[med-svn] [Git][med-team/python-biopython][master] 3 commits: skip-scipy-in-codonalign.patch: also skip on mips64el.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / python-biopython


Commits:
3fb9c7ee by Étienne Mollier at 2024-10-18T11:27:10+02:00
skip-scipy-in-codonalign.patch: also skip on mips64el.

The symptom of scipy processing hanging up appeared already in
riscv64, now on mips64el.

- - - - -
415b471a by Étienne Mollier at 2024-10-18T11:28:14+02:00
d/rules: skip test of BWA on mips64el.

- - - - -
fc95017a by Étienne Mollier at 2024-10-18T11:30:20+02:00
Ready for upload to unstable.

- - - - -


3 changed files:

- debian/changelog
- debian/patches/skip-scipy-in-codonalign.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+python-biopython (1.84+dfsg-3) unstable; urgency=medium
+
+  * skip-scipy-in-codonalign.patch: also skip on mips64el.
+    The symptom of scipy processing hanging up appeared already in
+    riscv64, now on mips64el.
+  * d/rules: skip test of BWA on mips64el.
+
+ -- Étienne Mollier <emollier at debian.org>  Fri, 18 Oct 2024 11:30:13 +0200
+
 python-biopython (1.84+dfsg-2) unstable; urgency=medium
 
   * d/t/run-unit-test: disable PDB_binary_cif for s390x in autopkgtest too.


=====================================
debian/patches/skip-scipy-in-codonalign.patch
=====================================
@@ -18,9 +18,9 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  
 +        import os
 +        import sys
-+        if os.uname().machine == 'riscv64':
++        if os.uname().machine == 'riscv64' or os.uname().machine == 'mips64':
 +            print('note: tests involving scipy skipped, '
-+                    'they hang on riscv64.', file=sys.stderr)
++                    'they hang on riscv64 and mips64.', file=sys.stderr)
 +            return
          try:
              import scipy
@@ -35,9 +35,9 @@ index d4bcd52..2f9c41d 100644
  
 +        import os
 +        import sys
-+        if os.uname().machine == 'riscv64':
++        if os.uname().machine == 'riscv64' or os.uname().machine == 'mips64':
 +            print('note: tests involving scipy skipped, '
-+                    'they hang on riscv64.', file=sys.stderr)
++                    'they hang on riscv64 and mips64.', file=sys.stderr)
 +            return
          try:
              import scipy


=====================================
debian/rules
=====================================
@@ -49,6 +49,17 @@ ifeq ($(BUILDARCH),riscv64)
     EXCLUDEARCH+=NCBI_BLAST_tools
 endif
 
+ifeq ($(BUILDARCH),mips64el)
+    # FIXME: bwa on mips64el is affected by the following issue, so
+    # skipping for now:
+    #
+    #   Bio.Application.ApplicationError: Non-zero return code 138 from
+    #   'bwa mem BWA/human_g1k_v37_truncated.fasta
+    #   BWA/HNSCC1_1_truncated.fastq BWA/HNSCC1_2_truncated.fastq',
+    #   message '[M::bwa_idx_load_from_disk] read 0 ALT contigs'
+    EXCLUDEARCH+=BWA_tool
+endif
+
 ifeq ($(BUILDARCH),s390x)
     # PDB binary cif parsing is non-working on big endian platforms.
     # The parsing is fed to C code which would need potientially



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/b02520908486d28e92cf86004312338cfca4c7bb...fc95017a23de6ead7be57971126bdda35a2504d9

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/b02520908486d28e92cf86004312338cfca4c7bb...fc95017a23de6ead7be57971126bdda35a2504d9
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