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Fix #213, remove pipestat_project_name, refactor pipestat_sample_name…
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… to pipestat_record_identifier, update doc strings
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donaldcampbelljr committed Feb 19, 2024
1 parent 65ed31d commit 94806df
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Showing 2 changed files with 16 additions and 3 deletions.
6 changes: 6 additions & 0 deletions docs/changelog.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,11 @@
# Changelog

## [0.15.0] -- 2024-xx-xx
### Changed
- remove pipestat_project_name from PipelineManager parameters
- refactor pipestat_sample_name to pipestat_record_identifier in PipelineManager parameters


## [0.14.0] -- 2023-12-22
### Changed
- refactor for pipestat v0.6.0 release
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13 changes: 10 additions & 3 deletions pypiper/manager.py
Original file line number Diff line number Diff line change
Expand Up @@ -112,6 +112,12 @@ class PipelineManager(object):
protect from a case in which a restart begins upstream of a stage
for which a checkpoint file already exists, but that depends on the
upstream stage and thus should be rerun if it's "parent" is rerun.
:param str pipestat_record_identifier: record_identifier to report results via pipestat
:param str pipestat_schema: output schema used by pipestat to report results
:param str pipestat_results_file: path to file backend for reporting results
:param str pipestat_config_file: path to pipestat configuration file
:param str pipestat_pipeline_type: Sample or Project level pipeline
:param pipestat_result_formatter: function used to style reported results, defaults to result_formatter_markdown
:raise TypeError: if start or stop point(s) are provided both directly and
via args namespace, or if both stopping types (exclusive/prospective
and inclusive/retrospective) are provided.
Expand All @@ -136,8 +142,7 @@ def __init__(
output_parent=None,
overwrite_checkpoints=False,
logger_kwargs=None,
pipestat_project_name=None,
pipestat_sample_name=None,
pipestat_record_identifier=None,
pipestat_schema=None,
pipestat_results_file=None,
pipestat_config=None,
Expand Down Expand Up @@ -330,7 +335,9 @@ def __init__(
signal.signal(signal.SIGTERM, self._signal_term_handler)

# pipestat setup
self.pipestat_record_identifier = pipestat_sample_name or DEFAULT_SAMPLE_NAME
self.pipestat_record_identifier = (
pipestat_record_identifier or DEFAULT_SAMPLE_NAME
)
self.pipestat_pipeline_type = pipestat_pipeline_type or "sample"

# don't force default pipestat_results_file value unless
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