feat: add gitfile option to make it possible to use local git repos when importing modules

[Smeds]

Feat: add gitfile option to make it possible to use local git repos when importing modules.

Should make it possible to include module like this:

module dna_seq:
    snakefile: gitfile("file:///beegfs-storage/LOCAL_PATH/dna-seq-gatk-variant-calling", path="workflow/Snakefile", tag="main")
    config: config

solves issues:

• LocalGitFile never opend due to variable passed as string #1372
• Unable to use LocalGitFile #1308

[johanneskoester]

Thanks a lot. Some comments below. Apart from that, can you add some test case(s)?

[Smeds]

Thanks a lot. Some comments below. Apart from that, can you add some test case(s)?

I have updated the code now.

I could add small git repo in the tests folder with commits that a workflow will have to use.

[Smeds]

I need some thoughts of how to handle tests for this pull-request. I have create "module" use to test the new functionality:
1 - A successfull use of gitfile
2 - A case where a rule is missing
3 - A case where a schema is missing

But to be able to run the test I would have to include a .git folder with the module, which git isn't alllowing me to do.

The only solution I can think of now is to compress the folder and decompress it before running the different tests.

@johanneskoester Do you have any good suggestion of how to handle this?

[Smeds]

Could git Submodules be a acceptable solution?

[Smeds]

Could git Submodules be a acceptable solution?

Didn't work

[Smeds]

)

I have added test cases now

[johanneskoester]

We are getting there! See below.

[Smeds]

@johanneskoester would there be any point of supporting relative path when importing a module using gitfile? At the moment I believe the could requires an absolute path.

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

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0.9% Duplication

[Smeds]

done

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

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No Coverage information
0.8% Duplication

[Smeds]

@johanneskoester it should now allow for relative paths

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.6% Duplication