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Multirun capabilities and other improvements #10

Merged
merged 53 commits into from
Jun 11, 2024
Merged

Multirun capabilities and other improvements #10

merged 53 commits into from
Jun 11, 2024

Commits on May 27, 2024

  1. partial thoughts -- not working

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    mmcdermott committed May 27, 2024
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  2. New structure based on conversation with Nassim

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    mmcdermott authored May 27, 2024
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  3. Updated configs further and started README documentation for this.

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    mmcdermott committed May 27, 2024
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  4. Got the custom OmegaConf resolvers working for populating the stage c… 

    …onfig.
    @mmcdermott
    mmcdermott committed May 27, 2024
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  5. Got tests to pass (including integration) on the extraction scripts w… 

    …ith the new hydra setup and custom resolvers
    @mmcdermott
    mmcdermott committed May 27, 2024
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Commits on May 28, 2024

  1. Updated MIMIC examples

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    mmcdermott committed May 28, 2024
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Commits on May 30, 2024

  1. Added some content to README that still needs to be re-worked a bit

    @mmcdermott
    mmcdermott committed May 30, 2024
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  2. Added joint script demonstrating joblib launcher

    @mmcdermott
    mmcdermott committed May 30, 2024
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Commits on May 31, 2024

  1. Minor changes mostly to joint script

    @mmcdermott
    mmcdermott committed May 31, 2024
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  2. Made the locking process more robust

    @mmcdermott
    mmcdermott committed May 31, 2024
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  3. Added a slurm script -- yet untested

    @mmcdermott
    mmcdermott committed May 31, 2024
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  4. Updates to pipeline.yaml

    @mmcdermott
    mmcdermott committed May 31, 2024
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  5. cleaned files

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    mmcdermott committed May 31, 2024
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  6. Not remotely working; moving to local for dev

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    mmcdermott committed May 31, 2024
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Commits on Jun 1, 2024

  1. Updated configs and added a resolver to get informative help messages… 

    … from the right sources
    @mmcdermott
    mmcdermott committed Jun 1, 2024
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  2. Starting eICU scripts and configs

    @mmcdermott
    mmcdermott committed Jun 1, 2024
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  3. Added (again untested) allergy table

    @mmcdermott
    mmcdermott committed Jun 1, 2024
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  4. Improved the structure of the pipeline and added a bunch more tables.… 

    … Still untested.
    @mmcdermott
    mmcdermott committed Jun 1, 2024
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  5. Forgot table configs -- likely currently malformed.

    @mmcdermott
    mmcdermott committed Jun 1, 2024
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  6. Added soon to be deleted microlab table

    @mmcdermott
    mmcdermott committed Jun 1, 2024
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  7. docs update

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    mmcdermott committed Jun 1, 2024
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  8. Added partial event configs for all tables.

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    mmcdermott committed Jun 1, 2024
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  9. Revised main script

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    mmcdermott committed Jun 1, 2024
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  10. Fixed a variety of lint errors

    @mmcdermott
    mmcdermott committed Jun 1, 2024
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  11. Adjusted a tiny thing in the yaml

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    mmcdermott committed Jun 1, 2024
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  12. Updated scripts to have help messages and to error if any internal pi… 

    …ece errors.
    @mmcdermott
    mmcdermott committed Jun 1, 2024
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  13. Every column in the raw files should apparently be lowercase... also … 

    …other typos
    @mmcdermott
    mmcdermott committed Jun 1, 2024
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  14. Fixing a typo in config for diagnosis

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    mmcdermott committed Jun 1, 2024
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  15. Fixed numerous typos and issues. Makes it through much of the files n… 

    …ow in the pre-MEDS stage
    @mmcdermott
    mmcdermott committed Jun 1, 2024
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  16. Linted

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    mmcdermott committed Jun 1, 2024
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  17. Corrected more typos

    @mmcdermott
    mmcdermott committed Jun 1, 2024
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  18. Working most of the way through. Some error about vitalsaperiodic and… 

    … floats vs. ints occurring during the event conversion currently, though
    @mmcdermott
    mmcdermott committed Jun 1, 2024
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Commits on Jun 2, 2024

  1. Incorporating fixes from #8 -- thanks @prenc!

    @mmcdermott
    mmcdermott committed Jun 2, 2024
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  2. Merge branch 'multirun' into eICU

    @mmcdermott
    mmcdermott committed Jun 2, 2024
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  3. Merge branch 'multirun' into docstrings

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    mmcdermott committed Jun 2, 2024
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  4. Make log dir stage dependent

    @mmcdermott
    mmcdermott committed Jun 2, 2024
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Commits on Jun 6, 2024

  1. Made submitit launcher script work

    @mmcdermott
    mmcdermott committed Jun 6, 2024
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  2. Added singleton sbatch script

    @mmcdermott
    mmcdermott committed Jun 6, 2024
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  3. Adding inits to make tests pass despite shared 'pre_MEDS.py' name

    @mmcdermott
    mmcdermott committed Jun 6, 2024
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  4. Make it always retype numerical values

    @mmcdermott
    mmcdermott committed Jun 6, 2024
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  5. typo fix

    @mmcdermott
    mmcdermott committed Jun 6, 2024
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  6. Undoing recent changes as they don't help

    @mmcdermott
    mmcdermott committed Jun 6, 2024
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  7. Merged with main

    @mmcdermott
    mmcdermott committed Jun 6, 2024
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  8. Use diagonal relaxed to combine the event subshards

    @mmcdermott
    mmcdermott committed Jun 6, 2024
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  9. Merge branch 'eICU' of github.com:mmcdermott/MEDS_polars_functions in… 

    …to eICU
    @mmcdermott
    mmcdermott committed Jun 6, 2024
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  10. fixed error in joint script help message for eICU. should apply to MI… 

    …MIC as well.
    @mmcdermott
    mmcdermott committed Jun 6, 2024
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Commits on Jun 7, 2024

  1. Fixed up sbatch script

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    mmcdermott committed Jun 7, 2024
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Commits on Jun 8, 2024

  1. Allowing for skipping the unique-by in the merge stage.

    @mmcdermott
    mmcdermott committed Jun 8, 2024
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  2. Added a note to eICU example

    @mmcdermott
    mmcdermott committed Jun 8, 2024
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  3. Updated scripts and added note to README.md for eICU

    @mmcdermott
    mmcdermott committed Jun 8, 2024
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Commits on Jun 11, 2024

  1. Merged

    @mmcdermott
    mmcdermott committed Jun 11, 2024
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  2. Updated some docstrings

    @mmcdermott
    mmcdermott committed Jun 11, 2024
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  3. Merge pull request #7 from mmcdermott/docstrings 

    Updated configs and added a resolver to get informative help messages from either the config or the script docstrings.
    @mmcdermott
    mmcdermott authored Jun 11, 2024
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