* A heterogeneous morphology consists of zero or more homogeneous and at least one heterogeneous neurite trees extending from the soma; 
* 'heterogeneous neurite trees ' is called a 'mixed subtree' for brevity
* this is a breaking change with how NeuroM<=3.x works
* this will fix #975

Remove deprecated modules and deprecation warning. viewer module was not included to be treated separately

Switch to using the morphio readonly morphology instead of mut

Co-authored-by: Mike Gevaert <michael.gevaert@epfl.ch>

Removes viewer deprecated module and hides plot_tree, plot_tree3d, plot_soma, plot_soma3d from neurom.view

Co-authored-by: Zisis Eleftherios <zisis@bb-fvfd24cfmnhx.epfl.ch>

…oint (#1030)

Use soma center as a reference point for morphology-level radial distance features.

Radial distance features on the morphology level were using
as reference point the root of each neurite. While this is ok
when per-neurite features are calculated, it is incorrect when
the radial distance features are calculated for the entire cell.

This change renders soma as the reference point for calculating
the radial distances, not the root of each neurite. When the same
features are used per-neurite the old behavior of using the neurite
root is still the same.

Co-authored-by: Adrien Berchet <adrien.berchet@gmail.com>

* Updating copyright year (#1028)

Co-authored-by: Alexander Dietz <alexander.dietz@epfl.ch>

* Updating copyright year (#1029)

Co-authored-by: Alexander Dietz <alexander.dietz@epfl.ch>

* Remove duplicated deps jinja, sphinx (#1043)

Co-authored-by: bbpgithubaudit <86652185+bbpgithubaudit@users.noreply.github.com>
Co-authored-by: Alexander Dietz <alexander.dietz@epfl.ch>
Co-authored-by: stefanoantonel <stefanoantonel@users.noreply.github.com>

Co-authored-by: Adrien Berchet <adrien.berchet@gmail.com>

Make file paths absolute in Population init, but not resolve symlinks.

Co-authored-by: Adrien Berchet <adrien.berchet@gmail.com>

* Maintain mut/immut after transformation
* Add tests

Co-authored-by: Eleftherios Zisis <eleftherios.zisis@epfl.ch>

* Updating copyright year (#1028)

Co-authored-by: Alexander Dietz <alexander.dietz@epfl.ch>

* Updating copyright year (#1029)

Co-authored-by: Alexander Dietz <alexander.dietz@epfl.ch>

* Remove duplicated deps jinja, sphinx (#1043)

* remove single point contour somas in h5 and asc tests (#1045)

* this is in prep for MorphIO to be more consistent and picky with contour somas

* Fix view cli (#1051)

* Fix coverage (#1056)

Co-authored-by: bbpgithubaudit <86652185+bbpgithubaudit@users.noreply.github.com>
Co-authored-by: Alexander Dietz <alexander.dietz@epfl.ch>
Co-authored-by: stefanoantonel <stefanoantonel@users.noreply.github.com>
Co-authored-by: MikeG <michael.gevaert@epfl.ch>
Co-authored-by: Alexis Arnaudon <alexis.arnaudon@epfl.ch>

---------

Co-authored-by: Eleftherios Zisis <eleftherios.zisis@epfl.ch>

* Fix NeuriteType for Python 3.12.3

* Coverage

…_segments (#1054)

* Improve iter_segments and add segment methods in core objects

* Rename iterator_type into section_iterator

* Remove iter_* methods and use consistent properties

* Use iter_sections instead of obj.sections in check.morphtree

* Update doc

* Expose soma methods as free functions.
* Allow using both morphio and neurom soma in soma functions.
* Keep backward compatibility with the soma methods.
* Disallow storing soma values to avoid issues with mutation of soma.
---------

Co-authored-by: Adrien Berchet <adrien.berchet@epfl.ch>