/scitbx/SConscript
-+++ b/work/cctbx_sources/scitbx/SConscript
-@@ -9,7 +9,6 @@ env_etc.scitbx_common_includes = [
-   env_etc.scitbx_include,
-   env_etc.omptbx_include,
-   env_etc.boost_adaptbx_include,
--  env_etc.boost_include,
- ]
- 
- SConscript("error/SConscript")
-diff --git a/work/cctbx_sources/scitbx/libtbx_config b/work/cctbx_sources/scitbx/libtbx_config
-index 87cc3c7..d147819 100644
---- a/work/cctbx_sources/scitbx/libtbx_config
-+++ b/work/cctbx_sources/scitbx/libtbx_config
-@@ -1,4 +1,4 @@
- {
--  "modules_required_for_build": ["boost"],
-+  "modules_required_for_build": [],
-   "modules_required_for_use": ["boost_adaptbx", "omptbx"],
- }
-diff --git a/work/cctbx_sources/scitbx/libtbx_refresh.py b/work/cctbx_sources/scitbx/libtbx_refresh.py
-index 10d4ee0..c8374b2 100644
---- a/work/cctbx_sources/scitbx/libtbx_refresh.py
-+++ b/work/cctbx_sources/scitbx/libtbx_refresh.py
-@@ -13,8 +13,7 @@ if (self.env.is_ready_for_build()):
-   generate_all.refresh(array_family=os.path.dirname(target_dir))
-   #
-   warn_if_unexpected_md5_hexdigest(
--    path=self.env.under_dist(
--      module_name="boost", path="boost/random/mersenne_twister.hpp"),
-+    path="@GENTOO_PORTAGE_EPREFIX@/usr/include/boost/random/mersenne_twister.hpp",
-     expected_md5_hexdigests=[
-       "a2533c79a21f0f773f2e0d29a37371b0", # CVS revision 1.21
-       "378432b5b280c9c0c894f7c80f0dad92", # CVS revision 1.20
-diff --git a/work/cctbx_sources/smtbx/SConscript b/work/cctbx_sources/smtbx/SConscript
-index f5031ee..02f81a4 100644
---- a/work/cctbx_sources/smtbx/SConscript
-+++ b/work/cctbx_sources/smtbx/SConscript
-@@ -7,7 +7,6 @@ env_etc.smtbx_common_includes = [
-   env_etc.cctbx_include,
-   env_etc.scitbx_include,
-   env_etc.chiltbx_include,
--  env_etc.boost_include,
- ]
- 
- env = env_base.Clone(
-diff --git a/work/cctbx_sources/spotfinder/SConscript b/work/cctbx_sources/spotfinder/SConscript
-index 1d280d4..9dc9195 100644
---- a/work/cctbx_sources/spotfinder/SConscript
-+++ b/work/cctbx_sources/spotfinder/SConscript
-@@ -13,7 +13,6 @@ env_etc.spotfinder_common_includes = [
-   env_etc.iotbx_include,
-   os.path.dirname(env_etc.spotfinder_dist),
-   env_etc.boost_adaptbx_include,
--  env_etc.boost_include,
-   env_etc.annlib_dist,
-   env_etc.annlib_include[0],
-   env_etc.annlib_include[1],
-diff --git a/work/cctbx_sources/tntbx/SConscript b/work/cctbx_sources/tntbx/SConscript
-index e773186..ee29f10 100755
---- a/work/cctbx_sources/tntbx/SConscript
-+++ b/work/cctbx_sources/tntbx/SConscript
-@@ -10,7 +10,6 @@ env_etc.tntbx_common_includes = [
-   env_etc.tntbx_include,
-   env_etc.tntbx_tnt_include,
-   env_etc.scitbx_include,
--  env_etc.boost_include,
- ]
- 
- Import("env_base", "env_etc")
--- 
-1.7.1.1
diff --git a/sci-libs/cctbx/files/2010.03.29.2334-clipper.patch b/sci-libs/cctbx/files/2010.03.29.2334-clipper.patch
deleted file mode 100644
index 8830dd8a054e..000000000000
--- a/sci-libs/cctbx/files/2010.03.29.2334-clipper.patch
+++ /dev/null
@@ -1,77 +0,0 @@
-diff --git a/cctbx_sources/clipper_adaptbx/SConscript b/cctbx_sources/clipper_adaptbx/SConscript
-index 9cce49e..1046ed0 100644
---- a/cctbx_sources/clipper_adaptbx/SConscript
-+++ b/cctbx_sources/clipper_adaptbx/SConscript
-@@ -1,56 +1,13 @@
- import libtbx.load_env
- Import("env_base", "env_etc")
- 
--env_etc.clipper_dist = libtbx.env.dist_path("clipper")
--env_etc.clipper_include = env_etc.clipper_dist
--
- env = env_base.Clone(
-   SHLINKFLAGS=env_etc.shlinkflags,
-   LIBS=env_etc.libm)
--env.Prepend(CPPPATH=[env_etc.clipper_include])
--
--if (env_etc.static_libraries): builder = env.StaticLibrary
--else:                          builder = env.SharedLibrary
--builder(target='#lib/clipper',
--  source = ["../clipper/clipper/core/"+file_name for file_name in """
--  atomsf.cpp
--  cell.cpp
--  clipper_memory.cpp
--  clipper_message.cpp
--  clipper_stats.cpp
--  clipper_types.cpp
--  clipper_util.cpp
--  container.cpp
--  container_hkl.cpp
--  container_map.cpp
--  container_types.cpp
--  coords.cpp
--  derivs.cpp
--  hkl_compute.cpp
--  hkl_data.cpp
--  hkl_datatypes.cpp
--  hkl_info.cpp
--  hkl_lookup.cpp
--  hkl_operators.cpp
--  map_interp.cpp
--  map_utils.cpp
--  nxmap.cpp
--  nxmap_operator.cpp
--  ramachandran.cpp
--  resol_basisfn.cpp
--  resol_fn.cpp
--  resol_targetfn.cpp
--  rotation.cpp
--  spacegroup.cpp
--  spacegroup_data.cpp
--  symop.cpp
--  xmap.cpp
--""".split()])
--# fftmap_sparse.cpp
--# fftmap.cpp
- 
- env_exe = env.Clone()
--env_exe.Prepend(LIBS=["clipper"])
-+env_exe.Prepend(LIBS=["clipper-minimol","clipper-mmdb","clipper-cns","clipper-cif","clipper-contrib","clipper-ccp4","clipper-phs","clipper-core"])
-+env_exe.Prepend(SHLINKFLAGS=["-Wl,--as-needed"])
- 
- exe = env_exe.Program(
-   target='#exe_dev/'+env["PROGPREFIX"]+'clipper.symtest'
-@@ -76,12 +33,10 @@ if (hasattr(env_etc, "cctbx_include")):
-     env_etc.include_registry.append(
-       env=env_clipper_boost_python_ext,
-       paths=[
--        env_etc.clipper_include,
-         env_etc.libtbx_include,
-         env_etc.cctbx_include,
-         env_etc.scitbx_include,
-         env_etc.boost_adaptbx_include,
--        env_etc.boost_include,
-         env_etc.python_include])
-     Export("env_clipper_boost_python_ext")
--    SConscript("clipper/SConscript")
-+
diff --git a/sci-libs/cctbx/files/2010.03.29.2334-flags.patch b/sci-libs/cctbx/files/2010.03.29.2334-flags.patch
deleted file mode 100644
index 8a8033234713..000000000000
--- a/sci-libs/cctbx/files/2010.03.29.2334-flags.patch
+++ /dev/null
@@ -1,94 +0,0 @@
-diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
-index 16d22b6..f85b664 100644
---- a/cctbx_sources/libtbx/SConscript
-+++ b/cctbx_sources/libtbx/SConscript
-@@ -5,6 +5,7 @@ from libtbx.str_utils import show_string
- from libtbx.path import norm_join, full_command_path
- import platform
- import sys, os
-+import SCons.Util
- 
- if (hasattr(Environment, "Clone")):
-   Environment.Copy = Environment.Clone # XXX backward compatibility 2008_03_30
-@@ -132,9 +133,7 @@ if (env_etc.compiler == "unix_icpc"):
- static_exe = libtbx.env.build_options.static_exe
- 
- def gcc_common_warn_options():
--  result = ["-Wall", "-Wno-sign-compare", "-Wno-unknown-pragmas"]
--  if (env_etc.gcc_version >= 40000):
--    result.append("-Winit-self")
-+  result = [""]
-   return result
- 
- def enable_more_warnings(env):
-@@ -355,16 +354,22 @@ else:
-     cc = env_etc.compiler.replace("unix_", "")
-     cxx = cc.replace("gcc", "g++")
-     env_etc.gcc_version = libtbx.env_config.get_gcc_version(command_name=cc)
-+#    linkerflags = os.environ.get("LDFLAGS")
-+#    link_flags=env_etc.ldflags
-+    link_flags=os.environ.get("LDFLAGS")
-+    linker_options=SCons.Util.CLVar(os.environ['LDFLAGS'])
-     env_base.Replace(
-       CC=cc,
-       SHCC=cc,
-       CXX=cxx,
-       LINK=cxx,
-+      LINKFLAGS=linker_options,
-       SHCXX=cxx,
-       SHLINK=cxx,
-       SHLIBSUFFIX=env_etc.shlibsuffix,
-     )
--    env_etc.c_link = cc
-+#    linkerflags = env_etc.ldflags
-+#    env_etc.c_link = cc + " " + linkerflags
-     env_etc.ccflags_base = [
-       "-fPIC",
-       "-fno-strict-aliasing"]
-@@ -380,7 +385,7 @@ else:
-       warn_options = gcc_common_warn_options() + ["-Werror"]
-     env_etc.ccflags_base.extend(warn_options)
-     if (libtbx.env.build_options.optimization):
--      opts = ["-DNDEBUG", "-O3", "-ffast-math"]
-+      opts = ["-DNDEBUG"]
-       if (env_etc.gcc_version >= 40300):
-         opts.append("-fno-associative-math")
-       opts.append("-ftrapping-math")
-@@ -401,6 +406,7 @@ else:
-       env_base.Prepend(LINKFLAGS=["-static"])
-       static_exe = None
-     env_etc.shlinkflags = ["-shared"]
-+    env_etc.shlinkflags.append(linker_options)
-     env_etc.shlinkflags_bpl = env_etc.shlinkflags
-     if (libtbx.env.build_options.mode == "profile"):
-       env_base.Prepend(LINKFLAGS=["-pg"])
-diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
-index ca510b9..68c58ea 100644
---- a/cctbx_sources/libtbx/env_config.py
-+++ b/cctbx_sources/libtbx/env_config.py
-@@ -1608,6 +1608,7 @@ class build_options:
-       self.env_cxxflags = ""
-       self.env_cflags = ""
-       self.env_cppflags = ""
-+      self.env_ldflags = ""
-       flg = os.environ.get("CXXFLAGS")
-       if flg is not None:
-         self.env_cxxflags = flg
-@@ -1617,6 +1618,9 @@ class build_options:
-       flg = os.environ.get("CPPFLAGS")
-       if flg is not None:
-         self.env_cppflags = flg
-+      flg = os.environ.get("LDFLAGS")
-+      if flg is not None:
-+        self.env_ldflags = flg
- 
-   def report(self, f=None):
-     if (f is None): f = sys.stdout
-@@ -1640,6 +1644,7 @@ class build_options:
-       print >>f, "  CXXFLAGS = ", self.env_cxxflags
-       print >>f, "  CFLAGS = ", self.env_cflags
-       print >>f, "  CPPFLAGS = ", self.env_cppflags
-+      print >>f, "  LDFLAGS = ", self.env_ldflags
- 
- class include_registry:
- 
diff --git a/sci-libs/cctbx/files/2010.03.29.2334-format-security.patch b/sci-libs/cctbx/files/2010.03.29.2334-format-security.patch
deleted file mode 100644
index 057c135f9953..000000000000
--- a/sci-libs/cctbx/files/2010.03.29.2334-format-security.patch
+++ /dev/null
@@ -1,117 +0,0 @@
- cctbx_sources/scitbx/lbfgsb/raw.h | 54 +++++++++++++++++++--------------------
- 1 file changed, 27 insertions(+), 27 deletions(-)
-
-diff --git a/cctbx_sources/scitbx/lbfgsb/raw.h b/cctbx_sources/scitbx/lbfgsb/raw.h
-index 21afed7..5b15055 100644
---- a/cctbx_sources/scitbx/lbfgsb/raw.h
-+++ b/cctbx_sources/scitbx/lbfgsb/raw.h
-@@ -853,7 +853,7 @@ namespace raw {
-     if (iprint >= 99) {
-       printf(" LINE SEARCH%12d times; norm of step =  %.15G\n",
-              iback, xstep);
--      printf(fmt_2001, iter,f,sbgnrm);
-+      printf("%s %i %f %f", fmt_2001, iter,f,sbgnrm);
-       if (iprint > 100) {
-         write_ref1(" X =", x);
-         write_ref1(" G =", g);
-@@ -862,7 +862,7 @@ namespace raw {
-     else if (iprint > 0) {
-       int imod = iter % iprint;
-       if (imod == 0) {
--        printf(fmt_2001, iter,f,sbgnrm);
-+        printf("%s %i %f %f", fmt_2001, iter,f,sbgnrm);
-       }
-     }
-     if (iprint >= 1) {
-@@ -967,9 +967,9 @@ namespace raw {
-       "                  2 rounding error dominate computation.\n";
-     if (task.substr(0,5) == "ERROR") goto lbl_999;
-     if (iprint >= 0) {
--      printf(fmt_3003);
--      printf(fmt_3004);
--      printf(fmt_3005, n,iter,nfgv,nintol,nskip,nact,sbgnrm,f);
-+      printf("%s", fmt_3003);
-+      printf("%s", fmt_3004);
-+      printf("%s %i %i %i %i %i %i %f %f", fmt_3005, n,iter,nfgv,nintol,nskip,nact,sbgnrm,f);
-       if (iprint >= 100) {
-         write_ref1(" X =", x);
-       }
-@@ -977,40 +977,40 @@ namespace raw {
-     }
-     lbl_999:
-     if (iprint >= 0) {
--      printf(fmt_3009, task.c_str());
-+      printf("%s %s", fmt_3009, task.c_str());
-       if (info != 0) {
--        if (info == -1) printf(fmt_9011);
--        if (info == -2) printf(fmt_9012);
--        if (info == -3) printf(fmt_9013);
--        if (info == -4) printf(fmt_9014);
--        if (info == -5) printf(fmt_9015);
-+        if (info == -1) printf("%s", fmt_9011);
-+        if (info == -2) printf("%s", fmt_9012);
-+        if (info == -3) printf("%s", fmt_9013);
-+        if (info == -4) printf("%s", fmt_9014);
-+        if (info == -5) printf("%s", fmt_9015);
-         if (info == -6) {
-           printf("  Input nbd(%12d) is invalid.\n", k);
-         }
-         if (info == -7) {
-           printf("  l(%12d) > u(%12d).  No feasible solution.\n", k, k);
-         }
--        if (info == -8) printf(fmt_9018);
--        if (info == -9) printf(fmt_9019);
-+        if (info == -8) printf("%s", fmt_9018);
-+        if (info == -9) printf("%s", fmt_9019);
-       }
--      if (iprint >= 1) printf(fmt_3007, cachyt,sbtime,lnscht);
--      printf(fmt_3008, time);
-+      if (iprint >= 1) printf("%s %f %f %f", fmt_3007, cachyt,sbtime,lnscht);
-+      printf("%s %f", fmt_3008, time);
-       if (iprint >= 1) {
-         if (info == -4 || info == -9) {
--          printf(fmt_3002,
-+          printf("%s %i %i %i %i %s %i %f %f", fmt_3002,
-                  iter,nfgv,nint,nact,word.c_str(),iback,stp,xstep); // itfile
-         }
--        printf(fmt_3009, task.c_str()); // itfile
-+        printf("%s %s", fmt_3009, task.c_str()); // itfile
-         if (info != 0) {
--          if (info == -1) printf(fmt_9011); // itfile
--          if (info == -2) printf(fmt_9012); // itfile
--          if (info == -3) printf(fmt_9013); // itfile
--          if (info == -4) printf(fmt_9014); // itfile
--          if (info == -5) printf(fmt_9015); // itfile
--          if (info == -8) printf(fmt_9018); // itfile
--          if (info == -9) printf(fmt_9019); // itfile
-+          if (info == -1) printf("%s", fmt_9011); // itfile
-+          if (info == -2) printf("%s", fmt_9012); // itfile
-+          if (info == -3) printf("%s", fmt_9013); // itfile
-+          if (info == -4) printf("%s", fmt_9014); // itfile
-+          if (info == -5) printf("%s", fmt_9015); // itfile
-+          if (info == -8) printf("%s", fmt_9018); // itfile
-+          if (info == -9) printf("%s", fmt_9019); // itfile
-         }
--        printf(fmt_3008, time); // itfile
-+        printf("%s %f", fmt_3008, time); // itfile
-       }
-     }
-   }
-@@ -3902,7 +3902,7 @@ namespace raw {
-       "   refresh the lbfgs memory and restart the iteration.\n";
-     if (info != 0) {
-       // singular triangular system detected; refresh the lbfgs memory.
--      if(iprint >= 1) printf(fmt_1005);
-+      if(iprint >= 1) printf("%s", fmt_1005);
-       info   = 0;
-       col    = 0;
-       head   = 1;
-@@ -3968,7 +3968,7 @@ namespace raw {
-     if (info != 0) {
-       // singular triangular system detected;
-       // refresh the lbfgs memory and restart the iteration.
