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 <[email protected]> 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 <[email protected]> Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1058474 Forwarded: not-needed -Last-Update: 2024-05-22 +Reviewed-By: Adrian Bunk <[email protected]> +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.
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