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Reorganize package dependencies #506

Merged
merged 22 commits into from
Nov 21, 2023
Merged

Reorganize package dependencies #506

merged 22 commits into from
Nov 21, 2023

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fcogidi
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@fcogidi fcogidi commented Nov 15, 2023

PR Type

Fix.

Short Description

  • Move MONAI from a required dependency in the base cyclops installation to an optional dependency in the models extra.
  • Move report package dependencies to the base cyclops installation since the model report is a highlight of cyclops

Tests Added

  • Updated test in tests/package/base.py
  • Updated test in tests/package/models.py
  • Removed test tests/package/report.py

@fcogidi fcogidi added the refactor Refactor existing code, with same or similar functionality label Nov 15, 2023
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codecov bot commented Nov 15, 2023

Codecov Report

Merging #506 (4e2de73) into main (262b854) will increase coverage by 0.00%.
Report is 2 commits behind head on main.
The diff coverage is 59.45%.

Additional details and impacted files

Impacted file tree graph

@@           Coverage Diff            @@
##             main     #506    +/-   ##
========================================
  Coverage   63.36%   63.36%            
========================================
  Files          95       95            
  Lines        9315     9427   +112     
========================================
+ Hits         5902     5973    +71     
- Misses       3413     3454    +41     
Files Coverage Δ
...scripts/medical_imagefolder/medical_imagefolder.py 100.00% <100.00%> (ø)
...etrics/experimental/distributed_backends/mpi4py.py 36.73% <100.00%> (ø)
...rimental/distributed_backends/torch_distributed.py 31.37% <100.00%> (-1.32%) ⬇️
cyclops/monitor/reductor.py 72.63% <100.00%> (ø)
cyclops/monitor/tester.py 86.15% <100.00%> (ø)
cyclops/utils/optional.py 100.00% <100.00%> (ø)
cyclops/tasks/classification.py 31.46% <50.00%> (ø)
cyclops/models/wrappers/pt_model.py 80.05% <66.66%> (-0.11%) ⬇️
cyclops/data/features/medical_image.py 35.23% <52.00%> (-2.81%) ⬇️
cyclops/data/transforms.py 48.27% <48.27%> (+48.27%) ⬆️

... and 16 files with indirect coverage changes

Impacted file tree graph

@amrit110 amrit110 self-assigned this Nov 21, 2023
@fcogidi fcogidi marked this pull request as ready for review November 21, 2023 21:56
@fcogidi fcogidi changed the title Make the use of MONAI optional Reorganize package dependencies Nov 21, 2023
@fcogidi fcogidi merged commit 8a0ef2f into main Nov 21, 2023
6 of 8 checks passed
@fcogidi fcogidi deleted the make_monai_optional branch November 21, 2023 23:18
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3 participants