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silence warnings PDBConstructionWarning in test_PDB_StructureAlignment.py #1877
Description
Setup
Seen with latest code from git while preparing the 1.73 release on Linux, but applies to all platforms.
Expected behaviour
$ python run_tests.py test_PDB_StructureAlignment.py
Python version: 2.7.15 | packaged by conda-forge | (default, Jul 27 2018, 10:26:36)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
Operating system: posix linux2
test_PDB_StructureAlignment ... ok
----------------------------------------------------------------------
Ran 1 test in 0.958 seconds
Actual behaviour
$ python run_tests.py test_PDB_StructureAlignment.py
Python version: 2.7.15 | packaged by conda-forge | (default, Jul 27 2018, 10:26:36)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
Operating system: posix linux2
test_PDB_StructureAlignment ... /tmp/biopython-1.73/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.py:91: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 13298.
PDBConstructionWarning)
/tmp/biopython-1.73/build/lib.linux-x86_64-2.7/Bio/PDB/StructureBuilder.py:91: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 13344.
PDBConstructionWarning)
ok
----------------------------------------------------------------------
Ran 1 test in 0.958 seconds
Steps to reproduce
Use python run_tests.py --offline test_PDB_StructureAlignment.py or similar.
We need to catch and ignore the PDBConstructionWarning here, see for example:
https://github.com/biopython/biopython/blob/biopython-172/Tests/test_PDB.py#L107
i.e. Wrap as few lines as possible in the context manager
Activity
konqr commentedon Dec 20, 2018
Hey. Beginner here. I am on it. :)
konqr commentedon Dec 20, 2018
@peterjc Done. PR added.
konqr commentedon Dec 21, 2018
Hey Peter. Thanks for the email. Sorry for the wrong PR. I understood what you want to be done. I'm on it, thanks.
konqr commentedon Dec 21, 2018
Please check #1881 for PR. Hope this runs well.
Silence PDBConstructionWarning in test_PDB_StructureAlignment
Silence PDBConstructionWarning in test_PDB_StructureAlignment
Silence PDBConstructionWarning in test_PDB_StructureAlignment