Upgrade versioneer, fix flake8 + other misc fixes

[DimitriPapadopoulos]

https://lgtm.com/projects/g/bids-standard/bids-validator/?severity=error

Fix the first of two errors, the fix seems rather obvious.

The other error is in _version.py and has been fixed upstream in python-versioneer/python-versioneer#250.

[codecov]

Codecov Report

Merging #1336 (9b5ebe3) into master (7cc3947) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #1336   +/-   ##
=======================================
  Coverage   84.78%   84.78%           
=======================================
  Files          82       82           
  Lines        3372     3372           
  Branches      999      999           
=======================================
  Hits         2859     2859           
  Misses        434      434           
  Partials       79       79           

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[sappelhoff]

for the _version related problem, we could update our vendored versioneer version: https://github.com/python-versioneer/python-versioneer#updating-versioneer

That should fix it, be backward compatible, and give us an up to date versioneer that is now being maintained by our very own @effigies

[DimitriPapadopoulos]

CI fails with:

bids-validator/bids_validator/_version.py:339:80: E501 line too long (84 > 79 characters)

I don't want to modify the _version.py file generated by versioneer, I cannot find a versioneer option to obtain a different _version.py file. The only option I can think of is to change the CI configuration to accept lines < 85 characters instead of lines < 80 characters. Or perhaps < 89 characters like black?

[sappelhoff]

you can setup a section on flake8 in our setup.cfg to ignore the versioneer files.

Example how to do it

Place where to do it here

[DimitriPapadopoulos]

Should be OK for flake8.

Not sure how to fix that for pytest:

setup.cfg files are general purpose configuration files, used originally by distutils, and can also be used to hold pytest configuration if they have a [tool:pytest] section.
[...]

Warning:

Usage of setup.cfg is not recommended unless for very simple use cases. .cfg files use a different parser than pytest.ini and tox.ini which might cause hard to track down problems. When possible, it is recommended to use the latter files, or pyproject.toml, to hold your pytest configuration.

Is it OK to create a pytest.ini file?

[DimitriPapadopoulos]

Actually not OK for flake8, because as far as I can see, it is run from bids-validator, not from bids-validator/bids-validator.

[sappelhoff]

Is it OK to create a pytest.ini file?

if you can figure out a minimal solution that involves us having to add a file, that'd still be fine I think.

But reusing existing config files would be better :) (if possible)

[effigies]

Pytest can be configured in setup.cfg.

[DimitriPapadopoulos]

I know, but the pytest documentation warns:

Warning:

Usage of setup.cfg is not recommended unless for very simple use cases. .cfg files use a different parser than pytest.ini and tox.ini which might cause hard to track down problems. When possible, it is recommended to use the latter files, or pyproject.toml, to hold your pytest configuration.

Hopefully this is a very simple case 😃

[DimitriPapadopoulos]

OK, all options have been added to setup.cfg.

Now I need to tell Code Climate not to bother with versioneer.py and _version.py.

[DimitriPapadopoulos]

See #1341 for shutting up Cold Climate. Hopefully it'll work...

[DimitriPapadopoulos]

Still these codeclimate errors. I just don't know how to exclude the versioneer files. Any clues?

The ci/circleci: test_docker failure looks like a more general problem, unrelated to this PR.

[sappelhoff]

I think code climate only complains on new changes. So after committing the versioneer files initially, it won't be a problem in the next prs.

It's not as satisfying, but I don't know how else to fix it.

[DimitriPapadopoulos]

I thought #1341 would help:

exclude_patterns:
  - "**/versioneer.py"
  - "**/_version.py"

It should according to the documentation, but doesn't :-(

[sappelhoff]

In 754bf25 I tried whether the exclude patterns work when they are absolute (relative to the .codeclimate.yml file), instead of globs. That didn't work.

Now I am wondering whether .codeclimate.yml is perhaps ignored in general, and should be at the root of the REPO, not nested inside the bids-validator directory 🤔

[DimitriPapadopoulos]

Now I am wondering whether .codeclimate.yml is perhaps ignored in general, and should be at the root of the REPO, not nested inside the bids-validator directory thinking

Makes sense. I'm moving it around in #1347.

[DimitriPapadopoulos]

Eventually got CodeClimate to work properly by (I think) moving bids-validator/.codeclimate.yml to .codeclimate.yml (#1347).

[sappelhoff]

wonderful, thanks for sticking with this.