Pin `numpy` to 1.X.X
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Description
Downloading pyensembl in a fresh environment yielded:
Traceback (most recent call last): File "/opt/mamba/envs/pyensembl/bin/pyensembl", line 8, in <module>
sys.exit(run())
File "/opt/mamba/envs/pyensembl/lib/python3.10/site-packages/pyensembl/shell.py", line 281, in run
genome.index(overwrite=args.overwrite)
File "/opt/mamba/envs/pyensembl/lib/python3.10/site-packages/pyensembl/genome.py", line 280, in index
self.db.connect_or_create(overwrite=overwrite)
File "/opt/mamba/envs/pyensembl/lib/python3.10/site-packages/pyensembl/database.py", line 286, in connect_or_create
return self.create(overwrite=overwrite)
File "/opt/mamba/envs/pyensembl/lib/python3.10/site-packages/pyensembl/database.py", line 206, in create
df = self._load_gtf_as_dataframe(
File "/opt/mamba/envs/pyensembl/lib/python3.10/site-packages/pyensembl/database.py", line 613, in _load_gtf_as_dataframe
df = read_gtf(
File "/opt/mamba/envs/pyensembl/lib/python3.10/site-packages/gtfparse/read_gtf.py", line 257, in read_gtf
result_df = result_df.to_pandas()
File "/opt/mamba/envs/pyensembl/lib/python3.10/site-packages/polars/dataframe/frame.py", line 2093, in to_pandas
return self._to_pandas_without_object_columns(
File "/opt/mamba/envs/pyensembl/lib/python3.10/site-packages/polars/dataframe/frame.py", line 2144, in _to_pandas_without_object_columns
record_batches = df._df.to_pandas()
File "/opt/mamba/envs/pyensembl/lib/python3.10/site-packages/pyarrow/__init__.py", line 65, in <module>
import pyarrow.lib as _lib
AttributeError: _ARRAY_API not found
It seems like pyarrow is not pinning numpy correctly, but I think you'll have a hard time making changes in that library in a timely fashion.
Would enforce in gtfparse. Reinstalling to the latest 1.X.X, eg:
pip install numpy==1.24.3
Fixes the issue.
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the dependency configuration for gtfparse and reproduce the failure through read_gtf.py in a fresh environment. Pin numpy to a 1.x release as requested, then verify that the pyarrow import no longer raises the reported _ARRAY_API error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- numpy, python
- Domain
- bioinformatics, data
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100