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Add progress bar for the EDA calculation in spatial LDA #680

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merged 7 commits into from
Sep 27, 2022

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alex-l-kong
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What is the purpose of this PR?

Begins addressing #566. Our repo includes a lot of intensive functions, so we'll need to ensure the user receives progress updates for these so they don't get left in the dark.

How did you implement your changes

Use the tqdm function in the tqdm.notebook function.

Based on our research and discussion with @ackagel, the only function that needs this for now is spLDA.preprocessing.compute_topic_modeling. There are various reasons others don't need them:

  • They already have a progress bar or print outs per every n iterations
  • They are direct calls to an external package, which we can't wrap easily in tqdm short of making a contribution to said package
  • In the case of neighborhood analysis, progress will be delayed until after the MIBI workshop

@alex-l-kong
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Also needed to update the start_docker.sh script, since it was attempting to pull a non-existant spatial-ark-test image. Added the site-packages reference back for the time being too.

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@ngreenwald ngreenwald left a comment

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You'll need to coordinate with Adam about the plan for the local version of ark

@alex-l-kong
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@ngreenwald just updated start_docker.sh to reflect @ackagel's work in main.

ark/spLDA/processing.py Show resolved Hide resolved
@ngreenwald ngreenwald merged commit e0f3f6f into main Sep 27, 2022
@ngreenwald ngreenwald deleted the progress_bars branch September 27, 2022 21:32
@srivarra srivarra added the enhancement New feature or request label Oct 3, 2022
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3 participants