Revert "sci-biology/ncbi-tools++: drop py2 only version"

This reverts commit e8d4a8bc048182c0db34a3b995ac6a5c24fcdbb8.

Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>

3 files changed, 371 insertions, 1 deletions

diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest
index 5529c7d24..9dd3a53d8 100644
--- a/sci-biology/ncbi-tools++/Manifest
+++ b/sci-biology/ncbi-tools++/Manifest
@@ -1,2 +1,3 @@
+DIST ncbi_cxx--12_0_0.tar.gz 37925914 BLAKE2B 45490961293d8b3ace24c21602f4039041003f9b45d9f1763957c97ba1e55d6d336c33b6116262b2e774cc26b9366cc3d61bead0c0c7fbd4c461cad2921d80d4 SHA512 1a79f2d95960efde6263289814102499460ec235dad36337dd398d668665e44015e06e40fd0e66a8fb16f526d326949adcaadcb667debeba5d8570b1a92e30ed
 DIST ncbi_cxx--18_0_0.tar.gz 69807228 BLAKE2B 2221232e4ab38845708a9ec5601a94f1dd25c5dd6fff265bde3c3d64b9108eec00b8480a1888d2517881f25abe9127e547ba88528b95398480ecd09d133482a7 SHA512 70dd07597aafa3f48881640530bf2aeebcac6fa13843fada4c590ca101cb8fdfa1aabf240ed0177d371a1fc36c6d231d667125279096006cd1eba119ea9514f5
 DIST ncbi_cxx--22_0_0.tar.gz 56042079 BLAKE2B 8a358f9f09e2844c4007b99f4b1c5212e254f804237c26c2eb6620448755b88029d492ff124fff3fdb515189219400f3edaaa195eb4f0fa539ac7b122af4d7e1 SHA512 f6624b09aae1f27b30196b7036f3d962125f2c57e1369bef013b15c116828e2daf264e018a1c1e71fb57c55462d71c5df7580e429fcf9d736e02f89c71cbfbd0
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
new file mode 100644
index 000000000..ed50801fc
--- /dev/null
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -0,0 +1,369 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+
+MY_TAG="Jun_15_2010"
+MY_Y="${MY_TAG/*_/}"
+MY_PV="12_0_0"
+MY_P="ncbi_cxx--${MY_PV}"
+#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
+
+# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
+DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
+HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
+SRC_URI="
+	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
+#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
+
+# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
+# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
+LICENSE="public-domain"
+SLOT="0"
+IUSE="
+	debug static-libs static threads pch
+	test wxwidgets odbc
+	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+	sablotron sqlite tiff xerces xalan xml xpm xslt X"
+#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64"
+RESTRICT="!test? ( test )"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+# sys-libs/db should be compiled with USE=cxx
+# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
+DEPEND="
+	<sys-devel/gcc-10:=
+	!sci-biology/sra_sdk
+	app-arch/cpio
+	berkdb? ( sys-libs/db:4.3[cxx] )
+	boost? ( dev-libs/boost[tools] )
+	curl? ( net-misc/curl )
+	sqlite? ( dev-db/sqlite:3 )
+	mysql? ( virtual/mysql )
+	fltk? ( x11-libs/fltk )
+	opengl? ( virtual/opengl media-libs/glew:0= )
+	mesa? ( media-libs/mesa[osmesa] )
+	glut? ( media-libs/freeglut )
+	freetype? ( media-libs/freetype )
+	gnutls? ( net-libs/gnutls )
+	python? ( ${PYTHON_DEPS} )
+	cppunit? ( dev-util/cppunit )
+	icu? ( dev-libs/icu )
+	expat? ( dev-libs/expat )
+	sablotron? ( app-text/sablotron )
+	xml? ( dev-libs/libxml2 )
+	xslt? ( dev-libs/libxslt )
+	xerces? ( dev-libs/xerces-c )
+	xalan? ( dev-libs/xalan-c )
+	muparser? ( dev-cpp/muParser )
+	hdf5? ( sci-libs/hdf5[cxx] )
+	gif? ( media-libs/giflib )
+	jpeg? ( virtual/jpeg:0= )
+	png? ( media-libs/libpng:0= )
+	tiff? ( media-libs/tiff:0= )
+	xpm? ( x11-libs/libXpm )
+	dev-libs/lzo
+	app-arch/bzip2
+	dev-libs/libpcre"
+# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
+# Intentionally omitted USE flags:
+#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
+#                              The default (heavily patched) embedded copy should work, or you can
+#                              leave it off altogether -- the only public apps that make use of it are
+#                              samples and tests, since NCBI's database servers are of course firewalled.
+
+# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+		"${FILESDIR}"/${P}-conf-opts.patch
+		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
+		"${FILESDIR}"/${P}-linkage-tuneups.patch
+		"${FILESDIR}"/${P}-more-patches.patch
+		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
+		"${FILESDIR}"/${P}-configure.patch
+		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
+		"${FILESDIR}"/${P}-fix-install.patch
+		"${FILESDIR}"/${P}-bdb6.patch
+		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
+		)
+
+src_prepare() {
+	default
+#	filter-ldflags -Wl,--as-needed
+#	append-ldflags -Wl,--no-undefined
+#	sed -i -e 's/-print-file-name=libstdc++.a//' \
+#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
+#		src/build-system/configure || die
+#	epatch \
+#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
+#		"${FILESDIR}"/curl-types.patch \
+#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
+#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
+#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
+#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
+#		"${FILESDIR}"/report_project_settings_configure.patch \
