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Bioinformatics

Bioinformatics is an interdisciplinary field that intersects with biology, computer science, mathematics and statistics. It concerns itself with the development and use of methods and software tools for collecting and analyzing biological data.

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dash
peterjc
peterjc commented Dec 18, 2018

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
scanpy
yuanx749
yuanx749 commented Jan 27, 2021

Hi,

Thank you for the great tool. I think this is not a bug.

Recently I upgraded some packages and found my results were different from the previous runs. I figured out that it is caused by different versions of pynndescent (0.4.7 vs 0.5.1), which is recommended to use in UMAP. So I think pynndescent should be included in the output of sc.logging.print_header().

Versions

<d

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