--      if(iprint >= 1)  printf(fmt_1005);
-+      if(iprint >= 1)  printf("%s", fmt_1005);
-       info   = 0;
-       col    = 0;
-       head   = 1;
diff --git a/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.6.patch b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.6.patch
deleted file mode 100644
index e54cfa16838b..000000000000
--- a/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.6.patch
+++ /dev/null
@@ -1,29 +0,0 @@
- cctbx_sources/scitbx/array_family/detail/misc.h    |    1 +
- .../scitbx/fortran_io/details/istream_scanner.h    |    2 +-
- 2 files changed, 2 insertions(+), 1 deletions(-)
-
-diff --git a/cctbx_sources/scitbx/array_family/detail/misc.h b/cctbx_sources/scitbx/array_family/detail/misc.h
-index 6ed881e..d7f7f52 100644
---- a/cctbx_sources/scitbx/array_family/detail/misc.h
-+++ b/cctbx_sources/scitbx/array_family/detail/misc.h
-@@ -2,6 +2,7 @@
- #define SCITBX_ARRAY_FAMILY_MISC_H
- 
- #include <scitbx/array_family/type_traits.h>
-+#include <memory>
- 
- namespace scitbx { namespace af {
- 
-diff --git a/cctbx_sources/scitbx/fortran_io/details/istream_scanner.h b/cctbx_sources/scitbx/fortran_io/details/istream_scanner.h
-index 8a0ac25..03a0e20 100644
---- a/cctbx_sources/scitbx/fortran_io/details/istream_scanner.h
-+++ b/cctbx_sources/scitbx/fortran_io/details/istream_scanner.h
-@@ -32,7 +32,7 @@ class istream_scanner
-     }
- 
-   private:
--    mutable std::basic_istream<CharType> &input;
-+    std::basic_istream<CharType> &input;
-     mutable value_t current;
- };
- 
diff --git a/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch
deleted file mode 100644
index 96cb21531bbf..000000000000
--- a/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch
+++ /dev/null
@@ -1,154 +0,0 @@
- .../scitbx/math/boost_python/distributions.cpp     |   60 +++++++++++++------
- cctbx_sources/scitbx/rigid_body/spatial_lib.h      |    1 +
- cctbx_sources/scitbx/rigid_body/tardy.h            |    4 +-
- .../refinement/boost_python/weighting_schemes.cpp  |    4 +-
- .../smtbx/structure_factors/direct/standard_xray.h |    4 +-
- 5 files changed, 48 insertions(+), 25 deletions(-)
-
-diff --git a/cctbx_sources/scitbx/math/boost_python/distributions.cpp b/cctbx_sources/scitbx/math/boost_python/distributions.cpp
-index a676798..68818e7 100644
---- a/cctbx_sources/scitbx/math/boost_python/distributions.cpp
-+++ b/cctbx_sources/scitbx/math/boost_python/distributions.cpp
-@@ -59,29 +59,51 @@ namespace {
-   {
-     typedef Distribution wt;
- 
-+    #define NEW_MEMBER(name)                \
-+    static FloatType name(wt const &self) { \
-+      return boost::math::name(self);                    \
-+    }
-+
-+    NEW_MEMBER(mean);
-+    NEW_MEMBER(median);
-+    NEW_MEMBER(mode);
-+    NEW_MEMBER(variance);
-+    NEW_MEMBER(standard_deviation);
-+    NEW_MEMBER(skewness);
-+    NEW_MEMBER(kurtosis);
-+
-+    #undef NEW_MEMBER
-+
-+    #define NEW_MEMBER(name)                               \
-+    static FloatType name(wt const &self, FloatType arg) { \
-+      return boost::math::name(self, arg);                              \
-+    }
-+
-+    NEW_MEMBER(pdf);
-+    NEW_MEMBER(cdf);
-+    NEW_MEMBER(quantile);
-+
-+    #undef NEW_MEMBER
-+
-+    static scitbx::af::shared<FloatType> quantiles(wt const &self, std::size_t n) {
-+      return scitbx::math::quantiles<FloatType>(self, n);
-+    }
-+
-     static void
-     wrap()
-     {
-       using namespace boost::python;
--      def("mean", (FloatType(*)(wt const&)) boost::math::mean);
--      def("median", (FloatType(*)(wt const&)) boost::math::median);
--      def("mode", (FloatType(*)(wt const&)) boost::math::mode);
--      def("variance", (FloatType(*)(wt const&)) boost::math::variance);
--      def("standard_deviation",
--        (FloatType(*)(wt const&)) boost::math::standard_deviation);
--      def("skewness", (FloatType(*)(wt const&)) boost::math::skewness);
--      def("kurtosis", (FloatType(*)(wt const&)) boost::math::kurtosis);
--      def("pdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::pdf);
--      def("cdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::cdf);
--      def("quantile", (FloatType(*)(wt const&, FloatType const&))
--        boost::math::quantile);
--      def("quantiles",
--#if BOOST_WORKAROUND(__EDG_VERSION__, BOOST_TESTED_AT(306))
--        (scitbx::af::shared<FloatType>(*)(wt const&, std::size_t)) quantiles
--#else
--        quantiles<FloatType, wt>
--#endif
--        );
-+      def("mean"              , mean);
-+      def("median"            , median);
-+      def("mode"              , mode);
-+      def("variance"          , variance);
-+      def("standard_deviation", standard_deviation);
-+      def("skewness"          , skewness);
-+      def("kurtosis"          , kurtosis);
-+      def("pdf"               , pdf);
-+      def("cdf"               , cdf);
-+      def("quantile"          , quantile);
-+      def("quantiles"         , quantiles);
-     }
-   };
- 
-diff --git a/cctbx_sources/scitbx/rigid_body/spatial_lib.h b/cctbx_sources/scitbx/rigid_body/spatial_lib.h
-index a084f0f..e377292 100755
---- a/cctbx_sources/scitbx/rigid_body/spatial_lib.h
-+++ b/cctbx_sources/scitbx/rigid_body/spatial_lib.h
-@@ -2,6 +2,7 @@
- #define SCITBX_RIGID_BODY_SPATIAL_LIB_H
- 
- #include <scitbx/rotr3.h>
-+#include <scitbx/rigid_body/matrix_helpers.h>
- #include <scitbx/array_family/versa_matrix.h>
- 
- namespace scitbx { namespace rigid_body {
-diff --git a/cctbx_sources/scitbx/rigid_body/tardy.h b/cctbx_sources/scitbx/rigid_body/tardy.h
-index 104f16b..a8f76cc 100755
---- a/cctbx_sources/scitbx/rigid_body/tardy.h
-+++ b/cctbx_sources/scitbx/rigid_body/tardy.h
-@@ -346,7 +346,7 @@ namespace tardy {
-       unsigned nb = this->bodies_size();
-       af::shared<af::small<ft, 7> > result((af::reserve(nb)));
-       af::shared<af::small<ft, 6> >
--        tau_array = f_ext_as_tau(f_ext_array().const_ref());
-+        tau_array = this->f_ext_as_tau(f_ext_array().const_ref());
-       for(unsigned ib=0;ib<nb;ib++) {
-         result.push_back(
-           this->bodies[ib]->joint->tau_as_d_e_pot_d_q(tau_array[ib]));
-@@ -379,7 +379,7 @@ namespace tardy {
-     qdd_array()
-     {
-       if (!qdd_array_) {
--        qdd_array_ = forward_dynamics_ab(
-+        qdd_array_ = this->forward_dynamics_ab(
-           /*tau_array*/ af::const_ref<af::small<ft, 6> >(0, 0),
-           f_ext_array().const_ref(),
-           /*grav_accn*/ af::const_ref<ft>(0, 0));
-diff --git a/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp b/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp
-index ce0c27b..904e8d7 100644
---- a/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp
-+++ b/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp
-@@ -25,9 +25,9 @@ namespace smtbx { namespace refinement { namespace least_squares {
-       : base_t(name, boost::python::no_init)
-     {
-       using namespace boost::python;
--      def("__call__", &wt::operator(),
-+      this->def("__call__", &wt::operator(),
-           (arg("fo_sq"), arg("sigma"), arg("fc_sq")));
--      def("__call__", weights,
-+      this->def("__call__", weights,
-           (arg("fo_sq"), arg("sigmas"), arg("fc_sq")));
-     }
-   };
-diff --git a/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h b/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h
-index 5e2df76..911bfde 100644
---- a/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h
-+++ b/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h
-@@ -161,7 +161,7 @@ namespace smtbx { namespace structure_factors { namespace direct {
-         for (int k=0; k < hr_ht.groups.size(); ++k) {
-           hr_ht_group<float_type> const &g = hr_ht.groups[k];
-           float_type hrx = g.hr * scatterer.site;
--          complex_type f = exp_i_2pi(hrx + g.ht);
-+          complex_type f = this->exp_i_2pi(hrx + g.ht);
-           if (scatterer.flags.use_u_aniso()) {
-             float_type dw = debye_waller_factor_u_star(g.hr, scatterer.u_star);
-             f *= dw;
-@@ -336,7 +336,7 @@ namespace smtbx { namespace structure_factors { namespace direct {
-         for (int k=0; k < hr_ht.groups.size(); ++k) {
-           hr_ht_group<float_type> const &g = hr_ht.groups[k];
-           float_type hrx = g.hr * scatterer.site;
--          complex_type f = exp_i_2pi(hrx + g.ht);
-+          complex_type f = this->exp_i_2pi(hrx + g.ht);
-           float_type fa = f.real(), fb = f.imag();
-           if (scatterer.flags.use_u_aniso()) {
-             float_type dw = debye_waller_factor_u_star(g.hr, scatterer.u_star);
diff --git a/sci-libs/cctbx/files/2010.03.29.2334-soname.patch b/sci-libs/cctbx/files/2010.03.29.2334-soname.patch
deleted file mode 100644
index 2c0efcabeb13..000000000000
--- a/sci-libs/cctbx/files/2010.03.29.2334-soname.patch
+++ /dev/null
@@ -1,123 +0,0 @@
-diff --git a/cctbx_sources/ccp4io_adaptbx/SConscript b/cctbx_sources/ccp4io_adaptbx/SConscript
-index 4ff2232..2ee3991 100644
---- a/cctbx_sources/ccp4io_adaptbx/SConscript
-+++ b/cctbx_sources/ccp4io_adaptbx/SConscript
-@@ -40,6 +40,7 @@ def replace_printf(file_name):
- 
- env = env_base.Clone(
-   SHLINKFLAGS=env_etc.shlinkflags)
-+env.Append(SHLINKFLAGS=["-Wl,-soname,libccp4io.so.0.0"])
- env.Append(CCFLAGS=env_etc.ccp4io_defines)
- env.Append(SHCCFLAGS=env_etc.ccp4io_defines)
- env_etc.include_registry.append(
-diff --git a/cctbx_sources/cctbx/SConscript b/cctbx_sources/cctbx/SConscript
-index 6ec7c93..7f2e788 100644
---- a/cctbx_sources/cctbx/SConscript
-+++ b/cctbx_sources/cctbx/SConscript
-@@ -15,6 +15,7 @@ env_etc.cctbx_common_includes = [
- 
- env = env_base.Clone(
-   SHLINKFLAGS=env_etc.shlinkflags)
-+env.Append(SHLINKFLAGS=["-Wl,-soname,libcctbx.so.0.0"])
- env_etc.include_registry.append(
-   env=env,
-   paths=env_etc.cctbx_common_includes)
-diff --git a/cctbx_sources/iotbx/mtz/SConscript b/cctbx_sources/iotbx/mtz/SConscript
-index c0a4bb0..d3c1e45 100644
---- a/cctbx_sources/iotbx/mtz/SConscript
-+++ b/cctbx_sources/iotbx/mtz/SConscript
-@@ -6,6 +6,7 @@ ccp4io_lib = getattr(env_etc, "ccp4io_lib", "cmtz")
- env.Prepend(LIBS=["cctbx", ccp4io_lib]+env_etc.libm)
- env.Append(CXXFLAGS=env_etc.ccp4io_defines)
- env.Append(SHCXXFLAGS=env_etc.ccp4io_defines)
-+env.Append(SHLINKFLAGS=["-Wl,-soname,libiotbx_mtz.so.0.0"])
- env_etc.enable_more_warnings(env=env)
- if (env_etc.static_libraries): builder = env.StaticLibrary
- else:                          builder = env.SharedLibrary
-diff --git a/cctbx_sources/iotbx/pdb/SConscript b/cctbx_sources/iotbx/pdb/SConscript
-index c1415c8..9e1af8d 100644
---- a/cctbx_sources/iotbx/pdb/SConscript
-+++ b/cctbx_sources/iotbx/pdb/SConscript
-@@ -2,6 +2,7 @@ Import("env_base", "env_etc")
- 
- env = env_base.Clone(
-   SHLINKFLAGS=env_etc.shlinkflags)
-+env.Append(SHLINKFLAGS=["-Wl,-soname,libiotbx_pdb.so.0.0"])
- env_etc.enable_more_warnings(env=env)
- env_etc.include_registry.append(
-   env=env,
-diff --git a/cctbx_sources/mmtbx/masks/SConscript b/cctbx_sources/mmtbx/masks/SConscript
-index e70ab3c..cf2f530 100755
---- a/cctbx_sources/mmtbx/masks/SConscript
-+++ b/cctbx_sources/mmtbx/masks/SConscript
-@@ -17,7 +17,9 @@ builder(
-   target="#lib/mmtbx_masks",
-   source=lib_sources)
- 
--env = env.Clone()
-+env = env.Clone(
-+  SHLINKFLAGS=env_etc.shlinkflags)
-+env.Append(SHLINKFLAGS=["-Wl,-soname,libmmtbx_masks.so.0.0"])
- env.Prepend(LIBS=["mmtbx_masks", "iotbx_pdb", "cctbx_sgtbx_asu"])
- env.Program( target = "tst_mask",  source="tst_mask.cpp")
- 
-diff --git a/cctbx_sources/omptbx/SConscript b/cctbx_sources/omptbx/SConscript
-index 43aac91..ce4b4f3 100644
---- a/cctbx_sources/omptbx/SConscript
-+++ b/cctbx_sources/omptbx/SConscript
-@@ -7,6 +7,7 @@ env_etc.omptbx_include = os.path.dirname(env_etc.omptbx_dist)
- 
- env = env_base.Clone(
-   SHLINKFLAGS=env_etc.shlinkflags)
-+env.Append(SHLINKFLAGS=["-Wl,-soname,libomptbx.so.0.0"])
- env_etc.include_registry.append(
-   env=env,
-   paths=[env_etc.omptbx_include])
-diff --git a/cctbx_sources/rstbx/SConscript b/cctbx_sources/rstbx/SConscript
-index 2213c2f..cae7542 100644
---- a/cctbx_sources/rstbx/SConscript
-+++ b/cctbx_sources/rstbx/SConscript
-@@ -15,6 +15,7 @@ env_etc.rstbx_common_includes = [
- ]
- 
- env = env_base.Clone(SHLINKFLAGS=env_etc.shlinkflags)
-+env.Append(SHLINKFLAGS=["-Wl,-soname,librstbx.so.0.0"])
- env.Append(LIBS=["cctbx"] + env_etc.libm)
- env_etc.include_registry.append(
-   env=env,
-diff --git a/cctbx_sources/scitbx/boost_python/SConscript b/cctbx_sources/scitbx/boost_python/SConscript
-index 6f221d0..c4698d8 100644
---- a/cctbx_sources/scitbx/boost_python/SConscript
-+++ b/cctbx_sources/scitbx/boost_python/SConscript
-@@ -4,6 +4,7 @@ Import("env_scitbx_boost_python_ext")
- env = env_base.Clone(
-   SHLINKFLAGS=env_etc.shlinkflags)
- env_etc.enable_more_warnings(env=env)
-+env.Append(SHLINKFLAGS=["-Wl,-soname,libscitbx_boost_python.so.0.0"])
- env.Append(CXXFLAGS=env_etc.cxxflags_bpl_defines_base)
- env.Append(SHCXXFLAGS=env_etc.cxxflags_bpl_defines_base)
- env.Append(LIBS=["boost_python"])
-diff --git a/cctbx_sources/scitbx/minpack/SConscript b/cctbx_sources/scitbx/minpack/SConscript
-index 7c325cb..cc23a04 100644
---- a/cctbx_sources/scitbx/minpack/SConscript
-+++ b/cctbx_sources/scitbx/minpack/SConscript
-@@ -3,6 +3,7 @@ Import("env_base", "env_etc")
- env = env_base.Clone(
-   SHLINKFLAGS=env_etc.shlinkflags)
- env_etc.enable_more_warnings(env=env)
-+env.Append(SHLINKFLAGS=["-Wl,-soname,libscitbx_minipack.so.0.0"])
- env_etc.include_registry.append(
-   env=env,
-   paths=env_etc.scitbx_common_includes)
-diff --git a/cctbx_sources/scitbx/slatec/SConscript b/cctbx_sources/scitbx/slatec/SConscript
-index ca9b6da..9c79d47 100644
---- a/cctbx_sources/scitbx/slatec/SConscript
-+++ b/cctbx_sources/scitbx/slatec/SConscript
-@@ -3,6 +3,7 @@ Import("env_base", "env_etc")
- env = env_base.Clone(
-   SHLINKFLAGS=env_etc.shlinkflags)
- env_etc.enable_more_warnings(env=env)
-+env.Append(SHLINKFLAGS=["-Wl,-soname,libscitbx_slatec.so.0.0"])
- env.Append(LIBS=env_etc.libm)
- if (env_etc.static_libraries): builder = env.StaticLibrary
- else:                          builder = env.SharedLibrary
diff --git a/sci-libs/cctbx/files/2010.03.29.2334-tst_server.py.patch b/sci-libs/cctbx/files/2010.03.29.2334-tst_server.py.patch
deleted file mode 100644
index f6509260d313..000000000000
--- a/sci-libs/cctbx/files/2010.03.29.2334-tst_server.py.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-diff --git a/mmtbx/monomer_library/tst_server.py b/mmtbx/monomer_library/tst_server.py
-index 519d203..91ba783 100644
---- cctbx_sources/mmtbx/monomer_library/tst_server.py
-+++ cctbx_sources/mmtbx/monomer_library/tst_server.py
-@@ -86,8 +86,8 @@ def exercise():
-     for base_code in ["A", "C", "G"]:
-       rna_atoms = srv.get_comp_comp_id_direct(base_code+"r").atom_dict()
-       dna_atoms = srv.get_comp_comp_id_direct(base_code+"d").atom_dict()
--      for as,bs,c in [(rna_atoms,dna_atoms,"d"), (dna_atoms,rna_atoms,"r")]:
--        for a in as.keys():
-+      for as_,bs,c in [(rna_atoms,dna_atoms,"d"), (dna_atoms,rna_atoms,"r")]:
-+        for a in as_.keys():
-           b = bs.get(a, None)
-           if (b is None):
-             print "Not in %s: %s" % (base_code+c, a)
diff --git a/sci-libs/cctbx/metadata.xml b/sci-libs/cctbx/metadata.xml
deleted file mode 100644
index d9a960529560..000000000000
--- a/sci-libs/cctbx/metadata.xml
+++ /dev/null
@@ -1,20 +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>
-	<longdescription>
-		The Computational Crystallography Toolbox (cctbx) is being developed
-		as the open source component of the PHENIX system. The goal of
-		the PHENIX project is to advance automation of macromolecular structure
-		determination. PHENIX depends on the cctbx, but not vice versa. This
-		hierarchical approach enforces a clean design as a reusable library.
-		The cctbx is therefore also useful for small-molecule crystallography
-		and even general scientific applications.
-	</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">cctbx</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/clipper/Manifest b/sci-libs/clipper/Manifest
deleted file mode 100644
index 456def844116..000000000000
--- a/sci-libs/clipper/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST clipper-2.1.20140911.tar.gz 1922753 BLAKE2B 0bf0b98a2ea52b40adf2ff648f69943e5a511d3f948c51372a3e427a6ece93537bd57aa6c7824cd9fee398ef314028ae7ac47a69bf6e48ec0000cf5e163a110a SHA512 1306bd68d40ea6a7d828f58ce276d6f5d05637af8712eeec3528cf0e4b637263b8ab068ec132765fc4167723bf1d43cbb9ffe0eca43dea3742ec273f34947912
-DIST clipper-2.1.20140911_p20160914-fix-c++14.patch.bz2 10551 BLAKE2B 9db14dce9f98de766acc1b552dd66ef47966b8ad581848cf2968b20edbbcda8e69b52a71e302457fc8dd653a88167c3cc818e6dcb5a9e128d76e1f80fb2d9771 SHA512 b18a059eb1bfaec18d1f6f104639001074d92b73768ab6ef412828fc21d891d93d15cd50cd41fca1187f4b4f90399e20bf3e6290af695c6bffbff2c85ca028eb
-EBUILD clipper-2.1.20140911-r1.ebuild 1434 BLAKE2B 7b8428aa4f24e5fec238db6ef12c5e5e469b0c56452644dac45b8b6b1810e07ecbf6c7721c121cfd20c721bef02b0ff2329c5398d6a39d178c49c0d305688007 SHA512 34816cca8354bccf6508b15e24a699cbf980508b03f3d582f1e3e977e5397354927e75ca8ca0f368ef7e96fdc776bb0968dbfeb1a4a6a3d49efc13d5ebae2558
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-libs/clipper/clipper-2.1.20140911-r1.ebuild b/sci-libs/clipper/clipper-2.1.20140911-r1.ebuild
deleted file mode 100644
index 249ac435d41b..000000000000
--- a/sci-libs/clipper/clipper-2.1.20140911-r1.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-FORTRAN_NEEDED=fortran
-
-inherit flag-o-matic fortran-2
-
-DESCRIPTION="Object-oriented libraries for crystallographic data and computation"
-HOMEPAGE="http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html"
-SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-2.1.20140911_p20160914-fix-c++14.patch.bz2"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="fortran static-libs test"
-
-RDEPEND="
-	sci-libs/libccp4
-	sci-libs/fftw:2.1
-	sci-libs/mmdb:2"
-DEPEND="${RDEPEND}
-	test? ( app-shells/tcsh )"
-
-PATCHES=(
-	# fix building with GCC 6, #585540
-	"${WORKDIR}/${PN}-2.1.20140911_p20160914-fix-c++14.patch"
-)
-
-src_configure() {
-	# Recommended on ccp4bb/coot ML to fix crashes when calculating maps
-	# on 64-bit systems
-	append-flags -fno-strict-aliasing
-
-	econf \
-		--enable-shared \
-		$(use_enable static-libs static) \
-		$(use_enable fortran) \
-		--enable-ccp4 \
-		--enable-cif \
-		--enable-cns \
-		--enable-contrib \
-		--enable-minimol \
-		--enable-mmdb \
-		--enable-phs
-#		--enable-cctbx
-}
-
-src_test() {
-	emake -C examples check
-	cd examples || die
-	sed -e '/mtzdump/d' -i test.csh || die
-	PATH="${S}/examples:${PATH}" csh test.csh || die
-}
-
-src_install() {
-	default
-
-	# package provides .pc files
-	find "${D}" -name '*.la' -delete || die
-}
