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geff

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Validate when writing geffs (#342) # Proposed Change Closes #333 I considered a few different approaches to how to make sure we didn't write an invalid geff. A major constraint is that our structural validation function takes a StoreLike as input which means that the geff has to be written before we can validate the structure. Given this constraint, I introduced a utility function that deletes a geff that we have written while doing its best to handle the different possible types in StoreLike and avoiding delete any members of the zarr that aren't geff members. Alternatively, I considered generalizing the `validate_structure` function to operate on either a StoreLike or an InMemoryGeff but the approaches that I tried were leading to a ton of code duplication and maintenance overhead. I think the deleting option is going to be easier to maintain in the long run even if its slightly less elegant and a bit inefficient. # Types of Changes What types of changes does your code introduce? Delete those that do not apply. - Bugfix (non-breaking change which fixes an issue) Which topics does your change affect? Delete those that do not apply. - Core io - Validate # Checklist Put an x in the boxes that apply. You can also fill these out after creating the PR. If you're unsure about any of them, don't hesitate to ask. We're here to help! This is simply a reminder of what we are going to look for before merging your code. - [x] I have read the [developer/contributing](https://github.com/live-image-tracking-tools/geff/blob/main/CONTRIBUTING) docs. - [x] I have added tests that prove that my feature works in various situations or tests the bugfix (if appropriate). - [x] I have checked that I maintained or improved code coverage. - [x] I have written docstrings and checked that they render correctly by looking at the docs preview (link left as a comment on the PR). --------- Co-authored-by: Caroline Malin-Mayor <malinmayorc@janelia.hhmi.org>

main

5 days ago

Merge branch 'main' into 333-validate-during-write

333-validate-during-write

5 days ago

Remove and consolidate duplicate test cases to speed up testing time (#354) # Proposed Change Starts to address #337 and #188 by refactor our tests for `geff._graph_libs` - Removes direct tests of different backends and instead tests all backends through api_wrapper tests - Eliminates some parametrization by consolidating many different data types into a single test case with multiple properties instead of testing each data type individually # Types of Changes What types of changes does your code introduce? Delete those that do not apply. - Tests Which topics does your change affect? Delete those that do not apply. - Implementations (`geff._graph_libs`) # Checklist Put an x in the boxes that apply. You can also fill these out after creating the PR. If you're unsure about any of them, don't hesitate to ask. We're here to help! This is simply a reminder of what we are going to look for before merging your code. - [x] I have read the [developer/contributing](https://github.com/live-image-tracking-tools/geff/blob/main/CONTRIBUTING) docs. - [x] I have added tests that prove that my feature works in various situations or tests the bugfix (if appropriate). - [x] I have checked that I maintained or improved code coverage. - [x] I have written docstrings and checked that they render correctly by looking at the docs preview (link left as a comment on the PR). --------- Co-authored-by: Caroline Malin-Mayor <malinmayorc@janelia.hhmi.org>

main

5 days ago

Fix logic when testing for sg num axes vs. ndim

test-deduplication

6 days ago

Fix typo in error message Co-authored-by: Caroline Malin-Mayor <malinmayorc@janelia.hhmi.org>

test-deduplication

6 days ago

Catch errors with deleting invalid geff and add to raised error message

333-validate-during-write

6 days ago

Add test for create_empty_geff

test-deduplication

6 days ago

test-deduplication

6 days ago

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ci(pre-commit.ci): autoupdate

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6 days ago

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ci(dependabot): bump peter-evans/commit-comment from 3 to 4

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