GNU bug report logs - #40265
[PATCH] gnu: python-intervaltree: Update to 3.0.2.

Previous Next

Full log

View this message in rfc822 format

From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Jakub Kądziołka <kuba <at> kadziolka.net>
Subject: bug#40265: closed (Re: [PATCH v2] gnu: python-intervaltree:
 Update to 3.0.2.)
Date: Sun, 05 Apr 2020 18:45:01 +0000

[Message part 1 (text/plain, inline)]

Your bug report

#40265: [PATCH] gnu: python-intervaltree: Update to 3.0.2.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 40265 <at> debbugs.gnu.org.

-- 
40265: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=40265
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

[Message part 2 (message/rfc822, inline)]

From: Jakub Kądziołka <kuba <at> kadziolka.net>
To: Marius Bakke <mbakke <at> fastmail.com>
Cc: efraim <at> flashner.co.il, 40265-done <at> debbugs.gnu.org
Subject: Re: [PATCH v2] gnu: python-intervaltree: Update to 3.0.2.
Date: Sun, 5 Apr 2020 20:44:48 +0200

[Message part 3 (text/plain, inline)]

On Thu, Apr 02, 2020 at 05:54:14PM +0200, Marius Bakke wrote:
> Jakub Kądziołka <kuba <at> kadziolka.net> writes:
> 
> > * gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2.
> > [arguments]: Don't skip the tests, work around the problematic
> > sanity-check instead.
> 
> LGTM.

Thanks! Pushed as 7fe746e071e3177e76dad9e2bcd1d53e87187f1a.

[signature.asc (application/pgp-signature, inline)]

[Message part 5 (message/rfc822, inline)]

From: Jakub Kądziołka <kuba <at> kadziolka.net>
To: guix-patches <at> gnu.org
Cc: rekado <at> elephly.net
Subject: [PATCH] gnu: python-intervaltree: Update to 3.0.2.
Date: Sat, 28 Mar 2020 00:51:25 +0100

* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2.
[arguments]: Don't skip the tests.
---

It turns out I need python-intervaltree 3.0 as a dependency for one of
the packages I'm working on.

Cc: Ricardo - you added python-pygenometracks, the only dependent. Could
you re-test it, just in case?

 gnu/packages/bioinformatics.scm | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index da3fe1d2c9..a8e4c830ae 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16,6 +16,7 @@
 ;;; Copyright © 2019 Brian Leung <bkleung89 <at> gmail.com>
 ;;; Copyright © 2019 Brett Gilio <brettg <at> gnu.org>
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling <at> bjoernhoefling.de>
+;;; Copyright © 2020 Jakub Kądziołka <kuba <at> kadziolka.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -13548,17 +13549,22 @@ allowing the insertion of arbitrary types into the tree.")
 (define-public python-intervaltree
   (package
     (name "python-intervaltree")
-    (version "2.1.0")
+    (version "3.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "intervaltree" version))
        (sha256
         (base32
-         "02w191m9zxkcjqr1kv2slxvhymwhj3jnsyy3a28b837pi15q19dc"))))
+         "0wz234g6irlm4hivs2qzmnywk0ss06ckagwh15nflkyb3p462kyb"))))
     (build-system python-build-system)
-    ;; FIXME: error when collecting tests
-    (arguments '(#:tests? #f))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'import-mismatch-error-workaround
+           (lambda _
+             (setenv "PY_IGNORE_IMPORTMISMATCH" "1")
+             #t)))))
     (propagated-inputs
      `(("python-sortedcontainers" ,python-sortedcontainers)))
     (native-inputs
-- 
2.26.0

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.