These are two different group of variables with really different precedence. I've placed lots of variables to role/vars and, seems, that should be reviewed.

We have recently dropped Python 2 support, so the following lines can be removed: from __future__ import division from __future__ import print_function There is at least one division import, and lo...

Most modern machines have better typefaces shipped by default. It's worth using them as defaults and fallback on webfonts selectively.

The following modules are not tested because of failing doctests: Bio.AlignIO.MauveIO Bio.Cluster Bio.Data.CodonTable Bio.ExPASy Bio.ExPASy.cellosaurus Bio.File Bio.Medline Bio.motifs.jaspar.db Bio...

The docstrings for the PAML run methods seem a little confusing/out-of-date about the return values. https://github.com/biopython/biopython/blob/biopython-172/Bio/Phylo/PAML/_paml.py#L88 "...

As part of the upgrade to support Python 3.6+ only, many checks for sys.version_info are no longer required. Here is an approximate list: $ grep "version_info" Bio/*.py Bio/*/*.py...

See #26 (comment); we should just print debug messages, if debug is enabled. This change should be done for the complete project.

From redmine XML Blast parser: miscellaneous bug fixes and cleanup Most of the cleanup, bug fixes were done. The last comment was: We could perhaps deprecate record.database_letters immediately, an...

This is a spin out from #2008, where we have agreed to adopt the black code formatting tool for Biopython: https://github.com/psf/black That issue focused on applying black to the main code base (B...

We have now dropped Python 2 support, which means we can take advantage of many of the unittest framework methods where were not present on Python 2. This issue is specifically for using assertIn a...

We have now dropped Python 2 support, which means we can take advantage of many of the unittest framework methods where were not present on Python 2. This issue is specifically for using assertIsIn...

This issue comes from the benchmark in #3230. The first item in the residue id of HETATMs is "H_" + res.resname. Because the PDB format is a column-delimited format, we don&#3...

This is a spin out from #2700 and #2835, on a related set of stylistic improvements to our use of the unittest testing framework, which can be spotted using flake8-assertive: $ pip install flake8-a...

Related problem No response Describe the solution you'd like It would be really useful if you could specify a custom startup script to run for a login shell. Describe alternatives you&#...

Related problem People can't find what they're looking for. Describe the solution you'd like It would be nice to add search terms to extra_usage so that when people use help...

Describe the bug the extra_usage text was accidentally removed from open when porting open, because open doesn't do encoding/decoding any longer. it needs to be put back in, at some point, ...

The book still mentions insert as the way to add a new column to a table: https://www.nushell.sh/book/working_with_tables.html#changing-data-in-a-table insert has been deprecated in favour of updat...