Disable progress bar while linting with --hide-progress

[mashehu]

No description provided.

[codecov]

Codecov Report

Merging #1769 (e30ebb4) into dev (d404374) will increase coverage by 0.06%.
The diff coverage is 88.46%.

❗ Current head e30ebb4 differs from pull request most recent head f4449ea. Consider uploading reports for the commit f4449ea to get more accurate results

@@            Coverage Diff             @@
##              dev    #1769      +/-   ##
==========================================
+ Coverage   69.22%   69.28%   +0.06%     
==========================================
  Files          59       59              
  Lines        7142     7147       +5     
==========================================
+ Hits         4944     4952       +8     
+ Misses       2198     2195       -3     

Impacted Files	Coverage Δ
nf_core/modules/modules_json.py	74.65% <ø> (ø)
nf_core/modules/modules_repo.py	84.21% <66.66%> (+1.35%)	⬆️
nf_core/__main__.py	53.50% <100.00%> (+0.72%)	⬆️
nf_core/lint/__init__.py	74.18% <100.00%> (+0.10%)	⬆️
nf_core/modules/lint/__init__.py	82.56% <100.00%> (+0.08%)	⬆️

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

[ewels]

Awesome!

What do you think about putting this at the top level instead, alongside --verbose etc? As it is (a) uncommon to use and (b) used by many commands.

Also, it would be nice to be able to set these with environment variables (much cleaner for this use case for example). Can do that for all options with auto_envvar_prefix, or just this one with envvar. See click docs

[mashehu]

Okay, auto_envvar_prefix is now enabled with prefix NFCORE (I think NF_CORE would have been too confusing, because _ separates subcommands).

I don't know how to nicely pass the option from the main command to the subcommands, so it is still on an individual command level. There is also no global option for rich to disable progress bars, but only on an per instance basis, therefore I think this approach makes it a bit more future proof.

[ewels]

I don't know how to nicely pass the option from the main command to the subcommands

You use click "context" for this, see the click docs. But if we already have it working then it's not a particularly high priority (especially when it's not used on all commands).

[ewels]

Happy with this, thanks! 🙌🏻

[ewels]

Hah, hadn't thought about this - that the env var would be different for different commands.

Ok so then this would be a vote for using an explicit env="HIDE_PROGRESS" on the commands so that we could have one env var that covers the entire tool (or using it on root in one place).

Again low priority. Basically this current setup is fine, might be nice to refactor one day (especially if we add more progress bars) but no needed.