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theislab / ehrapy

Electronic Health Record Analysis with Python.
https://ehrapy.readthedocs.io/
Apache License 2.0
232 stars 19 forks source link

read only file systems and example data download #699

Closed bio-la closed 6 months ago

bio-la commented 7 months ago

Report

adata = ep.dt.diabetes_130_raw(encoded=False) [...] OSError: [Errno 30] Read-only file system: '/ehrapy_data'

maybe add info how to prepare the project directory for download?

Version information

anndata 0.10.7 ehrapy 0.7.0 matplotlib 3.8.4 pandas 2.2.2 seaborn 0.13.2 session_info 1.0.0

PIL 10.3.0 appnope 0.1.4 asttokens NA autograd NA autograd_gamma NA bs4 4.12.3 cachetools 5.3.3 category_encoders 2.6.3 causallearn NA certifi 2024.02.02 charset_normalizer 3.3.2 comm 0.2.2 cvxopt 1.3.2 cycler 0.12.1 cython_runtime NA dateutil 2.9.0 db_dtypes 1.2.0 ... Python 3.10.14 | packaged by conda-forge | (main, Mar 20 2024, 12:53:34) [Clang 16.0.6 ] macOS-14.4.1-x86_64-i386-64bit

eroell commented 7 months ago

Hm, the ehrapy_data directory should typically be generated with not just read permissions The way to solve on unix would be to go to the ehrapy directory and there do chmod +wx ehrapy_data.

Not sure under what circumstances read-only permissions are set to this created directory