Morphio

Latest version: v3.4.0

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3.4.0

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Improvements:
* New SWC parser:
* handles `locale` correctly, so decimal numbers using comma are allowed
* ~800 line SWC parse time goes from 0.976 to 0.699
* Doesn't create changes to bifurcations at the root nodes of SWC files
* More strict Neuromorpho 3 point soma checks
* disallow repeated Sample IDs
* Follow https://swc-specification.readthedocs.io/en/latest/swc.html more closely
* Allow only positive integer Sample IDs
* Allow for the type of neurite to change at bifurcation points
* Allow Window style `End of Lines`
* allow trailing spaces on sample lines

* Since this is a large change to the SWC parser, the minor release was increased

3.3.10

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* This is primarily so that 3.13 wheels exist before the new SWC parser is put into production.
* try to work around removal of older MSVC tools
* Remove Errorlevel::Info; it's not an error if it's only informative
* Update upload/download actions to v4.
* update HDF5 url
* Update HighFive to 2.10.0

3.3.9

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* remove embarrassing debug print; Hat-tip SarahM

3.3.8

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* Make ThreePointSoma use relative tolerance (494)
* Fix incorrect warning types for `OnlyChild` and `DisconnectedNeurite` (487)
* Better error handling, allows for non-global errors and collecting the errors for a single morphology load,
see https://morphio.readthedocs.io/en/latest/warnings.html for an example on how to use a `warning_handler` (#482)

Improvements:
* work w/ clang17 (486)
* Turn on -Wno-poison-system-directories on clang (489)
* follow libsonata's example, and publish wheels that statically use hdf5, to reduce h5py version conflicts (493)
* update to pybind11 v2.12.0 (495)

3.3.7

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* Change license from LGPL-3.0 to Apache-2.0 467
* Switch to HDF5 1.14 for all wheels
* Add wheel building for python 3.12
* Add wheel building for ARM64 Apple Silicon
* Better write for soma types 411

3.3.6

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Improvements:
* don't allow negative IDs in SWC, except for the special parent == -1, for the first sample (466)
* Bump HighFive to v2.7.1 (449)
* Increase allowed section type to 19 (462)
* Have warnings for incompatible soma-types (458):
* SWC files should have soma that are either a point, or a set of stacked cylinders.
* H5 & ASC consider the soma to be a contour
* allow assignment of soma type for mutable soma
* add errors for soma access / write if wrong size
- ERROR_SOMA_INVALID_SINGLE_POINT
- ERROR_SOMA_INVALID_THREE_POINT_CYLINDER
- ERROR_SOMA_INVALID_CONTOUR
* increased test coverage and cleanup

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