Closed github-actions[bot] closed 2 months ago
The centralized nightlies job failed on Wednesday (2024-06-12) in run 9475617750
TileDB-Py failed to create a wheel. I restarted the job and it failed reproducibly.
I think this is another numpy Issue. During the standard build (which passed), it installed numpy 1.26.4. But during the wheel build (which failed), it installed numpy 2.0.0
Compiling tiledb/libtiledb.pyx because it depends on /home/runner/work/centralized-tiledb-nightlies/centralized-tiledb-nightlies/.eggs/numpy-2.0.0rc2-py3.11-linux-x86_64.egg/numpy/__init__.cython-30.pxd.
I suspect this is related to https://github.com/TileDB-Inc/TileDB-Py/pull/1989. @kounelisagis do you have any ideas for troubleshooting this?
The centralized nightlies job failed on Wednesday (2024-06-12) in run 9492584193
The centralized nightlies job failed on Thursday (2024-06-13) in run 9509565633
The TileDB-Py wheel build is continuing to fail. There are a bunch of error messages about "not declared in this scope", eg
.eggs/numpy-2.0.0rc2-py3.11-linux-x86_64.egg/numpy/__init__.cython-30.pxd:351:13: error: ‘PyArray_MultiIter_ITERS’ was not declared in this scope; did you mean ‘PyArray_MultiIter_NEXT’?
The centralized nightlies job failed on Friday (2024-06-14) in run 9524695087
The centralized nightlies job failed on Saturday (2024-06-15) in run 9532591390
The centralized nightlies job failed on Sunday (2024-06-16) in run 9540908808
The centralized nightlies job failed on Monday (2024-06-17) in run 9557834549
In last night's run, the tiledbsoma-py tests passed. I assume this is due to the recently merged https://github.com/single-cell-data/TileDB-SOMA/commit/6025c8db824a029bf5249e6ef2d318e2ff7e8814 (https://github.com/single-cell-data/TileDB-SOMA/pull/2745), which required numpy<2.0
in the setup.py
. Looking at the build log, numpy 2 was initially installed, but then it was downgraded to numpy 1.26.4.
In contrast, tiledbvcf-py continues to fail the import test:
python -c "import tiledbvcf; print(tiledbvcf.version)"
## A module that was compiled using NumPy 1.x cannot be run in
## NumPy 2.0.0 as it may crash. To support both 1.x and 2.x
## versions of NumPy, modules must be compiled with NumPy 2.0.
## Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
##
## If you are a user of the module, the easiest solution will be to
## downgrade to 'numpy<2' or try to upgrade the affected module.
## We expect that some modules will need time to support NumPy 2.
##
## Traceback (most recent call last): File "<string>", line 1, in <module>
## File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/tiledbvcf/__init__.py", line 2, in <module>
## import pyarrow
## File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/pyarrow/__init__.py", line 65, in <module>
## import pyarrow.lib as _lib
## AttributeError: _ARRAY_API not found
## Traceback (most recent call last):
## File "<string>", line 1, in <module>
## File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/tiledbvcf/__init__.py", line 2, in <module>
## import pyarrow
## File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/pyarrow/__init__.py", line 65, in <module>
## import pyarrow.lib as _lib
## File "pyarrow/lib.pyx", line 37, in init pyarrow.lib
## ImportError: numpy.core.multiarray failed to import
The centralized nightlies job failed on Tuesday (2024-06-18) in run 9575041254
The tiledbvcf-py build is failing with the same numpy-related import error as before. However, now the tiledbsoma-py tests are failing with the error message tiledb.cc.TileDBError: Group: Cannot open group; Group does not exist.
The tiledbsoma-py test failures were fixed by https://github.com/single-cell-data/TileDB-SOMA/pull/2753#pullrequestreview-2128833193 (confirmed in https://github.com/jdblischak/centralized-tiledb-nightlies/actions/runs/9585883108/job/26433519955#step:12:348)
The centralized nightlies job failed on Wednesday (2024-06-19) in run 9590553151
Still only the tiledbvcf-py import error
The centralized nightlies job failed on Thursday (2024-06-20) in run 9607203617
The tiledbvcf-py import error should be fixed when the pin numpy<2 is merged upstream in https://github.com/TileDB-Inc/TileDB-VCF/pull/731
The centralized nightlies job failed on Friday (2024-06-21) in run 9622093821
The centralized nightlies job failed on Saturday (2024-06-22) in run 9630033186
The centralized nightlies job failed on Sunday (2024-06-23) in run 9638470261
Nightly tiledbvcf-py build should be fixed by https://github.com/TileDB-Inc/TileDB-VCF/commit/f5707027301a2e0910cd2f276419a3101cf4267a (https://github.com/TileDB-Inc/TileDB-VCF/pull/734), confirmed in https://github.com/jdblischak/centralized-tiledb-nightlies/actions/runs/9650757378
The centralized nightlies job failed on Tuesday (2024-06-11) in run 9475617750