[med-svn] [Git][med-team/python-skbio][master] 2 commits: Fix cython issue

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / python-skbio


Commits:
4ca6bc43 by Andreas Tille at 2024-01-26T13:39:52+01:00
Fix cython issue

- - - - -
6b6382c1 by Andreas Tille at 2024-01-26T13:54:53+01:00
Upload to unstable

- - - - -


7 changed files:

- debian/changelog
- + debian/patches/cython3.patch
- debian/patches/series
- − skbio/alignment/_ssw_wrapper.c
- − skbio/diversity/_phylogenetic.c
- − skbio/metadata/_intersection.c
- − skbio/stats/__subsample.c


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+python-skbio (0.5.9-3) unstable; urgency=medium
+
+  * Fix cython issue
+    Closes: #1056047
+
+ -- Andreas Tille <tille at debian.org>  Fri, 26 Jan 2024 13:44:30 +0100
+
 python-skbio (0.5.9-2) unstable; urgency=medium
 
   * Add loong64 support


=====================================
debian/patches/cython3.patch
=====================================
@@ -0,0 +1,16 @@
+Description: Fix cython issue
+Bug-Debian: https://bugs.debian.org/1056047
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 26 Jan 2024 13:38:38 +0100
+
+--- a/skbio/alignment/_ssw_wrapper.pyx
++++ b/skbio/alignment/_ssw_wrapper.pyx
+@@ -581,7 +581,7 @@ cdef class StripedSmithWaterman:
+         # Set up our mask_length
+         # Mask is recommended to be max(query_sequence/2, 15)
+         if mask_auto:
+-            self.mask_length = len(query_sequence) // 2
++            self.mask_length = int(len(query_sequence) // 2)
+             if self.mask_length < mask_length:
+                 self.mask_length = mask_length
+         else:


=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ local_inventory
 modify-test.patch
 numpy-1.24.patch
 python3.12-xfail-tests.patch
+cython3.patch


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skbio/alignment/_ssw_wrapper.c deleted
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The diff for this file was not included because it is too large.

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skbio/diversity/_phylogenetic.c deleted
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The diff for this file was not included because it is too large.

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skbio/metadata/_intersection.c deleted
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The diff for this file was not included because it is too large.

=====================================
skbio/stats/__subsample.c deleted
=====================================
The diff for this file was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/76da8f3a033222d9d67a3f34570a432d4cbc541d...6b6382c1bab2b3d06ab70c89f16b8f99c736fdca

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/76da8f3a033222d9d67a3f34570a432d4cbc541d...6b6382c1bab2b3d06ab70c89f16b8f99c736fdca
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