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Change locations for zarr image in single image workflows #345

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merged 1 commit into from
Oct 5, 2023

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annshress
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Adds nesting for zarr file locations for single image workflows ( Closes #343 )
Previously, zarr directory structure was affected by scale-format-string argument in bf2raw command which has been removed.

Update SEM neuroglancer metadata to new format (Closes #342 )

This PR doesn't introduce any:

  • Binary files
  • Temporary files, auto-generated files
  • Secret keys
  • Local debugging print statements
  • Unwanted comments (e.g: # Gets user from environment for code os.environ['user'] )

This PR contains valid:

  • tests

@annshress annshress force-pushed the fix/single-image-zarr-nest branch 2 times, most recently from 46ee92d to 5702cfa Compare October 5, 2023 16:27
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github-actions bot commented Oct 5, 2023

Coverage report

The coverage rate went from 64.77% to 64.77% ➡️
The branch rate is 47%.

None of the new lines are part of the tested code. Therefore, there is no coverage data about them.

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Can you use the ZarrImage.path interface?

em_workflows/brt/flow.py Outdated Show resolved Hide resolved
@annshress annshress force-pushed the fix/single-image-zarr-nest branch from 163e329 to 1765bdd Compare October 5, 2023 18:17
Adds nesting for zarr file locations for single image workflows (Closes #343)
Previously, zarr directory structure was affected by `scale-format-string`
argument in bf2raw command which has been removed.

Update SEM neuroglancer metadata to new format (Closes #342)
@annshress annshress force-pushed the fix/single-image-zarr-nest branch from 1765bdd to 255ef6c Compare October 5, 2023 18:53
@philipmac philipmac merged commit f6f0767 into main Oct 5, 2023
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@philipmac philipmac deleted the fix/single-image-zarr-nest branch October 5, 2023 19:49
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