DEV: Improve CLI #307
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DEV: Improve CLI #307
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- Update setup.py documentation.
- Update cli using subclass.
- Common functions for cli.
- Add output path in common.
- Enable all inputs for tests
- Pass all the decorators from a common module
- Move cli functions from utils.misc to cli.common
Codecov Report
@@ Coverage Diff @@
## develop #307 +/- ##
===========================================
+ Coverage 99.82% 99.84% +0.02%
===========================================
Files 54 55 +1
Lines 5146 5169 +23
Branches 893 877 -16
===========================================
+ Hits 5137 5161 +24
Misses 2 2
+ Partials 7 6 -1
Continue to review full report at Codecov.
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- Fix help if no input provided. - Remove redundant code. - Use common click options for consistency.
- Fix help if no input provided.
shaneahmed
commented
Mar 4, 2022
- Update slide_thumbnail according to new structure.
- Update for default values.
shaneahmed
commented
Mar 4, 2022
- Update for default values.
John-P
reviewed
Mar 4, 2022
John-P
reviewed
Mar 4, 2022
John-P
approved these changes
Mar 4, 2022
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John-P
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John-P
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Looks OK to me. I am not super familiar with click, so I can't give feedback specific if this is the 'right' way to do it. But if it works, then I am happy. Certainly looks a bit tidier.
- Update click options for default value..
- Remove default values from function docstring.
- Update slide-thumbnail according to new options.
- Remove redundant code.
- Skip test to show on travis.
- Improve documentation of common.py.
- Fix mode and verbose conflicts.
- Move img_input check to common.py
- Update read_bounds.py cli
- Fix tests for tissue_mask.py cli
- Move overlapping function to common.py
- Improve input choice for tissue_mask.py.
- Add input type to mode.
- Update stain_norm.py for method.
- Fix tests for stain_norm.
- Rearrange inputs to stain_norm.py
- Fix deepsource bugs - unused imports - unnecessary else
- Fix coverage issues as some parts in the code cannot be reached.
- Update patch_predictor.py with common.py.
- Use prepare_file_dir_cli in stain_norm.py.
- Use prepare_file_dir_cli in save_tiles.py.
- Fix patch predictor test
- Fix patch_predictor test.
- Remove mode from prepare_model_cli.
- Update semantic_segment.py for cli.
- Update nucleus_instance_segment.py for cli.
- Remove unexpected keyword
- Reduce duplicate code. - Define function for ioconfig.
- Lazy import in common.
- Lazy imports for efficiency.
- Import iosegment config from relevant module.
John-P
reviewed
Mar 11, 2022
Comment on lines
+1645
to
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| @pytest.mark.skipif( | ||
| utils.env_detection.running_on_travis(), | ||
| reason="No need to display image on travis.", | ||
| ) |
Contributor
There was a problem hiding this comment.
Just wondering why this is added? Is it slow on travis?
Member
Author
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Just avoiding the clunky output on travis.
John-P
approved these changes
Mar 11, 2022
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