The nightly build job failed on Sunday (2024-06-16)

[github-actions[bot]]

The nightly build job failed on Sunday (2024-06-16) in run 9541271764

[awenocur]

There was a problem importing Numpy. I'm rerunning to rule out a trivial time-bound solving error, and will revisit if it fails again.

[github-actions[bot]]

The nightly build job failed on Monday (2024-06-17) in run 9541271764

[awenocur]

Looking further, maybe this is a NumPy v1 vs. v2 thing?

[github-actions[bot]]

The nightly build job failed on Monday (2024-06-17) in run 9558253578

[jdblischak]

My centralized nightly build of tiledbvcf-py is failing with the same import error as the ubuntu-latest-libtiledb-dev build.

Note that TileDB-SOMA recently pinned numpy<2.0 in setup.py to avoid numpy 2 problems (https://github.com/single-cell-data/TileDB-SOMA/pull/2745). Perhaps we need to do something similar here.

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/3.10.14/x64/lib/python3.10/site-packages/tiledbvcf/__init__.py", line 2, in <module>
##     import pyarrow
##   File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/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/3.10.14/x64/lib/python3.10/site-packages/tiledbvcf/__init__.py", line 2, in <module>
##     import pyarrow
##   File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/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

[github-actions[bot]]

The nightly build job failed on Wednesday (2024-06-19) in run 9575445387

[github-actions[bot]]

The nightly build job failed on Thursday (2024-06-20) in run 9590926967

[github-actions[bot]]

The nightly build job failed on Thursday (2024-06-20) in run 9607596493

[jdblischak]

@awenocur has pinned numpy<2 in #731/#732, which should fix the nightlies

[github-actions[bot]]

The nightly build job failed on Friday (2024-06-21) in run 9622381067

[github-actions[bot]]

The nightly build job failed on Sunday (2024-06-23) in run 9630294442

[github-actions[bot]]

The nightly build job failed on Sunday (2024-06-23) in run 9638851637

[jdblischak]

Fixed by #734