[med-svn] [Git][med-team/python-cutadapt][master] Replace the patch to fix the failing test in i386

[Lance Lin (@linqigang)]

Lance Lin pushed to branch master at Debian Med / python-cutadapt


Commits:
52e7e12e by Lance Lin at 2023-09-22T21:52:17+07:00
Replace the patch to fix the failing test in i386

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/Update__kmer_finder.pyx_to_always_use_a_64-bit_integer.patch
- − debian/patches/add_error_catching_for_test_in_i386.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -12,8 +12,8 @@ python-cutadapt (4.4-1) UNRELEASED; urgency=medium
     to /dev/null
   * d/patches/xfail_cutadapt_executable_test.patch: Remove patch so that test
     is run during autopkgtest
-  * d/patches/add_error_catching_for_test_in_i386.patch: Allow test to pass in
-    i386 with error catching
+  * d/patches/Update__kmer_finder.pyx_to_always_use_a_64-bit_integer.patch:
+    Allow test to pass in i386 with 64-bit integer
 
  -- Lance Lin <lq27267 at gmail.com>  Tue, 19 Sep 2023 22:46:11 +0700
 


=====================================
debian/patches/Update__kmer_finder.pyx_to_always_use_a_64-bit_integer.patch
=====================================
@@ -0,0 +1,25 @@
+Bug: https://github.com/marcelm/cutadapt/issues/730, https://github.com/marcelm/cutadapt/pull/731
+Description: Update _kmer_finder.pyx to always use a 64-bit integer
+Author: Lance Lin <lq27267 at gmail.com>
+Date: 2023-09-22
+
+--- a/src/cutadapt/_kmer_finder.pyx
++++ b/src/cutadapt/_kmer_finder.pyx
+@@ -4,7 +4,7 @@
+ from libc.string cimport memcpy, memset, strlen
+ 
+ from cpython.unicode cimport PyUnicode_CheckExact, PyUnicode_GET_LENGTH
+-from libc.stdint cimport uint8_t
++from libc.stdint cimport uint8_t, uint64_t
+ 
+ from ._match_tables import matches_lookup
+ 
+@@ -47,7 +47,7 @@
+ # Dnaio conveniently ensures that all sequences are ASCII only.
+ DEF BITMASK_INDEX_SIZE = 128
+ 
+-ctypedef size_t bitmask_t
++ctypedef uint64_t bitmask_t
+ 
+ cdef extern from "Python.h":
+     void *PyUnicode_DATA(object o)


=====================================
debian/patches/add_error_catching_for_test_in_i386.patch deleted
=====================================
@@ -1,29 +0,0 @@
-Bug: https://github.com/marcelm/cutadapt/issues/730
-Description: Add error catching for test run in i386 architecture
-Author: Lance Lin <lq27267 at gmail.com>
-Date: 2023-09-21
-
---- a/tests/test_kmer_finder.py
-+++ b/tests/test_kmer_finder.py
-@@ -82,12 +82,15 @@
- 
- 
- def test_kmer_finder_initialize_total_greater_than_max():
--    kmer_finder = KmerFinder([(0, None, ["A" * 31, "B" * 31, "C" * 31, "D" * 43])])
--    assert kmer_finder.kmers_present("X" * 100 + "A" * 31)
--    assert kmer_finder.kmers_present("X" * 100 + "B" * 31)
--    assert kmer_finder.kmers_present("X" * 100 + "C" * 31)
--    assert kmer_finder.kmers_present("X" * 100 + "D" * 43)
--    assert not kmer_finder.kmers_present(string.ascii_letters)
-+    try:
-+        kmer_finder = KmerFinder([(0, None, ["A" * 31, "B" * 31, "C" * 31, "D" * 43])])
-+        assert kmer_finder.kmers_present("X" * 100 + "A" * 31)
-+        assert kmer_finder.kmers_present("X" * 100 + "B" * 31)
-+        assert kmer_finder.kmers_present("X" * 100 + "C" * 31)
-+        assert kmer_finder.kmers_present("X" * 100 + "D" * 43)
-+        assert not kmer_finder.kmers_present(string.ascii_letters)
-+    except ValueError as error:
-+        assert ("D" * 43) in str(error)
- 
- 
- def test_kmer_finder_finds_all():


=====================================
debian/patches/series
=====================================
@@ -1 +1 @@
-add_error_catching_for_test_in_i386.patch
+Update__kmer_finder.pyx_to_always_use_a_64-bit_integer.patch



View it on GitLab: https://salsa.debian.org/med-team/python-cutadapt/-/commit/52e7e12e2597e2d96fa5d79b162d77176b0ef884

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-cutadapt/-/commit/52e7e12e2597e2d96fa5d79b162d77176b0ef884
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