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Making the interface re-usable and importable. #29

Merged
merged 32 commits into from
Jul 16, 2024
Merged

Making the interface re-usable and importable. #29

merged 32 commits into from
Jul 16, 2024

Commits on Jun 25, 2024

  1. Moving things around in preparation for installable package.

    @mmcdermott
    mmcdermott committed Jun 25, 2024
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Commits on Jun 26, 2024

  1. Trying a major re-arrangement. Likely not final structure.

    @mmcdermott
    mmcdermott committed Jun 26, 2024
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  2. Starting further re-arranging

    @mmcdermott
    mmcdermott committed Jun 26, 2024
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  3. Greater use of utils functions

    @mmcdermott
    mmcdermott committed Jun 26, 2024
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  4. Move script over

    @mmcdermott
    mmcdermott committed Jun 26, 2024
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  5. Moved shard_events script over.

    @mmcdermott
    mmcdermott committed Jun 26, 2024
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Commits on Jun 27, 2024

  1. moved all extraction scripts to main folder

    @mmcdermott
    mmcdermott committed Jun 27, 2024
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  2. Removed an unneeded function to simplify.

    @mmcdermott
    mmcdermott committed Jun 27, 2024
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  3. More simplifications

    @mmcdermott
    mmcdermott committed Jun 27, 2024
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  4. Fixed some tests and streamlined some accesses

    @mmcdermott
    mmcdermott committed Jun 27, 2024
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  5. Got tests working for extraction pipeline.

    @mmcdermott
    mmcdermott committed Jun 27, 2024
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Commits on Jul 4, 2024

  1. Manually ported over the change.

    @mmcdermott
    mmcdermott committed Jul 4, 2024
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  2. Not yet tested, but added map_over interfaces to some pre-processing … 

    …scripts.
    @mmcdermott
    mmcdermott committed Jul 4, 2024
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  3. Merge branch 'dev' into reusable_interface

    @mmcdermott
    mmcdermott committed Jul 4, 2024
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  4. Merge branch 'dev' into reusable_interface

    @mmcdermott
    mmcdermott committed Jul 4, 2024
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  5. Adding a note about overwriting the stages

    @mmcdermott
    mmcdermott committed Jul 4, 2024
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  6. Some more movement and renaming; still in progress.

    @mmcdermott
    mmcdermott committed Jul 4, 2024
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  7. Moved outliers, started adding a filters README

    @mmcdermott
    mmcdermott committed Jul 4, 2024
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Commits on Jul 5, 2024

  1. Likely missing needed changes to make things work, but moved all the … 

    …scripts over.
    @mmcdermott
    mmcdermott committed Jul 5, 2024
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  2. Fixed some typos causing test failures.

    @mmcdermott
    mmcdermott committed Jul 5, 2024
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  3. Added missing test

    @mmcdermott
    mmcdermott committed Jul 5, 2024
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Commits on Jul 12, 2024

  1. Moved configs around so stage configs with default args live in re-us… 

    …able yaml files to take advantage of hydra groups
    @mmcdermott
    mmcdermott committed Jul 12, 2024
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Commits on Jul 13, 2024

  1. Removed unneeded extraction specific script in favor of simply updati… 

    …ng the config name on the command line.
    @mmcdermott
    mmcdermott committed Jul 13, 2024
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Commits on Jul 15, 2024

  1. Moved help string for merge step to merge script.

    @mmcdermott
    mmcdermott committed Jul 15, 2024
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  2. Moved split and shard patients help string to main docstring.

    @mmcdermott
    mmcdermott committed Jul 15, 2024
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  3. Finished moving over the rest of the help strings.

    @mmcdermott
    mmcdermott committed Jul 15, 2024
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  4. Standardized main function docstring format and added more simple doc… 

    …tests to extraction scripts.
    @mmcdermott
    mmcdermott committed Jul 15, 2024
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  5. Fixed test for updated polars

    @mmcdermott
    mmcdermott committed Jul 15, 2024
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  6. Fixed polars errors and warnings in local testing.

    @mmcdermott
    mmcdermott committed Jul 15, 2024
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Commits on Jul 16, 2024

  1. Made merge to MEDS test have a deterministic output.

    @mmcdermott
    mmcdermott committed Jul 16, 2024
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  2. Set up script targets and config installation support for extraction … 

    …scripts.
    @mmcdermott
    mmcdermott committed Jul 16, 2024
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  3. Updated the way the current_script_name works.

    @mmcdermott
    mmcdermott committed Jul 16, 2024
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