bug#40265: closed ([PATCH] gnu: python-intervaltree: Update to 3.0.2.)

[GNU bug Tracking System]

Your message dated Sun, 5 Apr 2020 20:44:48 +0200
with message-id <20200405184448.ek2qernpt6ixbfj4@gravity>
and subject line Re: [PATCH v2] gnu: python-intervaltree: Update to 3.0.2.
has caused the debbugs.gnu.org bug report #40265,
regarding [PATCH] gnu: python-intervaltree: Update to 3.0.2.
to be marked as done.

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40265: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=40265
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> --- Begin Message ---
>
>
>
> 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 <address@hidden>
>  ;;; Copyright © 2019 Brett Gilio <address@hidden>
>  ;;; Copyright © 2020 Björn Höfling <address@hidden>
> +;;; Copyright © 2020 Jakub Kądziołka <address@hidden>
>  ;;;
>  ;;; 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
>
>
>
>
> --- End Message ---

--- Begin Message --- Subject: Re: [PATCH v2] gnu: python-intervaltree: Update to 3.0.2. Date: Sun, 5 Apr 2020 20:44:48 +0200

On Thu, Apr 02, 2020 at 05:54:14PM +0200, Marius Bakke wrote:
> Jakub Kądziołka <address@hidden> 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.

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