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Cellfinder config + path change#64

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sfmig merged 17 commits intomainfrom
smg/cellfinder-config
Jan 10, 2024
Merged

Cellfinder config + path change#64
sfmig merged 17 commits intomainfrom
smg/cellfinder-config

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@sfmig sfmig commented Dec 20, 2023

Implemented some feedback from the workflows code review, specifically issues #36 and #35:

  • defined required, optional and internal attributes in the CellfinderConfig class (Cellfinder config improvements #36)
  • refactored class methods
  • changed default directory where to output results and place downloaded data

I simplified the tests to run only with default/simplest config or skipped them for now, since tests are the focus of PR #62.

@sfmig sfmig force-pushed the smg/cellfinder-config branch from 7216821 to 574733c Compare December 22, 2023 12:31
This was linked to issues Dec 22, 2023
@sfmig sfmig marked this pull request as ready for review January 9, 2024 17:49
@sfmig sfmig requested a review from alessandrofelder January 9, 2024 17:59
@sfmig sfmig marked this pull request as draft January 9, 2024 19:04
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codecov bot commented Jan 9, 2024

Codecov Report

Attention: 28 lines in your changes are missing coverage. Please review.

Comparison is base (0c242b1) 82.37% compared to head (bedd3ba) 81.01%.
Report is 1 commits behind head on main.

❗ Current head bedd3ba differs from pull request most recent head a1fab20. Consider uploading reports for the commit a1fab20 to get more accurate results

Files Patch % Lines
benchmarks/cellfinder_core.py 0.00% 12 Missing ⚠️
tests/cellfinder_core/test_unit/test_cellfinder.py 70.27% 11 Missing ⚠️
...globe_workflows/cellfinder_core/cellfinder_core.py 96.52% 4 Missing ⚠️
tests/cellfinder_core/conftest.py 91.66% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #64      +/-   ##
==========================================
- Coverage   82.37%   81.01%   -1.37%     
==========================================
  Files          27       27              
  Lines        1538     1522      -16     
==========================================
- Hits         1267     1233      -34     
- Misses        271      289      +18     

☔ View full report in Codecov by Sentry.
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@sfmig sfmig marked this pull request as ready for review January 10, 2024 07:10
@sfmig sfmig mentioned this pull request Jan 10, 2024
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@alessandrofelder alessandrofelder left a comment

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Looks good - tiny comments about comments 😂 - thanks

@sfmig sfmig merged commit 017f005 into main Jan 10, 2024
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Cellfinder config improvements Cellfinder workflow paths

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