Bug with Topaz

[win5tan]

Hi there, it looks like there's a bug with Topaz. The line where it is erroring is bad. 

It should be:

pd.concat(groups_train, axis=0)

Instead of

pd.concat(groups_train, 0) <--- BAD!

Could the developers please debug/fix it? Thanks a lot.

[DarnellGranberry]

What file and line is it referencing in your error? Also, what branch are you using?

[win5tan]

Hi Darnell,

It was when I execute the Topaz path in cryosparc. IT officer from my institute thinks it's a bug error.

I used the following Topaz path: /stornext/System/data/software/rhel/9/base/structbio/topaz/0.2.5/bin/topaz

Thanks, Winnie

On Wed, Oct 16, 2024 at 12:12 AM Darnell Granberry @.***> wrote:

What file and line is it referencing in your error?

— Reply to this email directly, view it on GitHub https://github.com/tbepler/topaz/issues/207#issuecomment-2413879031, or unsubscribe https://github.com/notifications/unsubscribe-auth/BBBYF6OYMV6JS7Z36KMYORTZ3UICZAVCNFSM6AAAAABP6J6DMSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJTHA3TSMBTGE . You are receiving this because you authored the thread.Message ID: @.***>

[DarnellGranberry]

The only instances of pd.concat I can find all use that keyword argument. Can you try re-installing topaz? It would be helpful if you could paste the full traceback output when your error appears.

[vatese]

Hey! Hope this helps. Ran into something similar.

I see this was updated on the master branch https://github.com/tbepler/topaz/commit/25cb2cb8de2a0f995da42a472eb86b7011c8535a.

Topaz was installed with pip install topaz-em.

Traceback (most recent call last):
File "/sw/topaz/bin/topaz", line 8, in <module>
sys.exit(main())
File "/sw/topaz/lib64/python3.9/site-packages/topaz/main.py", line 148, in main
args.func(args)
File "/sw/topaz/lib64/python3.9/site-packages/topaz/commands/train_test_split.py", line 108, in main
targets_train = pd.concat(groups_train, 0)
TypeError: concat() takes 1 positional argument but 2 were given

Current version provided by pip:

./topaz --version
TOPAZ 0.2.5a

[DarnellGranberry]

Please update your installations and let us know if there are further issues

[DarnellGranberry]

Hi @win5tan . If you are still having issues, that should be fixed in v0.3.5.