+#		"${FILESDIR}"/make_install.patch
+
+#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
+
+#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
+#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
+#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
+#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
+#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
+
+#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
+
+# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
+#       "${FILESDIR}"/${P}-as-needed.patch
+#       "${FILESDIR}"/${P}-fix-creaders-linking.patch
+#       "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch
+#		)
+		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
+	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
+	# https://bugs.gentoo.org/show_bug.cgi?id=514706
+
+	tc-export CXX CC
+
+	cd src/build-system || die
+#	eautoreconf
+
+	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
+	# eautoconf # keep it disabled until we can ensure 2.59 is installed
+	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
+}
+
+# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
+src_configure() {
+	local myconf=()
+	#--without-optimization  turn off optimization flags in non-debug mode
+	#--with-profiling        build profiled versions of libs and apps
+	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
+	#--with-plugin-auto-load always enable the plugin manager by default
+	#--with-bundles          build bundles in addition to dylibs on Mac OS X
+	#--with-bin-release      build executables suitable for public release
+	#	no dll and such
+	#--with-64               compile to 64-bit code
+	#--with-universal        build universal binaries on Mac OS X
+	#--with-universal=CPUs   build universal binaries targeting the given CPUs
+	#--without-exe           do not build executables
+	#--with-relative-runpath=P specify an executable-relative DLL search path
+	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
+	#--with-limited-linker   don't attempt to build especially large projects
+	#--with-extra-action=    script to call after the configuration is complete
+	#--with-autodep          automatic generation of dependencies (GNU make)
+	#--with-fake-root=DIR    appear to have been built under DIR
+	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
+	#--without-execopy       do not copy built executables to the BIN area
+	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
+	#--with-lib-rebuilds=ask ask whether to update each app's libraries
+	#--without-deactivation  keep old copies of libraries that no longer build
+	#--without-makefile-auto-update  do not auto-update generated makefiles
+	#--with-projects=FILE    build projects listed in FILE by default
+	#--without-flat-makefile do not generate an all-encompassing flat makefile
+	#--with-configure-dialog allow interactive flat makefile project selection
+	#--with-saved-settings=F load configuration settings from the file F
+	#--with-check-tools=...  use the specified tools for testing
+	#--with-ncbi-public      ensure compatibility for all in-house platforms
+	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
+	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
+	#--without-sp            do not use SP libraries
+	#--without-orbacus       do not use ORBacus CORBA libraries
+	#--with-orbacus=DIR      use ORBacus installation in DIR
+	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
+	#--with-sablot=DIR       use Sablotron installation in DIR
+	#--without-sablot,       do not use Sablotron
+	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
+	#--without-oechem        do not use OEChem
+	#--with-sge=DIR          use Sun Grid Engine installation in DIR
+	#--without-sge           do not use Sun Grid Engine
+	#--with-magic=DIR        use libmagic installation in DIR
+	#--without-magic         do not use libmagic
+	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
+	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
+	#--without-connext       do not build non-public CONNECT library extensions
+	#--without-serial        do not build the serialization library and tools
+	#--without-objects       do not generate/build serializeable objects from ASNs
+	#--without-dbapi         do not build database connectivity libraries
+	#--without-app           do not build standalone applications like ID1_FETCH
+	#--without-gui           do not build most graphical projects
+	#--without-algo          do not build CPU-intensive algorithms
+	#--without-internal      do not build internal projects
+	#--with-gbench           ensure that Genome Workbench can be built
+	#--without-gbench        do not build Genome Workbench
+	myconf+=(
+	--with-dll
+	--with-lfs
+	--with-build-root="${S}"_build
+	--without-suffix
+	--without-hostspec
+	--without-version
+	--with-bincopy
+	--without-strip
+	--without-ccache
+	--without-distcc
+#	--with-ncbi-c
+	--without-ctools
+#	--with-sss
+#	--with-sssutils
+#	--with-sssdb
+#	--with-included-sss
+	--with-z="${EPREFIX}/usr"
+	--with-bz2="${EPREFIX}/usr"
+	--without-sybase
+	--with-autodep
