biomart_annotations still creates cache when use_cache=False

[PauBadiaM]

Please make sure these conditions are met

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of scanpy.
• (optional) I have confirmed this bug exists on the master branch of scanpy.

What happened?

When using sc.queries.biomart_annotations, it still generates the file .pybiomart.sqlite even when use_cache=False is used.

To me this is a problem because the generated hidden file interferes with Omnipath and makes it crash. It used to be the case that use_cache used to work but not anymore.

Thank you for your time.

Minimal code sample

import scanpy as sc

annot = sc.queries.biomart_annotations(
    'hsapiens',
    ['ensembl_gene_id', 'external_gene_name'],
    use_cache=False
)

Error output

No response

Versions

-----
anndata     0.10.3
scanpy      1.9.8
-----
PIL                 10.2.0
asttokens           NA
attr                23.1.0
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dateutil            2.8.2
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decorator           5.1.1
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future              0.18.3
h5py                3.10.0
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igraph              0.11.2
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kiwisolver          1.4.5
leidenalg           0.10.1
llvmlite            0.41.1
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mpl_toolkits        NA
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packaging           23.2
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pexpect             4.8.0
pickleshare         0.7.5
platformdirs        3.11.0
prompt_toolkit      3.0.39
psutil              5.9.5
ptyprocess          0.7.0
pure_eval           0.2.2
pyarrow             15.0.0
pybiomart           0.2.0
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pyparsing           3.1.1
pytz                2024.1
requests            2.31.0
requests_cache      1.1.1
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six                 1.16.0
sklearn             1.3.2
socks               1.7.1
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-----
IPython             8.17.2
jupyter_client      8.6.0
jupyter_core        5.5.0
-----
Python 3.11.6 | packaged by conda-forge | (main, Oct  3 2023, 10:40:35) [GCC 12.3.0]
Linux-6.5.0-17-generic-x86_64-with-glibc2.35
-----
Session information updated at 2024-02-16 11:40

[ivirshup]

Do you know when this used to work?

And would you be up for submitting a bugfix?

[PauBadiaM]

Hi @ivirshup, it used to work 6 months ago. As discussed in saezlab/omnipath#54 (comment), it seems it was an error with the package requests_cache. Installing the latest version from GitHub solves the issue so I'll close this then, thanks!