Arbor Library v0.7

What's Changed

Neuroscience/documentation

• prep extracellular potentials tutorial. Updated corresponding example by @espenhgn in #1825
• Add documentation on faster NMODL. by @thorstenhater in #1840
• Add tstop doc in recipe API doc by @schmitts in #1852
• Use list comprehension to speed up creation of connections by @schmitts in #1864
• Support markers in neurolucida ascii files by @bcumming in #1867
• simplified create_polygon function in lfpykit example by @espenhgn in #1881
• Better key for the lfpykit intersphinx mapping by @Helveg in #1878
• Sort (in python) the mechanism names (for convenience). by @thorstenhater in #1882
• Always emit weight expression. by @thorstenhater in #1875
• Add support for epoch callbacks by @bcumming in #1873
• Add introspection for global properties. by @thorstenhater in #1890
• Add point probes to demo by @schmitts in #1891
• Tut/use avail threads by @brenthuisman in #1900
• Allen tutorial by @brenthuisman in #1781
• New policy 'round_robin_halt' by @jlubo in #1868
• Axial Diffusion by @thorstenhater in #1729
• Add some convenience to simulation creation. by @thorstenhater in #1904
• Predefine SWC Regions. by @thorstenhater in #1911
• Diffusion Example Improvements (and a bit of clean-up) by @thorstenhater in #1914
• Inhomogeneous parameters by @AdhocMan in #1887
• Fix line numbers in tutorials and assorted doc corrections by @brenthuisman in #1917

Core

• Be more lenient when accepting args to file I/O by @thorstenhater in #1819
• modcc: generate missing node_index read needed for reading time t in the mechanisms by @noraabiakar in #1866
• Add Developer Documentation by @thorstenhater in #1639
• Isolate external catalogues from libarbor.a. by @thorstenhater in #1837

Build, testing, CI

• Build Python 3.10 binary wheels. Add v0.6 to spackfile. by @brenthuisman in #1817
• export API by @boeschf in #1824
• export doc by @boeschf in #1849
• Include CMAKE+CUDA iff NVCC is needed. by @thorstenhater in #1855
• Bit more on Spack, fix in tutorial by @brenthuisman in #1838
• json submodule added by @brenthuisman in #1871
• Fix a bug where Debian/Ubuntu's Python malfunctions by @brenthuisman in #1894
• Have dependency version policy by @brenthuisman in #1865
• random123 submodule added by @brenthuisman in #1872
• Fix tool installation paths. by @thorstenhater in #1905
• Adopt Black for Python. by @thorstenhater in #1906
• add cmake checks for non-bundled random123 by @bcumming in #1907
• Temporarily disable A64FX CI by @bcumming in #1910
• Adopt flake8 by @thorstenhater in #1908
• Move Python build to pyproject.toml, bump Python minver to 3.7, fix macos wheel generation by @brenthuisman in #1916
• Weekly CI Python wheel build pushes to Test.PyPI.org by @brenthuisman in #1921

Fixes, optimization

• Users may not give dt < 0. by @thorstenhater in #1821
• Fix ubenches compilation errors by @noraabiakar in #1828
• death test: wrong signal by @boeschf in #1858
• Make brunel.py setup faster. by @thorstenhater in #1854
• add a better error. by @thorstenhater in #1846
• Fix load_component for label-dict by @noraabiakar in #1859
• Found out the hard way that this is still needed :/ by @thorstenhater in #1860
• Elide memcpy where not needed by @thorstenhater in #1863
• Bug fix: Fix voltage vector size in threshold_watcher contstructor by @noraabiakar in #1820
• remove test statements for move ctor by @boeschf in #1899
• Code Quality: PVS Studio Finds by @thorstenhater in #1901
• Two context decomp swaps were forgotten by @brenthuisman in #1912

New Contributors

• @jlubo made their first contribution in #1868
• @AdhocMan made their first contribution in #1887