Archngv

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Fixed
~~~~~

- The bounding box for the microdomains is now consistent with the region of interest that has been selected.
- Replaces the use of the unmaintained python package TNS by the Neurots one.

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Fixed
~~~~~

- Fixed the snakemake syntax and code style by adding snakefmt requirement and command into the lint target of tox.ini
- Move module release from 2023-03 to 2023-05 because of a libsonata issue: ImportError: cannot import name 'CircuitConfigStatus' from 'libsonata'

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Improvements
~~~~~~~~~~~~

- Limit the microdomains to the region of interest.[`BBPP152-76`_]
- thread separately the non connected component [`BBPP152-111`_]
- Switch to the new Spatial_index package version. Use multi index [`BBPP152-109`_]
- Synthesis step improvement [`BBPP152-112`_]
- Generate tetrahedral meshes [`BBPP152-113`_]
- Adapt the build microdomains step for a negative entry for the region_mask.voxel_dimension [`BBPP152-155`_]
- Add the optional use of a ROI mask [`BBPP152-176`_]

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Improvements
~~~~~~~~~~~~

- Simplified NGV exporters and removed a lot of redundant code. [`NSETM-1927`_]
- Make the NGV population types consistent with the SONATA documentation, and maintain backward
backward compatibility with the legacy types. [`NSETM-1923`_]

Fixed
~~~~~

- Output the correct key entry 'endfeet_meshes_file' for the endfeet meshes path in the SONATA
config. Maintain backward compatibility with the old 'endfeet_meshes' entry. [`NSETM-1904`]

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New Features
~~~~~~~~~~~~

- NGV building supports circuit-build manifests, where the ngv specific configuration has to be
under a root entry 'ngv', [`NSETM-1872`_]

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Improvements
~~~~~~~~~~~~

- Endfeet meshes file layout has been converted to the grouped properties one. [`NSETM-1830`_]
- Merge microdomain files into a single file at the build root level. [`NSETM-1807`_]
- Use a generic file layout for grouped properties to store the microdomains that can be extended
with and arbitrary number of additional properties. [`NSETM-1807`_]
- Multiple yaml configuration files merged into the main MANIFEST.yaml. [`NSETM-1746`_]
- Refactored the neuroglial connectivity out of ngv.py to reduce its size. [`NSETM-1768`_]
- Refactored the gliovascular connectivity out of ngv.py to reduce its size.
- The app cli has been compressed into the ngv.py module. [`NSETM-1740`_]

New Features
~~~~~~~~~~~~
- Resampling was added in synthesis to create an upper bound in morphology points [`NSETM-1778`_].

Removed
~~~~~~~

- SONATA config no longer stores the bioname parameters. [`NSETM-1746`_]
- The deprecated `extras` subpackage has been removed.

.. _`NSETM-1927`: https://bbpteam.epfl.ch/project/issues/browse/NSETM-1927
.. _`NSETM-1923`: https://bbpteam.epfl.ch/project/issues/browse/NSETM-1923
.. _`NSETM-1904`: https://bbpteam.epfl.ch/project/issues/browse/NSETM-1904
.. _`NSETM-1872`: https://bbpteam.epfl.ch/project/issues/browse/NSETM-1872
.. _`NSETM-1830`: https://bbpteam.epfl.ch/project/issues/browse/NSETM-1830
.. _`NSETM-1778`: https://bbpteam.epfl.ch/project/issues/browse/NSETM-1778
.. _`NSETM-1807`: https://bbpteam.epfl.ch/project/issues/browse/NSETM-1807
.. _`NSETM-1746`: https://bbpteam.epfl.ch/project/issues/browse/NSETM-1746
.. _`NSETM-1768`: https://bbpteam.epfl.ch/project/issues/browse/NSETM-1768
.. _`NSETM-1740`: https://bbpteam.epfl.ch/project/issues/browse/NSETM-1740