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Add file_share param into workflows #297

Merged
merged 4 commits into from
Sep 12, 2023
Merged

Add file_share param into workflows #297

merged 4 commits into from
Sep 12, 2023

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annshress
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@annshress annshress commented Sep 5, 2023

Addresses

Changes

  • Uses a mapper over env
  • FilePath initialization requires share_name argument (previously not required)
  • Config. proj_dir and assets_dir requires share_name argument (previously relied on env)

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

@@ -23,6 +23,7 @@ def test_brt(mock_nfs_mount):
TargetNumberOfBeads=20,
LocalAlignments=0,
THICKNESS=30,
file_share="test",
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@annshress annshress Sep 5, 2023

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The new api call will have an added file_share string parameter. The possible strings are defined in FileShareEnum.

from enum import Enum


class FileShareEnum(Enum):
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ShareNames are a type of Enum.

em_workflows/config.py Show resolved Hide resolved
@annshress annshress marked this pull request as ready for review September 5, 2023 20:31
em_workflows/enums.py Outdated Show resolved Hide resolved
@annshress annshress marked this pull request as draft September 11, 2023 19:45
@annshress annshress marked this pull request as ready for review September 11, 2023 19:48
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github-actions bot commented Sep 11, 2023

Coverage report

The coverage rate went from 69.27% to 69.84% ⬆️
The branch rate is 50%.

94.87% of new lines are covered.

Diff Coverage details (click to unfold)

em_workflows/utils/utils.py

100% of new lines are covered (57.71% of the complete file).

em_workflows/czi/flow.py

100% of new lines are covered (36.11% of the complete file).

em_workflows/dm_conversion/flow.py

100% of new lines are covered (89.26% of the complete file).

em_workflows/enums.py

100% of new lines are covered (100% of the complete file).

em_workflows/lrg_2d_rgb/flow.py

100% of new lines are covered (93.5% of the complete file).

em_workflows/config.py

83.33% of new lines are covered (74.54% of the complete file).
Missing lines: 91, 95

em_workflows/file_path.py

100% of new lines are covered (83.96% of the complete file).

em_workflows/config.py Outdated Show resolved Hide resolved
@philipmac philipmac merged commit a9f5b7d into main Sep 12, 2023
2 checks passed
@philipmac philipmac deleted the feature/file_share branch September 12, 2023 16:40
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2 participants