diff --git a/sci-libs/clipper/metadata.xml b/sci-libs/clipper/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-libs/clipper/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-libs/coot-data/Manifest b/sci-libs/coot-data/Manifest
deleted file mode 100644
index 5c33a87918e8..000000000000
--- a/sci-libs/coot-data/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST coot-data-3.tar.gz 6728787 BLAKE2B 0238ac1fe5364e637f009a4e8e2cb0fc512815ebfe5c9fdc2767f42f4f177028dfd782ed2a388adb2c4ef71a99ec46973de062a541f6677e0a8f21d08cac8175 SHA512 7ebe28a619a577b18fc66e714f0bc8347121ebb12f372ac29c1d2d96013e608632921ea26caea3b62744252ae356949de8e04a6513f1a1e0ba30865708c26ffe
-EBUILD coot-data-3.ebuild 879 BLAKE2B c9b616621183022bce528f60222b568e27997582b3c2d8d495c761e29f62f56ca044f941d75aa4abd8eb1bf2bb383e01accaeb217e1ef9b6ea5b28b7dc0a1692 SHA512 2d17e550cb072038aa77c63f1b7f5ef55e367da6cb0e0db4990632758b6427ae18b6ede4d4501b390e65fe7178924da86c0185c0ef90396d68b723f520f503e7
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-libs/coot-data/coot-data-3.ebuild b/sci-libs/coot-data/coot-data-3.ebuild
deleted file mode 100644
index c0ab79993bea..000000000000
--- a/sci-libs/coot-data/coot-data-3.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="Data for the Crystallographic Object-Oriented Toolkit"
-HOMEPAGE="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/"
-SRC_URI="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/dependencies/reference-structures.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE=""
-
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}"
-
-src_install() {
-	insinto /usr/share/coot
-	doins -r reference-structures
-
-	# Coot looks in the wrong spot for the monomer library
-	# Listens to ccp4's CCP4_LIB rather than CLIBD_MON
-	cat >> "${T}"/coot <<- EOF
-	COOT_REFMAC_LIB_DIR="${EPREFIX}/usr/share/"
-	COOT_REF_STRUCTS="${EPREFIX}/usr/share/coot/reference-structures/"
-	EOF
-
-	newenvd "${T}"/coot 20coot
-}
diff --git a/sci-libs/coot-data/metadata.xml b/sci-libs/coot-data/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-libs/coot-data/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-libs/dcmtk/Manifest b/sci-libs/dcmtk/Manifest
index b5ed7ad53ea0..ec8c397ecb60 100644
--- a/sci-libs/dcmtk/Manifest
+++ b/sci-libs/dcmtk/Manifest
@@ -2,5 +2,7 @@ AUX dcmtk-3.6.3-dcmqrdb-cfg.patch 3031 BLAKE2B 9fd21949e42c7f0c479db7d9b81c13383
 AUX dcmtk-3.6.3-fix-gcc9.patch 2620 BLAKE2B 101faae609065ab9e37a4b9edd1363562a4b86a6bca0f7e9cce5d85aeb2aca6f8e61761657ee31eaa64c8a1c3c9b8d64af950b5d7988f66c393c96a46e4c0232 SHA512 f2de58f58234ab1a7ccfb5c2dd04e3a46f71a8875f32fd1aa8d139e14527d34624686a967d087040281c5dc3a62266321384a4dc9504562f117fdcde1321bf4a
 AUX dcmtk-3.6.3-nostrip.patch 7049 BLAKE2B 57d7b4d2cc3bdd683cb6c51c6d9c7e37023ddaf255655cf3f6c1473484d4e41d4a75b3bcb452a3caa06b8c751cfca47a14b0cd10372c1ebde936f7dec3046ed0 SHA512 00f28de0995c2d38b32b59298ac1c97878248647d403df86244d16a16cfd4c7ba47e7fe400592e5ac0f935a3704733a768fa3b94c9625903e86ab5f714d093bd
 DIST dcmtk-3.6.3.tar.gz 6269785 BLAKE2B 8f0797840fa5ab4ffb60e46f65b16739d3ed0cb7591b20cbfba81a59de97344a663f73bed8fc7f349a99accc46fd2fde3cff021861bde6f07957a433a4db67a3 SHA512 5b907422d2d80e417ae8239e159d1300da4ed8db7e92cee619cc1d37116165e8824f8a9103605e07a95b1bffe94bbd2d5e05125f068281d241e8e78755d0b5e8
+DIST dcmtk-3.6.4.tar.gz 6402734 BLAKE2B 2d362789e7819089b7da46a9601fa5d53b8e8aab1ac7d30bf1180b3da0645d015a177c97188dc9255c6962a9d7246cf287b20824a78fbe9612b9bc277e68d294 SHA512 735f85d04410437a5163b154f43c8a299aff7a8f810605ce6c5027ae4569ff1323a69f70a2603805cec9d826a31166fd904bb53c3edc1137bfc41ba2902c2261
 EBUILD dcmtk-3.6.3.ebuild 2039 BLAKE2B 655b3b3d424ebdba0d96f629b2308d1bd5650c03ebf48e575f05a8a9c3295928aff91cf34086b1a2f19a41907ff4811394f6c4622f3fd0ba3b2501dbe5a44d2c SHA512 7b92fda743f4ad39112f440b63db6549547a0e12510b9feb2c2a04cbea1a96db49d3c4ee04a8bf4e61bf500c0a94325332a997cc1f5f2434040b1b6a59b24211
+EBUILD dcmtk-3.6.4-r1.ebuild 1931 BLAKE2B 03b414dc9a763d562598760d9adae6f0ddea24431e13dbc517197ce84e4cf4261edd702b68398040674a7e11bc48b3b21b2564993d579902e40e914c75da1149 SHA512 6cb6d226886c6b7d29366986f6ce319d45f4f96d61b8c794cddcc1867bc8aa3518474c23b8c56e51e6d81bad03fbe309fa06364213a1327063aca852e76897c4
 MISC metadata.xml 317 BLAKE2B cad6b71cf9d8e4f626ee594c2eaad2e75f8ae288ea53206ae8ba37f0be04168f2ce7adeef7e45876d1358250e7ec6f2d9a07cc1c0ea4cf929323f1292ae4853a SHA512 0c6bb7cc6f8d56a7809354d0630ee49f33b63f7b60ad0a0ccbbfd7f28391a4c6b0c9f56caeb7cefcc74bf169ed6d46adda4fd204ef633311376b3cc3f7193d68
diff --git a/sci-libs/dcmtk/dcmtk-3.6.4-r1.ebuild b/sci-libs/dcmtk/dcmtk-3.6.4-r1.ebuild
new file mode 100644
index 000000000000..f701d3e9f5b5
--- /dev/null
+++ b/sci-libs/dcmtk/dcmtk-3.6.4-r1.ebuild
@@ -0,0 +1,87 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake-utils
+
+DESCRIPTION="The DICOM Toolkit"
+HOMEPAGE="https://dicom.offis.de/dcmtk.php.en"
+SRC_URI="http://dicom.offis.de/download/dcmtk/release/${P}.tar.gz"
+
+LICENSE="OFFIS"
+KEYWORDS="~amd64 ~arm ~x86"
+SLOT="0"
+IUSE="doc png ssl tcpd tiff +threads xml zlib"
+
+RDEPEND="
+	dev-libs/icu:=
+	virtual/jpeg:0
+	png? ( media-libs/libpng:* )
+	ssl? ( dev-libs/openssl:0= )
+	tcpd? ( sys-apps/tcp-wrappers )
+	tiff? ( media-libs/tiff:0 )
+	xml? ( dev-libs/libxml2:2 )
+	zlib? ( sys-libs/zlib )"
+DEPEND="${RDEPEND}
+	media-gfx/graphviz
+	doc? ( app-doc/doxygen )"
+
+src_prepare() {
+	cmake-utils_src_prepare
+
+	sed -e "s:share/doc/dcmtk:&-${PV}:" \
+		-e "s:DIR \"/:DIR \"/usr/:" \
+		-e "s:usr/etc:etc:" \
+		-e "s:/lib\":/$(get_libdir)\":" \
+		-e "s:COPYRIGHT::" \
+		-i CMakeLists.txt || die
+	sed -e 's:${CMAKE_INSTALL_PREFIX}/::' \
+		-i dcmwlm/data/CMakeLists.txt doxygen/CMakeLists.txt || die
+	# Temporary workaround: docs are not built with CMake
+	sed -i -e '/include/d' doxygen/Makefile.in || die
+
+	# fix -D deprecation warnings
+	sed -i -e "s|_BSD_SOURCE|_DEFAULT_SOURCE|g" \
+		"${S}"/config/configure.in \
+		"${S}"/CMakeLists.txt || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_SHARED_LIBS=ON
+		-DCMAKE_INSTALL_SYSCONFDIR=/etc
+		-DDCMTK_WITH_ICU=ON
+		-DDCMTK_WITH_TIFF=$(usex tiff)
+		-DDCMTK_WITH_PNG=$(usex png)
+		-DDCMTK_WITH_XML=$(usex xml)
+		-DDCMTK_WITH_ZLIB=$(usex zlib)
+		-DDCMTK_WITH_OPENSSL=$(usex ssl)
+		-DDCMTK_WITH_DOXYGEN=$(usex doc)
+		-DDCMTK_WITH_THREADS=$(usex threads)
+	)
+
+	cmake-utils_src_configure
+
+	if use doc; then
+		cd "${S}"/doxygen || die
+		econf
+	fi
+}
+
+src_compile() {
+	cmake-utils_src_compile
+
+	if use doc; then
+		emake -C "${S}"/doxygen
+	fi
+}
+
+src_install() {
+	doman doxygen/manpages/man1/*
+
+	if use doc; then
+		local HTML_DOCS=( "${S}"/doxygen/htmldocs/. )
+	fi
+	cmake-utils_src_install
+}
diff --git a/sci-libs/dealii/Manifest b/sci-libs/dealii/Manifest
new file mode 100644
index 000000000000..64faa4294ea6
--- /dev/null
+++ b/sci-libs/dealii/Manifest
@@ -0,0 +1,6 @@
+AUX dealii-9.1.1-no-ld-flags.patch 1044 BLAKE2B fed995fbd5563bfee6b4dd232d5d9aaecd8f0d206f06679b5d79022420c83ac2752414417499ac9181c25ddc594e492bf8d6b6af19fdfd1f047e7e089193de5d SHA512 15346b31f4ac5df3b1a3a3dcb215d4bd49e3e67480c86d4c78dbd5d27ae33f6cfa8b03fdc561e38090a2c22ae8ba71d13cd9b1bbdda3eedefd498f5cedfd0a09
+DIST dealii-9.1.1-offline_documentation.tar.gz 211103151 BLAKE2B ef7cf48aa8019a2d42a38804744ff72cc7f744255fa27df852f8f93c86a02f2125458e0e525e57510bb98adc27aed933fefa27d556d8203c991dae9866c7d57a SHA512 5e2b71e9bdeb80875772356e2c873bc1f065f2a8c5c47923b74b471d464e4867c257e3a47b32341aa60af98e74e3ed2eceba8dedb4b157ab872681576ecbd5db
+DIST dealii-9.1.1.tar.gz 19911088 BLAKE2B e8488833f11339ccffd4791b9b46ab77f1982cbbdeb11fab7f6b74ca2e17c3d648a2940f4462d0ac9c68bd619b3c4f43b4d8052d2903cbb9cae2fece93d81987 SHA512 02dd91e2b0f395960f900f4cbe00bd307a4762ffbc5f3838dcc34828937e96727efbbcc66fc3d357d6b00b0dddcbc6cd7709c4c03f067d92a8f72d4631b88bf1
+EBUILD dealii-9.1.1.ebuild 5262 BLAKE2B f7518d6570851c50513608bd6e8d4a84bdbe29579d86db3d2d30f4cd5739714199611245f74a393a34473a510d0b5419b2cde670eebaa5b2ef64dd3e3037ae3c SHA512 ad603ec9c6265054571006b8d244674e11abccc817af640f7851380105ba77d6feb24c6e5986389b1e7a3eb0c0004ed0090e12f9136fa34c3b4207eb0c9132a5
+EBUILD dealii-9999.ebuild 5295 BLAKE2B 4d3c6a8bf1e481e06426cad5dc37cd4fac7ae9190da3ca5a51a5f2a7e35b6fc3c77891198ce9feae6687a58bf6b99cfdebc39dbc1a9ec36e7514c19808f5db14 SHA512 36e338671b9cf44f18f57289797aa0fd8e0209da756320ea254efeb989bdc620851c97d157d45ed8cb9d45e1c4533430220232b0c30588706664348198352375
+MISC metadata.xml 2569 BLAKE2B 55b26d8d83d1203492fd10737e5845259a4eb7db5aed5f5e310616c812bd56b2d03fe389541ad28a7547be9331a6a587b09b3847172d1a70a98ca7c006168bab SHA512 738e28a559017ac76fbf595eb134f91932ed94fb56831ee125dca7aa31eb46db2439f3594b5b104f6a417d0715db149d94cb263d30ba2d32f76fc8deb5195526
diff --git a/sci-libs/dealii/dealii-9.1.1.ebuild b/sci-libs/dealii/dealii-9.1.1.ebuild
new file mode 100644
index 000000000000..f4aeb21e9f00
--- /dev/null
+++ b/sci-libs/dealii/dealii-9.1.1.ebuild
@@ -0,0 +1,161 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake-utils eutils multilib
+
+# deal.II uses its own FindLAPACK.cmake file that calls into the system
+# FindLAPACK.cmake module and does additional internal setup. Do not remove
+# any of these modules:
+CMAKE_REMOVE_MODULES_LIST=""
+
+DESCRIPTION="Solving partial differential equations with the finite element method"
+HOMEPAGE="http://www.dealii.org/"
+
+if [[ ${PV} = *9999* ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/dealii/dealii.git"
+	SRC_URI=""
+	KEYWORDS=""
+else
+	MY_PV="${PV//0_rc/rc}"
+	MY_P="${PN}-${MY_PV}"
+	SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${MY_PV}/${MY_P}.tar.gz -> ${P}.tar.gz
+		doc? (
+			https://github.com/${PN}/${PN}/releases/download/v${MY_PV}/${MY_P}-offline_documentation.tar.gz
+			-> ${P}-offline_documentation.tar.gz
+			)"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+	S="${WORKDIR}/${PN}-${MY_PV}"
+fi
+
+LICENSE="LGPL-2.1+"
+SLOT="0"
+IUSE="
+	adolc assimp arpack cpu_flags_x86_avx cpu_flags_x86_avx512f
+	cpu_flags_x86_sse2 cuda +debug doc +examples gmsh +gsl hdf5 +lapack
+	metis mpi muparser nanoflann opencascade netcdf p4est petsc scalapack
+	slepc +sparse static-libs sundials symengine +tbb trilinos
+"
+
+# TODO: add slepc use flag once slepc is packaged for gentoo-science
+REQUIRED_USE="
+	p4est? ( mpi )
+	slepc? ( petsc )
+	trilinos? ( mpi )"
+
+RDEPEND="dev-libs/boost
+	app-arch/bzip2
+	sys-libs/zlib
+	adolc? ( sci-libs/adolc )
+	arpack? ( sci-libs/arpack[mpi=] )
+	assimp? ( media-libs/assimp )
+	cuda? ( dev-util/nvidia-cuda-sdk )
+	gmsh? ( sci-libs/gmsh )
+	gsl? ( sci-libs/gsl )
+	hdf5? ( sci-libs/hdf5[mpi=] )
+	lapack? ( virtual/lapack )
+	metis? ( >=sci-libs/parmetis-4 )
+	mpi? ( virtual/mpi )
+	muparser? ( dev-cpp/muParser )
+	nanoflann? ( sci-libs/nanoflann )
+	netcdf? ( sci-libs/netcdf-cxx:0 )
+	opencascade? ( sci-libs/opencascade:* )
+	p4est? ( sci-libs/p4est[mpi] )
+	petsc? ( sci-mathematics/petsc[mpi=] )
+	scalapack? ( sci-libs/scalapack )
+	slepc? ( sci-mathematics/slepc[mpi=] )
+	sparse? ( sci-libs/umfpack )
+	sundials? ( sci-libs/sundials )
+	symengine? ( >=sci-libs/symengine-0.4:= )
+	tbb? ( dev-cpp/tbb )
+	trilinos? ( sci-libs/trilinos )"
+
+DEPEND="${RDEPEND}
+	virtual/pkgconfig
+	doc? ( app-doc/doxygen[dot] dev-lang/perl )"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-9.1.1-no-ld-flags.patch
+)
+
+src_configure() {
+	# deal.II needs a custom build type:
+	local CMAKE_BUILD_TYPE=$(usex debug DebugRelease Release)
+
+	local mycmakeargs=(
+		-DDEAL_II_PACKAGE_VERSION=9999
+		-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=OFF
+		-DDEAL_II_ALLOW_AUTODETECTION=OFF
+		-DDEAL_II_ALLOW_BUNDLED=OFF
+		-DDEAL_II_ALLOW_PLATFORM_INTROSPECTION=OFF
+		-DDEAL_II_COMPILE_EXAMPLES=OFF
+		-DDEAL_II_DOCHTML_RELDIR="share/doc/${P}/html"
+		-DDEAL_II_DOCREADME_RELDIR="share/doc/${P}"
+		-DDEAL_II_COMPILE_EXAMPLES=OFF
+		-DDEAL_II_EXAMPLES_RELDIR="share/doc/${P}/examples"
+		-DDEAL_II_LIBRARY_RELDIR="$(get_libdir)"
+		-DDEAL_II_SHARE_RELDIR="share/${PN}"
+		-DDEAL_II_WITH_ZLIB=ON
+		-DDEAL_II_WITH_ADOLC="$(usex adolc)"
+		-DDEAL_II_WITH_ASSIMP="$(usex assimp)"
+		-DDEAL_II_WITH_ARPACK="$(usex arpack)"
+		-DDEAL_II_WITH_CUDA="$(usex cuda)"
+		-DDEAL_II_COMPONENT_DOCUMENTATION="$(usex doc)"
+		-DDEAL_II_COMPONENT_EXAMPLES="$(usex examples)"
+		-DDEAL_II_WITH_GMSH="$(usex gmsh)"
+		-DDEAL_II_WITH_GSL="$(usex gsl)"
+		-DDEAL_II_WITH_HDF5="$(usex hdf5)"
+		-DDEAL_II_WITH_LAPACK="$(usex lapack)"
+		-DDEAL_II_WITH_METIS="$(usex metis)"
+		-DDEAL_II_WITH_MPI="$(usex mpi)"
+		-DDEAL_II_WITH_MUPARSER="$(usex muparser)"
+		-DDEAL_II_WITH_NANOFLANN="$(usex nanoflann)"
+		-DDEAL_II_WITH_NETCDF="$(usex netcdf)"
+		-DDEAL_II_WITH_OPENCASCADE="$(usex opencascade)"
+		-DDEAL_II_WITH_P4EST="$(usex p4est)"
+		-DDEAL_II_WITH_PETSC="$(usex petsc)"
+		-DDEAL_II_WITH_SCALAPACK="$(usex scalapack)"
+		-DDEAL_II_WITH_SLEPC="$(usex slepc)"
+		-DDEAL_II_WITH_SUNDIALS="$(usex sundials)"
+		-DDEAL_II_WITH_SYMENGINE="$(usex symengine)"
+		-DDEAL_II_WITH_UMFPACK="$(usex sparse)"
+		-DBUILD_SHARED_LIBS="$(usex !static-libs)"
+		-DDEAL_II_PREFER_STATIC_LIBS="$(usex static-libs)"
+		-DDEAL_II_WITH_THREADS="$(usex tbb)"
+		-DDEAL_II_WITH_TRILINOS="$(usex trilinos)"
+	)
+
+	# Do a little dance for purely cosmetic "QA" reasons.
+	use opencascade && mycmakeargs+=( -DOPENCASCADE_DIR="${CASROOT}" )
+
+	# Do a little dance for purely cosmetic "QA" reasons. The build system
+	# does query for the highest instruction set first and skips the other
+	# variables if a "higher" variant is set
+	if use cpu_flags_x86_avx512f; then
+		mycmakeargs+=( -DDEAL_II_HAVE_AVX512=yes )
+	elif use cpu_flags_x86_avx; then
+		mycmakeargs+=( -DDEAL_II_HAVE_AVX=yes )
+	elif use cpu_flags_x86_avx; then
+		mycmakeargs+=( -DDEAL_II_HAVE_SSE2=yes )
+	fi
+
+	cmake-utils_src_configure
+}
+
+src_install() {
+	if use doc && [[ ${PV} != *9999* ]]; then
+		# copy missing images to the build directory:
+		cp -r "${WORKDIR}"/doc/doxygen/deal.II/images \
+			"${BUILD_DIR}"/doc/doxygen/deal.II || die
+		# replace links:
+		sed -i \
+			's#"http://www.dealii.org/images/steps/developer/\(step-.*\)"#"images/\1"#g' \
+			"${BUILD_DIR}"/doc/doxygen/deal.II/step_*.html || die "sed failed"
+	fi
+	cmake-utils_src_install
+
+	# decompress the installed example sources:
+	use examples && docompress -x /usr/share/doc/${PF}/examples
+}
diff --git a/sci-libs/dealii/dealii-9999.ebuild b/sci-libs/dealii/dealii-9999.ebuild
new file mode 100644
index 000000000000..dbaa10c592be
--- /dev/null
+++ b/sci-libs/dealii/dealii-9999.ebuild
@@ -0,0 +1,162 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake-utils eutils multilib
+
+# deal.II uses its own FindLAPACK.cmake file that calls into the system
+# FindLAPACK.cmake module and does additional internal setup. Do not remove
+# any of these modules:
+CMAKE_REMOVE_MODULES_LIST=""
+
+DESCRIPTION="Solving partial differential equations with the finite element method"
+HOMEPAGE="http://www.dealii.org/"
+
+if [[ ${PV} = *9999* ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/dealii/dealii.git"
+	SRC_URI=""
+	KEYWORDS=""
+else
+	MY_PV="${PV//0_rc/rc}"
+	MY_P="${PN}-${MY_PV}"
+	SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${MY_PV}/${MY_P}.tar.gz -> ${P}.tar.gz
+		doc? (
+			https://github.com/${PN}/${PN}/releases/download/v${MY_PV}/${MY_P}-offline_documentation.tar.gz
+			-> ${P}-offline_documentation.tar.gz
+			)"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+	S="${WORKDIR}/${PN}-${MY_PV}"
+fi
+
+LICENSE="LGPL-2.1+"
+SLOT="0"
+IUSE="
+	adolc assimp arpack cpu_flags_x86_avx cpu_flags_x86_avx512f
+	cpu_flags_x86_sse2 cuda +debug doc +examples gmsh +gsl hdf5 +lapack
+	metis mpi muparser nanoflann opencascade netcdf p4est petsc scalapack
+	slepc +sparse static-libs sundials symengine +tbb trilinos
+"
+
+# TODO: add slepc use flag once slepc is packaged for gentoo-science
+REQUIRED_USE="
+	p4est? ( mpi )
+	slepc? ( petsc )
+	trilinos? ( mpi )"
+
+RDEPEND="dev-libs/boost
+	app-arch/bzip2
+	sys-libs/zlib
+	adolc? ( sci-libs/adolc )
+	arpack? ( sci-libs/arpack[mpi=] )
+	assimp? ( media-libs/assimp )
+	cuda? ( dev-util/nvidia-cuda-sdk )
+	gmsh? ( sci-libs/gmsh )
+	gsl? ( sci-libs/gsl )
+	hdf5? ( sci-libs/hdf5[mpi=] )
+	lapack? ( virtual/lapack )
+	metis? ( >=sci-libs/parmetis-4 )
+	mpi? ( virtual/mpi )
+	muparser? ( dev-cpp/muParser )
+	nanoflann? ( sci-libs/nanoflann )
+	netcdf? ( sci-libs/netcdf-cxx:0 )
+	opencascade? ( sci-libs/opencascade:* )
+	p4est? ( sci-libs/p4est[mpi] )
+	petsc? ( sci-mathematics/petsc[mpi=] )
+	scalapack? ( sci-libs/scalapack )
+	slepc? ( sci-mathematics/slepc[mpi=] )
+	sparse? ( sci-libs/umfpack )
+	sundials? ( sci-libs/sundials )
+	symengine? ( >=sci-libs/symengine-0.4:= )
+	tbb? ( dev-cpp/tbb )
+	trilinos? ( sci-libs/trilinos )"
+
+DEPEND="${RDEPEND}
+	virtual/pkgconfig
+	doc? ( app-doc/doxygen[dot] dev-lang/perl )"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-9.1.1-no-ld-flags.patch
+)
+
+src_configure() {
+	# deal.II needs a custom build type:
+	local CMAKE_BUILD_TYPE=$(usex debug DebugRelease Release)
+
+	local mycmakeargs=(
+		-DDEAL_II_PACKAGE_VERSION=9999
+		-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=OFF
+		-DDEAL_II_ALLOW_AUTODETECTION=OFF
+		-DDEAL_II_ALLOW_BUNDLED=OFF
+		-DDEAL_II_ALLOW_PLATFORM_INTROSPECTION=OFF
+		-DDEAL_II_COMPILE_EXAMPLES=OFF
+		-DDEAL_II_DOCHTML_RELDIR="share/doc/${P}/html"
+		-DDEAL_II_DOCREADME_RELDIR="share/doc/${P}"
+		-DDEAL_II_COMPILE_EXAMPLES=OFF
+		-DDEAL_II_EXAMPLES_RELDIR="share/doc/${P}/examples"
+		-DDEAL_II_LIBRARY_RELDIR="$(get_libdir)"
+		-DDEAL_II_SHARE_RELDIR="share/${PN}"
+		-DDEAL_II_WITH_ZLIB=ON
+		-DDEAL_II_WITH_ADOLC="$(usex adolc)"
+		-DDEAL_II_WITH_ASSIMP="$(usex assimp)"
+		-DDEAL_II_WITH_ARPACK="$(usex arpack)"
+		-DDEAL_II_WITH_CUDA="$(usex cuda)"
+		-DDEAL_II_COMPONENT_DOCUMENTATION="$(usex doc)"
+		-DDEAL_II_COMPONENT_EXAMPLES="$(usex examples)"
+		-DDEAL_II_WITH_GMSH="$(usex gmsh)"
+		-DDEAL_II_WITH_GSL="$(usex gsl)"
+		-DDEAL_II_WITH_HDF5="$(usex hdf5)"
+		-DDEAL_II_WITH_LAPACK="$(usex lapack)"
+		-DDEAL_II_WITH_METIS="$(usex metis)"
+		-DDEAL_II_WITH_MPI="$(usex mpi)"
+		-DDEAL_II_WITH_MUPARSER="$(usex muparser)"
+		-DDEAL_II_WITH_NANOFLANN="$(usex nanoflann)"
+		-DDEAL_II_WITH_NETCDF="$(usex netcdf)"
+		-DOPENCASCADE_DIR="${CASROOT}"
+		-DDEAL_II_WITH_OPENCASCADE="$(usex opencascade)"
+		-DDEAL_II_WITH_P4EST="$(usex p4est)"
+		-DDEAL_II_WITH_PETSC="$(usex petsc)"
+		-DDEAL_II_WITH_SCALAPACK="$(usex scalapack)"
+		-DDEAL_II_WITH_SLEPC="$(usex slepc)"
+		-DDEAL_II_WITH_SUNDIALS="$(usex sundials)"
+		-DDEAL_II_WITH_SYMENGINE="$(usex symengine)"
+		-DDEAL_II_WITH_UMFPACK="$(usex sparse)"
+		-DBUILD_SHARED_LIBS="$(usex !static-libs)"
+		-DDEAL_II_PREFER_STATIC_LIBS="$(usex static-libs)"
+		-DDEAL_II_WITH_THREADS="$(usex tbb)"
+		-DDEAL_II_WITH_TRILINOS="$(usex trilinos)"
+	)
+
+	# Do a little dance for purely cosmetic "QA" reasons.
