* [bug#40265] [PATCH] gnu: python-intervaltree: Update to 3.0.2.
@ 2020-03-27 23:51 Jakub Kądziołka
2020-03-31 14:58 ` Marius Bakke
2020-04-01 14:24 ` [bug#40265] [PATCH v2] " Jakub Kądziołka
0 siblings, 2 replies; 6+ messages in thread
From: Jakub Kądziołka @ 2020-03-27 23:51 UTC (permalink / raw)
To: 40265; +Cc: rekado
* 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@gmail.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
+;;; Copyright © 2020 Jakub Kądziołka <kuba@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
^ permalink raw reply related [flat|nested] 6+ messages in thread* [bug#40265] [PATCH] gnu: python-intervaltree: Update to 3.0.2.
2020-03-27 23:51 [bug#40265] [PATCH] gnu: python-intervaltree: Update to 3.0.2 Jakub Kądziołka
@ 2020-03-31 14:58 ` Marius Bakke
2020-04-01 5:47 ` Efraim Flashner
2020-04-01 14:24 ` [bug#40265] [PATCH v2] " Jakub Kądziołka
1 sibling, 1 reply; 6+ messages in thread
From: Marius Bakke @ 2020-03-31 14:58 UTC (permalink / raw)
To: Jakub Kądziołka, 40265; +Cc: rekado
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Jakub Kądziołka <kuba@kadziolka.net> writes:
> + (arguments
> + `(#:phases
> + (modify-phases %standard-phases
> + (add-before 'check 'import-mismatch-error-workaround
> + (lambda _
> + (setenv "PY_IGNORE_IMPORTMISMATCH" "1")
> + #t)))))
Can you add a comment about what this does?
Also, I guess this package should be moved out of bioinformatics.scm,
assuming the software you are packaging is not bioinfo-related?
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^ permalink raw reply [flat|nested] 6+ messages in thread
* [bug#40265] [PATCH] gnu: python-intervaltree: Update to 3.0.2.
2020-03-31 14:58 ` Marius Bakke
@ 2020-04-01 5:47 ` Efraim Flashner
0 siblings, 0 replies; 6+ messages in thread
From: Efraim Flashner @ 2020-04-01 5:47 UTC (permalink / raw)
To: Marius Bakke; +Cc: Jakub Kądziołka, rekado, 40265
[-- Attachment #1: Type: text/plain, Size: 1121 bytes --]
On Tue, Mar 31, 2020 at 04:58:43PM +0200, Marius Bakke wrote:
> Jakub Kądziołka <kuba@kadziolka.net> writes:
>
> > + (arguments
> > + `(#:phases
> > + (modify-phases %standard-phases
> > + (add-before 'check 'import-mismatch-error-workaround
> > + (lambda _
> > + (setenv "PY_IGNORE_IMPORTMISMATCH" "1")
> > + #t)))))
>
> Can you add a comment about what this does?
It seems to me there is some import mismatch and this is a workaround
for it. I assume it's related to deprecated python naming/modules and
may break on a python upgrade. IMO the phase name is descriptive enough,
and I assume if we were to remove it then it'd make a lot more sense
after seeing the error message.
>
> Also, I guess this package should be moved out of bioinformatics.scm,
> assuming the software you are packaging is not bioinfo-related?
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
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^ permalink raw reply [flat|nested] 6+ messages in thread
* [bug#40265] [PATCH v2] gnu: python-intervaltree: Update to 3.0.2.
2020-03-27 23:51 [bug#40265] [PATCH] gnu: python-intervaltree: Update to 3.0.2 Jakub Kądziołka
2020-03-31 14:58 ` Marius Bakke
@ 2020-04-01 14:24 ` Jakub Kądziołka
2020-04-02 15:54 ` Marius Bakke
1 sibling, 1 reply; 6+ messages in thread
From: Jakub Kądziołka @ 2020-04-01 14:24 UTC (permalink / raw)
To: 40265; +Cc: mbakke, efraim
* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2.
[arguments]: Don't skip the tests, work around the problematic
sanity-check instead.
---
Thanks for your helpful comments. I have added a comment, which, in
hindsight, should've been there in the first place :D
I will defer moving the package until committing the new dependent
(pwntools, #40265), as this is best done in a separate commit anyway.
gnu/packages/bioinformatics.scm | 19 +++++++++++++++----
1 file changed, 15 insertions(+), 4 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d69c2aea63..943369b275 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16,6 +16,7 @@
;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
+;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -13552,17 +13553,27 @@ 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
+ ;; pytest seems to have a check to make sure the user is testing
+ ;; their checked-out code and not an installed, potentially
+ ;; out-of-date copy. This is harmless here, since we just installed
+ ;; the package, so we disable the check to avoid skipping tests
+ ;; entirely.
+ (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
^ permalink raw reply related [flat|nested] 6+ messages in thread
end of thread, other threads:[~2020-04-05 18:45 UTC | newest]
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-- links below jump to the message on this page --
2020-03-27 23:51 [bug#40265] [PATCH] gnu: python-intervaltree: Update to 3.0.2 Jakub Kądziołka
2020-03-31 14:58 ` Marius Bakke
2020-04-01 5:47 ` Efraim Flashner
2020-04-01 14:24 ` [bug#40265] [PATCH v2] " Jakub Kądziołka
2020-04-02 15:54 ` Marius Bakke
2020-04-05 18:44 ` bug#40265: " Jakub Kądziołka
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