Update package.py to Snudda 2.0.1

@hjorth any constraints regarding the open3d package? The version in spack's current stable is quite old (and pins us to an really old version of fmt that conflicts with other top-level packages).

Hej Eric, feel free to change the version of the open3d package. I think it should be fine.

BTW. open3d is a messy package (in terms building it, especially its handling of dependencies) — I don't say we can't get it integrated into the ESD, but after quite a few changes it's still not yet done, and as of now, it feels ugly (and it's getting more ugly when comparing older version against newer versions of the package — i.e. open3d upstream might not even care?).

→ !525 (merged)

As far as I can see, you are not yet "heavily" invested in it (I looked at this)… so, all EBRAINS things aside, I just wanted to communicate, that IMHO it might be a dependency that you might to reevaluate in terms of functionality vs. technical debt that it introduces.

(Yeah, I know I shouldn't throw stones — my own packages (the BrainScaleS things) also depend on quite a few bad packages (and I can't blame anyone else :/ )… but the pain to keep stuff working despite bad dependencies (or even getting rid of those packages) increases my level of awareness nowadays ;) .)

changed target branch from master to update-snudda

merged

Hi @hjorth, open3d was indeed a messy package, so it took some more time than expected, but now it's finally in the ESD (see !525 (merged), !528 (merged)). py-snudda@2.0.1 is now available in the experimental kernel in the Lab, please test and let me know if there are any problems :)

Great thanks! I just test ran the old Striatum notebook and (after updating the JSON network and input config files to the new format) things worked nicely!

(Maybe we could aim for integrating some of this notebook code into a test for the package :) — for one of the upcoming releases?)

There is a series of unit tests available here: https://github.com/Hjorthmedh/Snudda/tree/master/tests

and mirrored here: https://gitlab.ebrains.eu/hjorth/snudda/-/tree/main/tests?ref_type=heads

This particular test uses most part of the pipeline: https://gitlab.ebrains.eu/hjorth/snudda/-/blob/main/tests/test_cli.py?ref_type=heads

(but of course it would be good to run all tests, but they would take some 8-10 minutes to run).

mentioned in issue #60