still need data dir when using alias option?

neuroquery / pubget

Collecting papers from PubMed Central and extracting text, metadata and stereotactic coordinates.

https://neuroquery.github.io/pubget/

MIT License

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still need data dir when using alias option? #36

Closed koudyk closed 1 year ago

koudyk commented 1 year ago

I just pulled pubget and installed it with pip install -e . in the pubget folder
I ran pubget run -q "fMRI[Abstract] AND music[Title]" --labelbuddy --alias fmri_music
I got this error: pubget run: error: the following arguments are required: data_dir

On the poster, we use the alias option without specifying a data directory. Is this how it's supposed to work? Or do we need both? If so, maybe we should update the code on the poster.

jeromedockes commented 1 year ago

sorry I missed this! yes we still need the data_dir, which is the root of all pubget data. the alias symlink and the query directory go inside the data_dir. As you know we fixed the poster. what we could consider is have a default for the data dir, such as the current working directory. It would certainly make some examples look a bit simpler, but I think in most cases users will want to specify a specific data directory. WDYT?