[bug#33032] [PATCH] gnu: update python-biopython to 1.72

[Ludovic Courtès]

Hi Brett,

Brett Gilio <address@hidden> skribis:

> ---
>  gnu/packages/bioinformatics.scm | 5 +++--
>  1 file changed, 3 insertions(+), 2 deletions(-)

[...]

>      (name "python-biopython")
> -    (version "1.70")
> +    (version "1.72")

I applied the patch and built tried to build the packages that depend on
it, as returned by:

  guix refresh -l python-biopython python2-biopython

Unfortunately that triggers a test failure in ‘seqmagic’ (I didn’t see
whether others are failing):

--8<---------------cut here---------------start------------->8---
ERROR: test_dna_protein_nogap_stop 
(seqmagick.test.test_transform.TranslateTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File 
"/tmp/guix-build-seqmagick-0.7.0.drv-0/seqmagick-0.7.0/seqmagick/test/test_transform.py",
 line 513, in test_dna_protein_nogap_stop
    self.assertEqual(expected, [str(i.seq) for i in actual])
  File 
"/tmp/guix-build-seqmagick-0.7.0.drv-0/seqmagick-0.7.0/seqmagick/test/test_transform.py",
 line 513, in <listcomp>
    self.assertEqual(expected, [str(i.seq) for i in actual])
  File 
"/tmp/guix-build-seqmagick-0.7.0.drv-0/seqmagick-0.7.0/seqmagick/transform.py", 
line 703, in translate
    protein = seq.translate(table, to_stop=to_stop)
  File 
"/gnu/store/ng8rrazi7kwchsmnhmhkjdfgjsv3lngv-python-biopython-1.72/lib/python3.6/site-packages/Bio/Seq.py",
 line 1163, in translate
    cds, gap=gap)
  File 
"/gnu/store/ng8rrazi7kwchsmnhmhkjdfgjsv3lngv-python-biopython-1.72/lib/python3.6/site-packages/Bio/Seq.py",
 line 2543, in _translate_str
    dual_coding = [c for c in stop_codons if c in forward_table]
  File 
"/gnu/store/ng8rrazi7kwchsmnhmhkjdfgjsv3lngv-python-biopython-1.72/lib/python3.6/site-packages/Bio/Seq.py",
 line 2543, in <listcomp>
    dual_coding = [c for c in stop_codons if c in forward_table]
  File 
"/tmp/guix-build-seqmagick-0.7.0.drv-0/seqmagick-0.7.0/seqmagick/transform.py", 
line 663, in __getitem__
    elif '-' in codon:
TypeError: argument of type 'int' is not iterable
-------------------- >> begin captured logging << --------------------
root: INFO: Applying translation generator: operation to perform is 
dna2proteinstop.
--------------------- >> end captured logging << ---------------------

----------------------------------------------------------------------
Ran 164 tests in 1.530s

FAILED (errors=7, skipped=7)
Test failed: <unittest.runner.TextTestResult run=164 errors=7 failures=0>
error: Test failed: <unittest.runner.TextTestResult run=164 errors=7 failures=0>
Backtrace:
           5 (primitive-load "/gnu/store/hg9qrk8cr2aw2y4ylxdcnlvpb3y…")
In ice-9/eval.scm:
   191:35  4 (_ _)
In srfi/srfi-1.scm:
    640:9  3 (for-each #<procedure 94c140 at /gnu/store/5sy3815dpjc…> …)
In 
/gnu/store/5sy3815dpjcvxhssaba6g2ilxm29va9n-module-import/guix/build/gnu-build-system.scm:
   799:31  2 (_ _)
In 
/gnu/store/5sy3815dpjcvxhssaba6g2ilxm29va9n-module-import/guix/build/python-build-system.scm:
    142:8  1 (check #:tests? _ #:test-target _ #:use-setuptools? _)
In 
/gnu/store/5sy3815dpjcvxhssaba6g2ilxm29va9n-module-import/guix/build/utils.scm:
    616:6  0 (invoke _ . _)

/gnu/store/5sy3815dpjcvxhssaba6g2ilxm29va9n-module-import/guix/build/utils.scm:616:6:
 In procedure invoke:
Throw to key `srfi-34' with args `(#<condition &invoke-error [program: "python" 
arguments: ("-c" "import setuptools, 
tokenize;__file__='setup.py';f=getattr(tokenize, 'open', 
open)(__file__);code=f.read().replace('\\r\\n', 
'\\n');f.close();exec(compile(code, __file__, 'exec'))" "test") exit-status: 1 
term-signal: #f stop-signal: #f] 99fec0>)'.
builder for `/gnu/store/a6zljh5pn0agm0rdf8bhx7c8hk9hia1d-seqmagick-0.7.0.drv' 
failed with exit code 1
--8<---------------cut here---------------end--------------->8---

Could you take a look?

Thank you!

Ludo’.