[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 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(-)

Toggle diff (41 lines)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

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 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.

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 פלשנר
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Confidentiality 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 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(-)

Toggle diff (46 lines)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

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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