Pipestat compatibility and move table function to pipestat

pepkit / looper

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http://looper.databio.org

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Pipestat compatibility and move table function to pipestat #409

Closed donaldcampbelljr closed 10 months ago

donaldcampbelljr commented 11 months ago

This PR addresses: https://github.com/pepkit/looper/issues/390

It aligns looper compatibility with pipestat 0.5.0 and greater as well as migrating looper table to pipestat.table.

It removes unused htmlreporting code as well as TableOld, ReportOld, CheckOld, requiring the user to properly configure pipestat if they wish to use these functions.

donaldcampbelljr commented 10 months ago

This requires dev branches of eido (0.2.2.dev0), yacman (0.9.2.dev1) and Peppy (0.40.0a3) to pass tests locally.

donaldcampbelljr commented 10 months ago

[x] Per discussion, change how looper determines pipestat configuration, i.e. instead of relying on pipestat's config file, the looper config file should supply the proper information to use pipestat. #

donaldcampbelljr commented 10 months ago

Passing tests locally except for:

FAILED tests/smoketests/test_run.py::TestLooperConfig::test_init_config_file[run] - Failed: DID RAISE: 'Namespace' object has no attribute 'config_file'
FAILED tests/smoketests/test_run.py::TestLooperConfig::test_init_config_file[runp] - Failed: DID RAISE: 'Namespace' object has no attribute 'config_file'

These failing tests were pulled in from Dev so I believe its not related to this PR's code changes.