[python/ci] Run SO copying workflow on macos-13 to avoid SIP #2435
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
ryan-williams
approved these changes
Apr 11, 2024
|
Fantastic work @jdblischak -- thank you!!! |
johnkerl
added a commit
that referenced
this pull request
Apr 12, 2024
* AlreadyExistsError; use for DataFrame in tiledbsoma.io * apply in `_create_or_open_collection` * apply in _create_from_matrix * apply in _ingest_uns_ndarray * lint * Run SO copying workflow on macos-13 to avoid SIP (#2435) * AlreadyExistsError; use for DataFrame in tiledbsoma.io * apply in `_create_or_open_collection` * apply in _create_from_matrix * apply in _ingest_uns_ndarray * lint * neaten * neaten * Update raises-notes * code-review feedback Co-authored-by: nguyenv <[email protected]> --------- Co-authored-by: John Blischak <[email protected]> Co-authored-by: nguyenv <[email protected]>
github-actions bot
pushed a commit
that referenced
this pull request
Apr 12, 2024
* AlreadyExistsError; use for DataFrame in tiledbsoma.io * apply in `_create_or_open_collection` * apply in _create_from_matrix * apply in _ingest_uns_ndarray * lint * Run SO copying workflow on macos-13 to avoid SIP (#2435) * AlreadyExistsError; use for DataFrame in tiledbsoma.io * apply in `_create_or_open_collection` * apply in _create_from_matrix * apply in _ingest_uns_ndarray * lint * neaten * neaten * Update raises-notes * code-review feedback Co-authored-by: nguyenv <[email protected]> --------- Co-authored-by: John Blischak <[email protected]> Co-authored-by: nguyenv <[email protected]>
johnkerl
added a commit
that referenced
this pull request
Apr 12, 2024
* AlreadyExistsError; use for DataFrame in tiledbsoma.io * apply in `_create_or_open_collection` * apply in _create_from_matrix * apply in _ingest_uns_ndarray * lint * Run SO copying workflow on macos-13 to avoid SIP (#2435) * AlreadyExistsError; use for DataFrame in tiledbsoma.io * apply in `_create_or_open_collection` * apply in _create_from_matrix * apply in _ingest_uns_ndarray * lint * neaten * neaten * Update raises-notes * code-review feedback --------- Co-authored-by: John Kerl <[email protected]> Co-authored-by: John Blischak <[email protected]> Co-authored-by: nguyenv <[email protected]>
johnkerl
changed the title
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Issue and/or context:
Closes #2237
We have a flaky macOS job that fails too often. Sometimes the macOS System Integrity Protection (SIP) unsets
DYLD_LIBRARY_PATH, which preventslibtiledbsoma.dylibfrom findinglibtiledb.dylibChanges:
There is no way to disable SIP during a run. Fortunately the GitHub Actions runner
macos-13has it disabled by default, so I switched to it. If SIP is enabled in the future, then we'll have to revisit.Notes for Reviewer:
I added a step to run
csrutil status, which will help us troubleshoot in the future if SIP is enabledSo far this has passed twice on my fork
https://github.com/jdblischak/TileDB-SOMA/actions/runs/8652010719/job/23723973384
https://github.com/jdblischak/TileDB-SOMA/actions/runs/8652049846/job/23724080889