+	use opencascade && mycmakeargs+=( -DOPENCASCADE_DIR="${CASROOT}" )
+
+	# Do a little dance for purely cosmetic "QA" reasons. The build system
+	# does query for the highest instruction set first and skips the other
+	# variables if a "higher" variant is set
+	if use cpu_flags_x86_avx512f; then
+		mycmakeargs+=( -DDEAL_II_HAVE_AVX512=yes )
+	elif use cpu_flags_x86_avx; then
+		mycmakeargs+=( -DDEAL_II_HAVE_AVX=yes )
+	elif use cpu_flags_x86_avx; then
+		mycmakeargs+=( -DDEAL_II_HAVE_SSE2=yes )
+	fi
+
+	cmake-utils_src_configure
+}
+
+src_install() {
+	if use doc && [[ ${PV} != *9999* ]]; then
+		# copy missing images to the build directory:
+		cp -r "${WORKDIR}"/doc/doxygen/deal.II/images \
+			"${BUILD_DIR}"/doc/doxygen/deal.II || die
+		# replace links:
+		sed -i \
+			's#"http://www.dealii.org/images/steps/developer/\(step-.*\)"#"images/\1"#g' \
+			"${BUILD_DIR}"/doc/doxygen/deal.II/step_*.html || die "sed failed"
+	fi
+	cmake-utils_src_install
+
+	# decompress the installed example sources:
+	use examples && docompress -x /usr/share/doc/${PF}/examples
+}
diff --git a/sci-libs/dealii/files/dealii-9.1.1-no-ld-flags.patch b/sci-libs/dealii/files/dealii-9.1.1-no-ld-flags.patch
new file mode 100644
index 000000000000..69c2c09e679c
--- /dev/null
+++ b/sci-libs/dealii/files/dealii-9.1.1-no-ld-flags.patch
@@ -0,0 +1,20 @@
+diff --git a/cmake/config/config_debug.pc.in b/cmake/config/config_debug.pc.in
+index 5ea03885cd..32e45d8121 100644
+--- a/cmake/config/config_debug.pc.in
++++ b/cmake/config/config_debug.pc.in
+@@ -8,4 +8,4 @@ Version: @DEAL_II_VERSION@
+ URL: https://dealii.org/
+ 
+ Cflags: @DEAL_II_CXX_FLAGS@ @DEAL_II_CXX_FLAGS_DEBUG@ @CONFIG_INCLUDE_DIRS_PC@
+-Libs: @DEAL_II_LINKER_FLAGS@ @DEAL_II_LINKER_FLAGS_DEBUG@ @CONFIG_LIBRARIES_DEBUG_PC@ @CONFIG_RPATH_DEBUG_PC@
++Libs: @CONFIG_LIBRARIES_DEBUG_PC@ @CONFIG_RPATH_DEBUG_PC@
+diff --git a/cmake/config/config_release.pc.in b/cmake/config/config_release.pc.in
+index 726a35d040..8a879d07e8 100644
+--- a/cmake/config/config_release.pc.in
++++ b/cmake/config/config_release.pc.in
+@@ -8,4 +8,4 @@ Version: @DEAL_II_VERSION@
+ URL: https://dealii.org/
+ 
+ Cflags: @DEAL_II_CXX_FLAGS@ @DEAL_II_CXX_FLAGS_RELEASE@ @CONFIG_INCLUDE_DIRS_PC@
+-Libs: @DEAL_II_LINKER_FLAGS@ @DEAL_II_LINKER_FLAGS_RELEASE@ @CONFIG_LIBRARIES_RELEASE_PC@ @CONFIG_RPATH_RELEASE_PC@
++Libs: @CONFIG_LIBRARIES_RELEASE_PC@ @CONFIG_RPATH_RELEASE_PC@
diff --git a/sci-libs/dealii/metadata.xml b/sci-libs/dealii/metadata.xml
new file mode 100644
index 000000000000..235d8ffe8218
--- /dev/null
+++ b/sci-libs/dealii/metadata.xml
@@ -0,0 +1,45 @@
+<?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@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+deal.II is a C++ program library targeted at the computational solution
+of partial differential equations using adaptive finite elements. It uses
+state-of-the-art programming techniques to offer you a modern interface
+to the complex data structures and algorithms required.
+</longdescription>
+	<use>
+		<flag name="adolc">Adds support for ADOL-C (<pkg>sci-libs/adolc</pkg>)</flag>
+		<flag name="arpack">Adds support for ARPACK (<pkg>sci-libs/arpack</pkg>)</flag>
+		<flag name="debug">
+Build an additional debug library with extra debug codepaths, like asserts
+and extra output. If you want to get meaningful backtraces see
+&lt;http://www.gentoo.org/proj/en/qa/backtraces.xml&gt;</flag>
+		<flag name="gmsh">Add support for gmsh (<pkg>sci-libs/gmsh</pkg>)</flag>
+		<flag name="metis">Add support for metis (<pkg>sci-libs/metis</pkg>)</flag>
+		<flag name="muparser">Add support for muparser (<pkg>dev-cpp/muParser</pkg>)</flag>
+		<flag name="nanoflann">Adds support for nanoflann (<pkg>sci-libs/nanoflann</pkg>)</flag>
+		<flag name="opencascade">Add support for opencascade (<pkg>sci-libs/opencascade</pkg>)</flag>
+		<flag name="p4est">Add support for p4est (<pkg>sci-libs/p4est</pkg>)</flag>
+		<flag name="petsc">Add support for petsc (<pkg>sci-mathematics/petsc</pkg>)</flag>
+		<flag name="scalapack">Add support for ScaLAPACK (<pkg>sci-libs/scalapack</pkg>)</flag>
+		<flag name="slepc">Add support for slepc (<pkg>sci-mathematics/slepc</pkg>)</flag>
+		<flag name="sparse">Add support for suitesparse (<pkg>sci-libs/suitesparse</pkg>)</flag>
+		<flag name="symengine">Add support for symengine (<pkg>sci-libs/symengine</pkg>)</flag>
+		<flag name="tbb">Add threading support with the help of the tbb library (<pkg>dev-cpp/tbb</pkg>)</flag>
+		<flag name="trilinos">Add support for trilinos (<pkg>sci-libs/trilinos</pkg>)</flag>
+		<flag name="assimp">Add support for assimp (<pkg>media-libs/assimp</pkg>)</flag>
+		<flag name="cuda">Add support for cuda assimp (<pkg>dev-util/nvidia-cuda-sdk</pkg>)</flag>
+		<flag name="sundials">Add support for sundials assimp (<pkg>sci-libs/sundials</pkg>)</flag>
+	</use>
+	<upstream>
+		<remote-id type="github">dealii/dealii</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-libs/dlib/Manifest b/sci-libs/dlib/Manifest
index 42d185ea3618..f43a45f87ec0 100644
--- a/sci-libs/dlib/Manifest
+++ b/sci-libs/dlib/Manifest
@@ -5,5 +5,5 @@ DIST dlib-19.9.tar.gz 8892457 BLAKE2B d18548e09f8169bbc9d7f339599bd58b940410839b
 EBUILD dlib-19.16.ebuild 2950 BLAKE2B 5b5193177d42cbdac7cc02ca06e46b41642175fdec40e4f432b4ace2efab2193ee9e3f92a4524dc304c5cc3f7d59aa6c8b44c932efaaa672812dc0744396de7f SHA512 67b7938ff4e696154021eb4c5a16ca1ceff75082c29e04ee87ad7610bab67ad35e7653609839e0b8b54fae33f49abf510d2cbee0faf2e37f1540695a5fe13394
 EBUILD dlib-19.4.ebuild 1797 BLAKE2B 45fd4d3b434852fa3a8d1571e30fee6ffbdb254ed471433fac534c26854ab69352b981dae4ad45b404cc6ff8525a92bb22915bd058c18e0f00d4c3cce9157164 SHA512 ef2172c18b446cf98c79e9b6a4dcf622ca62d05cc353d82d35385a16a334a94d5689af5117f9fee26e9e32346da57227beb83ca35b4b216135ad15b214042328
 EBUILD dlib-19.7.ebuild 1795 BLAKE2B beb38d516fb6c854f7958c6d63d83d5612acfdd384986df8ef7cfc58bca1a2c323078d96711882f4a2adeef775520fdef9e08caee550667d2493eead4fa7e9c8 SHA512 e3b82055fc6e093d2cbd7850b91354cf3e5b62cbf0d614b1c62316cdcf7aed0082808400161ea072d21a4296f901d5edeebc039ff5db73aaa0a921b6cba106ee
-EBUILD dlib-19.9.ebuild 1991 BLAKE2B 10801b1369fbc58eac0b7dbb8bfb9c4bc2ba270333545a85957f0ba3b047f3b83d61fa6e19a68fd73fb0ea38f712af4bc18da6da69f9e31e3ecb6f1213ad32e2 SHA512 cc886fb9acc3b97bed94dcd938a33537a0d4c3041103caf569f72884102579b523eabfc0198143747a1bdacdbb5770aceb66181b3eec56231532db21a66311e6
+EBUILD dlib-19.9.ebuild 2041 BLAKE2B 8ee1766f6ed036417412468206428a0712553942da092c7e71b33ac629db0d9ed90ad619d1b11567faf8c15b46ebefb0599ef37d9189f7c734e37ac56aa2df09 SHA512 b668d2317a8e4057b7214791f5f56523a249be48d790e6ef59e5e0b625bdc364d7f442285a5424828c16f98a011230eecae9f4861cb068e78cfc543967539eda
 MISC metadata.xml 1002 BLAKE2B 899d622186d6ed4ab0c8c448bdbe312be12f0eeeec5e4d4ae031de4dcb26d73f0489b697375893d4c4bd16651c6b2d40ac156b67be0b376ec270d7d99a6f465a SHA512 1977d192107b78b97d5336d3e5b2e43a7ea12ede631a864ce14aeab2f9d328526f815fab0d62ae1417842cdfe9e1e7c0494fcf79be535dbfc4e3ca9342447b5c
diff --git a/sci-libs/dlib/dlib-19.9.ebuild b/sci-libs/dlib/dlib-19.9.ebuild
index 555dc500ca7d..28049b0cd64a 100644
--- a/sci-libs/dlib/dlib-19.9.ebuild
+++ b/sci-libs/dlib/dlib-19.9.ebuild
@@ -13,6 +13,7 @@ LICENSE="Boost-1.0"
 SLOT="0/${PV}"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="cblas debug cuda examples gif jpeg lapack mkl png python sqlite static-libs test X"
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
 
 # doc needs a bunch of deps not in portage
 
diff --git a/sci-libs/gmsh/Manifest b/sci-libs/gmsh/Manifest
new file mode 100644
index 000000000000..734e9e99c16e
--- /dev/null
+++ b/sci-libs/gmsh/Manifest
@@ -0,0 +1,3 @@
+DIST gmsh-4.4.1-source.tgz 13227645 BLAKE2B 68df0a54655d2a85012d2961daafbe92f0295661f6f71b0be4c7a78b7c814af21b39b29e65a201c4918d7e31462ac391b208fcceca356c4d9974c5de3c88da13 SHA512 cfdd353de051d1deffca90bfa31a007a466d39c145e704612b92441556dec0c8d7b58ab07c2fa3166de893d99f0308ffb66b4f321172ea60da0b6db907aa7a2e
+EBUILD gmsh-4.4.1.ebuild 1740 BLAKE2B 77ac37edcdc391cf69151c289b2958e8f6d3d1ddd482bee66695d573dc8a9435b6bab4c4be9ae9f03b492c58502be85d1621382912392d205e6153091d400fa5 SHA512 5ac483d00af4d61871a6391b730b83fe6c36426dd511efd1ad7c3f20b0ee3e07068c80f11e47d2c916e1427e7a7e26739c30900209e70b3147204d26a9551f80
+MISC metadata.xml 737 BLAKE2B fc604a0966c3106fabcd1379cf0cecbd28bd80c9068330206127cd35e134436a5ec3f43b19dfe0793e2a7a299a4b8f335b11cf2f723b6451a3b341077d27a6c7 SHA512 03f6a246c66264a58638c5ef89ec10737cbb15bd6d443f2f866fc77d21bf052c3ff4e00ca919546aa0da5b91c31a96af8dea5609a72dbb92a20c534e6a6f639b
diff --git a/sci-libs/gmsh/gmsh-4.4.1.ebuild b/sci-libs/gmsh/gmsh-4.4.1.ebuild
new file mode 100644
index 000000000000..fa56d3eae139
--- /dev/null
+++ b/sci-libs/gmsh/gmsh-4.4.1.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils flag-o-matic fortran-2 python-any-r1 toolchain-funcs
+
+DESCRIPTION="A three-dimensional finite element mesh generator"
+HOMEPAGE="http://www.geuz.org/gmsh/"
+SRC_URI="http://www.geuz.org/gmsh/src/${P}-source.tgz"
+
+LICENSE="GPL-3 free-noncomm"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+## cgns is not compiling ATM, maybe fix cgns lib first
+IUSE="blas cgns examples jpeg lua med metis mpi netgen opencascade petsc png python X zlib"
+
+RDEPEND="
+	virtual/fortran
+	X? ( x11-libs/fltk:1 )
+	blas? ( virtual/blas virtual/lapack sci-libs/fftw:3.0 )
+	cgns? ( sci-libs/cgnslib )
+	jpeg? ( virtual/jpeg:0 )
+	lua? ( dev-lang/lua:0 )
+	med? ( sci-libs/med )
+	opencascade? ( sci-libs/opencascade:* )
+	png? ( media-libs/libpng:0 )
+	petsc? ( sci-mathematics/petsc )
+	zlib? ( sys-libs/zlib )
+	mpi? ( virtual/mpi[cxx] )"
+
+DEPEND="${RDEPEND}
+	${PYTHON_DEPS}
+	virtual/pkgconfig
+	python? ( dev-lang/swig:0 )
+	"
+
+S=${WORKDIR}/${P}-source
+
+pkg_setup() {
+	fortran-2_pkg_setup
+}
+
+src_configure() {
+	local mycmakeargs=( )
+
+	use blas && \
+		mycmakeargs+=(-DCMAKE_Fortran_COMPILER=$(tc-getF77))
+
+	mycmakeargs+=(
+		-DENABLE_BLAS_LAPACK="$(usex blas)"
+		-DENABLE_CGNS="$(usex cgns)"
+		-DENABLE_FLTK="$(usex X)"
+		-DENABLE_GRAPHICS="$(usex X)"
+		-DENABLE_MED="$(usex med)"
+		-DENABLE_METIS="$(usex metis)"
+		-DENABLE_NETGEN="$(usex netgen)"
+		-DENABLE_OCC="$(usex opencascade)"
+		-DENABLE_PETSC="$(usex petsc)"
+		-DENABLE_WRAP_PYTHON="$(usex python)")
+
+	cmake-utils_src_configure mycmakeargs
+}
+
+src_install() {
+	cmake-utils_src_install
+
+	if use examples ; then
+		insinto /usr/share/doc/${PF}
+		doins -r demos tutorial
+	fi
+}
diff --git a/sci-libs/gmsh/metadata.xml b/sci-libs/gmsh/metadata.xml
new file mode 100644
index 000000000000..20c781af95c5
--- /dev/null
+++ b/sci-libs/gmsh/metadata.xml
@@ -0,0 +1,20 @@
+<?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@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<use>
+		<flag name="cgns"> Enables cgns output support</flag>
+		<flag name="metis"> Enables metis support</flag>
+		<flag name="med"> Enables med support</flag>
+		<flag name="netgen"> Enable 3D Frontal triangulation using netgen lib</flag>
+		<flag name="petsc"> Enable sci-mathematics/petsc support</flag>
+		<flag name="opencascade"> Enable OpenCASCADE support</flag>
+	</use>
+</pkgmetadata>
diff --git a/sci-libs/gpp4/Manifest b/sci-libs/gpp4/Manifest
deleted file mode 100644
index a8aa3e3bc239..000000000000
--- a/sci-libs/gpp4/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST gpp4-1.3.1.tar.gz 694533 BLAKE2B 4c995a86dcd0753aba09a46e172bcd5a72f7b9b0a1cb66f17e83878a94ae9855b8664fcfa880222ed9e44421c098e151242f54c5d9d5f1cc4f522936f300ab92 SHA512 b24b26ecb38406bf5895f1dd43e847836f9aeecf7b5bc54df602e23e828b5cf8ae4a8902e294065d67edfb3507763e3d7496acbd6373e7dbc5e85d049c044920
-EBUILD gpp4-1.3.1.ebuild 586 BLAKE2B eafe298202e6a2e754847db44ebfd22e2fef78a3101a791d75d2c99e6f2c8e9f1e09e199c02a2b185632b686bb397ab1758b957eb2f6bc38797ab0b57542e4b5 SHA512 0053fdda411d272cba46232ed11208d0d71fc1d75424c1a35364d8b2fa61a98ff368c9794cc0cde134472281efacd95a0578fb5b1df34452cb95cdd836382551
-MISC metadata.xml 337 BLAKE2B 4d7bad2bc4fb50f30f170758c6b5e54cc408a5b940c41f222846732c60a543d546ef892f2c465d3787413f859167acdd34cb76b55b9f5b150594df163502dc04 SHA512 2291e4105f0f16ba3018cdadfceaed49d56418067ad6c9fdc68b5f2a3893654a66891456846284a30b32b8e29efc2b7c6bc2b919140d8745792405a70d993c92
diff --git a/sci-libs/gpp4/gpp4-1.3.1.ebuild b/sci-libs/gpp4/gpp4-1.3.1.ebuild
deleted file mode 100644
index 75be7d629f2c..000000000000
--- a/sci-libs/gpp4/gpp4-1.3.1.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-
-inherit fortran-2
-
-DESCRIPTION="A standalone, drop-in replacement for the CCP4 library"
-HOMEPAGE="https://launchpad.net/gpp4/"
-SRC_URI="https://launchpad.net/${PN}/1.3/${PV}/+download/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="fortran static-libs"
-
-RDEPEND="sci-libs/mmdb:0="
-DEPEND="${RDEPEND}"
-
-src_configure() {
-	econf \
-		$(use_with fortran fortran-api) \
-		$(use_enable static-libs static)
-}
diff --git a/sci-libs/gpp4/metadata.xml b/sci-libs/gpp4/metadata.xml
deleted file mode 100644
index 046af6ea9df6..000000000000
--- a/sci-libs/gpp4/metadata.xml
+++ /dev/null
@@ -1,11 +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>
-	<upstream>
-		<remote-id type="launchpad">gpp4</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-libs/libccp4/Manifest b/sci-libs/libccp4/Manifest
deleted file mode 100644
index a27f604c7e6d..000000000000
--- a/sci-libs/libccp4/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST libccp4-6.4.6.tar.gz 934709 BLAKE2B 43412152c9408bef1980c61610d013f3c5f0eab5ae4a474a0874f43250306cad4478e0fde06e01c1aa8b80ec563bcb019f2ce362f5272a0c1e06e24f9437599c SHA512 38893d7c8bec99b6d1245586695d98900284543dfe7f87e0cab81a7f7f93b3dac0780c3ea576fb910fc3712d7b9226814ebe05530948ace136860f398e11daf6
-EBUILD libccp4-6.4.6.ebuild 597 BLAKE2B 845c6e57d4c721bb5504cfe91e731a5d9fedfa1d06d298d4ba85b26daf73ab851bfc61538bd2aa456d64540771600ab79bd441ec013129781a1bb592b8f51e91 SHA512 29f519f7ea0ec6c6e9b043523cfe406accbbd0f0c84287085aa9e480ba6fe12b8dfd3646942b9b2af3fae2101165ec90fa257b10441f9ae408817c1361827c85
-MISC metadata.xml 265 BLAKE2B d5a98b9309829a0486c4b8a4336c2d24a0fe34e926d52afd0cc87e16fcc887ca4c18851e58afb33866823121fa8f221a90e0d726dbd85552a4caf66cf03b7b4a SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a
diff --git a/sci-libs/libccp4/libccp4-6.4.6.ebuild b/sci-libs/libccp4/libccp4-6.4.6.ebuild
deleted file mode 100644
index a2f7940a036c..000000000000
--- a/sci-libs/libccp4/libccp4-6.4.6.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-
-inherit autotools-utils fortran-2
-
-DESCRIPTION="The CCP4 C and F77 subroutine library"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-3 LGPL-3"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="fortran static-libs"
-
-RDEPEND="sci-libs/mmdb:2"
-DEPEND="${RDEPEND}
-"
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-src_configure() {
-	myeconfargs=(
-		$(use_enable fortran)
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-libs/med/Manifest b/sci-libs/med/Manifest
new file mode 100644
index 000000000000..7f3fba95a489
--- /dev/null
+++ b/sci-libs/med/Manifest
@@ -0,0 +1,3 @@
+DIST med-4.0.0.tar.gz 47849098 BLAKE2B 0bc6710f7b5156e09962e3125349573989429e614a203f649843f00dea06217040ebee70e481eed9c0dd304cb7d167efcd216c3600f6954a74f262cc845fff63 SHA512 2840437010481fc5f12a56e3282f8ca5e94df541899e2b511756702f86d0f87dbf2f6e086d8e591e2bd370d8f4bab8089e7f7f939fea16354a23e2b5a4d96cd7
+EBUILD med-4.0.0.ebuild 855 BLAKE2B b10da966988f792f38bacee9d3262429f7d8f5da33b3e0d4785c77fdcf216b22ce1af488407938ad1e1a3154b139fc0385418bb35d4ced76023ee62bdf111727 SHA512 20cc36592197be6d7365cbe6410dfd3701b9236e79dfaa00d147afbff3d27151137d1f13945e2aa74be016bdae196b7a90a5e0b247ff5d14bae5cd4b466e18e6
+MISC metadata.xml 361 BLAKE2B fbd2fb8f0943722292e127f49064380cbe92df453a9c30ac6e0f4767866d81c3ca69b2605cb6269d8cc02604507068dbb967317b6cdc2d1184420bff2d592200 SHA512 a25fbe30ddfa3b62d7c7fff16a022a19145e161099fc59cb2df072461452f2c8a2a0246da7bbc3e18dd580789e514f6a85232b908e921a9762eff18059c85f94
diff --git a/sci-libs/med/med-4.0.0.ebuild b/sci-libs/med/med-4.0.0.ebuild
new file mode 100644
index 000000000000..721d2173d35b
--- /dev/null
+++ b/sci-libs/med/med-4.0.0.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils flag-o-matic
+
+DESCRIPTION="Modeling and Exchange of Data library"
+HOMEPAGE="https://www.salome-platform.org/user-section/about/med"
