Upgrade black to 21.7b0

[jalaziz]

Upgrade to the latest release of black.

This allows downstream projects like Github's super-linter to upgrade black as well.

I am seeing some test failures, but haven't been able to pin down what about the black upgrade is causing the breakage.

[mbhall88]

@bricoletc any idea why changing the black version would cause these 2 grammar tests to fail?

[jalaziz]

@mbhall88 seems like it was an issue with the dev dependencies. By only upgrading black (poetry update --no-dev black) all the tests now pass.

[jalaziz]

If do a full update, I get:

Package operations: 5 installs, 26 updates, 1 removal

  • Removing chardet (4.0.0)
  • Updating decorator (4.4.2 -> 5.0.9)
  • Updating six (1.15.0 -> 1.16.0)
  • Updating attrs (20.3.0 -> 21.2.0)
  • Updating docutils (0.16 -> 0.17.1)
  • Updating pyrsistent (0.17.3 -> 0.18.0)
  • Updating smmap (3.0.5 -> 4.0.0)
  • Updating certifi (2020.12.5 -> 2021.5.30)
  • Installing charset-normalizer (2.0.4)
  • Updating gitdb (4.0.5 -> 4.0.7)
  • Updating idna (2.10 -> 3.2)
  • Updating more-itertools (8.7.0 -> 8.8.0)
  • Updating packaging (20.9 -> 21.0)
  • Installing typing-extensions (3.10.0.0)
  • Updating urllib3 (1.26.3 -> 1.26.6)
  • Updating configargparse (1.3 -> 1.5.1)
  • Installing connection-pool (0.0.3)
  • Updating gitpython (3.1.14 -> 3.1.20)
  • Updating nbformat (5.1.2 -> 5.1.3)
  • Updating pathspec (0.8.1 -> 0.9.0)
  • Updating pycodestyle (2.6.0 -> 2.7.0)
  • Updating pyflakes (2.2.0 -> 2.3.1)
  • Updating regex (2020.11.13 -> 2021.7.6)
  • Updating requests (2.25.1 -> 2.26.0)
  • Updating smart-open (4.2.0 -> 5.1.0)
  • Installing stopit (1.1.2)
  • Installing tabulate (0.8.9)
  • Updating zipp (3.4.0 -> 3.5.0)
  • Updating flake8 (3.8.4 -> 3.9.2)
  • Updating isort (5.7.0 -> 5.9.3)
  • Updating pytest-cov (2.11.1 -> 2.12.1)
  • Updating snakemake (6.0.1 -> 6.6.1)

Seems like the snakemake update may be the reason for the grammar tests failing. If I pin it to 6.0.1, the grammar tests no longer fail.

[jalaziz]

The one non-grammar test seems to fail because of the pathspec update. If I downgrade pathspec and snakemake all tests pass.

Not quite sure why updating pathspec would cause a newline to be removed, but that's a battle for another day. The PR as of my most recent push should be pass all tests now.

[jalaziz]

@mbhall88 Just wanted to follow up and see what I could do to unblock this?

[mbhall88]

Waiting on input from @bricoletc

[codecov]

Codecov Report

Merging #116 (c8a4a99) into master (c81a570) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #116   +/-   ##
=======================================
  Coverage   98.21%   98.21%           
=======================================
  Files          12       12           
  Lines         951      951           
  Branches      174      174           
=======================================
  Hits          934      934           
  Misses         10       10           
  Partials        7        7           

Flag	Coverage Δ
unittests	98.21% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

[bricoletc]

Looks good to me, though now this would make us require python 3.6.2 not 3.6.1 @mbhall88. I guess I'm ok with that though snakemake supports 3.5+

@jalaziz seems like for the super-linter issue, where black version was being pinned by snakefmt, is solved? So do you still need this black version update?

Anyway, I'm happy doing this update as it doesn't break anything

[jalaziz]

Looks good to me, though now this would make us require python 3.6.2 not 3.6.1 @mbhall88. I guess I'm ok with that though snakemake supports 3.5+

@jalaziz seems like for the super-linter issue, where black version was being pinned by snakefmt, is solved? So do you still need this black version update?

Anyway, I'm happy doing this update as it doesn't break anything

@bricoletc Unfortunately the super-linter fix didn't actually work and had to be reverted.