[med-svn] [Git][med-team/gubbins][master] 3 commits: remove-numba-temporarily.patch: update.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / gubbins


Commits:
b8f9256d by Étienne Mollier at 2026-02-21T09:19:15+01:00
remove-numba-temporarily.patch: update.

Cleanup occurrences of numba in python/setup.py.

Thanks: Adrian Bunk
Closes: #1128512

- - - - -
301b4cc4 by Étienne Mollier at 2026-02-21T09:30:11+01:00
d/clean: also cleanup leftover csv files.

Closes: #1044465

- - - - -
bee55ed6 by Étienne Mollier at 2026-02-21T09:37:56+01:00
d/changelog: ready for upload to unstable.

- - - - -


3 changed files:

- debian/changelog
- debian/clean
- debian/patches/remove-numba-temporarily.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+gubbins (3.4.3-3) unstable; urgency=medium
+
+  * remove-numba-temporarily.patch: update.
+    Cleanup occurrences of numba in python/setup.py.
+    Thanks to Adrian Bunk (Closes: #1128512)
+  * d/clean: also cleanup leftover csv files. (Closes: #1044465)
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 21 Feb 2026 09:30:44 +0100
+
 gubbins (3.4.3-2) unstable; urgency=medium
 
   [ Alexandre Detiste ]


=====================================
debian/clean
=====================================
@@ -1 +1,2 @@
 tests/run_all_tests-*
+src/*.csv


=====================================
debian/patches/remove-numba-temporarily.patch
=====================================
@@ -3,15 +3,15 @@ Description: disable numba in upstream code.
  Ideally, numba should be simply recommended, and the code to proceed to
  numba JIT compilation should be capable of shifting gears to no-optimization
  in order to support situations where numba is not available.
-
 Author: Étienne Mollier <emollier at debian.org>
 Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1058474
 Forwarded: not-needed
-Last-Update: 2024-05-22
+Reviewed-By: Adrian Bunk <bunk at debian.org>
+Last-Update: 2026-02-21
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- a/python/gubbins/pyjar.py
-+++ b/python/gubbins/pyjar.py
+--- gubbins.orig/python/gubbins/pyjar.py
++++ gubbins/python/gubbins/pyjar.py
 @@ -16,8 +16,6 @@
  from Bio import AlignIO
  from math import log, exp
@@ -150,3 +150,25 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  def int_to_seq(seq,out_seq):
  
      for i,b in enumerate(seq):
+--- gubbins.orig/python/setup.py
++++ gubbins/python/setup.py
+@@ -34,8 +34,7 @@
+         "multiprocess >= 0.70",
+         "scipy >= 1.5.3",
+         "numpy >= 1.19",
+-        "ska >= 1.0",
+-        "numba > 0.0"
++        "ska >= 1.0"
+     ],
+     long_description="""\
+       Gubbins is a tool that generates a reconstruction of
+@@ -55,8 +54,7 @@
+         "dendropy  >= 4.0.2",
+         "multiprocess >= 0.70",
+         "scipy >= 1.5.3",
+-        "numpy >= 1.19",
+-        "numba > 0.0"
++        "numpy >= 1.19"
+     ],
+     license="GPL"
+ )



View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/compare/aeead48bdc138e75a6c185169c825e02cfef9579...bee55ed609138e47ff22c99b05a86b443031f6df

-- 
View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/compare/aeead48bdc138e75a6c185169c825e02cfef9579...bee55ed609138e47ff22c99b05a86b443031f6df
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20260221/0b096826/attachment-0001.htm>