+SRC_URI="https://files.salome-platform.org/Salome/other/${P}.tar.gz"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="mpi"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	>=sci-libs/hdf5-1.10.5[mpi=]
+	mpi? ( virtual/mpi )
+"
+
+DEPEND="
+	${DEPEND}
+"
+
+src_prepare() {
+	default
+	append-cppflags -DH5_USE_16_API
+}
+
+src_configure() {
+	local myconf=(
+		--docdir="/usr/share/doc/${PF}"
+		--disable-python
+	)
+
+	econf "${myconf[@]}"
+}
+
+src_install() {
+	default
+
+	mv "${ED}"/usr/$(get_libdir)/libmed3.settings \
+		"${ED}"/usr/share/doc/${PF}/ || die "mv failed"
+
+	rm -rf "${ED}"/usr/include/2.3.6 || die "rm failed"
+}
diff --git a/sci-libs/libccp4/metadata.xml b/sci-libs/med/metadata.xml
index da36ecbfcd6a..dd66d18ef4fd 100644
--- a/sci-libs/libccp4/metadata.xml
+++ b/sci-libs/med/metadata.xml
@@ -1,8 +1,12 @@
 <?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>
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
 	</maintainer>
 </pkgmetadata>
diff --git a/sci-libs/mmdb/Manifest b/sci-libs/mmdb/Manifest
deleted file mode 100644
index 207427681b12..000000000000
--- a/sci-libs/mmdb/Manifest
+++ /dev/null
@@ -1,10 +0,0 @@
-AUX mmdb-1.25.5-include-path.patch 362 BLAKE2B 930b83c0afe026aaa385853de8496ebbe5f49b4c78590a42a68ffa6c22697d4e67051897c29e7b110d2b1c61ac4e5efc7389afa5a0afd0db77d3d5d0a6b7cf8c SHA512 60b110b173867c4b3eb45ad370141950046e248dd94d6496e8c8a14a72051a24cdfe805a2401083d53b471893d4e528a8f953ed28935393ab40201a973921f3b
-DIST mmdb-1.25.5.tar.gz 732911 BLAKE2B 6c0d49ca028c0140df6cd513d66cd260087f747a755a85508dac2e24c63ed17d684b368e76fe2582c4921f1cf6bbb4cd7fa33cc5e47b6ef79af6fad1b5f1c8ef SHA512 19784f119422e176ff97c0f40256815584ddf2156570593047125ffaf509c961840619799ce20c43efb330d22f068f96c061d31aa5bc5851f538da1742152ba0
-DIST mmdb-1.25.6.1.tar.gz 992256 BLAKE2B cef269f4428b5a553075e6c2d33568ead3271ec4dd87fef5524072530723b8f59760a8dc5c523a985ccb922cef52bcdf88b18334626a71059994ce2a9b30ed8f SHA512 b253ee6096ea90202c061d579d98f324a53de17dad9db0a426e1a2106b23eecf6ec90667697f1e88a5f7b05fc45a0bbd2faada997de3ecca5b0f2b548520bd5c
-DIST mmdb2-2.0.1.tar.gz 721759 BLAKE2B ea79bbbeef345b1e9d7240ec31f67a217e7c9312827f0333d1b089be8b265bf09baf5b54f2d8edd7eee17a530dd9931bd4ec0b6377aa2a15cec67b6ec142e345 SHA512 00465204aa2b76867f805259d25653d48e0e4fe5eabb3929b86a9e3ae8d88345737ca187cfd21dc6c2808e6e8da9c9d61c11be2f587e733390bc69e5ef87b7cd
-DIST mmdb2-2.0.5.tar.gz 733138 BLAKE2B 8197fbd0331aa770144e9fa56ac6a3a89f58fb226d83f1e55afeb1d7df31f194ccaba6fe4a851cd326e77d7362bb5c1fb6d731823690cc9c7295d50d8b7427f8 SHA512 dfcbe9f84a62251976fc44f0a63dfd19306245aa147d7eb0cc7875d4c9295eac3d01bc4aeb165c04e0613e4d0b9bb0e8e6bcaf3872ed1da29e3e66ac4ec8bcc4
-EBUILD mmdb-1.25.5-r1.ebuild 487 BLAKE2B 6d600888c83ce61aa55575f4b1593b4144b741521ce345220f350e429efd5e734d73c10a77470ed676818f0ed9fa2710b9dab0168a2997a6b0f0aa7c7fa82c88 SHA512 983840011e3e1fe935b61b5687d80d21c2358b3b521768551f34c3c81a16522e6ba024d0d470d83d67dff17ae1bc6294c30855a269c29dbf0f91d84e8c2de62f
-EBUILD mmdb-1.25.6.1.ebuild 486 BLAKE2B 55ecf364e9567c6d98961eef9cd59a05fcfe7b83e1c7eb8286dafeeb951c43adfca391c9b44b055147fa3a5bea3324b02dccbc092d8f328ec2685c4152fa2501 SHA512 590b8d4cad702f7b7f6f37bac4eb50f56b09dae6c62e54143d5a6b6ea6fa172faada73119d3609c03f0bf7b93232a879f200b31d3d81cc4871e678e5bb66aa07
-EBUILD mmdb-2.0.1.ebuild 484 BLAKE2B 320fa1dfb1c044c237b78c902af2ba2bcbc8f98b453ae416ea69f624d8873a8087bee4895547546d4a958bce6767115622f288bac33bccb00e9c19822ed8b999 SHA512 a0cd76203854c4b8963e9d3ee5846d3538887b4f8d3d12644591d98b3659ce1b1ec95fecf118e76e21ca7f885e9ab8575976d1a66976ffe2262a71f5c5a97bee
-EBUILD mmdb-2.0.5-r1.ebuild 647 BLAKE2B 0613e0e8ca1597c315d87c96988ead8536e989388c6d85320f40408b2d54395cb8b0e8e190a80ecfed2990f6800f02ce123f566d3a3da34d9c5c9cc3646693ab SHA512 ca4927b4895437ae755a19c1e5572dde25bc7572cbc50e6b707d4a55a06452d072c4f9c280f633e53059f1f8f2b31c302711227c762204d7e028e7a9c28eff7c
-MISC metadata.xml 347 BLAKE2B c20fb359d6159c1526170b6a97b97413e4d13d6cd824ca18ffa1605e5afb5df030e88bed371d3716489dab5a23c6f482d995df74f31d2853ab0845c44f92f405 SHA512 4638d7dff2f4e4b84c0acb9f4084141bede8166faf8354ef61656597f69584493f64f7552c3f79849d8d910cdfb93292ad1625589e1f9aa175ea4e2e26af90f8
diff --git a/sci-libs/mmdb/files/mmdb-1.25.5-include-path.patch b/sci-libs/mmdb/files/mmdb-1.25.5-include-path.patch
deleted file mode 100644
index 52189f0a32f0..000000000000
--- a/sci-libs/mmdb/files/mmdb-1.25.5-include-path.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- mmdb.pc.in | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/mmdb.pc.in b/mmdb.pc.in
-index dd654a4..b3c28a9 100644
---- a/mmdb.pc.in
-+++ b/mmdb.pc.in
-@@ -1,7 +1,7 @@
- prefix=@prefix@
- exec_prefix=@exec_prefix@
- libdir=@libdir@
--includedir=@includedir@
-+includedir=@includedir@/mmdb
- 
- Name: mmdb
- Description: Macromolecular coordinate library
diff --git a/sci-libs/mmdb/metadata.xml b/sci-libs/mmdb/metadata.xml
deleted file mode 100644
index 8f40a97a08ad..000000000000
--- a/sci-libs/mmdb/metadata.xml
+++ /dev/null
@@ -1,11 +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>
-  <upstream>
-    <remote-id type="launchpad">mmdb</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild b/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild
deleted file mode 100644
index e62be82bfb06..000000000000
--- a/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils
-
-DESCRIPTION="The Coordinate Library for working with CCP4 coordinate files"
-HOMEPAGE="https://launchpad.net/mmdb/"
-SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz"
-
-LICENSE="GPL-2 LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="static-libs"
-
-PATCHES=( "${FILESDIR}"/${P}-include-path.patch )
diff --git a/sci-libs/mmdb/mmdb-1.25.6.1.ebuild b/sci-libs/mmdb/mmdb-1.25.6.1.ebuild
deleted file mode 100644
index d63c4003a026..000000000000
--- a/sci-libs/mmdb/mmdb-1.25.6.1.ebuild
+++ /dev/null
@@ -1,15 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="The Coordinate Library for working with CCP4 coordinate files"
-HOMEPAGE="https://launchpad.net/mmdb/"
-SRC_URI="https://launchpad.net/mmdb/1.25/${PV}/+download/${P}.tar.gz"
-
-LICENSE="GPL-2 LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="static-libs"
-
-PATCHES=( "${FILESDIR}"/${PN}-1.25.5-include-path.patch )
diff --git a/sci-libs/mmdb/mmdb-2.0.1.ebuild b/sci-libs/mmdb/mmdb-2.0.1.ebuild
deleted file mode 100644
index e227efcef4d9..000000000000
--- a/sci-libs/mmdb/mmdb-2.0.1.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils
-
-MY_P="${PN}2-${PV}"
-
-DESCRIPTION="The Coordinate Library for working with CCP4 coordinate files"
-HOMEPAGE="https://launchpad.net/mmdb/"
-SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${MY_P}.tar.gz"
-
-LICENSE="GPL-2 LGPL-3"
-SLOT="2"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="static-libs"
-
-S="${WORKDIR}"/${MY_P}
diff --git a/sci-libs/mmdb/mmdb-2.0.5-r1.ebuild b/sci-libs/mmdb/mmdb-2.0.5-r1.ebuild
deleted file mode 100644
index d9a8ad2243da..000000000000
--- a/sci-libs/mmdb/mmdb-2.0.5-r1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-MY_P="${PN}2-${PV}"
-
-DESCRIPTION="The Coordinate Library for working with CCP4 coordinate files"
-HOMEPAGE="https://launchpad.net/mmdb/"
-SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${MY_P}.tar.gz"
-
-LICENSE="GPL-2 LGPL-3"
-SLOT="2"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="static-libs"
-
-S="${WORKDIR}"/${MY_P}
-
-src_configure() {
-	econf \
-		--enable-shared \
-		$(use_enable static-libs static)
-}
-
-src_install() {
-	default
-	if ! use static-libs; then
-		find "${ED}" -name '*.la' -delete || die
-	fi
-}
diff --git a/sci-libs/monomer-db/Manifest b/sci-libs/monomer-db/Manifest
deleted file mode 100644
index ebe5a99c3f89..000000000000
--- a/sci-libs/monomer-db/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST refmac_dictionary_v5.41.tar.gz 28087020 BLAKE2B 0beb08e0885fe92e147dc412f1a74995baaf4fa0e0ccbb960a09a8ebd700c4690bf9c1b7b5527a2085739f32bbdf0ade2039bb3843e5323c07d9e9a5a4972e93 SHA512 4e694c63fb783d998ce30a65f8cd4111a13a9dcb6e45bd29ed4e7ad87d58a11e8004205ab7e108bb52723834bddfaaca1e7d9d7336e17f4d2ea38093cfd1be7c
-EBUILD monomer-db-5.41.ebuild 737 BLAKE2B 9b1a51ba9d1c7b5daa17b42d42f8e2e9857293584fedd7e47f717c1d0cdb1445b5de669572d64baa6ec581cb9fdb6f450116b8e2d42ba73cfaeaa0aedba53b31 SHA512 4205f735529141d5e49274e0d9eb206a80b0e5a2d470c0e137a31e84f44f5dff8e945fb8bd095af907675a2a256168eb84800ca89ba3a8d992b70b267ca9782f
-MISC metadata.xml 259 BLAKE2B dfc879984b6adce945d0e0a50f6ede2bca87147b9db99491359cdeccc2e74a20d56e14ae8903dbb80c94854f89bee539f14a4e3ce864204e277accf3f124a748 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706
diff --git a/sci-libs/monomer-db/metadata.xml b/sci-libs/monomer-db/metadata.xml
deleted file mode 100644
index 8425c0d53cb0..000000000000
--- a/sci-libs/monomer-db/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@gentoo.org</email>
-    <name>Gentoo Science Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-libs/monomer-db/monomer-db-5.41.ebuild b/sci-libs/monomer-db/monomer-db-5.41.ebuild
deleted file mode 100644
index 42a0643c4d6c..000000000000
--- a/sci-libs/monomer-db/monomer-db-5.41.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MY_PN="refmac_dictionary"
-
-DESCRIPTION="Monomer library used for macromolecular structure building and refinement"
-HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/"
-SRC_URI="http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/${MY_PN}_v${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="LGPL-3"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE=""
-
-RESTRICT="binchecks strip"
-
-S="${WORKDIR}"/monomers
-
-src_install() {
-	insinto /usr/share/data/monomers/
-	for i in {a..z} {0..9} *list *.cif *.txt *table *pdb; do
-		einfo "Installing ${i}** ..."
-		doins -r ${i}
-	done
-	dodoc *.txt
-}
diff --git a/sci-libs/openblas/Manifest b/sci-libs/openblas/Manifest
index 60a690d43e9b..bdc61767c453 100644
--- a/sci-libs/openblas/Manifest
+++ b/sci-libs/openblas/Manifest
@@ -1,4 +1,4 @@
 AUX shared-blas-lapack.patch 5557 BLAKE2B 1e41b18e5a9c12eec9283c835e9b09e4ca89c6512f47a2f158f29c8a8a822d0365ad350177e379bec13f7c7574d8debd55a2f612027ff661c67ac7b226bb2370 SHA512 baa23f0c2bc8b7bc3384d7b8fa20eb5e095f20e1d8859badb55e680ccd435a851da6099b20aa203e46d62096ac93663ea130bea04dabf19432522e53139d393b
 DIST openblas-0.3.6.tar.gz 11923774 BLAKE2B 0133b83a4449fd7f86d6379129be4e4477df338d0a402a7787eec317838922b175315c6e6b014a2c7ed6aa1c58509a28f6b48c641e043af067434c4315f1fdb1 SHA512 e432ae8bfbdc8e8c6336553e05181ab38576164c140ef2a6ddb2a66479f724bd4e60a2c90f7bc15bf18eefa7045e7775dedae421fb71296b8d250132c2407b07
-EBUILD openblas-0.3.6.ebuild 3508 BLAKE2B f0aad5a9f8977bea411144cc47d977e8fdf83e76a8475bbfec70efabfdb9db8c880ffe2cd03276e94f553f5dce9229719193b05c8b91d59cf12e2e437427bc3a SHA512 c74c40f9b3a9b7b3cc1adf697af94b87bb4f090f921b5084b7a20a429f8ab5276cfb637b89a312639d951e8fc78b5ae5063f6e6de58ae5afc8e36885ec699c0a
-MISC metadata.xml 945 BLAKE2B 19efdde0fefe0a22b2b9a1ceee091c037f6e1be3c9611263daf977b81a0620fe1e603cfa94277adbdef2bbfc47ab69488502f2f73fa61ec203193a90f87d9a19 SHA512 596ed3aca0e52076aac15a3ff3a10dd40a8da00b1069b2b120a690a91a735f4009f87cf5ef2236f2069883c7a39d3e0f4079148a171e3560f53cee180514326b
+EBUILD openblas-0.3.6.ebuild 3532 BLAKE2B b48e2a8dce76ebff23d42da60e867e97ceb5c2f7d9b610800472e8765373dc8547f86065bc35d3924e402b3f4d47650596a457845b2c5062e22f377318ada101 SHA512 0ac456ebe0043cd37be9e40186283895ed09c9bbdad9259b918b40053d3b083ef9df341e2806f7d140cb63dc39182b785e0da556d594edd1150f424c972b18b5
+MISC metadata.xml 884 BLAKE2B a2fa7ef571e7fa3a5390f73e40f58fe54b156e9a706c046e88b844de341b0689b8a5fe996fa31ea48f913bfbf064271983d065dd1ada7109212240bcb766317a SHA512 088a07f3bb464717bd8403c9547def9c361b1d0c9f3e5d3398d93c7d8f7b54b4ec47ec82b4d72409ad926a6e49fc297cdbe43b7ea199cf1d64ac27091930868d
diff --git a/sci-libs/openblas/metadata.xml b/sci-libs/openblas/metadata.xml
index 95b34d1ccda3..fa16b081f106 100644
--- a/sci-libs/openblas/metadata.xml
+++ b/sci-libs/openblas/metadata.xml
@@ -14,10 +14,9 @@
 	</longdescription>
 	<use>
 		<flag name="dynamic">Build dynamic architecture detection at run time (for multi targets)</flag>
-		<flag name="pthread">Build with pthread threadding model</flag>
-		<flag name="serial">Build without multi-thraedding</flag>
 		<flag name="eselect-ldso">Enable BLAS/LAPACK runtime switching</flag>
 		<flag name="index-64bit">Compile a separate INTERFACE64 OpenBLAS</flag>
+		<flag name="pthread">Build with pthread threading model</flag>
 	</use>
 	<upstream>
 		<remote-id type="github">xianyi/OpenBLAS</remote-id>
diff --git a/sci-libs/openblas/openblas-0.3.6.ebuild b/sci-libs/openblas/openblas-0.3.6.ebuild
index 19c3b79f2584..f52bf5c6ece1 100644
--- a/sci-libs/openblas/openblas-0.3.6.ebuild
+++ b/sci-libs/openblas/openblas-0.3.6.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
-inherit toolchain-funcs
+inherit fortran-2 toolchain-funcs
 
 DESCRIPTION="Optimized BLAS library based on GotoBLAS2"
 HOMEPAGE="http://xianyi.github.com/OpenBLAS/"
@@ -11,34 +11,38 @@ SRC_URI="https://github.com/xianyi/OpenBLAS/tarball/v${PV} -> ${P}.tar.gz"
 LICENSE="BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="dynamic openmp pthread serial static-libs eselect-ldso index-64bit"
-REQUIRED_USE="?? ( openmp pthread serial )"
+IUSE="dynamic eselect-ldso index-64bit openmp pthread"
+REQUIRED_USE="?? ( openmp pthread )"
 
 RDEPEND="
-eselect-ldso? ( >=app-eselect/eselect-blas-0.2
-				!app-eselect/eselect-cblas
-				>=app-eselect/eselect-lapack-0.2 )
-"
+	eselect-ldso? ( >=app-eselect/eselect-blas-0.2
+			!app-eselect/eselect-cblas
+			>=app-eselect/eselect-lapack-0.2 )"
+
 DEPEND="virtual/pkgconfig"
 
 PATCHES=( "${FILESDIR}/shared-blas-lapack.patch" )
 
-openblas_flags() {
-	local flags=()
+pkg_setup() {
+	fortran-2_pkg_setup
+	use openmp && tc-check-openmp
+	export CC=$(tc-getCC) FC=$(tc-getFC)
+
 	use dynamic && \
-		flags+=( DYNAMIC_ARCH=1 TARGET=GENERIC NUM_THREADS=64 NO_AFFINITY=1 )
+		export DYNAMIC_ARCH=1 TARGET=GENERIC NUM_THREADS=64 NO_AFFINITY=1
+
+	# disable submake with -j
+	export MAKE_NB_JOBS=-1
+
+	USE_THREAD=0
 	if use openmp; then
-		tc-check-openmp
-		flags+=( USE_THREAD=1 USE_OPENMP=1 )
+		USE_THREAD=1; USE_OPENMP=1;
 	elif use pthread; then
-		flags+=( USE_THREAD=1 USE_OPENMP=0 )
-	else
-		flags+=( USE_THREAD=0 ) # serial
+		USE_THREAD=1; USE_OPENMP=0;
 	fi
-	flags+=( DESTDIR="${D}" PREFIX="${EPREFIX}/usr" )
-	flags+=( OPENBLAS_INCLUDE_DIR='$(PREFIX)'/include/${PN} )
-	flags+=( OPENBLAS_LIBRARY_DIR='$(PREFIX)'/$(get_libdir) )
-	echo "${flags[@]}"
+	export USE_THREAD USE_OPENMP
+
+	export PREFIX="${EPREFIX}/usr"
 }
 
 src_unpack () {
@@ -50,15 +54,21 @@ src_unpack () {
 }
 
 src_compile () {
-	emake $(openblas_flags)
-	emake -Cinterface shared-blas-lapack $(openblas_flags)
+	emake
+	emake -Cinterface shared-blas-lapack
 	if use index-64bit; then
-		emake -C"${S}-index-64bit" $(openblas_flags) INTERFACE64=1 LIBPREFIX=libopenblas64
+		emake -C"${S}-index-64bit" INTERFACE64=1 LIBPREFIX=libopenblas64
 	fi
 }
 
+src_test() {
+	emake tests
+}
+
 src_install () {
-	emake install $(openblas_flags)
+	emake install DESTDIR="${D}" OPENBLAS_INCLUDE_DIR='$(PREFIX)'/include/${PN} \
+		OPENBLAS_LIBRARY_DIR='$(PREFIX)'/$(get_libdir)
+	dodoc GotoBLAS_*.txt *.md Changelog.txt
 
 	if use eselect-ldso; then
 		dodir /usr/$(get_libdir)/blas/openblas/
diff --git a/sci-libs/scikits/Manifest b/sci-libs/scikits/Manifest
index d5c0658febfb..6ab8091f613c 100644
--- a/sci-libs/scikits/Manifest
+++ b/sci-libs/scikits/Manifest
@@ -1,3 +1,4 @@
 DIST scikits.example-0.1.tar.gz 2401 BLAKE2B 4c67adb2e74be9c94d68e99bf44017eb75c054608b69045523c5cfeee18edb01384640e8ed3cba4765bc181e7dfb9a2e70d1a97ad2b6176d2df7112172adce55 SHA512 9e5534a9f12f5a11e7f9d7c3d4f16cdbfa34293b29882e6bc9ec597b6e7ac306cc65e2b197da8c0bfc8e319b01db31f34b06018b5420c3ad68e8cc3f490259e1
 EBUILD scikits-0.1-r1.ebuild 753 BLAKE2B f930539931f3399fdd4c82b9148e5996b43b2051d8c52429795a90b63db54bb6f91c77bcbd5aa8e77fb84fc2a9f2efa218e7bc06efbb6c23e18f447d2aab9d77 SHA512 4959c848f06b45d553e75c2429133e5e814d7307be1d3d2c78b1335a1a91225a2d6b4df14e0b10cea3692ac9653414cc803ce6a06c830b739c0a55e7a23df05d
