search

single-cell-data / TileDB-SOMA

Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell data at any scale.
https://tiledbsoma.readthedocs.io
MIT License
90 stars 25 forks source link

[python] Fix nightly-build failure / `pybind11` exception-mapping #2963

Closed johnkerl closed 1 month ago

johnkerl commented 1 month ago

Issue and/or context: Resolves #2961

Changes:

Do explicit try-catch. See also #783.

Notes for Reviewer:

It's not necessarily causal that this triggered on https://github.com/jdblischak/centralized-tiledb-nightlies/issues/21. It's true that the apis/python/tests/test_shape.py was recently introduced on the #2407 stack. However, whether un-rethrown errors (on implicit pybind body, as in the "before" parts of this PR) reach the Python level as tiledbsoma.SOMAError or RuntimeError or tiledb.cc.TileDBError has some element of randomness.

There's an attempt to globally register a rethrow: https://github.com/single-cell-data/TileDB-SOMA/blob/1.13.1/apis/python/src/tiledbsoma/pytiledbsoma.cc#L36-L50

However, @nguyenv and I have long found that some things come through as RuntimeError on one machine, and tiledb.cc.TileDBError in another. We suspect that TileDB-Py's exception registrar has a race condition with our own.

Regardless, a safe practice is explicit catch-and-rethrow at the boundary between C++ and Python, which is what we do more of here.

codecov[bot] commented 1 month ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 89.99%. Comparing base (796c168) to head (f29a82c). Report is 4 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #2963 +/- ## ========================================== + Coverage 89.89% 89.99% +0.09% ========================================== Files 39 39 Lines 4049 4057 +8 ========================================== + Hits 3640 3651 +11 + Misses 409 406 -3 ``` | [Flag](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2963/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | Coverage Δ | | |---|---|---| | [python](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2963/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `89.99% <ø> (+0.09%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data#carryforward-flags-in-the-pull-request-comment) to find out more. | [Components](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2963/components?src=pr&el=components&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | Coverage Δ | | |---|---|---| | [python_api](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2963/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `89.99% <ø> (+0.09%)` | :arrow_up: | | [libtiledbsoma](https://app.codecov.io/gh/single-cell-data/TileDB-SOMA/pull/2963/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=single-cell-data) | `∅ <ø> (∅)` | |