Neurom

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- Morphology class accepts only morphio objects, not files anymore. (1120)
- Replace ``iter_*`` methods by properties in core objects and improve ``iter_segments``. (1054)
- NeuriteType extended to allow mixed type declarations as tuple of ints. (1071)
- All features return built-in types (1064)
- Morphology class also allows mutable morphio objects to be passed explicitly. (1049)
- Morphology class uses morphio immutable class by composition, istead of inheritance. (979)
- Morphology level radial distance features use the soma as reference point. (1030)
- Make ``neurom.core.Population`` resolve paths. Symlinks are not resolved. (1047)
- Mixed subtree processing can be used in morph_stats app via the use_subtrees flag. (1034)
- ``neurom.view.[plot_tree|plot_tree3d|plot_soma|plot_soma3D]`` were hidden from the
neurom.view module. They can still be imported from neurom.view.matplotlib_impl. (1032)
- Mixed subtree processing. (981)
- Deprecated modules and classes were removed. (1026)

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- Fix neurom.app.morph_stats.extract_dataframe for Population objects with several workers (1080)
- Update readthedocs config (1077)
- Can pass List[Population] args to neurom.app.morph_stats.extract_dataframe (1076)
- Fix compatibility with MorphIO>=3.3.6 (1075)
- Check that soma is not empty when features need it (1073)

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- Fix QhullError warning (1063)

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- Fix: extract_stats could not work on single neurite (1060)
- Fix view cli to use 'equal' axis when available (1051)
- Remove single point contour somas in h5 and asc tests (1045)
- Remove duplicated deps jinja, sphinx (1043)

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- Add ``neurom.features.morphology.length_fraction_above_soma`` feature.
- List of multiple kwargs configurations are now allowed in``neurom.apps.morph_stats``.
- ``neurom.features.neurite.principal_direction_extents`` directions correspond to extents
ordered in a descending order.
- Add features ``neurom.features.morphology.(aspect_ration, circularity, shape_factor)
- Fix ``neurom.morphmath.principal_direction_extent`` to calculate correctly the pca extent.
- Fix ``neurom.features.neurite.segment_taper_rates`` to return signed taper rates.
- Fix warning system so that it doesn't change the pre-existing warnings configuration
- Fix ``neurom.features.bifurcation.partition_asymmetry`` Uylings variant to not throw
for bifurcations with leaves.
- Fix ``neurom.features.neurite.principal_direction_extents`` to remove duplicate points
when calculated.
- Add ``neurom.features.morphology.volume_density`` feature so that it is calculated
correctly when the entire morphology is taken into account instead of summing the per
neurite volume densities.
- Add support for py39 and py310 testing.
- Fix ``neurom.features.morphology.sholl_frequency`` to return an empty list when a
neurite_type that is not present in the morphology is specified.
- Fix ``neurom.features.morphology.trunk_origin_radii`` to warn and use only the root
section for the calculation of the path distances. Edge cases from the combination
of ``min_length_filter`` and ``max_length_filter`` are addressed.
- Fix ``neurom.features.morphology.sholl_frequency`` to use soma center in distance
calculation, instead of using the origin.
- Add ``neurom.features.morphology.trunk_angles_inter_types`` and
``neurom.features.morphology.trunk_angles_from_vector`` features, make
``neurom.features.morphology.trunk_angles`` more generic and add length filter to
``neurom.features.morphology.trunk_origin_radii``.
- Deprecate python3.6
- Add doc on spherical coordinates.

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- Add morphology features total_width, total_height and total_depth