Fede dev

[FedeClaudi]

I've made a few changes..

When downloading files the progress bar is now implemented with rich [on windows the looks are not the best, but on linux and macOs it should be better]:

I've removed tqdm from the requirements, it's only used in the atlas generation stuff now.

atlases list now doesn't show the remote path anymore, but I've added the local and online version of the atlas.

Also if an an atlas is outdated this is highlighted in the table (shown for an example here):

---

atlas update
When instatiating at atlas class it checks if it's the latest version, if not it prompts the user to update

Using the update command results in the current atlas folder being deleted and the new atlas being downloaded:

if force is not used, the atlas is not updated if the version matches the latest version online.

[adamltyson]

Hi @FedeClaudi, I ran this locally (after reinstalling, and deleting ~/.brainglobe). I installed an atlas with brainatlas_update -a allen_mouse_25um, but then brainatlas_list_atlases gives me:

(brainatlas_api) adam@garfield:~/projects/brainatlas-api$ brainatlas_list_atlases
                                                                                                  
                              Brainglobe Atlases                               
╭──────────────────┬────────────┬───────────────┬────────────────┬────────────╮
│ Name             │ Downloaded │ Local version │ Latest version │ Local path │
├──────────────────┼────────────┼───────────────┼────────────────┼────────────┤
│ allen_mouse_25um │    ---     │      ---      │      0.2       │ ---        │
╰──────────────────┴────────────┴───────────────┴────────────────┴────────────╯

Am I doing something wrong?

[FedeClaudi]

no, it looks like there's something off...

---

it's fixed now, I forgot one thing amongs commits and stuff.. thanks for checking!

[adamltyson]

Bingo, looks great now!

[vigji]

Looks good, will test as soon as I can!
Just a note looking at the code - could we use click for out command line functions? Is it very neat to read, just add a couple of function decorators to parse the arguments

[FedeClaudi]

could we use click for out command line functions? Is it very neat to read, just add a couple of function decorators to parse the arguments

I don't understand, what do you mean with out command line functions and what's click?

[vigji]

Sorry, our command line functions like this one for atlas update :)
Click is a library for parsing command line arguments for command line applications it’s very straightforward to use - not good for many parameters, but here we have one or two. I used it for the config module!

[FedeClaudi]

I see, instead of argparse we should use click?

[vigji]

Yep!

[FedeClaudi]

aaaaand, done. That's cool I didn't know about it.

[FedeClaudi]

among other things, brainatlas_api.list_atlases.list_atlases is now brainatlas_api.list_atlases.show_atlases.
The command line command is the same

[vigji]

Great! Good to merge for me.