Subject: [bug#40265] [PATCH v2] gnu: python-intervaltree: Update to 3.0.2.

From: Jakub Kądziołka <[email-masked]>
Date: Wed, 1 Apr 2020 16:24:48 +0200

* 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 <[email-masked]>
 ;;; Copyright © 2019 Brett Gilio <[email-masked]>
 ;;; Copyright © 2020 Björn Höfling <[email-masked]>
+;;; Copyright © 2020 Jakub Kądziołka <[email-masked]>
 ;;;
 ;;; 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+         ;; out-of-date copy.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