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Issue 492 refactor pipestat #496

Merged
merged 27 commits into from
Jun 4, 2024
Merged

Issue 492 refactor pipestat #496

merged 27 commits into from
Jun 4, 2024

Commits on May 22, 2024

  1. first pass at creating pipestat config and associating psms with pifaces

    @donaldcampbelljr
    donaldcampbelljr committed May 22, 2024
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Commits on May 23, 2024

  1. fix bug with pipestat key present but value being None

    @donaldcampbelljr
    donaldcampbelljr committed May 23, 2024
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  2. use_pipestat = is_pipestat_configured

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    donaldcampbelljr committed May 23, 2024
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  3. ensure a pipestatmanager is created if a config file does already exist

    @donaldcampbelljr
    donaldcampbelljr committed May 23, 2024
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  4. modify comprehensive tests to have correct paths

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    donaldcampbelljr committed May 23, 2024
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  5. refactor Checker code

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    donaldcampbelljr committed May 23, 2024
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  6. refactor Reporter code

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    donaldcampbelljr committed May 23, 2024
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  7. refactor Linker and Tabulator

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    donaldcampbelljr committed May 23, 2024
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  8. refactor Destroyer

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    donaldcampbelljr committed May 23, 2024
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  9. attempt refactor for obtaining project level pifaces and associated psms

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    donaldcampbelljr committed May 23, 2024
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Commits on May 24, 2024

  1. bump pipestat req to 0.9.2a1

    @donaldcampbelljr
    donaldcampbelljr committed May 24, 2024
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  2. set multi_pipelines to True so that sample and project pipelines can … 

    …be reported to the same results.yaml file.
    @donaldcampbelljr
    donaldcampbelljr committed May 24, 2024
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  3. Add warning for mismatched pipeline names

    @donaldcampbelljr
    donaldcampbelljr committed May 24, 2024
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Commits on Jun 3, 2024

  1. refactor _set_pipestat_namespace

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    donaldcampbelljr committed Jun 3, 2024
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  2. remove unused code, finish Destroyer refactor

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    donaldcampbelljr committed Jun 3, 2024
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  3. refactor func names

    @donaldcampbelljr
    donaldcampbelljr committed Jun 3, 2024
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  4. remove unnecessary variable duplication

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    donaldcampbelljr committed Jun 3, 2024
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  5. remove commented code

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    donaldcampbelljr committed Jun 3, 2024
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  6. add "--project" argument back to Looper

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    donaldcampbelljr committed Jun 3, 2024
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  7. refactor obtaining results_file_path during pipestat configuration cr… 

    …eation
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    donaldcampbelljr committed Jun 3, 2024
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  8. remove commented code

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    donaldcampbelljr committed Jun 3, 2024
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  9. remove print statements, change info to debug

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    donaldcampbelljr committed Jun 3, 2024
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  10. ensure we are checking for project level pipestat configuration if us… 

    …ing --project
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    donaldcampbelljr committed Jun 3, 2024
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  11. reduce looper verbosity by switching to logger.debug in some places

    @donaldcampbelljr
    donaldcampbelljr committed Jun 3, 2024
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  12. bumbp pipestat req to v0.9.2

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    donaldcampbelljr committed Jun 3, 2024
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  13. Merge branch 'dev' into dev_492_refactor_pipestat

    @donaldcampbelljr
    donaldcampbelljr authored Jun 3, 2024
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  14. add enum for pipeline type #360

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    donaldcampbelljr committed Jun 3, 2024
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