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Dorado update #142

Merged
merged 4 commits into from
Oct 22, 2024
Merged

Dorado update #142

merged 4 commits into from
Oct 22, 2024

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TomHarrop
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@TomHarrop
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Wait for a new container, this one fails with

Job in error state.. tool_id: dorado_pod5_convert, exit_code: 1, stderr: 
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.1.2 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 "/home/epi2melabs/conda/bin/pod5", line 5, in <module>
    from pod5.tools.main import main
  File "/home/epi2melabs/conda/lib/python3.12/site-packages/pod5/__init__.py", line 17, in <module>
    from .api_utils import (
  File "/home/epi2melabs/conda/lib/python3.12/site-packages/pod5/api_utils.py", line 11, in <module>
    import pyarrow as pa
  File "/home/epi2melabs/conda/lib/python3.12/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 "/home/epi2melabs/conda/bin/pod5", line 5, in <module>
    from pod5.tools.main import main
  File "/home/epi2melabs/conda/lib/python3.12/site-packages/pod5/__init__.py", line 17, in <module>
    from .api_utils import (
  File "/home/epi2melabs/conda/lib/python3.12/site-packages/pod5/api_utils.py", line 11, in <module>
    import pyarrow as pa
  File "/home/epi2melabs/conda/lib/python3.12/site-packages/pyarrow/__init__.py", line 65, in <module>
    import pyarrow.lib as _lib
  File "pyarrow/lib.pyx", line 36, in init pyarrow.lib
ImportError: numpy.core.multiarray failed to import
.

@TomHarrop TomHarrop merged commit 6961f31 into usegalaxy-au:master Oct 22, 2024
1 check passed
@TomHarrop TomHarrop deleted the dorado_update branch October 22, 2024 22:29
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