[Bug]: Fail to import in read-only file system

[alejoe91]

What happened?

I'm trying to import pynwb within an Apptainer container and I'm getting a Read-only filesystem error:

apptainer shell /allen/aind/scratch/alessio.buccino/singularity_cache_dir/ghcr.io-allenneuraldynamics-aind-ephys-pipeline-nwb-si-0.102.1.img

In the container

Apptainer> python
Python 3.11.5 (main, Sep 11 2023, 13:54:46) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pynwb
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/conda/lib/python3.11/site-packages/pynwb/__init__.py", line 250, in <module>
    __load_core_namespace()
  File "/opt/conda/lib/python3.11/site-packages/pynwb/__init__.py", line 219, in __load_core_namespace
    Path(__resources['cached_typemap_path']).unlink(missing_ok=True)
  File "/opt/conda/lib/python3.11/pathlib.py", line 1147, in unlink
    os.unlink(self)
OSError: [Errno 30] Read-only file system: '/opt/conda/lib/python3.11/site-packages/pynwb/core_typemap.pkl'

I think that the error might be related to running in an environment where I previously used an apptainer image with another pynwb version.

Anyways, I think that the code should have some try-except to avoid errors when unlinking the core_typemap

Steps to Reproduce

import pynwb # in an apptainer container

Traceback

Apptainer> python
Python 3.11.5 (main, Sep 11 2023, 13:54:46) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pynwb
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/conda/lib/python3.11/site-packages/pynwb/__init__.py", line 250, in <module>
    __load_core_namespace()
  File "/opt/conda/lib/python3.11/site-packages/pynwb/__init__.py", line 219, in __load_core_namespace
    Path(__resources['cached_typemap_path']).unlink(missing_ok=True)
  File "/opt/conda/lib/python3.11/pathlib.py", line 1147, in unlink
    os.unlink(self)
OSError: [Errno 30] Read-only file system: '/opt/conda/lib/python3.11/site-packages/pynwb/core_typemap.pkl'

Operating System

Linux

Python Executable

Conda

Python Version

3.11

Package Versions

pynwb == 2.8.3

Code of Conduct

• I agree to follow this project's Code of Conduct
• Have you checked the Contributing document?
• Have you ensured this bug was not already reported?

[stephprince]

Thanks for reporting this issue @alejoe91

I think that the error might be related to running in an environment where I previously used an apptainer image with another pynwb version.

I agree, I think the error is coming from an attempt to remove the previously cached type map from a different pynwb version. I will look into addressing this. (There is a related issue in #2048 with a similar write access error)