Add context handling with accept/reject

[arnaudon]

This PR adds an accept/reject mechanisms to allow for external modification of section and trunk growths via the generic context object.

[codecov]

Codecov Report

Merging #61 (29a57c3) into main (9d74824) will decrease coverage by 0.04%.
The diff coverage is 100.00%.

❗ Current head 29a57c3 differs from pull request most recent head 301455f. Consider uploading reports for the commit 301455f to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #61      +/-   ##
==========================================
- Coverage   97.76%   97.73%   -0.04%     
==========================================
  Files          39       39              
  Lines        2197     2211      +14     
  Branches      381      385       +4     
==========================================
+ Hits         2148     2161      +13     
  Misses         30       30              
- Partials       19       20       +1     

Flag	Coverage Δ
pytest	97.73% <100.00%> (-0.04%)	⬇️

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

Files	Coverage Δ
neurots/extract_input/input_parameters.py	97.56% <ø> (ø)
neurots/generate/orientations.py	100.00% <100.00%> (ø)
neurots/generate/section.py	100.00% <100.00%> (ø)
neurots/generate/tree.py	99.01% <100.00%> (-0.99%)	⬇️
neurots/utils.py	100.00% <100.00%> (ø)

[arnaudon]

@adrien-berchet , when you have 5min, if you can take a look at this to see if the general implementation makes sense. I will then use context to modify the prob() function.

[adrien-berchet]

@adrien-berchet , when you have 5min, if you can take a look at this to see if the general implementation makes sense. I will then use context to modify the prob() function.

Looks nice!

[arnaudon]

@lidakanari @adrien-berchet , this can be reviewed as well, again, it is experimental, so not fully tested

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.88%. Comparing base (38f8e66) to head (4b9cb8f).
Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #61      +/-   ##
==========================================
+ Coverage   97.86%   97.88%   +0.01%     
==========================================
  Files          39       39              
  Lines        2200     2217      +17     
  Branches      382      296      -86     
==========================================
+ Hits         2153     2170      +17     
  Misses         29       29              
  Partials       18       18              

Flag	Coverage Δ
pytest	97.88% <100.00%> (+0.01%)	⬆️

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

Files with missing lines	Coverage Δ
neurots/generate/orientations.py	100.00% <100.00%> (ø)
neurots/generate/section.py	100.00% <100.00%> (ø)
neurots/generate/tree.py	100.00% <100.00%> (ø)
neurots/utils.py	100.00% <100.00%> (ø)

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