BUG: Run WSI pipeline at scale.

[kenza-bouzid]

Small Fixes to make the WSI run at scale for PANDA cohort. Main changes:

• fix all parameters of PandaSlidesDataModule to avoid default behaviors
• set multiprocessing_context to "spawn" for WSI container
• add parameter save_tiles to outputs handler

[codecov]

Codecov Report

Merging #357 (07936d4) into main (325384b) will decrease coverage by 5.47%.
The diff coverage is 33.33%.

@@            Coverage Diff             @@
##             main     #357      +/-   ##
==========================================
- Coverage   80.86%   75.39%   -5.48%     
==========================================
  Files          28       51      +23     
  Lines        2383     2999     +616     
  Branches      352      412      +60     
==========================================
+ Hits         1927     2261     +334     
- Misses        354      661     +307     
+ Partials      102       77      -25     

Impacted Files	Coverage Δ
...logy/src/histopathology/datamodules/base_module.py	78.32% <ø> (ø)
...pathology/src/histopathology/utils/output_utils.py	50.00% <12.50%> (ø)
...c/histopathology/configs/classification/BaseMIL.py	65.86% <33.33%> (ø)
...pathology/configs/classification/DeepSMILEPanda.py	70.42% <66.66%> (ø)
...istopathology/src/histopathology/models/deepmil.py	90.96% <80.00%> (ø)
hi-ml/src/health_ml/utils/__init__.py
hi-ml/src/health_ml/utils/config_loader.py
hi-ml/src/health_ml/utils/lr_scheduler.py
hi-ml/src/health_ml/model_trainer.py
hi-ml/src/health_ml/utils/data_augmentations.py
... and 74 more

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[ant0nsc]

Changes look good from a code perspective. Now that we have the pipeline running, I'd love to see more details around the impact of the changes individually: Spawn alone, uint8 alone.

[vale-salvatelli]

Small suggestion save_output_tiles might be a bit more interpretable. From a first read I thought this was about saving all the randomly sampled tiles

[kenza-bouzid]

good point!