Added pephub support in looper

khoroshevskyi commented 1 year ago

Added option that supports pephub projects
[x] Add project level pipeline interface ~- [ ] Add changelog~ Will be added in dev branch
[x] Add documentation
[x] :warning: Wait for 1.4.0 release first
[x] include the example config in the docs to show how to set it up.
[x] ❗ add an example to hello_looper to show how to run it. (New repository with project?)
[x] ❗ update the looper init functionality to be able to also populate it with pifaces (still figuring out how to do it right ... should we add new arguments in this case?)
[x] Fixed initialization of generic pipeline interface.
[x] Add tests*

*Update about tests: I can't add full looper running test using pephub, because looper main method contains all running functionality and it means that I can't execute it without using cli. If I want to execute it as a command from terminal, I can't mock few functions, and consequently tests will need actual data from PEPhub.

khoroshevskyi commented 1 year ago

I added possibility of running looper using PEPhub projects.

Example:

looper run pephub::Khoroshevskyi/looper:default --output-dir . -S /path/to/pipeline_interface.yaml

HELP needed:

One of the tests is failing. It is smoke test and is running as subprocess, so I can't figure out where is problem. Additionally, I don't see anything that I added can influence this test. I would appreciate help with this test:)

Everything else done. looper config file still have to be added in Project config (#342). I didn't solve this issue.

nsheff commented 1 year ago

@Khoroshevskyi were you able to solve the broken test on this?

vreuter commented 1 year ago

@Khoroshevskyi were you able to solve the broken test on this?

@nsheff i didn't dig at the details, but when i merged to dev the changes from the attmap removal and the limit / skip work with @donaldcampbelljr , and then reconciled the merge conflicts when i pulled dev back into this feature branch, the test resolved.

https://github.com/pepkit/looper/pull/369/commits/bed956a9537ee906258bec4d88436ef089e8f204

pepkit / looper

Added pephub support in looper #369