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authorPacho Ramos <pacho@gentoo.org>2020-07-02 22:52:26 +0200
committerPacho Ramos <pacho@gentoo.org>2020-07-02 22:52:26 +0200
commit4af58d4365b1c323106e4fcf0c07266d1438a63a (patch)
treef2376419bbd13fe33e18a6bf2604c8a00f2d3b98 /sci-chemistry/autodock
parentdev-perl/constant-defer: -r bump for EAPI& + fixes (diff)
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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@gentoo.org>
Diffstat (limited to 'sci-chemistry/autodock')
-rw-r--r--sci-chemistry/autodock/autodock-4.2.6.ebuild68
-rw-r--r--sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch12
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