pypiper
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databio
Python toolkit for building restartable pipelines
Right now, [the docs](https://pep.databio.org/pypiper/pipestat/) suggest configuring pipestat via pypiper like this: ```python pm = pypiper.PipelineManager( ..., pipestat_schema="custom_results_schema.yaml", pipestat_results_file="custom_results_file.yaml", pipestat_sample_name="my_record", pipestat_project_name="my_namespace", pipestat_config="custom_pipestat_config.yaml", ) ``` meanwhile, pipestat is configured like this: ```python...
I am experiencing this as I use pypiper in Bedbase. `pm.report_result(key="bedtype", value=self.bed_type)` It expects value to be a dict, but it does not need to be a dict. It could...
In files like `ngstk.py`, it looks like there are some escape sequences in patterns for regex matching that are generating `DeprecationWarning` messages. This could likely be fixed by [prefixing with...
Currently, it appears that tests for pypiper are generating results in a tmp directory that is not being cleaned up once pytesting is finished.
I ran into a duplicate option name error when creating a pipeline using both `logmuse` and `pypiper`; namely, when composing `logmuse.add_logging_options` with `pypiper.add_pypiper_args`, e.g. ```python parser = argparse.ArgumentParser(...) ... ......
As far as I know, Pypiper runs commands of a pipeline sequentially, even if some commands can be run concurrently. Will you plan to support the concurrent execution in the...
Right now, a few test assertions use the value of a constant, rather than the constant. If the constant changes, these will likely break. But the test logic is about...
This checkpoint-related option is declared as one of three members of `CHECKPOINT_SPECIFICATIONS`, but it's not included in the `"checkpoint"` group. As far as I can tell, at the moment the...
`Pipeline.stages` suggests a collection of names, rather than callables, `Stage` instances, or the like. https://github.com/databio/pypiper/blob/master/pypiper/pipeline.py#L175-L179
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. ```...