[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/

[Andrew Ammerlaan]

commit:     e8d4a8bc048182c0db34a3b995ac6a5c24fcdbb8
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb  1 04:32:58 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb  1 04:32:58 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e8d4a8bc

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

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        | 369 ---------------------
 .../ncbi-tools++/ncbi-tools++-18.0.0.ebuild        |   2 +-
 2 files changed, 1 insertion(+), 370 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
deleted file mode 100644
index ed50801fc..000000000
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ /dev/null
@@ -1,369 +0,0 @@
-# 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 0aacd0511..5c0b619df 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=( python2_7 )
+PYTHON_COMPAT=( python3_{7,8,9} )
 
 inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs