The new flake8-bugbear 22.7.1 warns if a function defined inside a loop uses
a variable redefined in the loop, due to the late-binding closure gotcha:
https://docs.python-guide.org/writing/gotchas/#late-binding-closures
When possible/sensible, I've moved the function definition before the loop
(adding the variable(s) as parameters) which is clearly also a speed-up.
Most other cases are false alarms, e.g. if the function is used and
discarded within the loop iteration that defines it. In such cases, I've
annotated the offending lines with a `# noqa: B023`.
The only file where I've applied the suggested workaround of immediately
binding arguments is in `lib/galaxy/visualization/plugins/config_parser.py`
Also:
- Small refactorings, in particular to `scripts/apply_tags.py`
instead of directly loading it as YAML.
Will make it easier to uniformly deal with changes of format (e.g.
we are deprecating ini now).
Fix traceback:
```
Traceback (most recent call last):
File "scripts/config_parse.py", line 31, in <module>
main(args.config_file, args.setting)
File "scripts/config_parse.py", line 16, in main
gx_config = GalaxyAppConfiguration(**yaml.safe_load(open(config))["galaxy"])
File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/__init__.py", line 125, in safe_load
return load(stream, SafeLoader)
File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/__init__.py", line 81, in load
return loader.get_single_data()
File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/constructor.py", line 49, in get_single_data
node = self.get_single_node()
File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/composer.py", line 39, in get_single_node
if not self.check_event(StreamEndEvent):
File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/parser.py", line 98, in check_event
self.current_event = self.state()
File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/parser.py", line 171, in parse_document_start
raise ParserError(None, None,
yaml.parser.ParserError: expected '<document start>', but found '<scalar>'
in "/tmp/tmpsffm7of5/galaxy.ini", line 3, column 1
```
when starting Galaxy with a `galaxy.ini` config file (though Galaxy startup
will still fail later).
John Davis