+#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
+	# --without-downloaded-vdb is not available in 12.0.0 release yet
+	# preventing executing git to checkout during configure phase ncbi-vdb sources
+	# resulting in 'checking for ncbi-vdb... no' and
+	# '^PACKAGES:'
+	# '^  disabled: ... VDB'
+	# --without-downloaded-vdb
+	$(use_with debug)
+	$(use_with debug max-debug)
+	$(use_with debug symbols)
+	$(use_with static-libs static)
+	$(use_with static static-exe)
+	$(use_with threads mt)
+	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
+	$(use_with test check)
+	$(use_with pch)
+	$(use_with lzo lzo "${EPREFIX}/usr")
+	$(use_with pcre pcre "${EPREFIX}/usr")
+	$(use_with gnutls gnutls "${EPREFIX}/usr")
+	$(use_with mysql mysql "${EPREFIX}/usr")
+	$(use_with muparser muparser "${EPREFIX}/usr")
+	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
+	$(use_with opengl opengl "${EPREFIX}/usr")
+	$(use_with mesa mesa "${EPREFIX}/usr")
+	$(use_with opengl glut "${EPREFIX}/usr")
+	$(use_with opengl glew "${EPREFIX}/usr")
+	$(use_with opengl glew-mx)
+	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
+	$(use_with wxwidgets wxwidgets-ucs)
+	$(use_with freetype freetype "${EPREFIX}/usr")
+	$(use_with fastcgi fastcgi "${EPREFIX}/usr")
+	$(use_with berkdb bdb "${EPREFIX}/usr")
+	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
+	$(use_with python python "${EPREFIX}/usr")
+	$(use_with boost boost "${EPREFIX}/usr")
+	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
+	$(use_with icu icu "${EPREFIX}/usr")
+	$(use_with expat expat "${EPREFIX}/usr")
+	$(use_with xml libxml "${EPREFIX}/usr")
+	$(use_with xml libxslt "${EPREFIX}/usr")
+	$(use_with xerces xerces "${EPREFIX}/usr")
+	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
+	$(use_with xalan xalan "${EPREFIX}/usr")
+#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
+	--without-gif
+	$(use_with jpeg jpeg "${EPREFIX}/usr")
+	$(use_with tiff tiff "${EPREFIX}/usr")
+	$(use_with png png "${EPREFIX}/usr")
+	$(use_with xpm xpm "${EPREFIX}/usr")
+	$(use_with curl curl "${EPREFIX}/usr")
+#	$(use_with X x "${EPREFIX}/usr")
+#	$(use_with X x) # there is no --with-x option
+	)
+
+	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
+	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
+
+	# TODO
+	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
+	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
+
+	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
+
+#	ECONF_SOURCE="src/build-system" \
+#		econf \
+	bash \
+		./src/build-system/configure \
+		--srcdir="${S}" \
+		--prefix="${EPREFIX}/usr" \
+		--libdir=/usr/lib64 \
+		--with-flat-makefile \
+		${myconf[@]} || die
+#--without-debug \
+#		--with-bin-release \
+#		--with-bincopy \
+#		--without-static \
+#		--with-dll \
+#		--with-mt \
+#		--with-openmp \
+#		--with-lfs \
+#		--prefix="${ED}"/usr \
+#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
+#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
+#		|| die
+#	econf ${myconf[@]}
+}
+
+src_compile() {
+	## all_r would ignore the --with-projects contents and build more
+	## emake all_r -C GCC*-Release*/build || die
+	## all_p with compile only selected/required components
+	##cd "${S}"_build &&\
+	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
+	#emake all_p -C "${S}"_build/build
+
+	#
+	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
+	#
+	# The next release should automatically address such underlinking, albeit
+	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
+	# add or extend more DLL_LIB settings, to which end you may find the
+	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
+	# helpful.  For instance,
+	#
+	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
+	#
+	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
+	#
+	# DLL_LIB = xncbi
+	#
+	# (You can find the path to that makefile by examining
+	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
+	#
+	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
+	emake -C "${S}"_build/build -f Makefile.flat
+	#
+	# >=gcc-5.3.0 is not supported, see also bug #579248#c8
+	# configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++  5.3.0
+}
+
+src_install() {
+	rm -rvf "${S}"_build/lib/ncbi || die
+	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
+
+#	dobin "${S}"_build/bin/*
+#	dolib.so "${S}"_build/lib/*so*
+#	dolib.a "${S}"_build/lib/*.a
+#	doheader "${S}"_build/inc/*
+
+	# File collisions with sci-biology/ncbi-tools
+	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
+	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
+	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
+	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
+	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
+
+	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
+	doenvd "${S}/99${PN}"
+}
+
+pkg_postinst() {
+	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
+	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
+}
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 5c0b619df..0aacd0511 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python2_7 )
 
 inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs