Scanpy does not work with with few permissions
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Description
I'm running scanpy in a docker container with few privileges, e.g. the guest user.
Unfortunately, scanpy tries to create a folder in the local working directory:
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/scanpy/__init__.py", line 14, in <module>
from . import settings
File "/usr/local/lib/python3.6/site-packages/scanpy/settings.py", line 13, in <module>
os.makedirs('.scanpy/')
File "/usr/local/lib/python3.6/os.py", line 220, in makedirs
mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '.scanpy/'
Could you use a tempdir alternativley?
Contributor guide
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 scanpy/settings.py and reproduce importing scanpy as a user who cannot write to the current working directory. Check that initialization no longer fails with the shown PermissionError and that its required directory is created in a temporary location instead.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100