How can I avoid removing comments in CWL ?

[aleksandarbaburski]

Hi,
while formatting CWL code, the cwl-format will remove all comment lines.
Can I avoid that somehow? I would like to have some comments in the code.
Is there a reason for removing comments by default?

Thanks,
Aleksandar

[mr-c]

Hello @aleksandarbaburski

DId you see the first entry in https://github.com/rabix/cwl-format#rules ?

If there are useful comments, perhaps they would make more sense as label and doc entries?

[aleksandarbaburski]

Thanks @mr-c on quick response!

Yes, I sow that first rule, but I wasn't sure if that's some best practice specific for CWL or there is some other reason why classical comments (#) in the CWL code should be avoided?

[aleksandarbaburski]

Hi @mr-c,

I am trying to run the second use case in the "Use programmatically in Python" section:

from cwlformat.formatter import stringify_dict

as_dict = load_yaml(unformatted_text)
formatted_str = stringify_dict(as_dict)

1. I couldn't find load_yaml function. How to import it?
2. It looks like the first 2 rules do not apply to this use case. Here, all the comments (including comments before the actual CWL code) will be removed, right?

FYI @bhanu-gandham

[aleksandarbaburski]

@mr-c, what can be done to override the feature of removing comments within CWL?
On the other hand, if removing those comments is in line with CWL best practice we will use the cwl-format package as is.
Thanks

FYI @bhanu-gandham

[mr-c]

Yes, I sow that first rule, but I wasn't sure if that's some best practice specific for CWL or there is some other reason why classical comments (#) in the CWL code should be avoided?

If the comments would be meaningful to the user of the tool or workflow, then they would be better suited for the various doc and label fields

The choice to remove comments altogether was not mine; this tool was originally written by @kghose

[mr-c]

Replace load_yaml with your preferred yaml loader (pyyaml or ruamel.yaml, for example)

import ruamel.yaml
yaml = ruamel.yaml.YAML()
as_dict = yaml.load( ... )