feat: update how related regions are fetched

[xgui3783]

see FZJ-INM1-BDA/siibra-configurations#44

This PR is the companion PR for updating the SANDS reference within siibra.

Rather than relying on SANDS references of parcellation entity version, it is updated to use parcellation entity, which semantically more closely models SANDS model.

n.b. as this PR requires a specific branch of siibra configuration to function properly, this PR also aims to introduce the mechanism, by which, based on commit message, custom ref of siibra-configuration will be used.

These changes are not yet pushed, in order to follow the Red/Green light approach for TDD

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 28.88889% with 32 lines in your changes are missing coverage. Please review.

Project coverage is 49.50%. Comparing base (5a0e6b3) to head (e1cff22).
Report is 477 commits behind head on main.

Files	Patch %	Lines
siibra/core/region.py	28.88%	32 Missing ⚠️

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Additional details and impacted files

@@             Coverage Diff             @@
##             main     #582       +/-   ##
===========================================
+ Coverage   36.81%   49.50%   +12.68%     
===========================================
  Files          61       74       +13     
  Lines        5421     6961     +1540     
===========================================
+ Hits         1996     3446     +1450     
- Misses       3425     3515       +90     

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[xgui3783]

Expecting e2e tests to fail (specifically e2e/core/test_regions.py)

[xgui3783]

Tests should pass.

[xgui3783]

@AhmetNSimsek can you please take a look at this?

I have also managed to pull in the changes that allow a custom ref of siibra-configuration to be used with [ci:usecfg]<refname>

[AhmetNSimsek]

LGTM.
Could you add docstrings to RegionRelationAssessments members?

Also, thank you for implementing running tests with custom ref of siibra-configuration based on the commit message.

[xgui3783]

@AhmetNSimsek can you take a look? I added docstring as you requested.

[AhmetNSimsek]

Thanks, looks good.

For future reference, would you mind using numpy style as in

siibra-python/siibra/core/region.py

Lines 273 to 297 in 50d4d4c

	"""
	Find regions that match the given region specification in the subtree
	headed by this region.
	Parameters
	----------
	regionspec: str, regex, int, Region
	- a string with a possibly inexact name (matched both against the name and the identifier key)
	- a string in '/pattern/flags' format to use regex search (acceptable flags: aiLmsux, see at https://docs.python.org/3/library/re.html#flags)
	- a regex applied to region names
	- a Region object
	filter_children : bool, default: False
	If True, children of matched parents will not be returned
	find_topmost : bool, default: True
	If True (requires `filter_children=True`), will return parent
	structures if all children are matched, even though the parent
	itself might not match the specification.
	Returns
	-------
	list[Region]
	list of regions matching to the regionspec
	Tip
	---
	See example 01-003, find regions.
	"""

This should also work but better to have a unified style. Please don't waste time on it now tho. There are more urgent things atm.

[xgui3783]

Thanks, looks good.

For future reference, would you mind using numpy style as in

siibra-python/siibra/core/region.py

Lines 273 to 297 in 50d4d4c

	"""
	Find regions that match the given region specification in the subtree
	headed by this region.
	Parameters
	----------
	regionspec: str, regex, int, Region
	- a string with a possibly inexact name (matched both against the name and the identifier key)
	- a string in '/pattern/flags' format to use regex search (acceptable flags: aiLmsux, see at https://docs.python.org/3/library/re.html#flags)
	- a regex applied to region names
	- a Region object
	filter_children : bool, default: False
	If True, children of matched parents will not be returned
	find_topmost : bool, default: True
	If True (requires `filter_children=True`), will return parent
	structures if all children are matched, even though the parent
	itself might not match the specification.
	Returns
	-------
	list[Region]
	list of regions matching to the regionspec
	Tip
	---
	See example 01-003, find regions.
	"""

This should also work but better to have a unified style. Please don't waste time on it now tho. There are more urgent things atm.

Apologies, I have a lot on my plate right now.

Do you mind taking over the reformatting for me?

@AhmetNSimsek

[AhmetNSimsek]

Since the config branch had been merged and tagged, bumped the version (3b2d9fa) to test with the correct config.