From patchwork Tue Apr 22 14:00:31 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 41933 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 39B0C27BC4B; Tue, 22 Apr 2025 15:03:12 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 9E0F227BC49 for ; Tue, 22 Apr 2025 15:03:11 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u7ECU-00081O-2J; Tue, 22 Apr 2025 10:02:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u7ECL-0007ua-4F for guix-patches@gnu.org; Tue, 22 Apr 2025 10:02:05 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u7ECK-0006h6-9d for guix-patches@gnu.org; Tue, 22 Apr 2025 10:02:04 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=RSxJW3ITmoFvccy/rMrtTawzQyf6xxzl1iGP7VU3otU=; b=Z0mb2lZJvuvV+HwIql9EYNmHJVuK7cUiTZD44tykQLGKBqq0hCBSq+Uqyodpf5ziVUtjxgd9qGj4/pujJUwyPuEs8bXzbubccfH/hphY7VWcnjuAnHo+MLDjsYLCF9sJdFNaNKYX2nh3i3GMivIeor77P2WPkgVfpP6fQARWBVcB+Ji4N6XuA6zlJ6bTVEc1CY6hH3ofbKjqA0NDKRTTaeGzER+JJ8f0h+Qv+aXiKGCRiokqV/oqd0tPks2ycJbwEGw22Xb452AK2UKaamwU4lg44Ipmtt+mR5wPdNVdPZOk8m1XEDGCUDCXk5kUrBwXl7mEUrXMjmU//1WQHXLf6Q==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u7ECK-0005FM-0M for guix-patches@gnu.org; Tue, 22 Apr 2025 10:02:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77895] [PATCH v2 04/10] gnu: python-bed-reader: Improve phases' style. Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 22 Apr 2025 14:02:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77895 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77895@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 77895-submit@debbugs.gnu.org id=B77895.174533048020040 (code B ref 77895); Tue, 22 Apr 2025 14:02:03 +0000 Received: (at 77895) by debbugs.gnu.org; 22 Apr 2025 14:01:20 +0000 Received: from localhost ([127.0.0.1]:49102 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u7EBb-0005DA-Cy for submit@debbugs.gnu.org; Tue, 22 Apr 2025 10:01:19 -0400 Received: from 1.mo562.mail-out.ovh.net ([178.33.109.175]:51123) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u7EBO-0005BQ-H0 for 77895@debbugs.gnu.org; Tue, 22 Apr 2025 10:01:07 -0400 Received: from director3.derp.mail-out.ovh.net (director3.derp.mail-out.ovh.net [152.228.215.222]) by mo562.mail-out.ovh.net (Postfix) with ESMTPS id 4ZhkRM1FHrz1Ywt; Tue, 22 Apr 2025 14:01:03 +0000 (UTC) Received: from director3.derp.mail-out.ovh.net (director3.derp.mail-out.ovh.net. [127.0.0.1]) by director3.derp.mail-out.ovh.net (inspect_sender_mail_agent) with SMTP for <77895@debbugs.gnu.org>; Tue, 22 Apr 2025 14:01:03 +0000 (UTC) Received: from mta11.priv.ovhmail-u1.ea.mail.ovh.net (unknown [10.108.17.119]) by director3.derp.mail-out.ovh.net (Postfix) with ESMTPS id 4ZhkRM00Jmz86KW; Tue, 22 Apr 2025 14:01:02 +0000 (UTC) Received: from ngraves.fr (unknown [10.1.6.5]) by mta11.priv.ovhmail-u1.ea.mail.ovh.net (Postfix) with ESMTPSA id 94F5A263A0B; Tue, 22 Apr 2025 14:01:02 +0000 (UTC) Authentication-Results: garm.ovh; auth=pass (GARM-102R00449fe2d2b-5dd6-41e5-b315-bb9128b11539, 0A1BC1951B487096A19EF2AF6351B65704E5605C) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Tue, 22 Apr 2025 16:00:31 +0200 Message-ID: <20250422140051.2273-4-ngraves@ngraves.fr> X-Mailer: git-send-email 2.49.0 In-Reply-To: <20250422140051.2273-1-ngraves@ngraves.fr> References: <20250422140051.2273-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 11609998368165651170 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgddvgeefleduucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepleffjeetueethfefkeffffefvddukeejkefgleduiedthfekvefhiedvhfffgeegnecukfhppeduvdejrddtrddtrddupdeltddrledvrdduudejrddugeegnecuvehluhhsthgvrhfuihiivgeptdenucfrrghrrghmpehinhgvthepuddvjedrtddrtddruddpmhgrihhlfhhrohhmpehnghhrrghvvghssehnghhrrghvvghsrdhfrhdpnhgspghrtghpthhtohepvddprhgtphhtthhopeejjeekleehseguvggssghughhsrdhgnhhurdhorhhgpdhrtghpthhtohepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdfovfetjfhoshhtpehmohehiedvmgdpmhhouggvpehsmhhtphhouhht DKIM-Signature: a=rsa-sha256; bh=RSxJW3ITmoFvccy/rMrtTawzQyf6xxzl1iGP7VU3otU=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1745330463; v=1; b=y8yTm+ys7PEyZb+n/aSc5+0PK/Rn8RmjuQTRRfoVPDS5MmYQ9ipjMhCPfE/V2XabCiyqr2xV eh6VDrCsKFFd+TGv2YbTBwK/kam50U01CCan/C26YLJxQiHU/jovATSM5vg3yOWjHcJcPURMANI GXrHiGofPQgs/qV3W1tJgZ77TLKwV5DUXJjJk6IMMEgvX+UuM44usgSh2/eQ6pDkHzS/IHDb4Mj A7GEFEbVMFmu9JD5t7Z6EVzTApqWqNmCHzzvIHpZ/hVL2TSfSzg/QxlbFtJXtx0fem7PCsv+1S6 r9jZrlCewqAit94Z+pNDjU4vk2hWTgH7cDJJj+YJJFJsg== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-bed-reader) [arguments]{phases}: Improve phases 'install-python-library and 'check-python with site-packages procedure. --- gnu/packages/bioinformatics.scm | 22 ++++++++-------------- 1 file changed, 8 insertions(+), 14 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e1cac1f149..d4fa482851 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2333,26 +2333,20 @@ (define-public python-bed-reader (add-after 'build-python-module 'install-python-module (assoc-ref py:%standard-phases 'install)) (add-after 'install-python-module 'install-python-library - (lambda _ - (let ((site (string-append #$output "/lib/python" - #$(version-major+minor - (package-version python)) - "/site-packages/"))) - (mkdir-p (string-append site "bed_reader")) + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((site (py:site-packages inputs outputs))) + (mkdir-p (string-append site "/bed_reader")) (copy-file "target/release/libbed_reader.so" - (string-append site "bed_reader/bed_reader.so"))))) + (string-append site "/bed_reader/bed_reader.so"))))) (add-after 'install-python-library 'add-install-to-pythonpath (assoc-ref py:%standard-phases 'add-install-to-pythonpath)) (add-after 'add-install-to-pythonpath 'check-python - (lambda* (#:key tests? #:allow-other-keys) + (lambda* (#:key inputs outputs tests? #:allow-other-keys) (when tests? - (let ((site (string-append #$output "/lib/python" - #$(version-major+minor - (package-version python)) - "/site-packages/")) + (let ((site (py:site-packages inputs outputs)) (data-dir "bed_reader/tests/data")) (symlink (canonicalize-path data-dir) - (string-append site data-dir)) + (string-append site "/" data-dir)) (invoke "pytest" "-v" #$output ;; These test require a 84 GB file. "-k" (string-join @@ -2363,7 +2357,7 @@ (define-public python-bed-reader "test_optional_dependencies") " and not ")) (delete-file-recursively - (string-append site "bed_reader/tests")) + (string-append site "/bed_reader/tests")) (delete-file-recursively (string-append #$output "/.pytest_cache"))))))))) (native-inputs (list python-pytest