lint multiple tools at once (command line API change)

[peterjc]

Current usage:

Usage: planemo lint [OPTIONS] TOOL_PATH

e.g.

$ planemo lint --report_level warn ../pico_galaxy/tools/seq_filter_by_id
$ planemo lint --report_level warn ../pico_galaxy/tools/seq_filter_by_mapping

I would like to be able to list multiple paths in the same command, e.g.

$ planemo lint --report_level warn ../pico_galaxy/tools/seq_filter_by_id ../pico_galaxy/tools/seq_filter_by_mapping

This would then allow wildcard via the command line expansion, e.g.

$ planemo lint --report_level warn ../pico_galaxy/tools/seq_filter_by_*

[hexylena]

👍, also would like to see a -r flag to mirror shed_lint

[peterjc]

Good idea - I was thinking about that too, e.g.

$ planemo lint --report_level warn -r ../pico_galaxy/tools/

Worth a separate issue?

[jmchilton]

planemo lint is attempting to -r when you give it a directory - the fact that it doesn't is kind of a bug I think.

Update: In the sense it will lint everything in the directory - it is annoying that it is not going into subdirectories. I think this should just be the default behavior - objections?

[jmchilton]

@jmchilton But then it wouldn't match the semantics of test, maybe flagging it with -r is a good idea.

[hexylena]

👍 to planemo lint /dir/ meaning planemo lint /dir/*.xml and -r being separate.

[jmchilton]

@erasche Okay - that feels correcter to me for some reason so as long as that is not confusing to a not-@jmchilton I think that is what we should do. Also allowing multiple tools/directories to be passed is a no brainier - test should work that way to do.

[peterjc]

I'm happy to let you guys decide the API based on the existing usage patterns in the other planemo commands.

[peterjc]

Lovely - this is working nicely for me - thanks :)

[peterjc]

I'm unclear about the intended usage of planemo lint vs planemo shed_lint, but does that also need to allow multiple PROJECT arguments to match?

[jmchilton]

shed_lint first finds "tool shed repositories" (e.g. directories with .shed.yml files) and then lints "any included tool" (right now that just means everything other the .shed.yml file but in the future it will be smarter and only lint things that would be uploaded). lint --recurisive will just lint all tools - it doesn't need to find a .shed.yml file first. I guess shed_lint will assume the directory you give it corresponds to a tool shed repository if it cannot find any .shed.yml files - so perhaps in your case they look pretty simillair. There is also differences related to the way they are displayed - shed_lint tries to show tool linting in the context of the repository with a little + it is slight. The other big difference is that shed_lint lint tool shed artifacts as well.

But yeah - shed_lint should also allow multiple inputs.

[peterjc]

Thanks - and yes, since right now I have no .shed.yml files the two commands seemed very similar.

What does "tool shed artefacts" mean for shed_lint?

[jmchilton]

Tool Shed artifact linting means...

• Pretty much full XSD validation of repository_dependencies.xml files (at the top of shed repositories).
• Partial XSD validation of tool_dependencies.xml files (at the top of shed repositories).
• Checking README files ( linting: Check for suitable README file #89 ) ( linting: Check reStructuredText markup in any .rst files #91 ) (at the top of shed repositories)
• Basic checks of .shed.yml
  • is your repository name and owner valid
  • is the category extant
  • does the name match best practice (package_ for tool_dependency_definitions, etc...).

Can track progress on this at - #107

Basically the goal would be to ensure shed_create and shed_upload commands will work after linting. Obviously there is still a lot that linting is not catching - but it has caught some stuff (markdown readme files, malformed tool_dependencies.xml, mis-named repositories).

[peterjc]

Thanks - I should be using planemo shed_lint in preference to planemo lint for broader coverage.

[jmchilton]

If you want all your tools covered regardless of what happens with shed_lint it might be worth separating it out into two commands:

planemo lint -r .
planemo shed_lint -r .

and run shed_lint without --tools. Up to you though - I'll try to continue to support shed_lint without .shed.yml files.