scverse / squidpy

Spatial Single Cell Analysis in Python
https://squidpy.readthedocs.io/en/stable/
BSD 3-Clause "New" or "Revised" License
428 stars 79 forks source link

adjusted CellComposite and CellLabels loading in read_nanostring #766

Closed FrancescaDr closed 10 months ago

FrancescaDr commented 11 months ago

Description

How has this been tested?

Tested with two different patients from CosmX Lung (test/test_nanostring.py) and loading with data from CosmX bowel disease data

Closes

closes #585

giovp commented 11 months ago

hi @FrancescaDr could you please rebase from main ? it should fix tests. Also could you remove the tests for the reader? after that we can merge it!

codecov-commenter commented 11 months ago

Codecov Report

Merging #766 (6f48274) into main (c528ce7) will decrease coverage by 0.07%. The diff coverage is 0.00%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #766 +/- ## ========================================== - Coverage 69.94% 69.87% -0.07% ========================================== Files 39 39 Lines 5476 5481 +5 Branches 1024 1025 +1 ========================================== Hits 3830 3830 - Misses 1358 1363 +5 Partials 288 288 ``` | [Files](https://app.codecov.io/gh/scverse/squidpy/pull/766?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse) | Coverage Δ | | |---|---|---| | [src/squidpy/read/\_read.py](https://app.codecov.io/gh/scverse/squidpy/pull/766?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL3NxdWlkcHkvcmVhZC9fcmVhZC5weQ==) | `35.86% <0.00%> (-2.07%)` | :arrow_down: |