[med-svn] [Git][med-team/tombo][master] 3 commits: Add patch to fix FTBFS with cython3 (Closes: #1056041, #1056892)

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / tombo


Commits:
45aa7808 by Nilesh Patra at 2023-12-04T00:37:55+05:30
Add patch to fix FTBFS with cython3 (Closes: #1056041, #1056892)

- - - - -
c500284a by Nilesh Patra at 2023-12-04T00:38:47+05:30
Bump Standards-Version to 4.6.2 (no changes needed)

- - - - -
8b025770 by Nilesh Patra at 2023-12-04T00:38:59+05:30
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/cython3-fix.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+tombo (1.5.1-5) unstable; urgency=medium
+
+  * Team Upload.
+  * Add patch to fix FTBFS with cython3 (Closes: #1056041, #1056892)
+  * Bump Standards-Version to 4.6.2 (no changes needed)
+
+ -- Nilesh Patra <nilesh at debian.org>  Mon, 04 Dec 2023 00:38:50 +0530
+
 tombo (1.5.1-4) unstable; urgency=medium
 
   * Fix watch file


=====================================
debian/control
=====================================
@@ -19,7 +19,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-scipy <!nocheck>,
                python3-tqdm <!nocheck>,
                python3-nose2 <!nocheck>
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/tombo
 Vcs-Git: https://salsa.debian.org/med-team/tombo.git
 Homepage: https://github.com/nanoporetech/tombo


=====================================
debian/patches/cython3-fix.patch
=====================================
@@ -0,0 +1,27 @@
+--- a/tombo/_c_dynamic_programming.pyx
++++ b/tombo/_c_dynamic_programming.pyx
+@@ -324,7 +324,7 @@
+         bool return_z_scores=False):
+     cdef DTYPE_INT_t n_bases = fwd_pass.shape[0] - 1
+     cdef DTYPE_INT_t bandwidth = fwd_pass.shape[1]
+-    cdef DTYPE_INT_t half_bandwidth = bandwidth / 2
++    cdef DTYPE_INT_t half_bandwidth = bandwidth // 2
+     cdef DTYPE_INT_t n_events = event_means.shape[0]
+ 
+     # comment out when profiling
+--- a/tombo/_c_helper.pyx
++++ b/tombo/_c_helper.pyx
+@@ -1,3 +1,4 @@
++#cython: cpow=True
+ cimport cython
+ 
+ import numpy as np
+@@ -209,7 +210,7 @@
+     low = 0
+     high = sorted_arr.shape[0] - 1
+     while (low <= high):
+-        mid = (low + high) / 2
++        mid = (low + high) // 2
+         if (sorted_arr[mid] >= value):
+             high = mid - 1
+         else:


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 no_future.patch
 2to3.patch
 mathjax.patch
+cython3-fix.patch



View it on GitLab: https://salsa.debian.org/med-team/tombo/-/compare/35885964822467e6169645ea235b303bfba953c9...8b025770eb1542a5196ef25acb1b5d3c2a2b7bfa

-- 
View it on GitLab: https://salsa.debian.org/med-team/tombo/-/compare/35885964822467e6169645ea235b303bfba953c9...8b025770eb1542a5196ef25acb1b5d3c2a2b7bfa
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/20231203/42a40a90/attachment-0001.htm>