commit: 4af58d4365b1c323106e4fcf0c07266d1438a63a Author: Pacho Ramos <pacho <AT> gentoo <DOT> org> AuthorDate: Thu Jul 2 20:52:26 2020 +0000 Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org> CommitDate: Thu Jul 2 20:52:26 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4af58d43
sci-chemistry/autodock: Stop relying on python2 Also remove false positive configure warnings (#670690) and fix typo at install time (#543270) Closes: https://bugs.gentoo.org/543270 Closes: https://bugs.gentoo.org/670690 Package-Manager: Portage-2.3.100, Repoman-2.3.22 Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org> sci-chemistry/autodock/autodock-4.2.6.ebuild | 68 +++++++++++++--------- .../files/autodock-4.2.6-buildsystem.patch | 12 ++-- 2 files changed, 46 insertions(+), 34 deletions(-) diff --git a/sci-chemistry/autodock/autodock-4.2.6.ebuild b/sci-chemistry/autodock/autodock-4.2.6.ebuild index 6cfe76fbbfd..b4dce2e439b 100644 --- a/sci-chemistry/autodock/autodock-4.2.6.ebuild +++ b/sci-chemistry/autodock/autodock-4.2.6.ebuild @@ -1,38 +1,56 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -PYTHON_COMPAT=( python2_7 ) +# Tests require python2 +#PYTHON_COMPAT=( python2_7 ) -inherit autotools eutils python-any-r1 versionator +inherit autotools readme.gentoo-r1 #python-any-r1 MY_PN="autodocksuite" MY_P="${MY_PN}-${PV}" DESCRIPTION="A suite of automated docking tools" HOMEPAGE="http://autodock.scripps.edu/"; -SRC_URI="http://autodock.scripps.edu/downloads/autodock-registration/tars/dist$(delete_all_version_separators)/${MY_P}-src.tar.gz" +SRC_URI="http://autodock.scripps.edu/downloads/autodock-registration/tars/dist$(ver_rs 1- '')/${MY_P}-src.tar.gz" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="examples openmp test" -RESTRICT="!test? ( test )" + +IUSE="examples openmp" #test +#RESTRICT="!test? ( test )" + +# False positives caused by nested configure scripts +QA_CONFIGURE_OPTIONS=".*" RDEPEND="" -DEPEND="test? ( ${PYTHON_DEPS} )" +DEPEND="" +#DEPEND="test? ( ${PYTHON_DEPS} )" S="${WORKDIR}/src" +DISABLE_AUTOFORMATTING="yes" +DOC_CONTENTS=" +The AutoDock development team requests all users to fill out the +registration form at: + +http://autodock.scripps.edu/downloads/autodock-registration + +The number of unique users of AutoDock is used by Prof. Arthur J. +Olson and the Scripps Research Institude to support grant +applications. +" + PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) src_prepare() { - local i + default - epatch "${PATCHES[@]}" + local i sed \ -e "s/\tcsh/\tsh/" \ @@ -58,15 +76,15 @@ src_compile() { emake -C autogrid } -src_test() { - elog "Testing autodock" - cd "${S}/autodock/Tests" || die - cp ../*.dat . || die - ${EPYTHON} test_autodock4.py || die "AutoDock tests failed." - einfo "Testing autogrid" - cd "${S}/autogrid/Tests" || die - ${EPYTHON} test_autogrid4.py || die "AutoGrid tests failed." -} +#src_test() { +# elog "Testing autodock" +# cd "${S}/autodock/Tests" || die +# cp ../*.dat . || die +# ${EPYTHON} test_autodock4.py || die "AutoDock tests failed." +# einfo "Testing autogrid" +# cd "${S}/autogrid/Tests" || die +# ${EPYTHON} test_autogrid4.py || die "AutoGrid tests failed." +#} src_install() { if use openmp; then @@ -79,7 +97,7 @@ src_install() { insinto /usr/share/${PN} doins -r \ autodock/{AD4_parameters.dat,AD4_PARM99.dat} \ - $(usex examples "autodoc/EXAMPLES" "") + $(usex examples "autodock/EXAMPLES" "") DOCS=( RELEASENOTES @@ -88,15 +106,9 @@ src_install() { autodock/USERGUIDES/AutoDock4.2_UserGuide.pdf ) einstalldocs + readme.gentoo_create_doc } pkg_postinst() { - elog "The AutoDock development team requests all users to fill out the" - elog "registration form at:" - echo - elog "\thttp://autodock.scripps.edu/downloads/autodock-registration"; - echo - elog "The number of unique users of AutoDock is used by Prof. Arthur J." - elog "Olson and the Scripps Research Institude to support grant" - elog "applications." + readme.gentoo_print_elog } diff --git a/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch index ae44ffeb315..443dfcd868c 100644 --- a/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch +++ b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch @@ -1,11 +1,11 @@ - src/autodock/Makefile.am | 6 +++--- - src/autogrid/Makefile.am | 4 ++-- + a/autodock/Makefile.am | 6 +++--- + b/autogrid/Makefile.am | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/autodock/Makefile.am b/src/autodock/Makefile.am index 799a3c4..911897b 100644 ---- a/src/autodock/Makefile.am -+++ b/src/autodock/Makefile.am +--- a/autodock/Makefile.am ++++ b/autodock/Makefile.am @@ -459,7 +459,8 @@ endif BUILT_SOURCES = $(autodock4_SOURCES) default_parameters.h @@ -28,8 +28,8 @@ index 799a3c4..911897b 100644 diff --git a/src/autogrid/Makefile.am b/src/autogrid/Makefile.am index b531099..b78b380 100644 ---- a/src/autogrid/Makefile.am -+++ b/src/autogrid/Makefile.am +--- a/autogrid/Makefile.am ++++ b/autogrid/Makefile.am @@ -94,9 +94,9 @@ autogrid4_SOURCES = main.cpp \ BUILT_SOURCES = default_parameters.h
