Voxcell

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Improvements
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- Use sphinx-bluebrain-theme for documentation
- Add missing API to documentation

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Python 2 compatibility
~~~~~~~~~~~~~~~~~~~~~~

- Dropped Python 2 support


Bug Fixes
~~~~~~~~~

- Fixed issue with H5PY >= 3.0.0 string type behavior. Changes in H5py >= 3.0.0 API affected the
reading of h5 files by returning string fields as bytes fields. The recommended use of the method
`Dataset.asstr()` to return string field is implemented in this version.

Removed modules
~~~~~~~~~~~~~~~

- Removed deprecated module `voxcell.positions`

- Removed deprecated module `voxcell.build`

- Removed deprecated module `voxcell.core`

- Removed deprecated module `voxcell.voxell_data`

- Removed deprecated function `voxcell.vector_field.generate_homogeneous_field`:
- Removed deprecated function `voxcell.vector_field.calculate_fields_by_distance_from`:
- Removed deprecated function `voxcell.vector_field.calculate_fields_by_distance_to`:
- Removed deprecated function `voxcell.vector_field.calculate_fields_by_distance_between`:
- Removed deprecated function `voxcell.vector_field.compute_cylindrical_tangent_vectors`:
- Removed deprecated function `voxcell.vector_field.compute_hemispheric_spherical_tangent_fields`:

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Improvements
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- Remove the NodePopulation implementation and hard deprecate the class. Deprecate the
node_population.py module itself.

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New Features
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- Add a function to retrieve the region ids of layers in a brain region

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Bug Fixes
~~~~~~~~~

- Force the version of h5py to h5py<3.0.0. h5py==3.0.0 dropped the python2 support and changed the
string behaviors.

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- Set the nrrd header_ field `kinds` with the value `['vector', 'domain', 'domain', domain']` when saving an
nrrd file which holds a non-scalar vector field over a volume. This change enables visualization of
direction vectors (3D vector field) and orientations (quaternions, 4D) with ITK-SNAP_ and 3D Slicer_.

- Changed processing of properties of CellCollection that are pandas.Categorical. A special rule for
string properties is applied. If unique values of a property make less than half of its all values
then it is loaded as pandas.Categorical.

- Deprecated the Hierarchy class in profit of the RegionMap. The Hierarchy class should be removed
in 2.8.0. Redo the docs for the RegionMap object.

- Changed saving of `CellCollection`. Raise an error if there is a `None` or `np.NaN` in
`CellCollection`.

- Fixed the orientation loading for sonata files in `CellCollection`. Two different formats
exist : the euler's angles and the quaternions.

- use quaternions if all "orientation_[x|y|z]" are present
- if some of the "orientation_[x|y|z]" fields are here but not all. Raise.
- if orientations and rotation_angles are present use quaternions
- if no quaternions and some of the rotation_angles use the eulers angles
and assign 0 to the missing ones.

- Added a orientation_format property to the `CellCollection` class. This allows the user to choose
which sonata orientation format she/he wants to use.

- Added a size function to `CellCollection`.

- Check the sizes of the orientations/positions/properties before saving.