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>

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 6cfe76fbbfd0..b4dce2e439b4 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 ae44ffeb3159..443dfcd868ce 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