deal with local and remote atlas versions in validate_atlases.py

[viktorpm]

Describe the bug

• I transferred the newly generated Kim atlases (v1.1) to my local atlases folder to run the validation.py function on them.
• I received this warning:

brainglobe_atlasapi: kim_mouse_25um version 1.1is not the latest available (1.0). To update the atlas run in the terminal:
brainglobe update -a kim_mouse_25um

• The new atlases were overwritten by the older versions from the GIN repository.
• To work around the problem, I simply renamed the folders from kim_mouse_25um_v1.1 to kim_mouse_25um_v1.0.

Expected behaviour

• Detect the difference but don't replace the atlases automatically.

[adamltyson]

Detect the difference but don't replace the atlases automatically.

What was done automatically? Nothing in BrainGlobe should update the atlases without specific user interaction.

[viktorpm]

It started to download the atlases without me running the brainglobe update -a kim_mouse_25um (or any other) command.

[adamltyson]

What started to? What process was running?

[viktorpm]

I ran the validation.py function. This is the output:

(bg-atlasapi) vplattner@hpc-gw1:~/_projects/validation/brainglobe-atlasapi$ python brainglobe_atlasapi/atlas_generation/validate_atlases.py
example_mouse_100um 1.2
allen_mouse_10um 1.2
allen_mouse_25um 1.2
allen_mouse_50um 1.2
allen_mouse_100um 1.2
mpin_zfish_1um 1.0
allen_human_500um 0.1
/nfs/nhome/live/vplattner/_projects/validation/brainglobe-atlasapi/brainglobe_atlasapi/core.py:65: UserWarning: This atlas seems to be outdated as no additional_references list is found in metadata!
  warnings.warn(
kim_mouse_10um 1.0
brainglobe_atlasapi: kim_mouse_10um not found locally. Downloading...
Downloading... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0% • 645.2/645.2 MB • speed: 1.8 MB/s • ETA: 0:00:00
kim_mouse_25um 1.0
brainglobe_atlasapi: kim_mouse_25um version 1.1is not the latest available (1.0). To update the atlas run in the terminal:
    brainglobe update -a kim_mouse_25um
brainglobe_atlasapi: kim_mouse_25um version 1.1is not the latest available (1.0). To update the atlas run in the terminal:
    brainglobe update -a kim_mouse_25um
brainglobe_atlasapi: kim_mouse_25um version 1.1is not the latest available (1.0). To update the atlas run in the terminal:
    brainglobe update -a kim_mouse_25um
brainglobe_atlasapi: updating kim_mouse_25um
Downloading... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0% • 226.7/226.7 MB • speed: 1.1 MB/s • ETA: 0:00:00
brainglobe_atlasapi: kim_mouse_25um updated to version: 1.0
kim_mouse_50um 1.0
brainglobe_atlasapi: kim_mouse_50um version 1.1is not the latest available (1.0). To update the atlas run in the terminal:
    brainglobe update -a kim_mouse_50um
brainglobe_atlasapi: kim_mouse_50um version 1.1is not the latest available (1.0). To update the atlas run in the terminal:
    brainglobe update -a kim_mouse_50um
brainglobe_atlasapi: kim_mouse_50um version 1.1is not the latest available (1.0). To update the atlas run in the terminal:
    brainglobe update -a kim_mouse_50um
brainglobe_atlasapi: updating kim_mouse_50um
Downloading... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━ 87.8% • 167.2/190.5 MB • speed: 1.1 MB/s • ETA: 0:00:21

[adamltyson]

Can you link to that file?

[viktorpm]

Sure! https://github.com/brainglobe/brainglobe-atlasapi/blob/main/brainglobe_atlasapi/atlas_generation/validate_atlases.py

[adamltyson]

This isn't a bug in the atlasapi, the validation script explicitly updates the atlas. Maybe the validation script should have some logic to deal specifically with atlas versions that are newer than those on GIN?

[viktorpm]

Should I convert this into a discussion or close it?

[adamltyson]

You can keep it open, just maybe change the title so we know what the actual issue is.

As an aside, I've actually just disabled Discussions. We decided a while back to not use that feature (in favour of issues, Zulip & image.sc), and I didn't know we still had it enabled on this repo.