Release pypiper v0.13.0 with pipestat support #21
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donaldcampbelljr
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donaldcampbelljr
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* Work towards pypier utilizing pipestat changes. Related: pepkit/pipestat#21 * Refactor to align with pipestat refactoring. Create default output schema to satisfy pipestat requirements. * Call pipestat backend for setting status. Set status for pipeline.manager. * Pytest fixes. * Pytest fixes, revert old test. * Move make_sure_path_exists before creating PipestatManager Object * Ensure pypiper is calling pipestat interface and NOT the backend. * Removed redundant default output schema function and refactored. * Add clear_status to end of unit test. * Implement pipestat.report for reporting results and objects with and without annotations. * Fix unit test, reporting results, and refresh_stats. #187 * lint * remove report_object and simplify report_result * Add report_object back for backwards compatibility. * Add ability to pass result_format to pipestat and return formatted string. Added annotation for backwards compatibility. * Change to passing formatting function to pipestat instead of format flag. * Added default mark down formatter to pass during pipestatmanager creation. Fixed sample_name and pipeline_name mix up for pipeline manager. * Add passing multi flag to pipestatmanager during creation. * Add printing pipestat arguments to log file. * Polish output of pipestat object after initialization * Update docs * Update requirements * fix _failed property return * update changelog
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After pipestat API, back-end, and is finalized (e.g. #17), we should update pypiper again to use the latest pipestat.
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