[med-svn] [Git][med-team/python-skbio][master] Try fixing some issue for 32bit architectures

[Andreas Tille (@tille)]

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


Commits:
086d2b59 by Andreas Tille at 2023-01-29T11:26:08+01:00
Try fixing some issue for 32bit architectures

- - - - -


3 changed files:

- debian/changelog
- debian/patches/numpy-1.24.patch
- debian/salsa-ci.yml


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+python-skbio (0.5.8-2exp2) UNRELEASED; urgency=medium
+
+  * Try fixing some issue for 32bit architectures
+
+ -- Andreas Tille <tille at debian.org>  Sun, 29 Jan 2023 11:25:28 +0100
+
 python-skbio (0.5.8-2exp1) experimental; urgency=medium
 
   * Deactivate patch that builds against scipy 1.81. and building against


=====================================
debian/patches/numpy-1.24.patch
=====================================
@@ -6,7 +6,7 @@ Forwarded: https://github.com/biocore/scikit-bio/issues/1839
 
 --- a/skbio/alignment/_indexing.py
 +++ b/skbio/alignment/_indexing.py
-@@ -113,7 +113,10 @@
+@@ -113,7 +113,10 @@ class _Indexing(metaclass=ABCMeta):
          if isinstance(indexable, np.ndarray):
              pass
          elif hasattr(indexable, '__iter__'):
@@ -20,7 +20,7 @@ Forwarded: https://github.com/biocore/scikit-bio/issues/1839
  
 --- a/skbio/sequence/tests/test_sequence.py
 +++ b/skbio/sequence/tests/test_sequence.py
-@@ -459,7 +459,7 @@
+@@ -459,7 +459,7 @@ class TestSequence(TestSequenceBase, Rea
              Sequence(np.array([1, "23", 3]))
          with self.assertRaises(TypeError):
              # object
@@ -29,7 +29,7 @@ Forwarded: https://github.com/biocore/scikit-bio/issues/1839
  
          # invalid input type (non-numpy.ndarray input)
          with self.assertRaisesRegex(TypeError, r'tuple'):
-@@ -2212,7 +2212,7 @@
+@@ -2212,7 +2212,7 @@ class TestSequence(TestSequenceBase, Rea
                      yield i
                  else:
                      yield np.array([i], dtype=int)
@@ -38,3 +38,14 @@ Forwarded: https://github.com/biocore/scikit-bio/issues/1839
                    lambda x: pd.Series(tuple(x))):
              exp = np.arange(10, dtype=int)
              obs = s._munge_to_index_array(c(mixed()))
+--- a/skbio/io/format/fasta.py
++++ b/skbio/io/format/fasta.py
+@@ -880,7 +880,7 @@ def _parse_quality_scores(chunks):
+ 
+     qual_str = ' '.join(chunks)
+     try:
+-        quality = np.asarray(qual_str.split(), dtype=int)
++        quality = np.asarray(qual_str.split(), dtype=int64)
+     except ValueError:
+         raise QUALFormatError(
+             "Could not convert quality scores to integers:\n%s"


=====================================
debian/salsa-ci.yml
=====================================
@@ -4,7 +4,5 @@ include:
   - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
 
 variables:
-  # i386 is explicitly excluded
-  SALSA_CI_DISABLE_BUILD_PACKAGE_I386: 1
   # Build against scipy 1.10 in experimental
   RELEASE: 'experimental'



View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/commit/086d2b596a637c18c4d8ef9307ea941d24df5afc

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/commit/086d2b596a637c18c4d8ef9307ea941d24df5afc
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