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Traceback (most recent call last):
File "/usr/lib/python3.10/runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/usr/lib/python3.10/runpy.py", line 86, in _run_code
exec(code, run_globals)
File "/home/jk/work/github/bio2zarr/bio2zarr/__main__.py", line 22, in <module>
bio2zarr()
File "/home/jk/.local/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/home/jk/.local/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/jk/.local/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/jk/.local/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/jk/.local/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/jk/.local/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/jk/work/github/bio2zarr/bio2zarr/cli.py", line 366, in encode
vcf2zarr.encode(
File "/home/jk/work/github/bio2zarr/bio2zarr/vcf2zarr/vcz.py", line 970, in encode
vzw.encode_all_partitions(
File "/home/jk/work/github/bio2zarr/bio2zarr/vcf2zarr/vcz.py", line 936, in encode_all_partitions
pwm.submit(self.encode_partition, partition_index)
File "/home/jk/work/github/bio2zarr/bio2zarr/core.py", line 291, in submit
future = self.executor.submit(*args, **kwargs)
File "/home/jk/work/github/bio2zarr/bio2zarr/core.py", line 90, in submit
future.set_result(fn(*args, **kwargs))
File "/home/jk/work/github/bio2zarr/bio2zarr/vcf2zarr/vcz.py", line 643, in encode_partition
self.encode_id_partition(partition_index)
File "/home/jk/work/github/bio2zarr/bio2zarr/vcf2zarr/vcz.py", line 749, in encode_id_partition
for value in col.iter_values(partition.start, partition.stop):
File "/home/jk/work/github/bio2zarr/bio2zarr/vcf2zarr/icf.py", line 638, in iter_values
chunk_record_index = self.chunk_record_index(start_partition)
File "/home/jk/work/github/bio2zarr/bio2zarr/vcf2zarr/icf.py", line 601, in chunk_record_index
a = pickle.load(f)
ModuleNotFoundError: No module named 'numpy._core'
I'm not sure there's an awful lot we can do about this, unfortunately. Numpy 2.x and 1.x are going to coexist for some time, so it's not clear what we can do here.
The easy solution would be to pin to numpy > 2 and bump the ICF metadata version. However, pinning to numpy > 2 isn't helpful in the short term, I think.
The text was updated successfully, but these errors were encountered:
On reflection, the reasonable thing to do here is to catch the pickle-time error and raise a helpful error message. We don't need to support mixed numpy version environments, as it's an intermediate format after all.
We get a backtrace like:
I'm not sure there's an awful lot we can do about this, unfortunately. Numpy 2.x and 1.x are going to coexist for some time, so it's not clear what we can do here.
The easy solution would be to pin to numpy > 2 and bump the ICF metadata version. However, pinning to numpy > 2 isn't helpful in the short term, I think.
The text was updated successfully, but these errors were encountered: