3d trunk angles

[arnaudon]

@lidakanari @adrien-berchet , I've clean up the main code, once we agree on it, I'll clean up the schema/tests so we can merge. I'm done with it for now.

[arnaudon]

@lidakanari , I wait on your green light to start cleaning up test/schemas

[codecov[bot]]

Codecov Report

Merging #49 (c18688a) into main (01c941f) will increase coverage by 0.11%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main      #49      +/-   ##
==========================================
+ Coverage   97.44%   97.56%   +0.11%     
==========================================
  Files          38       39       +1     
  Lines        1954     2132     +178     
  Branches      288      324      +36     
==========================================
+ Hits         1904     2080     +176     
- Misses         34       35       +1     
- Partials       16       17       +1     

Flag	Coverage Δ
pytest	97.56% <100.00%> (+0.11%)	:arrow_up:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
neurots/astrocyte/grower.py	75.86% <ø> (ø)
neurots/astrocyte/tree.py	100.00% <ø> (ø)
neurots/extract_input/input_distributions.py	100.00% <ø> (ø)
neurots/extract_input/input_parameters.py	97.43% <ø> (ø)
neurots/generate/algorithms/tmdgrower.py	99.24% <ø> (-0.02%)	:arrow_down:
neurots/generate/tree.py	98.90% <ø> (-0.02%)	:arrow_down:
neurots/extract_input/from_neurom.py	96.49% <100.00%> (-3.51%)	:arrow_down:
neurots/generate/grower.py	100.00% <100.00%> (ø)
neurots/generate/orientations.py	100.00% <100.00%> (ø)
neurots/morphmath/sample.py	100.00% <100.00%> (ø)
... and 5 more

[arnaudon]

@adrien-berchet @lidakanari , if this is what you had in mind, I'll fix the tests

[arnaudon]

@adrien-berchet , I simplified the validation of bar length as well, as it is done in the preprocessing, no need to redo it in the grower later

[arnaudon]

@adrien-berchet , I'm not sure how to fix this failing test, locally it worked with latest numpy... could you have a quick look? thank you!

[arnaudon]

I think I bumped to the wrong version

[arnaudon]

ah no, so i don't know that this is..

[adrien-berchet]

It's not because of numpy, it's because you remove the skip_validation parameter from the TreeGrowerSpaceColonization constructor but in the test the skip_validation parameter is still given, so the parameters are shifted and thus the context is passed as a random number generator.

[arnaudon]

Finally! I can't spot what is not covered, maybe codecov needs some time to be up to date.

[arnaudon]

ALL GREEEEN!!!!!!

[adrien-berchet]

ALL GREEEEN!!!!!!

Yay :partying_face:

[lidakanari]

Finally double checking and all is good from my side to merge this one. @eleftherioszisis if you want to check for astrocytes please provide feedback for this, otherwise we are ok to merge this one.

[arnaudon]

great thanks! I'll then make a minor release of neurots, so we can merge the dependencies