Remove serialem code and revise context determination - #632

Merged

stephen-riggs merged 12 commits into

mainfrom

Jul 18, 2025

Commits on Jul 15, 2025

Add metadata options to _find_context
stephen-riggs
committed
f0dd9e8
Remove serialem logic
stephen-riggs
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be88af8
Tests for finding context
stephen-riggs
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cd98ad8
Avoid marking some metadata as SPA
stephen-riggs
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f95b861

Commits on Jul 17, 2025

Moved CLEM context determination logic to the start of the '_find_context' function, as it conflicts with some of the metadata determindation logic for SPA and Tomo
tieneupin
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07d7eeb
Simplified the conditions for determining the context for CLEM TIFF files; the loading of the 'analyse_created_directories' key should not be needed
tieneupin
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76f5284
Added examples of files from the CLEM workflow that are used to determine the context
tieneupin
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b1a165d
Removed the need for an instance environment when determining the context of CLEM files; removed the corresponding mocks in the test
tieneupin
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2e6b21b
Added example CLEM workflow files that cannot be used to determine context, and more files that can
tieneupin
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cdbedff
Resolved merge conflicts with 'main' branch
tieneupin
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446f6c0

Commits on Jul 18, 2025

Reinstate the [ form and test one more case
stephen-riggs
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0d363e7
Make note on problem
stephen-riggs
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4d926b6