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 <emoll...@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 <emoll...@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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