pepkit / pipestat

Pipeline results reporting package
https://pep.databio.org/pipestat/
BSD 2-Clause "Simplified" License
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Adapt yacman v0.9.3 #147

Closed nsheff closed 5 months ago

nsheff commented 5 months ago

Draft PR of changes to make pipestat compatible with yacman v0.9.3, in prep for yacman v1

codecov[bot] commented 5 months ago

Codecov Report

Attention: 3 lines in your changes are missing coverage. Please review.

Comparison is base (6c4797c) 54.51% compared to head (dc47361) 54.56%.

Files Patch % Lines
pipestat/pipestat.py 71.42% 2 Missing :warning:
pipestat/backends/file_backend/filebackend.py 90.90% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## dev #147 +/- ## ========================================== + Coverage 54.51% 54.56% +0.05% ========================================== Files 15 15 Lines 2328 2335 +7 ========================================== + Hits 1269 1274 +5 - Misses 1059 1061 +2 ```

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donaldcampbelljr commented 5 months ago

Ok, I think I've got this completed. One thing is that the new functionality is a bit messier to implement:

        self.cfg[CONFIG_KEY] = YAMLConfigManager(
            entries=config_dict, filepath=self.cfg["config_path"]
        )

becomes

        if config_dict is not None:
            self.cfg[CONFIG_KEY] = YAMLConfigManager.from_obj(entries=config_dict)
        elif self.cfg["config_path"] is not None:
            self.cfg[CONFIG_KEY] = YAMLConfigManager.from_yaml_file(filepath=self.cfg["config_path"])
        else:
            self.cfg[CONFIG_KEY] = YAMLConfigManager()