+EBUILD scikits-0.1-r2.ebuild 759 BLAKE2B 72d5ebeddf875a66f48606aea0d127098ab7d4c05ef10e156b0b3cd4c22550b4d5af95213a682411fdb8fac153481be555be926f99bc2390971073cc13a90ab8 SHA512 42d353358dc15c3061b7a300a8caa6a50a2071bd44a30b8beb9b5929faeed8f469de3a82770b90a3aa607bf7908d70fcc468ef2bfcf86dfef9d5ee7c4edc035b
 MISC metadata.xml 454 BLAKE2B 65b13370ebd7fdc79632a088b403f493076c87a0ccc49b64946c7ed0050fcfd85f7ac0fce2fa853e1be0944d0ee1628470dadb4124448e7a746bdb864ffe9977 SHA512 b33fed7d1199471c4a86dadf1aa90951035fe49c76df9310de4ed13c391b92782230308a55a33c7fa88f5bd42b8718fe5f6ac88c0a8c1818848a447c4c1d0eb8
diff --git a/sci-libs/scikits/scikits-0.1-r2.ebuild b/sci-libs/scikits/scikits-0.1-r2.ebuild
new file mode 100644
index 000000000000..0febd354ddb8
--- /dev/null
+++ b/sci-libs/scikits/scikits-0.1-r2.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} pypy )
+
+inherit python-r1
+
+DESCRIPTION="Common files for python scikits"
+HOMEPAGE="http://projects.scipy.org/scipy/scikits"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}.example/${PN}.example-${PV}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}"
+DEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+src_install() {
+	python_moduleinto scikits
+	python_foreach_impl python_domodule scikits.example*/scikits/__init__.py
+
+	if use examples; then
+		insinto /usr/share/doc/${PF}/examples
+		doins -r scikits.example*/*
+	fi
+}
diff --git a/sci-libs/scikits_image/Manifest b/sci-libs/scikits_image/Manifest
index 481add14dac2..238afc7f698e 100644
--- a/sci-libs/scikits_image/Manifest
+++ b/sci-libs/scikits_image/Manifest
@@ -1,3 +1,4 @@
 DIST scikit-image-0.13.0.tar.gz 26101533 BLAKE2B c28284f64abd58c7bafa8f5f0c781496e8bb28af79c5c730df7cbf2fede958eb88ea420fd7f89e7b8d0d91719a98dd0935af3b2cc50fe501cc8d8d1d0ee56cb9 SHA512 923015e373c406ae2fbbfdf83ce8b91e83790bdf7842c4439fdc9fd58cffe46efc0cfc7a1b0b06e1b2d092a909a6f085335640850883e7608dbccd1074046550
+EBUILD scikits_image-0.13.0-r1.ebuild 1802 BLAKE2B 90a39c2e5b940774e7450a8a105a15c91896542613209899717c6a9130f9bef94786a88db67e5abeabe05ed9781c1f71310f0a90338059aa10881aa0c23a7d84 SHA512 9ef9af8cc9d4d6fad1cded893a9b55d85a04ce38232cf79a6f42752789d2f0237a57f7c95ef240d041039a3a81e77d7e4839c600dcb6ad04fc2c48d4d931c6e2
 EBUILD scikits_image-0.13.0.ebuild 1800 BLAKE2B 46b48868ab892309c47488e038feb01be571ad545fbcfe0b7141ab75c409d2b78e50c1abb44683c1e938fe0a5a429e189fc089f882ab9cb44a0a77a829a05230 SHA512 4455e0d670565842ee64dc41ae699729afbb9efa8dbd01c3c8c3b755833d8ec279ff4f08d38a3b864111ecd00ada5993ef66880ad3ef10688e607b08a91b86ea
 MISC metadata.xml 834 BLAKE2B d6ed9731e0bfffb39fb127b1ccaa9d449e7cedc4038a5a4a915624fadad131d39df0d1d7123951539074758095d35c1b9730bb4a3da2278b02630903645eb769 SHA512 1c615479bc22c8c66b4f7a2189e38c69f9b8722f051c68473439069ef89598f0505dbd94fe06cbe56a07e41a1a6552f4d8d666703676ef9a165dbcf462e09e40
diff --git a/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild b/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild
new file mode 100644
index 000000000000..49f66eaba90b
--- /dev/null
+++ b/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+
+inherit distutils-r1 eutils virtualx
+
+MYPN="${PN/scikits_/scikit-}"
+MYP="${MYPN}-${PV}"
+
+DESCRIPTION="Image processing routines for SciPy"
+HOMEPAGE="https://scikit-image.org/"
+SRC_URI="mirror://pypi/${PN:0:1}/${MYPN}/${MYP}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc freeimage pyamg test"
+
+RDEPEND="
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/networkx[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pillow[${PYTHON_USEDEP}]
+	dev-python/pywavelets[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+	sci-libs/scipy[sparse,${PYTHON_USEDEP}]
+	freeimage? ( media-libs/freeimage )
+	pyamg? ( dev-python/pyamg[${PYTHON_USEDEP}] )"
+DEPEND="${RDEPEND}
+	>=dev-python/cython-0.23[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	test? (	dev-python/nose[${PYTHON_USEDEP}] )"
+
+S="${WORKDIR}/${MYP}"
+
+DOCS=( CONTRIBUTORS.txt DEPENDS.txt RELEASE.txt TASKS.txt TODO.txt )
+
+python_test() {
+	distutils_install_for_testing
+	cd "${TEST_DIR}" || die "no ${TEST_DIR} available"
+	echo "backend : Agg" > matplotlibrc || die
+	#echo "backend.qt4 : PyQt4" >> matplotlibrc || die
+	#echo "backend.qt4 : PySide" >> matplotlibrc || die
+	MPLCONFIGDIR=. virtx nosetests --exe -v skimage || die
+}
+
+pkg_postinst() {
+	optfeature "FITS io capability" dev-python/astropy
+	optfeature "GTK" dev-python/pygtk
+	optfeature "Parallel computation" dev-python/dask
+	# not in portage yet
+	#optfeature "io plugin providing a wide variety of formats, including specialized formats using in medical imaging." dev-python/simpleitk
+	#optfeature "io plugin providing most standard formats" dev-python/imread
+}
diff --git a/sci-libs/scikits_learn/Manifest b/sci-libs/scikits_learn/Manifest
index a374a97c87f1..1bd2d8aab788 100644
--- a/sci-libs/scikits_learn/Manifest
+++ b/sci-libs/scikits_learn/Manifest
@@ -11,5 +11,6 @@ EBUILD scikits_learn-0.17.ebuild 3101 BLAKE2B cb820e2a85478a08baee14de1a8c4f47ec
 EBUILD scikits_learn-0.18.1.ebuild 3129 BLAKE2B d27141520db85f89685949e3d62f1e4512de15f458ed2c77ab7250bec7fe834f9a8d560ea7f7566b7ea2e07a533150d04b40a28edb42fa8def30dcf10c56f9fd SHA512 28976162f6b03af48d4478e05e9d3e3dd56d809865df915abb5c322de078d9eafb8758cce118c295c875b0a67cef65d5c511abede23d64e4add522395d9bf36f
 EBUILD scikits_learn-0.18.2-r1.ebuild 3277 BLAKE2B 30df6d022a1ef0100f34fb6dbcbab2a80b61c083b6e58cb49205e2e7a8125868be52ba12fea55be305f302a012da1a77dc94712ee0def7078ada1018898d5cf7 SHA512 2bd0578062ab1a99862651e80ebf40569898d0159b2d86a4c85a548d4b192a81816b05f152d482c6a3a108bc77d377fea27a484c2f1c54b2024dd3cc6a9b17bc
 EBUILD scikits_learn-0.18.2.ebuild 3141 BLAKE2B 0c9220602cb8f67f4251f4eaf813553d81ef49d24b1c46ba90611a0f33f1e28c40534c0802319ab09c910cc581d7244936a8ede48209308085daf73277a1cfbb SHA512 34d010e3de4c67c940b8218c4d2fbf69968ccc34e7d81e73d93e644fae8641d33fb3d06a23be3adbef8714dff86eb0e12643311c649d353f8da60cff00df6f8f
+EBUILD scikits_learn-0.19.0-r1.ebuild 2821 BLAKE2B a267003f211e4e9a5b16dd50121965cfd1d48f11504e3d6818f4a667b8d5be735e0dd6b526ab0abf4234990258a32b0d810a7db323f22443241838ff8ac62dd2 SHA512 4db55b7807707db298c0a455bf0e18e9a7698d8434ea140416562ae3c061e5ab316e6e5ea80f519fe7e3c9fc9dc9419d3d110f77a9142ea025dc5a8b2fcc18da
 EBUILD scikits_learn-0.19.0.ebuild 2819 BLAKE2B f8e1f95c028c061d7b7f7d652e2a88854c4e5b4d24a5b4f4188de536279080e5515f9f1392d25502ba1fa6fbdf0879be7e07d7bec8e6f9ef2392818de4e0df4e SHA512 220cf1360fbdca2127330fff1beacfdc8103886ae04b8baf94a195638b242ef6dc6241b9814b40adcd90d4f7bf70ae10a14a3df2b638e0104e857ee58116691e
 MISC metadata.xml 605 BLAKE2B 46a657647a79f0a23cc07b39877b1e57158cdf94d9478c3aa4e7af0dbdbf60acf996d1431076697db764d42bec0d5e0517c1247e91dc36e85823a45784d00e71 SHA512 e14b6835108fa80eca44bab635c9a229da65f048ffcee16cd4ad7736c3a0fb364c94ff0bd9630030653bd3cd78d8dced191c43c7e5aacb3a7f6e61ac45b5bb3d
diff --git a/sci-libs/scikits_learn/scikits_learn-0.19.0-r1.ebuild b/sci-libs/scikits_learn/scikits_learn-0.19.0-r1.ebuild
new file mode 100644
index 000000000000..3184d4e85551
--- /dev/null
+++ b/sci-libs/scikits_learn/scikits_learn-0.19.0-r1.ebuild
@@ -0,0 +1,106 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+
+inherit distutils-r1 flag-o-matic
+
+MYPN="${PN/scikits_/scikit-}"
+MYP="${MYPN}-${PV}"
+
+DESCRIPTION="Python modules for machine learning and data mining"
+HOMEPAGE="https://scikit-learn.org"
+SRC_URI="mirror://pypi/${MYPN:0:1}/${MYPN}/${MYP}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples test"
+
+# tried to unbundle virtual/python-funcsigs, funcsigs, odict
+# but it is a large mess to maintain
+
+RDEPEND="
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/nose[${PYTHON_USEDEP}]
+	dev-python/numpy[lapack,${PYTHON_USEDEP}]
+	sci-libs/scikits[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	virtual/blas:=
+	virtual/cblas:=
+"
+
+DEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/numpy[lapack,${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	virtual/blas:=
+	virtual/cblas:=
+"
+
+S="${WORKDIR}/${MYP}"
+
+PATCHES=( "${FILESDIR}"/${PN}-0.18.1-system-cblas.patch )
+
+python_prepare_all() {
+	# bug #397605
+	[[ ${CHOST} == *-darwin* ]] \
+		&& append-ldflags -bundle "-undefined dynamic_lookup" \
+		|| append-ldflags -shared
+
+	# scikits-learn now uses the horrible numpy.distutils automagic
+	export SCIPY_FCONFIG="config_fc --noopt --noarch"
+
+	# remove bundled cblas
+	rm -r sklearn/src || die
+
+	# commented out, since it is a mess to maintain
+	# use system joblib
+	#rm -r sklearn/externals/joblib || die
+	#sed -i -e '/joblib/d' sklearn/externals/setup.py || die
+	#for f in sklearn/{*/,}*.py; do
+	#	sed -r -e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \
+	#		-e 's/from (sklearn|\.|)\.externals import/import/' -i $f || die
+	#done
+
+	# use system funcsigs and odict
+	#rm sklearn/externals/funcsigs.py || die
+	#rm sklearn/externals/odict.py || die
+	#for f in sklearn/{utils/fixes.py,gaussian_process/{tests/test_,}kernels.py}; do
+	#	sed -r -e 's/from (sklearn|\.|)\.externals\.funcsigs/from funcsigs/' -i $f || die
+	#done
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	distutils-r1_python_compile ${SCIPY_FCONFIG}
+}
+
+python_test() {
+	# doc builds and runs tests
+	use doc && return
+	distutils_install_for_testing ${SCIPY_FCONFIG}
+	esetup.py install \
+			  --root="${T}/test-${EPYTHON}" \
+			  --no-compile ${SCIPY_FCONFIG}
+	pushd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die > /dev/null
+	JOBLIB_MULTIPROCESSING=2 SKLEARN_SKIP_NETWORK_TESTS=1 nosetests -v sklearn --exe || die
+	popd > /dev/null
+}
+
+python_install() {
+	distutils-r1_python_install ${SCIPY_FCONFIG}
+}
+
+python_install_all() {
+	find "${S}" -name \*LICENSE.txt -delete
+	distutils-r1_python_install_all
+	if use examples; then
+		dodoc -r examples
+		docompress -x /usr/share/doc/${PF}/examples
+	fi
+
+}
diff --git a/sci-libs/scikits_optimization/Manifest b/sci-libs/scikits_optimization/Manifest
index 11fd515a8a44..c395d713a828 100644
--- a/sci-libs/scikits_optimization/Manifest
+++ b/sci-libs/scikits_optimization/Manifest
@@ -1,3 +1,4 @@
 DIST scikits.optimization-0.3.tar.gz 25297 BLAKE2B 1001ee772fb115e620f98547332f26f3876b38c9718e9f3c9a47e17863f2efbd6d9f6551da2340fda1ce612b385f757123bd32786764dcd3e287689313cac4ec SHA512 e8f33f4770d9b0514854e36127c53554823a159363c69d1ca0445a05ca9ebc55bc7105b35b2c615bfbef0c63a2b658d628befccb0ab09bcf98d91f8cb4d8be72
+EBUILD scikits_optimization-0.3-r1.ebuild 670 BLAKE2B f23b992a06db15ef1c2f3727197f153ce8a2f4a3eb3212aff542e25c385cbaaa91b175d5a60b4157f2b01da3a732dd35bfb2987e72243f6fd2e1e01cb483d142 SHA512 35902192f7f6437e3ee1d4c3cdc0bfeaaec6585002dff8a8d56b143cc8c23eb29b519b9a6aa54f3fdb95dda58d31670ef653bb2ab7a45b3d4cc7952d294375c6
 EBUILD scikits_optimization-0.3.ebuild 657 BLAKE2B 9fbf57298b6b2c4ada5656cdfb83af65df910b2222f31635d1bd208ff18e7993704cbb03ebd5c66379da43b6c35a59c61e55012fe7fdcfb1d965db16a3682cdf SHA512 cee7de81a15ecb2b9c6b08787ca5f8c04fe3732a6730263508c6af31d062c8fd7cd47745ed2b601254ee7a45e70de0c54f6f2e3834a9e8e3c6fac8107fc405e3
 MISC metadata.xml 441 BLAKE2B 503d22424542fd6a0f363f1a53c9f7fbd3945105ce8139e197266226b38464ce6b22b778d605ac502f9a990eb6e427a3333015c1c0e50b130e3299c17d867d9c SHA512 820c83082ab922e90874e753fee91b8d76d7bad211928dffc011d7ed44e11ca187d2d5fa75933defe673b7293770e6167148779fdfb28986c5784891d6843157
diff --git a/sci-libs/scikits_optimization/scikits_optimization-0.3-r1.ebuild b/sci-libs/scikits_optimization/scikits_optimization-0.3-r1.ebuild
new file mode 100644
index 000000000000..119808a32f92
--- /dev/null
+++ b/sci-libs/scikits_optimization/scikits_optimization-0.3-r1.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+
+inherit distutils-r1
+
+MY_P="${P/scikits_/scikits.}"
+
+DESCRIPTION="Python module for numerical optimization"
+HOMEPAGE="http://projects.scipy.org/scipy/scikits"
+SRC_URI="mirror://pypi/${PN:0:1}/scikits.optimization/${MY_P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/scikits[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}
+	dev-python/setuptools[${PYTHON_USEDEP}]"
+
+S="${WORKDIR}/${MY_P}"
+
+python_test() {
+	esetup.py test
+}
diff --git a/sci-libs/scikits_timeseries/Manifest b/sci-libs/scikits_timeseries/Manifest
index 26c86239d04d..0ea447334704 100644
--- a/sci-libs/scikits_timeseries/Manifest
+++ b/sci-libs/scikits_timeseries/Manifest
@@ -1,4 +1,5 @@
 DIST scikits.timeseries-0.91.3-html_docs.zip 907495 BLAKE2B e06c295bb4b093c2d7d5e767a8c03cb71e84ef3207790203c920ad9a9d57488f926c7a761ffb41fbc6829a9847327d40fa202776fa36fe473663066e41ecdee4 SHA512 9fb474e2a13dee865801fa5aa5f05bb74ea2387b7e14d716210898d9b338b63b7f1935f7a5514d72ffcd6f4a8552054094244fab199e18c819815d4b19cd3f23
 DIST scikits.timeseries-0.91.3.tar.gz 323771 BLAKE2B 74c14a1ec903dd02f8b3134867d4e371bac00d1a7b22de38962c3ca27afb603296b415e3ab2f21114b9c34890c24ea10379e5465d557778c6c794470235a311e SHA512 ea7292bf4d9bcce416b6f0e2c99fc40afe97a3a0210c535bd68f43a4a553d8a30cb77ce00f96ffc26340d5ff837faf5d480ea775385769495eccb5a196a88617
 EBUILD scikits_timeseries-0.91.3-r1.ebuild 1120 BLAKE2B 786204c02e544a40181b379465a04e77e81d661d26f21920e8d13923051a7c1958bd17a1930982ebe24054928c23bbb6ab4e58208dbad18c99da15308ddee7e6 SHA512 cb788db3f4233d299b101038f56f92c636a475532e6a343dc0dce8125bffc23dbbb0b8427ee43a78f457756efc47cdd4886100c5b7de4762a4e23cefc08246c7
+EBUILD scikits_timeseries-0.91.3-r2.ebuild 1133 BLAKE2B c4fc6118073aebf51e699d565c3235a2f33b5d4b10cbb60170056ede233a02b229a50cb16f1b1cda5cde50d06f1941c2966596b309060ff49d71fde40db91df0 SHA512 5487485fcee9b8220360359ffe2df21367d3169ec40b9e8efc0c8824373999ed4dbfb2d5f81401a13fa13530feb6b89fe6ae1ed3fb664c5a5127ac54372c7e81
 MISC metadata.xml 673 BLAKE2B 432205d6049ba9bcc3355436a0017b30b66c0865afed8900e5f62846885050958ff193d2524fb9818141dca6cce2a912cf11cea4075a10abce4ed6bff3964f28 SHA512 1bd1de5dfc98873bf2df5d6fa42a02b5d4c0736d965b712909ccb991d8caff4fc71827bc292643a659566c64578e2a52a780ddec2eead4339d3481683b778d43
diff --git a/sci-libs/scikits_timeseries/scikits_timeseries-0.91.3-r2.ebuild b/sci-libs/scikits_timeseries/scikits_timeseries-0.91.3-r2.ebuild
new file mode 100644
index 000000000000..7cbafda1d0b2
--- /dev/null
+++ b/sci-libs/scikits_timeseries/scikits_timeseries-0.91.3-r2.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+
+inherit distutils-r1
+
+MY_P="${P/scikits_/scikits.}"
+
+DESCRIPTION="SciPy module for manipulating, reporting, and plotting time series"
+HOMEPAGE="http://pytseries.sourceforge.net/index.html"
+SRC_URI="
+	mirror://sourceforge/pytseries/${MY_P}.tar.gz
+	doc? ( mirror://sourceforge/pytseries/${MY_P}-html_docs.zip )"
+
+LICENSE="BSD eGenixPublic-1.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc"
+
+DEPEND="
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )"
+RDEPEND="
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	sci-libs/scikits[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/pytables[${PYTHON_USEDEP}]"
+
+S="${WORKDIR}/${MY_P}"
+
+python_test() {
+	esetup.py test
+}
+
+python_install() {
+	distutils-r1_python_install
+	rm "${D}"$(python_get_sitedir)/scikits/__init__.py || die
+}
+
+python_install_all() {
+	use doc && HTMLDOCS=( "${WORKDIR}/html" )
+	distutils-r1_python_install_all
+}
diff --git a/sci-libs/ssm/Manifest b/sci-libs/ssm/Manifest
deleted file mode 100644
index fbe82fcd4fbc..000000000000
--- a/sci-libs/ssm/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST ssm-1.4.tar.gz 424785 BLAKE2B 3f28bc70aa431b4288467a0c1cc09868a4e19d28e396540799990ef8cdfec0054db2d5304f741a311052fe62738ac49e9e7ef5db6d98b66f7774fb8068906f99 SHA512 93b55c544eaf651544bb664b65701c081aa6e77707aaf680c1489b129f89598d9a9c348d2fae86cd6e7b3e97bfd26c3abe16220633da4b570c983dbceec8b15a
-EBUILD ssm-1.4.ebuild 575 BLAKE2B 3fcc47abe51a247f6cea53922e76f52fc72c688a2750609b1fa61e4b3ca31440c9dd3ccab3a9adda1d9d7666ffbddca653706c903353b8704f65aec22df1a948 SHA512 5f447c8751449830d09223aad5e3892da03b989058b5a8b6d2183360ca6c5005a2ce2606e6d6e9894e2f78091d5ad1ceef935bd3fe47ec02c519ab763a3f475a
-MISC metadata.xml 408 BLAKE2B d4f2c0f12c6462a24ce01d02439840478bfb32ea2e304221f67205e4be4cf8f2551cfcf97189d2cd80fa325d6892643eaabdd6cb7ade2565c47d41654c643b78 SHA512 2f93da2950c7ad7dcffc1652f67a4744e7507ae26e597f46b38e52587b9f71cfdb9961781b870c28b5ee81f91625381fa64117dfd31fb12652853096b3e55cc2
diff --git a/sci-libs/ssm/metadata.xml b/sci-libs/ssm/metadata.xml
deleted file mode 100644
index ba579239e43b..000000000000
--- a/sci-libs/ssm/metadata.xml
