Missing .gitmodules?

[kinow]

Hi,

I see .gitmodules was removed in this commit, but the directories janis-core and janis-assistant were kept, as well as the updatesubmodules.sh script. Should these be removed as well?

Cheers Bruno

[illusional]

Hey @kinow, thanks for noticing and raising this issue. I'm not sure why they were removed, but the submodules in this repository are more symbolic for a signpost janis release. You'll see that we make pretty frequent updates to the submodules (janis-core, assistant, bioinformatics and unix), but really only tag a release in this repository when we want to say:

• Hey we've been working on a heap of things, and people who watch this repository should know
• Or, we've made improvements to janisdk, which contains some handy utilities for:
  • generating tool wrappers from a container and a CLI help text (similar to aCLImatise, which can also generate Janis tool wrappers)
  • Converting a tool from CWL to janis (and soon, WDL to Janis)
  • Or running tests, declared in the tool wrappers (you'll see some of those tests run on pull requests in core and assistant).

I'll tag @rlupat and say that should probably be added back in at some point, but not urgently.

[kinow]

Hi @illusional !

Hey @kinow, thanks for noticing and raising this issue. I'm not sure why they were removed, but the submodules in this repository are more symbolic for a signpost janis release.

That makes sense, I also saw some README files mentioning the script used to generate documentation with docs/regeneratedocumentation.py (I think it uses submodules too when generating the docs?)

generating tool wrappers from a container and a CLI help text (similar to aCLImatise, which can also generate Janis tool wrappers)

#TodayILearned about aCLImatise, thanks!

I'll tag @rlupat and say that should probably be added back in at some point, but not urgently.

Thanks!