BodenmillerGroup / steinbock

A toolkit for processing multiplexed tissue images
https://bodenmillergroup.github.io/steinbock
MIT License
49 stars 14 forks source link

Enhanced error handling of corrupted IMC files with no recovery txt #190

Closed Milad4849 closed 1 year ago

Milad4849 commented 1 year ago

AS discussed in #184, now when an mcd file is corrupted and a recovery txt file is not found, an additional warning message is logged: "No corresponding recovery text file was found". I tested it using the corrupted mcd file provided by @nathansteenbuck.

jwindhager commented 1 year ago

Ah wait - why is this merged directly into main? In case you follow the previous strategy, I would merge feature branches into develop first, and only merge develop into main upon release. Aside from the develop branch, only hotfix branches should be merged into main. But you are of course free to change that model :)

codecov-commenter commented 1 year ago

Codecov Report

Patch coverage has no change and project coverage change: -0.02 :warning:

Comparison is base (bc10207) 30.66% compared to head (418a634) 30.65%.

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #190 +/- ## ========================================== - Coverage 30.66% 30.65% -0.02% ========================================== Files 66 66 Lines 2511 2512 +1 ========================================== Hits 770 770 - Misses 1741 1742 +1 ``` | [Impacted Files](https://app.codecov.io/gh/BodenmillerGroup/steinbock/pull/190?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup) | Coverage Δ | | |---|---|---| | [steinbock/preprocessing/imc.py](https://app.codecov.io/gh/BodenmillerGroup/steinbock/pull/190?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup#diff-c3RlaW5ib2NrL3ByZXByb2Nlc3NpbmcvaW1jLnB5) | `57.14% <0.00%> (-0.23%)` | :arrow_down: |

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Milad4849 commented 1 year ago

@jwindhager I considered this a bug fix earlier, therefore the direct merge into the main, perhaps not best described as a bug fix, will continue the aforementioned model!