+++ /dev/null
@@ -1,14 +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@gentoo.org</email>
-    <name>Gentoo Science Project</name>
-  </maintainer>
-  <use>
-    <flag name="ccp4">Link superpose with libccp4</flag>
-  </use>
-  <upstream>
-    <remote-id type="launchpad">ssm</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-libs/ssm/ssm-1.4.ebuild b/sci-libs/ssm/ssm-1.4.ebuild
deleted file mode 100644
index abcd8885a76c..000000000000
--- a/sci-libs/ssm/ssm-1.4.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils
-
-DESCRIPTION="A macromolecular coordinate superposition library"
-HOMEPAGE="https://launchpad.net/ssm"
-SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz"
-
-LICENSE="GPL-3 LGPL-2.1"
-SLOT="0/2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+ccp4 static-libs"
-
-DEPEND="
-	sci-libs/mmdb:2
-	ccp4? ( sci-libs/libccp4 )"
-RDEPEND="${DEPEND}"
-
-src_configure() {
-	local myeconfargs=( $(use_enable ccp4) )
-	autotools-utils_src_configure
-}
diff --git a/sci-libs/tensorflow-estimator/Manifest b/sci-libs/tensorflow-estimator/Manifest
index 56111102db9b..0e002ff60ead 100644
--- a/sci-libs/tensorflow-estimator/Manifest
+++ b/sci-libs/tensorflow-estimator/Manifest
@@ -1,6 +1,6 @@
 AUX 0001-pip_package-modularize-build-script-to-allow-distros.patch 4250 BLAKE2B 79702d82e629e2159cbe33efe8dd91536d904536f4bbf3d4ad02186916a09786cde6ce29a63acaafe3169dbd7904448461f2b557f33218651351fd87d42ed613 SHA512 42bb57433f61b3a9b1a93c897202bacdf44a8277ea0e64257ac3b60c9b964a6441345c9b222fb26afb1d66a53323fe38c29811adfd6354032cb5d3f85dde0816
 DIST tensorflow-estimator-1.13.0.tar.gz 530871 BLAKE2B 4f208ed20e10fa68e06d21c9865cd07623e14362bdcff456bc9b412431c8f12f289c8a8f8ad89cb1f0ec98b1432844632d7e1097ea29d40bf6f67b90b4968f93 SHA512 e4be92b805776d2be5f391f737f1043b994f42721173c4d4a7dbf3fac9b00121cb072091a474bf71c7dcd952fc8b330cf9254c7a5ad9d096ba1cdc12ba12078b
-DIST tensorflow-estimator-1.14.0_rc1.tar.gz 670908 BLAKE2B 8ffcf2228fe4c4af1e834ab28368a1472df9d5de011ecc0a6e8623d60b293f1c07c73fa2eae7b743fd1d910b1cdc7813c46a66fd645d290fd9cf87f7654839aa SHA512 59d9505b01c8bb1f88ab310f341c8a96c3699676e0440b04ade76d66a3940c94b50a2f8ba1704873aae9c6dde0be3d734f0c8f3cf99901b17baa82704d784085
-EBUILD tensorflow-estimator-1.13.0.ebuild 1333 BLAKE2B 0087323052bd5de42be018b255f21d50c499a18aba79a8540e6490cd1a9173be9a08b257cfd2da2b0378c274331b9a51f9048891688f0115a300a997279e1c55 SHA512 7c10982a4f1f1a7943c2497f3831f5825836a8589bc74c52665e0862d386a73e71039c474ee1f78f4505b9c5af4bd72ef34f73bc5b58c758f04beef19be691c8
-EBUILD tensorflow-estimator-1.14.0_rc1.ebuild 1242 BLAKE2B 0dc0e5c67af5912051fb35124fb81016c23ce4f13f614fca11fdcd5a536e4975b76b95a13583a756349afff5e24c57473dd1d075f14b501fffad3c76c9976705 SHA512 69d492ed326750faae953f41eb607853050395b9736de3493beacbedeb8a6119bfc07aece8d5dbf4ab82c18a328dee9a74941604502c35e8287ce8ef415e0ee8
+DIST tensorflow-estimator-1.14.0.tar.gz 670750 BLAKE2B d24bba87131605f965be05cd76103e77c45c606af685f08d478cf4acaf2975aba6134bfe9ea51d1837297cf4ce5339bad761af6c00077193ccbae3f1bbcaa667 SHA512 65d21f4d275edc57feb0b36775f275d7b7adc1f5c2958b8269dcf61bed0189570adcb2eaf981e2ae4ba7e6ccec6d4d467384a267a6a29c325dc8126b1bdced5a
+EBUILD tensorflow-estimator-1.13.0.ebuild 1336 BLAKE2B 8cb7993e004e31435ee8878335696befd20dc7e90f9156dc2c17a3e3668bdd63c14891b4960ace13d1c2e1da66f3580c4634f75de69ef2095d0f6566bfacc5f5 SHA512 9d7b99123345ae85268b8676d91aa34f62ba4e2fd8131630f26b1dc3bb969cbd40e37c2ac054800f48fd1df02a77cfd724d50bef9e787bbe1316225c9c484cc9
+EBUILD tensorflow-estimator-1.14.0.ebuild 1245 BLAKE2B 4d7a31587186446be9d72524801d95c193db6561558403c0c5b5b8e694b84955792c96e6fc81b2bbba3df2db88f1ffd954d2a028692375549639bb8bfcfd8eb3 SHA512 42259cdced6aabddc930dc07121e9b5f87639e4fb3fb9223c8123dc02f508f5393345873ee11f866b3c859466fdcec2b402d2f303fb8fb4c643edb2c93275e6f
 MISC metadata.xml 580 BLAKE2B fb81098968d0fdf34a3f28dabee76df16be5393cb9ea79ee4fa670af985ef3f70bb83f14be84a0cc0e564e6626007c2977851f8299460b483f88325be155f4cc SHA512 6aef6523502a3bcf0b2ca59cf7480b92032b53020cccfa715203e5a48c960ecc92c94fa75f98a234da2d51662d43e0c1a85a1537f3ab67287cdb8183476a0efa
diff --git a/sci-libs/tensorflow-estimator/tensorflow-estimator-1.13.0.ebuild b/sci-libs/tensorflow-estimator/tensorflow-estimator-1.13.0.ebuild
index a5aede9bca28..07240632c5d9 100644
--- a/sci-libs/tensorflow-estimator/tensorflow-estimator-1.13.0.ebuild
+++ b/sci-libs/tensorflow-estimator/tensorflow-estimator-1.13.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Jason Zaman
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
diff --git a/sci-libs/tensorflow-estimator/tensorflow-estimator-1.14.0_rc1.ebuild b/sci-libs/tensorflow-estimator/tensorflow-estimator-1.14.0.ebuild
index d72026f052a2..4d6fbccd5074 100644
--- a/sci-libs/tensorflow-estimator/tensorflow-estimator-1.14.0_rc1.ebuild
+++ b/sci-libs/tensorflow-estimator/tensorflow-estimator-1.14.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Jason Zaman
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
diff --git a/sci-libs/tensorflow/Manifest b/sci-libs/tensorflow/Manifest
index 798f74aad804..83b067841fbe 100644
--- a/sci-libs/tensorflow/Manifest
+++ b/sci-libs/tensorflow/Manifest
@@ -1,4 +1,8 @@
 AUX tensorflow-1.14.0-0001-systemlibs-unbundle-enum34.patch 1958 BLAKE2B 830ddb5ee1ffe84459879fb5cd9acdbc87d862d780cfa1e6e85f49bf46c2ca705fe25f915d8c8243bb5fae558d05b204268332bad471433b437cf15bb12a173b SHA512 73d6a225f77204daa36696d688721f8f58696dfc7cbb72a79dd2c5dbb938f26e3bd003e22a1755f0d31d2cfc8a532152c6a262cf2f1c7f49706d491021b9066f
+AUX tensorflow-1.14.0-0002-install_headers-fix-paths-of-generated-headers.patch 1059 BLAKE2B ca06d4a07ff5a55399ab84325f7c51fe2abbe969fe2a096bc50b9373b490a52c4a189559d3b92d5f95195c3895ef9bf184b4a876032122781a5edae590806b0d SHA512 c60e16fbcc104d18971cbd097d452ad9e688330a996705532ac2f2c4364bdfbc10641b3fbf42c65079b419bc469610398785f331b4ef1376c3c2f7424c7c51c0
+AUX tensorflow-1.14.0-0003-systemlibs-jsoncpp-update-header-symlinks-for-jsoncp.patch 792 BLAKE2B c51b247be2d9bc2f124c0dd07d48fa7f3685cda148b050328e45521b2eb6da555e59f89ff554057db777ec435daa58ddb786e9ef44779fcaed5cf29f76686031 SHA512 d5266f79efa9402de4cf53803d532711af8db8b40d2964ef1a6b27f6e7ac3ac95e112590c39fbd84873d9459367485e10b351f45e703ab7e095661683e5ba341
+AUX tensorflow-1.14.0-0004-pkgconfig-generate-tensorflow_cc-pkg-config-entry.patch 1420 BLAKE2B 528c26f6be43a3ecec5acbc932916a286086775deca66ccf4e87a46b63d49b0c67b787a0823ee5f5cf222e4c4e06a9b8e6d09048353c6b475efe8af945a0522d SHA512 de764fcacb035c2ffb7b02c583c5cee9297fb53ad3203bbaffbfb3cc63d3d48674c7a99a624cc77e1bf58cd70026fea5de8404a04ba6e7a0c61f2f108ddf639d
+AUX tensorflow-1.14.0-0005-gen_git_source-builtins-does-not-exist-in-python2.patch 865 BLAKE2B 3adb6688478452b6e8e093128a7ed50db5d10efa31192f0fa41d5adca1dc44004ec388171fc09a1a0579e116dd5816eabaec6431961e93719705b0186853b15b SHA512 ada76bfc06c56b19f1f2b7e88979d2dfea3bcac9a91a79e4d0dacaad3bdbf0ff4f450670ff26e49cdd6bf39062c7dfdfb17a61bc92c35a7bc748a42bedec23e0
 DIST ARM_NEON_2_x86_SSE-1200fe90bb174a6224a525ee60148671a786a71f.tar.gz 100612 BLAKE2B 84f81072d3298dde613b4c1ebabf852c67e04b5882a4ca0ed6f218b42e8fa3ea9598140b0c0009e8d6b62d08902622a6d57ee005ec3ad8a808c9fb21aa53430c SHA512 03a289d8099a5c4a5298cba8f516d2edb41220935d8db750970113ca7513372c78241c2c948d0ffcd60e84686e50ba1d7fd0b46efea6881dd320435eca92a7b9
 DIST abseil-cpp-389ec3f906f018661a5308458d623d01f96d7b23.tar.gz 1180190 BLAKE2B beec1338bf8cfa99d0de3bdb1631da5385317e68bf87f5da154ceab9455af7221f140838e41f4087d7d0064c22f93dce5860c484a8e4026b46efa103a52db307 SHA512 20d2cc8d23eb729607692d861049dccbd6b4af56fc4ed7733492348e3fe879d7acc6316f0d6e1c683f98188f028d460a40cab35667856cf334aa5f00fc830911
 DIST abseil-cpp-daf381e8535a1f1f1b8a75966a74e7cca63dee89.tar.gz 1275955 BLAKE2B eb6e0f9d55458a4ae6e8b86be89add9b0cc44d1ff5a11f6fa1ec93e2f46885c8ff87b8c1e674e1ba5ac13556ed303963864057f0e258fce41fa753d891846996 SHA512 56a827296e2948b90922766369f2040e04abd03320375240ad32fcc2925cdd1ffea312edcef1009a0c8abd79f521a61e433b7651dd4c2721d2b1ad13f48256de
@@ -25,6 +29,6 @@ DIST tensorflow-1.13.1.tar.gz 31614228 BLAKE2B 3e78309744747afd5a0929eebccb414ef
 DIST tensorflow-1.14.0-python-license.rst.txt 45132 BLAKE2B 8a8ace4b64fd9eda1932272704dd4fea002d2562cd9c2c94470d3ff5de58bb171ff849d3f998ea90cd779d1084d39af1267aca8400b74b701205d2e76e6a2628 SHA512 c79c42f4ceecf33c8f8778ca17b53595b75d5d0bdf30b11058cf01dd70a6351f530ca9dd846460aba14edc1d5876f7bf6fa0f9f49f7915590b0f54d267ce3856
 DIST tensorflow-1.14.0.tar.gz 41335204 BLAKE2B d91d84c5d86c838cc659c45e28cf3c8a9ec9a02f5854a1826680806dae41cdd00ea49a6d2c04f2019b3400c6e267c6ca6f3b28e43b244569dca174ff7f2c59d6 SHA512 ac9ea5a2d1c761aaafbdc335259e29c128127b8d069ec5b206067935180490aa95e93c7e13de57f7f54ce4ba4f34a822face22b4a028f60185edb380e5cd4787
 DIST tensorflow-python-license.rst.txt 45132 BLAKE2B 770ddd87adc745a021daac01a284131825a33f176002a28b20a2251246183bf7ab4686305620678285e4a216a37f01b3ad953fe7864fa79611cccde156d69ab6 SHA512 2d5a3783ec340f24797e89c78007ee95ab753eb5ee8198c739544f9e1159895f7abe816d6b3c66620f8d7b64641d2a7f44ff0a5b4f2f941928f4733157c7995e
-EBUILD tensorflow-1.13.1.ebuild 10008 BLAKE2B a960ab449ad040ed5974ff80bc69f8d4648b55d98668cfcc8c65920b5ccc85bb906fb565fd06345a49e87815ddc0c13f59d04ca9f92f11b3bfd035e09bf88a28 SHA512 15beb4bfa5b4d49d664278ef88d5411f1b9d9253ab061caab095e343f974f7f4181598e88402a4584ffcdcf4d3f7c5636fc8d0de42aac311939fab1821d9e403
-EBUILD tensorflow-1.14.0.ebuild 10280 BLAKE2B 101ea18384f252c67b56d307c296a81a108cde6443dd83c20c399cad3a531cc0ba29c9c24057c754ffa1ff1ae28c5b6c6359c75b723ff62f851b6ba17863ac1d SHA512 daabe065895473cdd3977b2b41264228641f3c1fd6f3d45b22eb5d568d64ed7e7cf591d1e46f4cde636d03942fd13ff3b91695d48e8e25af3188b4dfafe87ed7
+EBUILD tensorflow-1.13.1.ebuild 10011 BLAKE2B 8b151edc20f6b80ccaac0e6c99f2414b484eb23ec2e1706736e90f355c8e5d960d8bb5beb00adf54238243e192832f6765d0edab1a6a14d18b888a34d2be343b SHA512 d3aefaeca59c6ee8ad58c0cf0830dc1334d0c0d12d602bbb6fea3f6030d002e918414fb0a5eb900a0ad199012c454d6dba8bda889b218fe6da4daa1e55a6d95e
+EBUILD tensorflow-1.14.0-r1.ebuild 10688 BLAKE2B 272c017503db3301e972242af8e0b66aaf7e81befe37ece9dc39696dec838b139d873c79e6db4f19fdf91f1af968475848bd4176155fcf5df403b6ebea108b79 SHA512 015fc7b2a664d7b8617da22139e8a87cca5bb6f876ded8fdc441ad68c5456ab9d7c7d5ca624031bec0d38e35e39fee69db8e5a38fdfe9ff23cdb8377fd9df66a
 MISC metadata.xml 512 BLAKE2B 39a7fc6dc76945448a9f0e8e9d79866f364d0df5036500a2ab981b6ab6f1170ef8a15e29e3a5a3d39edc0dc441985feaa45ce8069fdfb815ca1419721ba9d870 SHA512 a6dc893a523fa7dab319173914e8602434b8247aee2af6a4adbde29be440097901b0e40193e5592f3849340414a4debce1218ae3895c2c6e7d5af171c463c82b
diff --git a/sci-libs/tensorflow/files/tensorflow-1.14.0-0002-install_headers-fix-paths-of-generated-headers.patch b/sci-libs/tensorflow/files/tensorflow-1.14.0-0002-install_headers-fix-paths-of-generated-headers.patch
new file mode 100644
index 000000000000..566f28743764
--- /dev/null
+++ b/sci-libs/tensorflow/files/tensorflow-1.14.0-0002-install_headers-fix-paths-of-generated-headers.patch
@@ -0,0 +1,38 @@
+From 5176e1feb22fac2f9d4ca9d8ad261ef6893d3c76 Mon Sep 17 00:00:00 2001
+From: Jason Zaman <jason@perfinion.com>
+Date: Mon, 29 Jul 2019 01:17:06 +0800
+Subject: [PATCH 2/3] install_headers: fix paths of generated headers
+
+Signed-off-by: Jason Zaman <jason@perfinion.com>
+---
+ tensorflow/BUILD | 7 +++++--
+ 1 file changed, 5 insertions(+), 2 deletions(-)
+
+diff --git a/tensorflow/BUILD b/tensorflow/BUILD
+index a04ddf9f8a..1e0cc9207b 100644
+--- a/tensorflow/BUILD
++++ b/tensorflow/BUILD
+@@ -703,8 +703,8 @@ genrule(
+     mkdir $@
+     for f in $(SRCS); do
+       d="$${f%/*}"
+-      d="$${d#bazel-out*genfiles/}"
+-      d="$${d#*external/eigen_archive/}"
++      d="$${d#bazel-out/*/genfiles/}"
++      d="$${d#bazel-out/*/bin/}"
+ 
+       if [[ $${d} == *local_config_* ]]; then
+         continue
+@@ -716,6 +716,9 @@ genrule(
+         if [[ $${TF_SYSTEM_LIBS:-} == *$${extname}* ]]; then
+           continue
+         fi
++
++        d="$${d#*external/farmhash_archive/src}"
++        d="$${d#*external/$${extname}/}"
+       fi
+ 
+       mkdir -p "$@/$${d}"
+-- 
+2.21.0
+
diff --git a/sci-libs/tensorflow/files/tensorflow-1.14.0-0003-systemlibs-jsoncpp-update-header-symlinks-for-jsoncp.patch b/sci-libs/tensorflow/files/tensorflow-1.14.0-0003-systemlibs-jsoncpp-update-header-symlinks-for-jsoncp.patch
new file mode 100644
index 000000000000..3ccdf4933732
--- /dev/null
+++ b/sci-libs/tensorflow/files/tensorflow-1.14.0-0003-systemlibs-jsoncpp-update-header-symlinks-for-jsoncp.patch
@@ -0,0 +1,27 @@
+From 22275f7dbfa2d483ed4778427b137e83144bac3d Mon Sep 17 00:00:00 2001
+From: Jason Zaman <jason@perfinion.com>
+Date: Fri, 2 Aug 2019 20:06:33 +0800
+Subject: [PATCH 3/3] systemlibs: jsoncpp: update header symlinks for jsoncpp
+ 1.9
+
+Signed-off-by: Jason Zaman <jason@perfinion.com>
+---
+ third_party/systemlibs/jsoncpp.BUILD | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/third_party/systemlibs/jsoncpp.BUILD b/third_party/systemlibs/jsoncpp.BUILD
+index 526fd0c418..7d54f9289b 100644
+--- a/third_party/systemlibs/jsoncpp.BUILD
++++ b/third_party/systemlibs/jsoncpp.BUILD
+@@ -6,6 +6,8 @@ filegroup(
+ )
+ 
+ HEADERS = [
++    "include/json/allocator.h",
++    "include/json/assertions.h",
+     "include/json/autolink.h",
+     "include/json/config.h",
+     "include/json/features.h",
+-- 
+2.21.0
+
diff --git a/sci-libs/tensorflow/files/tensorflow-1.14.0-0004-pkgconfig-generate-tensorflow_cc-pkg-config-entry.patch b/sci-libs/tensorflow/files/tensorflow-1.14.0-0004-pkgconfig-generate-tensorflow_cc-pkg-config-entry.patch
new file mode 100644
index 000000000000..5e65c413e776
--- /dev/null
+++ b/sci-libs/tensorflow/files/tensorflow-1.14.0-0004-pkgconfig-generate-tensorflow_cc-pkg-config-entry.patch
@@ -0,0 +1,46 @@
+From a8144189b257d515f1eb72a4b50098e9f4abd4ea Mon Sep 17 00:00:00 2001
+From: Jason Zaman <jason@perfinion.com>
+Date: Fri, 2 Aug 2019 22:21:25 +0800
+Subject: [PATCH 4/5] pkgconfig: generate tensorflow_cc pkg-config entry
+
+Signed-off-by: Jason Zaman <jason@perfinion.com>
+---
+ tensorflow/c/generate-pc.sh | 18 ++++++++++++++++--
+ 1 file changed, 16 insertions(+), 2 deletions(-)
+
+diff --git a/tensorflow/c/generate-pc.sh b/tensorflow/c/generate-pc.sh
+index 7184ad68fb..a4d51a1b3b 100755
+--- a/tensorflow/c/generate-pc.sh
++++ b/tensorflow/c/generate-pc.sh
+@@ -63,12 +63,26 @@ cat << EOF > tensorflow.pc
+ prefix=${TF_PREFIX}
+ exec_prefix=\${prefix}
+ libdir=\${exec_prefix}/${LIBDIR}
+-includedir=\${prefix}/include
++includedir=\${prefix}/include/tensorflow
+ 
+ Name: TensorFlow
+ Version: ${TF_VERSION}
+ Description: Library for computation using data flow graphs for scalable machine learning
+ Requires:
+-Libs: -L\${libdir} -ltensorflow
++Libs: -L\${libdir} -ltensorflow -ltensorflow_framework
++Cflags: -I\${includedir}
++EOF
++
++cat << EOF > tensorflow_cc.pc
++prefix=${TF_PREFIX}
++exec_prefix=\${prefix}
++libdir=\${exec_prefix}/${LIBDIR}
++includedir=\${prefix}/include/tensorflow
++
++Name: TensorFlow
++Version: ${TF_VERSION}
++Description: Library for computation using data flow graphs for scalable machine learning
++Requires:
++Libs: -L\${libdir} -ltensorflow_cc -ltensorflow_framework
+ Cflags: -I\${includedir}
+ EOF
+-- 
+2.21.0
+
diff --git a/sci-libs/tensorflow/files/tensorflow-1.14.0-0005-gen_git_source-builtins-does-not-exist-in-python2.patch b/sci-libs/tensorflow/files/tensorflow-1.14.0-0005-gen_git_source-builtins-does-not-exist-in-python2.patch
new file mode 100644
index 000000000000..fc2e1fe92cb4
--- /dev/null
+++ b/sci-libs/tensorflow/files/tensorflow-1.14.0-0005-gen_git_source-builtins-does-not-exist-in-python2.patch
@@ -0,0 +1,25 @@
+From bdbe7a572ed248bf8e53df200ffa5e66bf77b16f Mon Sep 17 00:00:00 2001
+From: Jason Zaman <jason@perfinion.com>
+Date: Fri, 2 Aug 2019 22:22:53 +0800
+Subject: [PATCH 5/5] gen_git_source: builtins does not exist in python2
+
+Signed-off-by: Jason Zaman <jason@perfinion.com>
+---
+ tensorflow/tools/git/gen_git_source.py | 1 -
+ 1 file changed, 1 deletion(-)
+
+diff --git a/tensorflow/tools/git/gen_git_source.py b/tensorflow/tools/git/gen_git_source.py
+index 6cefd3900b..4d52c1fccf 100755
+--- a/tensorflow/tools/git/gen_git_source.py
++++ b/tensorflow/tools/git/gen_git_source.py
+@@ -26,7 +26,6 @@ NOTE: this script is only used in opensource.
