From: "Andrew Ammerlaan" <andrewammerlaan@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/tigmint/
Date: Wed, 20 Oct 2021 13:12:24 +0000 (UTC) [thread overview]
Message-ID: <1634735534.9a13af8737903d7bb70f8667fa53e6056fd3d429.andrewammerlaan@gentoo> (raw)
commit: 9a13af8737903d7bb70f8667fa53e6056fd3d429
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 20 13:12:14 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Wed Oct 20 13:12:14 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9a13af87
sci-biology/tigmint: properly install python things
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
...igmint-1.2.4.ebuild => tigmint-1.2.4-r1.ebuild} | 33 +++++++++++++++-------
1 file changed, 23 insertions(+), 10 deletions(-)
diff --git a/sci-biology/tigmint/tigmint-1.2.4.ebuild b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
similarity index 57%
rename from sci-biology/tigmint/tigmint-1.2.4.ebuild
rename to sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
index 1b181ea44..6900ea7aa 100644
--- a/sci-biology/tigmint/tigmint-1.2.4.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
@@ -1,9 +1,10 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python3_{8..9} )
+DISTUTILS_USE_SETUPTOOLS=no
inherit distutils-r1
@@ -13,9 +14,10 @@ SRC_URI="https://github.com/bcgsc/tigmint/releases/download/v${PV}/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
RESTRICT="test"
+PROPERTIES="test_network"
RDEPEND="
dev-python/intervaltree[${PYTHON_USEDEP}]
@@ -29,10 +31,8 @@ RDEPEND="
distutils_enable_tests pytest
-# install the executable into /usr/bin
-# BUG: the read_fasta.py should be installed into python modules
-# so it can be imported into python
src_prepare(){
+ # install the executable into /usr/bin
sed -i Makefile -e 's#prefix=/usr/local#prefix=/usr#'
default
}
@@ -44,12 +44,25 @@ src_configure(){
# do not run src_compile step as it runs git, makefile2graph, gsed, tred
-src_install(){
- default
- distutils-r1_src_install
+python_install() {
+ # This is a bit unorthodox, but it allows us to get both a symlink from
+ # /usr/bin to our script using the correct python implementation
+ # *and* to import it from the python shell
+ python_domodule bin/*.py
+ python_domodule bin/tigmint-arcs-tsv
+ python_domodule bin/tigmint-cut
+
+ python_doscript bin/*.py
+ python_doscript bin/tigmint-arcs-tsv
+ python_doscript bin/tigmint-cut
+}
+
+python_install_all() {
+ dobin bin/tigmint
+ dobin bin/tigmint-make
}
src_test(){
default
- python_foreach_impl python_test
+ distutils-r1_src_test
}
next reply other threads:[~2021-10-20 13:12 UTC|newest]
Thread overview: 10+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-10-20 13:12 Andrew Ammerlaan [this message]
-- strict thread matches above, loose matches on Subject: below --
2023-01-13 7:43 [gentoo-commits] proj/sci:master commit in: sci-biology/tigmint/ Horea Christian
2021-10-21 8:59 Martin Mokrejs
2021-10-19 15:06 Martin Mokrejs
2021-10-19 14:24 Martin Mokrejs
2021-10-17 16:22 Martin Mokrejs
2021-10-17 12:25 Martin Mokrejs
2021-01-05 6:08 Horea Christian
2020-01-10 16:14 Martin Mokrejs
2018-04-21 11:39 Martin Mokrejs
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=1634735534.9a13af8737903d7bb70f8667fa53e6056fd3d429.andrewammerlaan@gentoo \
--to=andrewammerlaan@gentoo.org \
--cc=gentoo-commits@lists.gentoo.org \
--cc=gentoo-dev@lists.gentoo.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox