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Standardise contexts#844

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tieneupin merged 10 commits into
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standardise-contexts
Jul 24, 2026
Merged

Standardise contexts#844
tieneupin merged 10 commits into
mainfrom
standardise-contexts

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@tieneupin

@tieneupin tieneupin commented Jul 21, 2026

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The FIBContext and CLEMContext classes were written with their own versions of functions that we have now established to be shared across the classes. This PR standardises FIBContext and CLEMContext by replacing the _get_source and _file_transferred_to functions defined within the modules with the shared version of said functions. Also adds tests for the CLEMContext.

Actual code diff is +21/-111. The rest of the diff is due to the updating and adding of tests.

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codecov Bot commented Jul 21, 2026

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Codecov Report

❌ Patch coverage is 66.66667% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 54.41%. Comparing base (f97ffec) to head (d9bf915).

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #844      +/-   ##
==========================================
+ Coverage   53.56%   54.41%   +0.85%     
==========================================
  Files         103      103              
  Lines       11085    11042      -43     
  Branches     1477     1466      -11     
==========================================
+ Hits         5938     6009      +71     
+ Misses       4829     4713     -116     
- Partials      318      320       +2     
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  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@tieneupin
tieneupin marked this pull request as ready for review July 22, 2026 05:14
@tieneupin
tieneupin requested a review from d-j-hatton July 22, 2026 05:14
@tieneupin tieneupin self-assigned this Jul 22, 2026
@tieneupin tieneupin added enhancement New feature or request client Relates to the client component cryo-clem Part of the cryo-CLEM pipeline extension fib Part of the FIB pipeline extension labels Jul 22, 2026
@tieneupin
tieneupin force-pushed the standardise-contexts branch from abfae0b to 6fa3a04 Compare July 22, 2026 06:23
@tieneupin
tieneupin force-pushed the standardise-contexts branch from 6fa3a04 to d9bf915 Compare July 24, 2026 14:43
@tieneupin
tieneupin merged commit aedfa37 into main Jul 24, 2026
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@tieneupin
tieneupin deleted the standardise-contexts branch July 24, 2026 14:50
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