+ from __future__ import absolute_import
+ from __future__ import division
+ from __future__ import print_function
+-from builtins import bytes  # pylint: disable=redefined-builtin
+ import argparse
+ import json
+ import os
+-- 
+2.21.0
+
diff --git a/sci-libs/tensorflow/tensorflow-1.13.1.ebuild b/sci-libs/tensorflow/tensorflow-1.13.1.ebuild
index 319886a15f19..a0ff5d05f137 100644
--- a/sci-libs/tensorflow/tensorflow-1.13.1.ebuild
+++ b/sci-libs/tensorflow/tensorflow-1.13.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Jason Zaman
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
diff --git a/sci-libs/tensorflow/tensorflow-1.14.0.ebuild b/sci-libs/tensorflow/tensorflow-1.14.0-r1.ebuild
index 934280200207..8982469fb675 100644
--- a/sci-libs/tensorflow/tensorflow-1.14.0.ebuild
+++ b/sci-libs/tensorflow/tensorflow-1.14.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Jason Zaman
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -53,7 +53,7 @@ RDEPEND="
 	dev-db/lmdb
 	dev-db/sqlite
 	dev-libs/icu
-	>=dev-libs/jsoncpp-1.8.4
+	>=dev-libs/jsoncpp-1.9
 	dev-libs/libpcre
 	dev-libs/nsync
 	dev-libs/openssl:0=
@@ -62,7 +62,7 @@ RDEPEND="
 	media-libs/giflib
 	media-libs/libjpeg-turbo
 	media-libs/libpng:0
-	>=net-libs/grpc-1.16.0
+	>=net-libs/grpc-1.22.0
 	net-misc/curl
 	sys-libs/zlib
 	>=sys-apps/hwloc-2
@@ -82,9 +82,9 @@ RDEPEND="
 		>=dev-python/protobuf-python-3.6.0[${PYTHON_USEDEP}]
 		dev-python/six[${PYTHON_USEDEP}]
 		dev-python/termcolor[${PYTHON_USEDEP}]
-		dev-python/grpcio[${PYTHON_USEDEP}]
+		>=dev-python/grpcio-1.22.0[${PYTHON_USEDEP}]
 		>=dev-python/wrapt-1.11.1[${PYTHON_USEDEP}]
-		>=net-libs/google-cloud-cpp-0.9.0
+		>=net-libs/google-cloud-cpp-0.10.0
 		>=sci-libs/keras-applications-1.0.6[${PYTHON_USEDEP}]
 		>=sci-libs/keras-preprocessing-1.0.5[${PYTHON_USEDEP}]
 		>=sci-visualization/tensorboard-1.13.0[${PYTHON_USEDEP}]
@@ -112,7 +112,7 @@ BDEPEND="
 	)
 	!python? ( dev-lang/python )
 	python? (
-		dev-python/grpcio-tools
+		>=dev-python/grpcio-tools-1.22.0
 	)"
 REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
 
@@ -120,6 +120,10 @@ S="${WORKDIR}/${MY_P}"
 
 PATCHES=(
 	"${FILESDIR}/tensorflow-1.14.0-0001-systemlibs-unbundle-enum34.patch"
+	"${FILESDIR}/tensorflow-1.14.0-0002-install_headers-fix-paths-of-generated-headers.patch"
+	"${FILESDIR}/tensorflow-1.14.0-0003-systemlibs-jsoncpp-update-header-symlinks-for-jsoncp.patch"
+	"${FILESDIR}/tensorflow-1.14.0-0004-pkgconfig-generate-tensorflow_cc-pkg-config-entry.patch"
+	"${FILESDIR}/tensorflow-1.14.0-0005-gen_git_source-builtins-does-not-exist-in-python2.patch"
 )
 DOCS=( AUTHORS CONTRIBUTING.md ISSUE_TEMPLATE.md README.md RELEASE.md )
 CHECKREQS_MEMORY="5G"
@@ -328,7 +332,7 @@ src_install() {
 	# Generate pkg-config file
 	${PN}/c/generate-pc.sh --prefix="${EPREFIX}"/usr --libdir=$(get_libdir) --version=${MY_PV} || die
 	insinto /usr/$(get_libdir)/pkgconfig
-	doins ${PN}.pc
+	doins ${PN}.pc ${PN}_cc.pc
 
 	for l in libtensorflow{,_framework,_cc}.so; do
 		dolib.so bazel-bin/tensorflow/${l}
diff --git a/sci-libs/trilinos/Manifest b/sci-libs/trilinos/Manifest
new file mode 100644
index 000000000000..6bfeaa2d8a53
--- /dev/null
+++ b/sci-libs/trilinos/Manifest
@@ -0,0 +1,4 @@
+DIST trilinos-12.14.1-patches-r0.tar.xz 6448 BLAKE2B f852a4612c400ddfb6dcecb476e0b9b2cd0f38ac9cd74fd09fc1f99ccb2588a4703f8c8514689c81d23aa218aff3cdcbe9b5205becea8936723d6e339705d54d SHA512 206bd08f0a5b7f7107e60c9e9c1a15fa7e74916bacb5399cccdd936b426768834ff24424ea77e8d1706afa98d88bb5a098b3b0203039024a3b5f5388c4a9735b
+DIST trilinos-12.14.1.tar.gz 129036436 BLAKE2B e7401df2ff8408a7af4a8e90d93b1929df65228c4f5cf3c754d20ebdfa8f3835800f540e87c1198e0baf2fefe0920618ae497f59373720754ab0c9dc1da93136 SHA512 dfff0e0582cb5ad12614dd53e9635572c8d1ee86d96f432f5a6e046af63edb13f6bfa3037204ab89fbb0d27e9be9bd9661d47efb41ab2a6e421bca5eba6b6a87
+EBUILD trilinos-12.14.1.ebuild 6148 BLAKE2B d8ef14be03e34742e59292426af03336fb3997f3e50b02e0d6a9d6114a5d67c7d3530e93f44e645e247f395343b1a3045383714f8408a41a0434cf125f6006c5 SHA512 b96f197cfd8435366940237eba40dd8cd48e950e6c814ebcb18b6c04125f374d4475cecaea3c25a2ec60b3685e3db2d52ac025a9f6031111c67039cfa00be2d8
+MISC metadata.xml 2778 BLAKE2B 45cb2a647a1730c9b6b21271364b5f4acaf145f6ae33db356d0b9be7584705c29a645d3f96abfe0a9b87540ae55ab586ec202191776f4472b66291c274b9f24b SHA512 c58e98197353efe1c6fef038dd53d4a938e85aa66fc53f00cab0133d8ee89c629eead55c270c88583778b193f0a85b498c7235fc3f1e8f45a1abfff2d5f0cbec
diff --git a/sci-libs/trilinos/metadata.xml b/sci-libs/trilinos/metadata.xml
new file mode 100644
index 000000000000..8cbeddb082eb
--- /dev/null
+++ b/sci-libs/trilinos/metadata.xml
@@ -0,0 +1,47 @@
+<?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@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription lang="en">
+The Trilinos Project is an effort to develop algorithms and enabling
+technologies within an object-oriented software framework for the solution
+of large-scale, complex multi-physics engineering and scientific problems.
+</longdescription>
+	<use>
+		<flag name="adolc">Add support for adolc (<pkg>sci-libs/adolc</pkg>)</flag>
+		<flag name="arprec">Add support for arprec (<pkg>sci-libs/arprec</pkg>)</flag>
+		<flag name="boost">Add support for boost (<pkg>dev-libs/boost</pkg>)</flag>
+		<flag name="clp">Add support for clp (<pkg>sci-libs/coinor-clp</pkg>)</flag>
+		<flag name="cuda">Add support for cuda (<pkg>dev-util/nvidia-cuda-toolkit</pkg>)</flag>
+		<flag name="eigen">Add support for eigen (<pkg>dev-cpp/eigen</pkg>)</flag>
+		<flag name="glpk">Add support for glpk (<pkg>sci-mathematics/glpk</pkg>)</flag>
+		<flag name="gtest">Add support for gtest (<pkg>dev-cpp/gtest</pkg>)</flag>
+		<flag name="hwloc">Add support for hwloc (<pkg>sys-apps/hwloc</pkg>)</flag>
+		<flag name="hdf5">Add support for hdf5 (<pkg>sci-libs/hdf5</pkg>)</flag>
+		<flag name="hypre">Add support for hypre (<pkg>sci-libs/hypre</pkg>)</flag>
+		<flag name="matio">Add support for matio (<pkg>sci-libs/matio</pkg>)</flag>
+		<flag name="metis">
+Add support for metis (<pkg>sci-libs/metis</pkg> or <pkg>sci-libs/parmetis</pkg>)
+</flag>
+		<flag name="mkl">Add support for mkl (<pkg>sci-libs/mkl</pkg>)</flag>
+		<flag name="mumps">Add support for mumps (<pkg>sci-libs/mumps</pkg>)</flag>
+		<flag name="netcdf">Add support for netcdf (<pkg>sci-libs/netcdf</pkg>)</flag>
+		<flag name="petsc">Add support for petsc (<pkg>sci-mathematics/petsc</pkg>)</flag>
+		<flag name="qd">Add support for qd (<pkg>sci-libs/qd</pkg>)</flag>
+		<flag name="scalapack">Add support for scalapack (<pkg>sci-libs/scalapack</pkg>)</flag>
+		<flag name="scotch">Add support for scotch (<pkg>sci-libs/scotch</pkg>)</flag>
+		<flag name="sparse">Add support for sparse matrix solvers (<pkg>sci-libs/umfpack</pkg>)</flag>
+		<flag name="superlu">Add support for superlu (<pkg>sci-libs/superlu</pkg>)</flag>
+		<flag name="taucs">Add support for taucs (<pkg>sci-libs/taucs</pkg>)</flag>
+		<flag name="tbb">Add support for threading building blocks library (<pkg>dev-cpp/tbb</pkg>)</flag>
+		<flag name="tvmet">Add support for tvmet (<pkg>dev-libs/tvmet</pkg>)</flag>
+		<flag name="yaml">Add support for yaml (<pkg>dev-cpp/yaml-cpp</pkg>)</flag>
+	</use>
+</pkgmetadata>
diff --git a/sci-libs/trilinos/trilinos-12.14.1.ebuild b/sci-libs/trilinos/trilinos-12.14.1.ebuild
new file mode 100644
index 000000000000..affe878ba6ec
--- /dev/null
+++ b/sci-libs/trilinos/trilinos-12.14.1.ebuild
@@ -0,0 +1,211 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+CMAKE_MAKEFILE_GENERATOR=emake
+
+inherit cmake-utils toolchain-funcs multilib toolchain-funcs
+
+DESCRIPTION="Scientific library collection for large scale problems"
+HOMEPAGE="http://trilinos.sandia.gov/"
+MY_PV="${PV//\./-}"
+PATCHSET="r0"
+SRC_URI="https://github.com/${PN}/Trilinos/archive/${PN}-release-${MY_PV}.tar.gz -> ${P}.tar.gz
+	https://dev.gentoo.org/~tamiko/distfiles/${P}-patches-${PATCHSET}.tar.xz"
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+LICENSE="BSD LGPL-2.1"
+SLOT="0"
+
+IUSE="
+	adolc arprec boost clp cuda eigen glpk gtest hdf5 hwloc hypre
+	matio metis mkl mumps netcdf petsc qd scalapack scotch sparse
+	superlu taucs tbb test threads tvmet yaml zlib X
+"
+
+# TODO: fix export cmake function for tests
+RESTRICT="test"
+
+RDEPEND="
+	sys-libs/binutils-libs
+	virtual/blas
+	virtual/lapack
+	virtual/mpi
+	adolc? ( sci-libs/adolc )
+	arprec? ( sci-libs/arprec )
+	boost? ( dev-libs/boost )
+	clp? ( sci-libs/coinor-clp )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-3.2 )
+	eigen? ( dev-cpp/eigen:3 )
+	glpk? ( sci-mathematics/glpk )
+	gtest? ( dev-cpp/gtest )
+	hdf5? ( sci-libs/hdf5[mpi] )
+	hypre? ( sci-libs/hypre )
+	hwloc? ( sys-apps/hwloc )
+	matio? ( sci-libs/matio )
+	mkl? ( sci-libs/mkl )
+	metis? ( || ( sci-libs/parmetis sci-libs/metis ) )
+	mumps? ( sci-libs/mumps )
+	netcdf? ( sci-libs/netcdf )
+	petsc? ( sci-mathematics/petsc )
+	qd? ( sci-libs/qd )
+	scalapack? ( sci-libs/scalapack )
+	scotch? ( sci-libs/scotch )
+	sparse? ( sci-libs/cxsparse sci-libs/umfpack )
+	superlu? ( sci-libs/superlu )
+	taucs? ( sci-libs/taucs )
+	tbb? ( dev-cpp/tbb )
+	tvmet? ( dev-libs/tvmet )
+	yaml? ( dev-cpp/yaml-cpp )
+	zlib? ( sys-libs/zlib )
+	X? ( x11-libs/libX11 )"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/Trilinos-${PN}-release-${MY_PV}"
+
+PATCHES=(
+	"${WORKDIR}"/patches
+)
+
+trilinos_conf() {
+	local dirs libs d
+	for d in $($(tc-getPKG_CONFIG) --libs-only-L $1); do
+		dirs="${dirs};${d:2}"
+	done
+	[[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_DIRS=${dirs:1}" )
+	for d in $($(tc-getPKG_CONFIG) --libs-only-l $1); do
+		libs="${libs};${d:2}"
+	done
+	[[ -n ${libs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_NAMES=${libs:1}" )
+	dirs=""
+	for d in $($(tc-getPKG_CONFIG) --cflags-only-I $1); do
+		dirs="${dirs};${d:2}"
+	done
+	[[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_INCLUDE_DIRS=${dirs:1}" )
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_SHARED_LIBS=ON
+		-DCMAKE_INSTALL_PREFIX="${EPREFIX}"
+		-DCMAKE_SKIP_INSTALL_RPATH=ON
+		-DTrilinos_INSTALL_CONFIG_DIR="${EPREFIX}/usr/$(get_libdir)/cmake"
+		-DTrilinos_INSTALL_INCLUDE_DIR="${EPREFIX}/usr/include/trilinos"
+		-DTrilinos_INSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)/trilinos"
+		-DTrilinos_ENABLE_ALL_PACKAGES=ON
+		-DTrilinos_ENABLE_PyTrilinos=OFF
+		-DTrilinos_ENABLE_SEACASChaco=OFF
+		-DTrilinos_ENABLE_SEACASExodiff="$(usex netcdf)"
+		-DTrilinos_ENABLE_SEACASExodus="$(usex netcdf)"
+		-DTrilinos_ENABLE_TESTS="$(usex test)"
+		-DZoltan2_ENABLE_Experimental=ON
+		-DTPL_ENABLE_BinUtils=ON
+		-DTPL_ENABLE_BLAS=ON
+		-DTPL_ENABLE_LAPACK=ON
+		-DTPL_ENABLE_MPI=ON
+		-DTPL_ENABLE_ADOLC="$(usex adolc)"
+		-DTPL_ENABLE_AMD="$(usex sparse)"
+		-DTPL_ENABLE_ARPREC="$(usex arprec)"
+		-DTPL_ENABLE_BLACS="$(usex scalapack)"
+		-DTPL_ENABLE_BoostLib="$(usex boost)"
+		-DTPL_ENABLE_Boost="$(usex boost)"
+		-DTPL_ENABLE_Clp="$(usex clp)"
+		-DTPL_ENABLE_CSparse="$(usex sparse)"
+		-DTPL_ENABLE_CUDA="$(usex cuda)"
+		-DTPL_ENABLE_CUSPARSE="$(usex cuda)"
+		-DTPL_ENABLE_Eigen="$(usex eigen)"
+		-DTPL_ENABLE_GLPK="$(usex glpk)"
+		-DTPL_ENABLE_gtest="$(usex gtest)"
+		-DTPL_ENABLE_HDF5="$(usex hdf5)"
+		-DTPL_ENABLE_HWLOC="$(usex hwloc)"
+		-DTPL_ENABLE_HYPRE="$(usex hypre)"
+		-DTPL_ENABLE_Matio="$(usex matio)"
+		-DTPL_ENABLE_METIS="$(usex metis)"
+		-DTPL_ENABLE_MKL="$(usex mkl)"
+		-DTPL_ENABLE_MUMPS="$(usex mumps)"
+		-DTPL_ENABLE_Netcdf="$(usex netcdf)"
+		-DTPL_ENABLE_PARDISO_MKL="$(usex mkl)"
+		-DTPL_ENABLE_PETSC="$(usex petsc)"
+		-DTPL_ENABLE_Pthread="$(usex threads)"
+		-DTPL_ENABLE_QD="$(usex qd)"
+		-DTPL_ENABLE_SCALAPACK="$(usex scalapack)"
+		-DTPL_ENABLE_Scotch="$(usex scotch)"
+		-DTPL_ENABLE_SuperLU="$(usex superlu)"
+		-DTPL_ENABLE_TAUCS="$(usex taucs)"
+		-DTPL_ENABLE_TBB="$(usex tbb)"
+		-DTPL_ENABLE_Thrust="$(usex cuda)"
+		-DTPL_ENABLE_TVMET="$(usex tvmet)"
+		-DTPL_ENABLE_UMFPACK="$(usex sparse)"
+		-DTPL_ENABLE_X11="$(usex X)"
+		-DTPL_ENABLE_yaml-cpp="$(usex yaml)"
+		-DTPL_ENABLE_Zlib="$(usex zlib)"
+		-DML_ENABLE_SuperLU:BOOL=OFF
+	)
+
+	use eigen && \
+		mycmakeargs+=(
+		-DEigen_INCLUDE_DIRS="${EPREFIX}/usr/include/eigen3"
+	)
+	use hypre && \
+		mycmakeargs+=(
+		-DHYPRE_INCLUDE_DIRS="${EPREFIX}/usr/include/hypre"
+	)
+	use scotch && \
+		mycmakeargs+=(
+		-DScotch_INCLUDE_DIRS="${EPREFIX}/usr/include/scotch"
+	)
+
+	# cxsparse is a rewrite of csparse + extras
+	use sparse && \
+		mycmakeargs+=(
+		-DCSparse_LIBRARY_NAMES="cxsparse"
+	)
+
+	# mandatory blas and lapack
+	trilinos_conf blas BLAS
+	trilinos_conf lapack LAPACK
+	use superlu && trilinos_conf superlu SuperLU
+	use metis && trilinos_conf metis METIS
+
+	# blacs library is included in scalapack these days
+	if use scalapack; then
+		trilinos_conf scalapack SCALAPACK
+		mycmakeargs+=(
+			-DBLACS_LIBRARY_NAMES="scalapack"
+			-DBLACS_INCLUDE_DIRS="${EPREFIX}/usr/include/blacs"
+		)
+	fi
+
+	#
+	# Make sure we use the compiler wrappers in order to build trilinos.
+	#
+	export CC=mpicc CXX=mpicxx && tc-export CC CXX
+
+	#
+	# cmake-utils eclass patches the base directory CMakeLists.txt
+	# which does not work for complex Trilinos CMake modules
+	#
+	CMAKE_BUILD_TYPE=RELEASE cmake-utils_src_configure
+}
+
+src_install() {
+	cmake-utils_src_install
+
+	# Clean up the mess:
+	mv "${ED}"/bin "${ED}/usr/$(get_libdir)"/trilinos || die "mv failed"
+	if [ -f "${ED}"/lib/exodus.py ]; then
+		mv "${ED}"/lib/exodus.py "${ED}/usr/$(get_libdir)"/trilinos || die "mv failed"
+	fi
+
+	#
+	# register $(get_libdir)/trilinos in LDPATH so that the dynamic linker
+	# has a chance to pick up the libraries...
+	#
+	cat >> "${T}"/99trilinos <<- EOF
+	LDPATH="${EPREFIX}/usr/$(get_libdir)/trilinos"
+	PATH="${EPREFIX}/usr/$(get_libdir)/trilinos/bin"
+	EOF
+	doenvd "${T}"/99trilinos
+}