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

Jakub Kądziołka wrote on 28 Mar 2020 00:51

Recipients:(address . guix-patches@gnu.org)(address . rekado@elephly.net)

Message-ID:20200327235125.3250-1-kuba@kadziolka.net

* 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 ofthe packages I'm working on.
Cc: Ricardo - you added python-pygenometracks, the only dependent. Couldyou re-test it, just in case?
gnu/packages/bioinformatics.scm | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-)

Toggle diff (41 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 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

Marius Bakke wrote on 31 Mar 2020 16:58

Recipients:(address . rekado@elephly.net)

Message-ID:87sghotvto.fsf@devup.no

Jakub Kądziołka <kuba@kadziolka.net> writes:

Toggle quote (8 lines)

> + (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?

Efraim Flashner wrote on 1 Apr 2020 07:47

Recipients:(name . Marius Bakke)(address . mbakke@fastmail.com)

Message-ID:20200401054751.GM5436@E5400

On Tue, Mar 31, 2020 at 04:58:43PM +0200, Marius Bakke wrote:

Toggle quote (12 lines)> 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 workaroundfor it. I assume it's related to deprecated python naming/modules andmay 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 senseafter seeing the error message.

Toggle quote (6 lines)

> > 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 פלשנרGPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351Confidentiality cannot be guaranteed on emails sent or received unencrypted

Jakub Kądziołka wrote on 1 Apr 2020 16:24

[PATCH v2] gnu: python-intervaltree: Update to 3.0.2.

Recipients:(address . 40265@debbugs.gnu.org)

Message-ID:20200401142448.2683-1-kuba@kadziolka.net

* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2.[arguments]: Don't skip the tests, work around the problematicsanity-check instead.---Thanks for your helpful comments. I have added a comment, which, inhindsight, 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(-)

Toggle diff (46 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 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

Marius Bakke wrote on 2 Apr 2020 17:54

Recipients:(address . efraim@flashner.co.il)

Message-ID:87lfndsx21.fsf@devup.no

Jakub Kądziołka <kuba@kadziolka.net> writes:

Toggle quote (4 lines)

> * 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.

Jakub Kądziołka wrote on 5 Apr 2020 20:44

Recipients:(name . Marius Bakke)(address . mbakke@fastmail.com)

Message-ID:20200405184448.ek2qernpt6ixbfj4@gravity

On Thu, Apr 02, 2020 at 05:54:14PM +0200, Marius Bakke wrote:

Toggle quote (8 lines)

> Jakub Kądziołka <kuba@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.

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