v3.4.0

What's Changed

Two large changes to the SWC reader; this may impact reading, hence the increase in minor version number:

• Efficient swc build (#476)

  • 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 line

• Section change (#510)

  • A section within MorphIO is defined as a series of segments between
    bifurcation/multifurcation points. However, SWC files allow section
    change without a branch. Normal parsing of this will raise an
    exception, but can be allowed using the option UNIFURCATED_SECTION_CHANGE
  • Create a warning if the section type changes without a bifurcation
  • Add option to allow for sections changes in SWC files without bifurcation

Full Changelog: v3.3.10...v3.4.0

v3.3.10

v3.3.10

This is primarily so that 3.13 wheels exist before the new SWC parser is put into production.

What's Changed

• 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

Full Changelog: v3.3.9...v3.3.10

v3.3.9

v3.3.9

• remove embarrassing debug print; Hat-tip SarahM

v3.3.8

v3.3.8

• 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)

v3.3.7

• 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 #481
• Better write for soma types #411

v3.3.6

v3.3.6

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

v3.3.5

New Features

• Abstraction for morphology collection. (#444)

Improvements

• Don't ignore choice of MORPHIO_ENABLE_COVERAGE. (#452)
• enable windows py311, since new h5py release has wheels (#441)
• Update clang-format CI to 22.04. (#445)
• Make neurolucida state machine thread-safe (#440)
• Improve doc (#439)

v3.3.4

New Features

• Add operator-> for iterators, for better ergonomics (#408)
• Allow SWC and ASC morphologies to be built from strings (#407)

Fixes

• Replace assert by exception (#436)
• Render README as RST (#434)
• Fallback to using python 3.10 for ci tests (#430)
• Fix sscanf clammping of allowed inputs (#420)
• Fix section order after deleting section in mut morphology (#412)
• Enable test mistakenly disabled (#418)
• Freeze wheel build os versions (#391)
• Fix wrong section order when section is deleted (#412)
• Add 3.11 wheels Linux; macOS/Windows ones require h5py to release an updated wheel for python 3.11

Improvements

• Remove travis configuration and badge (#428)
• Update links to morphology documentation (#424)
• Update pybind11 to v2.10.0 release (#425)
• Cleanup tests (#421)
• Cleanup mutable morphology and soma (#413, #414, #415)
• Cleanup ascii reader (#405)
• Use Catch2 builtins to approximate comparisons (#394)
• Update lexertl14 to latest commit cd5a1f1 (#397)
• Update HighFive to v2.4.1 (#406)
• Update gsl-lite submodule to v0.40.0 (#395)
• Use non-exceptional methods wherever possible (#389)
• Rebuild morphologies only when modifiers are passed (#392)

v3.3.3: Fix windows-2022 wheels & MANIFEST.in warnings (#388)

What's Changed

• Add Vasculature section_offsets & section_connectivity by @eleftherioszisis in #352
• Add n_points methods for immutable Morphology & Vasculature by @eleftherioszisis in #359
• Update pybind11 version to v2.8.1 release by @eleftherioszisis in #362
• add isHeterogeneous for checking if neurites are mixed
• fix operator<< instances by @mgeplf in #364
• Update readthedocs python to 3.9 by @eleftherioszisis in #365
• Add section type exception for unsupported type in ascii writer by @eleftherioszisis in #370
• Have Section and MitoSection have value semantics for comparison by @mgeplf in #379
• dependencies: allow to use an external pybind11. by @matz-e in #351
• Handle missmatching soma pts diameters in swc/asc by @eleftherioszisis in #385
• Catch2: move to submodule and update to v2.13.8 by @matz-e in #386

Full Changelog: v3.3.2...v3.3.3

Fix wheels uploading

What's Changed

• Fix wheel uploading on new release tags by @eleftherioszisis in #355

Full Changelog: v3.3.1...v3.3.2