[PATCH] gnu: update python-biopython to 1.72

OpenSubmitted by Brett Gilio.
Details
4 participants
  • Andreas Enge
  • Brett Gilio
  • Sarah Morgensen
  • Ludovic Courtès
Owner
unassigned
Severity
normal
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Brett Gilio wrote on 13 Oct 2018 05:49
(address . guix-patches@gnu.org)(name . Brett Gilio)(address . brettg@posteo.net)
20181013034945.9545-1-brettg@posteo.net
--- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-)
Toggle diff (31 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 91bb94c54..2f59211ab 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -12,6 +12,7 @@ ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>+;;; Copyright © 2018 Brett Gilio <brettg@posteo.net> ;;; ;;; This file is part of GNU Guix. ;;;@@ -732,14 +733,14 @@ provide a coordinated and extensible framework to do computational biology.") (define-public python-biopython (package (name "python-biopython")- (version "1.70")+ (version "1.72") (source (origin (method url-fetch) ;; use PyPi rather than biopython.org to ease updating (uri (pypi-uri "biopython" version)) (sha256 (base32- "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))+ "18p5dk9hdjq1p8sz3fgld0yajsdf0bb28gbv4rk0rfdd8cj4jsxb")))) (build-system python-build-system) (arguments `(#:phases-- 2.19.1
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Ludovic Courtès wrote on 21 Oct 2018 23:40
(name . Brett Gilio)(address . brettg@posteo.net)(address . 33032@debbugs.gnu.org)
87o9bn6krx.fsf@gnu.org
Hi Brett,
Brett Gilio <brettg@posteo.net> skribis:
Toggle quote (4 lines)> ---> gnu/packages/bioinformatics.scm | 5 +++--> 1 file changed, 3 insertions(+), 2 deletions(-)
[...]
Toggle quote (4 lines)> (name "python-biopython")> - (version "1.70")> + (version "1.72")
I applied the patch and built tried to build the packages that depend onit, as returned by:
guix refresh -l python-biopython python2-biopython
Unfortunately that triggers a test failure in ‘seqmagic’ (I didn’t seewhether others are failing):
Toggle snippet (46 lines)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
Could you take a look?
Thank you!
Ludo’.
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Ludovic Courtès wrote on 27 Dec 2018 11:59
control message for bug #33032
(address . control@debbugs.gnu.org)
877efvb5g2.fsf@gnu.org
tags 33032 moreinfo
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Andreas Enge wrote on 5 Sep 2020 22:36
Update
(address . 33032@debbugs.gnu.org)
20200905203639.GA24538@jurong
Hello,
I just updated seqmagick to 0.8.0.
Then I tried to update python-biopython to the latest version, 1.78. With it,seqmagick fails to compile with the following message:
mportError: cannot import name 'triefind' from 'Bio' (/gnu/store/9cr6885z39yb5x3pbanva5h9nacmlkvz-python-biopython-1.78/lib/python3.8/site-packages/Bio/__init__.py)
======================================================================ERROR: Failure: ImportError (Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabetfor more information.)

Andreas
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Sarah Morgensen wrote on 14 Sep 05:32 +0200
(name . Andreas Enge)(address . andreas@enge.fr)(address . 33032@debbugs.gnu.org)
86o88vj0h3.fsf@mgsn.dev
Hello,
Andreas Enge <andreas@enge.fr> writes:
Toggle quote (17 lines)> Hello,>> I just updated seqmagick to 0.8.0.>> Then I tried to update python-biopython to the latest version, 1.78. With it,> seqmagick fails to compile with the following message:>> mportError: cannot import name 'triefind' from 'Bio'> (/gnu/store/9cr6885z39yb5x3pbanva5h9nacmlkvz-python-biopython-1.78/lib/python3.8/site-packages/Bio/__init__.py)>> ======================================================================> ERROR: Failure: ImportError (Bio.Alphabet has been removed from Biopython. In> many cases, the alphabet can simply be ignored and removed from scripts. In a> few cases, you may need to specify the ``molecule_type`` as an annotation on a> SeqRecord for your script to work correctly. Please see> https://biopython.org/wiki/Alphabet for more information.)
I think this may be fixed by updating seqmagick to 0.8.1 (currentrelease 0.8.4) and packaging its new dependency, pygtrie, which providesthat removed functionality.
--Sarah
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