`download-files-by-category` not exposed to CLI

[lucas-diedrich]

Hi, this is a very useful package, thank you so much!

I tried to run the download-files-by-category command as described in the README.

pridepy download-files-by-category -a PXD022105 -o ./data -c RAW -p ftp

which failed with the error

pridepy [OPTIONS] COMMAND [ARGS]...
Try 'pridepy --help' for help.
Error: No such command 'download-files-by-category'.

Can you provide me any guidance on how to resolve the error?

---

My environment (Python 3.12 on MacOS):

I tried to install both the latest version of the package from pip and from the main branch on GitHub.

anyio==4.12.1
boto3==1.42.39
botocore==1.42.39
certifi==2026.1.4
charset-normalizer==3.4.4
click==8.3.1
h11==0.16.0
httpcore==1.0.9
httpx==0.27.2
idna==3.11
jmespath==1.1.0
packaging @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_packaging_1769093650/work
pridepy==0.0.12
python-dateutil==2.9.0.post0
ratelimit==2.2.1
requests==2.32.5
s3transfer==0.16.0
setuptools==80.10.2
six==1.17.0
sniffio==1.3.1
tqdm==4.67.2
typing_extensions==4.15.0
urllib3==2.6.3
wheel==0.46.3

[lucas-diedrich]

Edit: Inspecting the CLI interface showed that the command name changed to download-all-public-category-files, which resolved the error. So the correctly working command would be

pridepy download-all-public-category-files -a PXD022105 -o ./data -c RAW -p ftp

Thanks!

[ypriverol]

Thanks looks we have fixed the README #83

[lucas-diedrich]

Awesome, thanks for the quick response!