Donald Campbell
Donald Campbell
This appears to be happening in all branches for me. Currently running PyTests and the terminal outputs many of these logging errors making it difficult to read testing results. ```...
Currently, Looper checks if Pipestat has been configured for **each sample** before adding the sample to the submission conductor. If pipestat can be successfully configured, looper generates a configuration file...
Addresses Issues for https://github.com/pepkit/looper/milestone/13 A couple issues on milestone 1.8.0 are still outstanding but they are lower priority. If they are not solved by EOD Friday, they will be moved...
Seeing some of these warnings in the testing suite via the `test_args_expansion` function: ``` PytestReturnNotNoneWarning: Expected None, but tests/test_comprehensive.py::test_args_expansion returned ['--dry-run'], which will be an error in a future version...
Related to this Pipestat enhancement: https://github.com/pepkit/pipestat/issues/125 Can Looper easily distinguish between using an input pep and sending an output pep for results reporting via pipestat? Pipestat now has the `pephub_path`...
Noticing this as I refactor Looper tests. ``` pep_config: project/project_config.yaml output_dir: "results" pipeline_interfaces: sample: - pipeline/pipeline_interface1_sample.yaml - pipeline/pipeline_interface2_sample.yaml ``` ``` pep_config: project/project_config.yaml output_dir: "results" pipeline_interfaces: sample: pipeline/pipeline_interface1_sample.yaml ``` The piface...
> However, Looper goes on to later call `prj.name` and it fails with the exception: `Project name inference isn't supported on a project that lacks a config file.` This would...
Will proceed with having Looper construct a new pipestat config file from a given pipestat config file AND the pipeline interfaces. Looper will use that config file to construct pipestat...
Related to: https://github.com/pepkit/looper/issues/392 https://github.com/pepkit/looper/issues/397 In my attempt to replicate #392, I noticed that, when using a looper config file for pipestat, if the pipestat initialization fails, Looper will raise an...
This is a workaround so that `looper runp` does not fail by not passing a record_identifier to pipestat during the initial pipestat instantiation when outputing results to different result files...