[Debian-med-packaging] Bug#1079439: python-biopython: autopkgtest stuck on riscv64

[Étienne Mollier]

Hi,

Err, I haven't forgotten about the issue, but I have been
banging my head on a weird import issue until I glued os and sys
import to point at which the logic of the skip for riscv64 is
implemented; see the patch below.  Now that the test suite goes
through, it is capable of reporting a couple of issues that were
hidden until then on riscv64 due to the cpu hog.  Relevant part
of the output for reference:

	======================================================================
	FAIL: test_fasta_db_nucl (test_NCBI_BLAST_tools.BlastDB.test_fasta_db_nucl)
	Test makeblastdb wrapper with nucleotide database.
	----------------------------------------------------------------------
	Traceback (most recent call last):
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/Tests/test_NCBI_BLAST_tools.py", line 344, in test_fasta_db_nucl
	    self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nhd"))
	AssertionError: False is not true
	
	======================================================================
	FAIL: test_fasta_db_prot (test_NCBI_BLAST_tools.BlastDB.test_fasta_db_prot)
	Test makeblastdb wrapper with protein database.
	----------------------------------------------------------------------
	Traceback (most recent call last):
	  File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/Tests/test_NCBI_BLAST_tools.py", line 251, in test_fasta_db_prot
	    self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.phd"))
	AssertionError: False is not true

It is a bit unclear to my why these nhd and phd files would be
missing.  This may be a problem with ncbi-blast+, but would need
further investigation to tell for sure.

Have a nice day,  :)
-- 
  .''`.  Étienne Mollier <emollier at debian.org>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/3, please excuse my verbosity
   `-


Description: skip scipy tests within test_Align_codonalign.
 This patch is introduced to give some breath to Risc-V CI runners while
 the core of the problem is investigated.

Author: Étienne Mollier <emollier at debian.org>
Bug-Debian: https://bugs.debian.org/1079439
Forwarded: not-needed
Last-Update: 2024-08-25
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- python-biopython.orig/Tests/test_Align_codonalign.py
+++ python-biopython/Tests/test_Align_codonalign.py
@@ -8230,6 +8230,12 @@
         self.assertAlmostEqual(dN, 0.0203, places=4)
         self.assertAlmostEqual(dS, 0.0164, places=4)
 
+        import os
+        import sys
+        if os.uname().machine == 'riscv64':
+            print('note: tests involving scipy skipped, '
+                    'they hang on riscv64.', file=sys.stderr)
+            return
         try:
             import scipy
         except ImportError:
--- python-biopython.orig/Tests/test_codonalign.py
+++ python-biopython/Tests/test_codonalign.py
@@ -307,6 +307,12 @@
         self.assertAlmostEqual(dN, 0.0203, places=4)
         self.assertAlmostEqual(dS, 0.0164, places=4)
 
+        import os
+        import sys
+        if os.uname().machine == 'riscv64':
+            print('note: tests involving scipy skipped, '
+                    'they hang on riscv64.', file=sys.stderr)
+            return
         try:
             import scipy
         except ImportError:
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