v3.3.1

What's Changed

• Imbue enums with numeric operations by @mgeplf in #330
• remove unused AccessMode enum by @mgeplf in #331
• don't compile c++ tests when creating python package by @mgeplf in #332
• use std::make_unique by @mgeplf in #333
• Rename CHANGLOG.md to CHANGELOG.md (typo fix) by @musicinmybrain in #336
• Change tmp dir by @mgeplf in #335
• Remove unused python mock dependency by @musicinmybrain in #339
• Don't run tests twice on push within a pull request by @mgeplf in #340
• Dendritic spine by @mgeplf in #321
• Remove explicit template class instantiation by @musicinmybrain in #338
• cleanup building and publishing wheels by @mgeplf in #343
• Update setup by @mgeplf in #344
• more reliable ASC (Neurolucida) parser by @asanin-epfl in #305
• Mg/windows build by @mgeplf in #342
• update documentation by @asanin-epfl in #346
• add authors by @mgeplf in #347
• Work around conda cmake finding HDF5 issues by building docs with libhdf5-dev already installed by @mgeplf in #348
• Exclude musllinux wheels building by @eleftherioszisis in #354

New Contributors

• @musicinmybrain made their first contribution in #336

Full Changelog: v3.3.0...v3.3.1

Introduce property `section_id` on `Marker` class

• Parse markers at any level of ASC morphology, introduce a new property section_id on Marker class. (#325, #329)
• better documentation of MorphIO warnings (#327)
• Consider 'Incomplete' as a marker (#328)

Use lexertl14, cleanup HDF5 processing and better specification docs

• cleanup morphologyHDF5 (#285)
• Revise specification documentation (#294)
• Cleanup properties & vasc/properties (#307)
• use lexertl14 (#304)
• Fix Lexertl sdist (#308)
• clean up after ourselves when running tests (#311)
• add copyright/funding info (#317)
• Move NeuroM morphology specs to MorphIO (#313)
• fix hdf5 when there is no soma (#319)
• should no longer need to unlink gcc8/gcc9 (#326)

Binding for ZERO_DIAMETER warning

• Create binding for ZERO_DIAMETER warning (#303)

Glial cell section types according to new spec

• use CHECK_THROW_AS from Catch2 (#282)
• Allow 2 point swc soma as a cylinder one. Solution to #265. (#280)
• clean and refactor README.rst (#283)
• Add SECTION_ALL to the python bindings (#290)
• migrate from nosetests to pytest (#291) (#302)
• Change glial cell section types according to new spec (#292)
• Add readthedocs links to README (#298)
• Warn about zero diameter in SWC morphology (#301)
• Warn about disconnected neurite only when there is a soma (#296)

Allow to throw warnings instead of writing them to stderr/stdout

• remove -j2 from cpp_test.sh - not an option for cmake (#269)
• Adding C++ tests (#263)
• Fix for compat with recent HighFive (#268)
• Minimal solution to raising of warning instead of writing them (#266)
• apply ignoring logic to raised warnings as well (#271)
• Consider custom section types from 5 up to 10 (#274)
• fix broken links and include README to readthedocs (#276)
• narrow conditions when WARNING_NEUROMORPHO_SOMA_NON_CONFORM is thrown (#275)
• fix README for pypi release (#278)

MorphIO no longer merge unifurcations

• MorphIO no longer merge unifurcations (#238)
• Fix deleteSection and appendSection for shared_ptr (#251)
• Simple lifetime check using nullptr (#253)
• Automatic documentation generation from sources (#254 , #248)
• Add coverage to C++ tests (#260)
• Extending std namespace is undefined behavior (#261)

Make Intel compiler happy

Make intel compiler happy (#246)

By fixing a narrow conversion

Refactor versioning #231

Refactor versioning (#231)

No longer use an enum as the return type of `Morphology::version()` but a tuple <string, int, int>. The three fields are:

- file format extension. One of "h5", "asc", "swc"
- major version for the given format
- minor version for the given format

So far the existing values are:
- ("swc", 1, 0)
- ("asc", 1, 0)
- ("h5", 1, 0)
- ("h5", 1, 1)
- ("h5", 1, 2)

The advantage is that versions can now be ordered within a given file format.

* Fix the metadata version field in H5. It is now 1.2 instead of 1.1 as per the spec:  https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html

Add support for markers that don't have a diameter

Allow markers to have no diameters (#233)

Markers may have only `(X Y Z)` specified instead of the more common `(X Y Z D)`. In this case, diameters are set to 0.

Also:
Strings in the middle of the list of points are now skipped.

ℹ️ The example file added in this commit is from C280999A-I4.asc

The following illustrates both use cases:

```lisp
( (Color Red)
  (   -0.97  -141.17    84.77)
  "<--4 boutons on a PC soma"
)  ;  End of text
```