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v1.0.0703a9293 · ·
Release 1.0.0 Overview ====================== This major release is the first attempt at producing a stable API, based on the section-tree representation of neurons. Various classes from the version 0 series have been re-worked to simplify the code. The code base is separated into a "stable" public API and an "unstable" developer one, where "stable" means that future changes in the version 1 series will be backwards compatible. It is intended that users interact only with the command line applications and the public python API. The APIs are defined thus: Stable public API ----------------- Symbols defined or imported into the following packages form the public API: * neurom * neurom.viewer * neurom.core * neurom.io * neurom.check * neurom.stats * neurom.exceptions Developer API (unstable) ------------------------ The stability of these modules is not guaranteed and is primarilly intended for developers of NeuroM. The intention is that parts of this API will be moved to the public API after some re-design and refinement. * neurom.fst * neurom.fst.sectionfunc * neurom.check.structural_checks * neurom.check.neuron_checks * neurom.core.types * neurom.core.tree * neurom.core._neuron * neurom.core._soma * neurom.core.point * neurom.core.dataformat * neurom.io.utils * neurom.io.swc * neurom.io.hdf5 * neurom.view * neurom.view.common * neurom.view.view * neurom.analysis * neurom.analysis.morphmath Point tree deprecation ---------------------- The original point tree representation of neurons has been moved to the module `neurom.point_neurite`. It is isolated from the rest of NeuroM and shall be removed in a future release. It is kept primarilly for debugging purposes. Additional checks ----------------- Additional checks have been implemented for the morph_check application. These are disabled by default. * z-jump * fat ends
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v0.1.25b8b5b3a · ·
Overview ======== This release has a considerable re-working of the `morph_check` application and related modules. The end-user functionality remains unchanged, with the exception of the `morph_check` configuration file structure, which now has two categories of checks structured thus: ``` checks: structural_checks: - is_single_tree - has_soma_points - has_sequential_ids - has_increasing_ids - has_valid_soma - has_valid_neurites neuron_checks: - has_basal_dendrite - has_axon - has_apical_dendrite - has_all_nonzero_segment_lengths - has_all_nonzero_section_lengths - has_all_nonzero_neurite_radii - has_all_monotonic_neurites - has_no_flat_neurites - has_nonzero_soma_radius ``` -
v0.1.2.dev09c79f10e · ·
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v0.1.1d654c67c · ·
Release 0.1.1 ------------- Overview ======== * This release sees a further migration of NeuroM functionality towards the more efficient section-tree neuron representation from the original point-tree representation. * Various minor big-fixes and improvements to the viewers, documentation and examples. * Deprecation of various point-tree modules. New Features ============ * Basic functionality in top level module * neurom.load_neuron(s). * neurom.get. * neurom.NeuriteType. * NeuriteType aliases AXON, BASAL_DENDRITE, APICAL_DENDRITE, SOMA, ANY_NEURITE. * Generic neurite section iteration over neuron, populations's neurites. * See neurom.fst.iter_sections. * Neurite section access by section ID. * Non-zero soma radius check in morph_check application. * Generalized 3D transformations of neurons, neurites. * More features added to [neurom.get](http://neurom.readthedocs.io/en/latest/_neurom_build/neurom.fst.get.html#neurom.fst.get). Deprecated modules ================== The following modules have been deprecated, and will be removed in the next major release (1.0). * neurom.ezy * neurom.points * neurom.segments * neurom.sections * neurom.triplets * neurom.bifurcations Note that there are other, generic modules whose functionality is tailored to point neurons which have not been explicitly deprecated yet. Their functionality will either be modified, or deprecated in a further minor release.
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