Arbor Library v0.6

What's Changed

Core API:

• Add S-Exp for CV Policies by @thorstenhater in #1511
• Clean-up and extend mech cat iterator interface. by @thorstenhater in #1564
• Mech ABI: The final step. by @thorstenhater in #1452
• Add dim3 to gridDim constructor in generated mechanism code by @noraabiakar in #1630
• Added an empty catalogue by @Helveg in #1677
• Allow to limit Poisson schedule with a stop time (closes #1617) by @schmitts in #1684
• Expose profiler to Python by @Helveg in #1688
• Added a debug mode to build-catalogue by @Helveg in #1686
• Write build-catalogue (c)make errors to stdout and stderr by @Helveg in #1679
• Makejobs arg by @Helveg in #1673
• Feature/python clean memory by @max9901 in #1670
• Feature/label dict by @apeyser in #1711
• Add locset expressions for proximal and distal translation of locations by @bcumming in #1671
• Gap Junction mechanisms by @noraabiakar in #1682
• Solve non-linear systems that are not kinetic schemes. by @noraabiakar in #1724
• Add cos and sin SVE implementations by @noraabiakar in #1744
• Deal with zero radius points in a morphology by @halfflat in #1719
• Simplify default proc_allocation generation. by @halfflat in #1725
• Find morphology location from a coordinate by @bcumming in #1751
• resurrect lmorpho by @schmitts in #1746
• Expose information about the CV discretization to the public inteface by @noraabiakar in #1758
• Allow the use of string s-expression CV-policies in pyarb by @noraabiakar in #1799
• Construct domain_decomposition given a list of group_descriptions. by @noraabiakar in #1788
• Profile externally loaded mechanisms by @noraabiakar in #1691
• Have option to set thread count to local maximum by @brenthuisman in #1716

CI/build/testing:

• Python unit test clean-up by @noraabiakar in #1595
• Add CI for the in-repo Spack package by @schmitts in #1544
• Ci/sanitize by @thorstenhater in #1521
• Update spack package to include fmt for arbor@0.5.3: by @bcumming in #1609
• Cache Spack for GHA by @schmitts in #1619
• Run examples via scripts (closes #1566) by @schmitts in #1631
• Build a catalogue in CI by @schmitts in #1632
• Switch to PyPA's cibuildwheel action repo's. by @Helveg in #1703
• Automatic test discovery sans boilerplate by @Helveg in #1693
• build external mechanism catalogues in release mode by @noraabiakar in #1713
• make VERBOSE=1 in verbose mode by @Helveg in #1715
• Bump pybind to 2.8.1 by @brenthuisman in #1742
• Better error reporting in python context interface by @bcumming in #1732
• Better error diagnostic in python when invalid cell properties are provided. by @bcumming in #1743
• Test separately built catalogues by @bcumming in #1748
• Weekly cron job checking for submodule updates by @brenthuisman in #1741
• Added local Python testsuite instructions by @Helveg in #1809
• CMake CUDA clean-up. by @thorstenhater in #1804
• Add dry run benchmark cell model for testing communication scaling by @bcumming in #1627
• v0.6-rc by @brenthuisman in #1814
• More robust build-catalogue by @thorstenhater in #1784

Documentation:

• arbor.mechanism_catalogue.extend() documentation added. by @brenthuisman in #1597
• zenodo 0.5.2 entry by @brenthuisman in #1598
• mpi.py updated for new synapse labelling by @brenthuisman in #1602
• Tutorial structure: remove deduplication, includify by @brenthuisman in #1575
• Docs mechabi by @brenthuisman in #1610
• Improved documentation about weights by @brenthuisman in #1620
• Adapt to changes in Pandas requiring unique indices by @brenthuisman in #1625
• Add implies default license by @kanzl in #1635
• Update Slack to Gitter by @brenthuisman in #1637
• Better Python installation instructions by @brenthuisman in #1622
• Add example based on LFPykit example Example_Arbor_swc.ipynb by @espenhgn in #1652
• Name and describe arguments to constructors where ambiguous. by @brenthuisman in #1678
• improved Github Issue templates by @brenthuisman in #1698
• Add some comments about units to network ring examples by @schmitts in #1697
• Fix link (closes #1664) by @schmitts in #1701
• Fix class members in cable example by @schmitts in #1641
• Correctify and seabornize dendrite tutorial by @brenthuisman in #1706
• Polish GJ example readme by @thorstenhater in #1726
• Completed the docs with more config() flags by @Helveg in #1708
• Make connectivity example more complete by @brenthuisman in #1721
• Add description of arbor and NEURON's nernst application rules to the docs. by @noraabiakar in #1638
• Show docs version info more prominently on RTD by @brenthuisman in #1737
• Update/fix tinyopt README.md by @halfflat in #1747
• Add python gap junction example by @kanzl in #1750
• Documentation: add expected nmodl units by @noraabiakar in #1756
• Fixed broken link from get_probes to probes by @Helveg in #1763
• Removed double preposition by @Helveg in #1762
• Fixed MD to RST typo by @Helveg in #1760
• Fix broken links in probe_sample.rst by @Helveg in #1761
• Docs/contrib updates by @brenthuisman in #1736
• Add Release procedure to docs by @brenthuisman in #1738
• Example and tutorial for two cells connected via a gap junction by @schmitts in #1771
• Have single source for citation info, compatible with Github citation UI by @brenthuisman in #1791
• Advertise GH Discussions for modelling by @brenthuisman in #1793
• Add release cycle info to docs by @brenthuisman in #1798
• Added a warning when users are reading latest docs. by @Helveg in #1800

Fixes/optimization:

• Fix GPU compile. by @thorstenhater in #1601
• Compile all arbor source files with -fvisibility=hidden by @noraabiakar in #1599
• Bug/assorted static analysis by @thorstenhater in #1615
• Fix ambiguous Region/Locset expressions by @thorstenhater in #1629
• Clean-up AVX routine and global def [EOM] by @thorstenhater in #1618
• Categorise ASSIGNED RANGE variables as STATE-ish. by @thorstenhater in #1624
• Check that mechanisms have the right kind by @noraabiakar in #1633
• Resolve uninitialised values. by @thorstenhater in #1616
• Correctly parse diameter in ASCII files by @bcumming in #1640
• Attempt fixing a64fx build by @bcumming in #1636
• Fix simulation::add_sampler cell_group dispatch by @noraabiakar in #1654
• Fix on-components on empty cable bug by @halfflat in #1658
• Fix cv_policy parse and write in ACC by @noraabiakar in #1665
• Fixed MRO and code duplication in setup.py by @Helveg in #1672
• Rephrase exception message in case of missing segment by @schmitts in #1659
• Fix modcc simd generation by @noraabiakar in #1681
• Segfault on instantiating mechanisms on empty regions by @thorstenhater in #1657
• Add missing closing bracket to mechanism repr (closes #1667) by @schmitts in #1699
• Better handling of errors during dynamic catalogue loading by @thorstenhater in #1702
• Swap && and || operator precedence in modcc by @noraabiakar in #1710
• Remove use of removed INSTRUMENT_MALLOC symbols from Glibc 2.34 by @brenthuisman in #1730
• Generate correct simd code for reading peer_index and v_peer by @noraabiakar in #1735
• fixes for non-standard code by @boeschf in #1769
• Modcc: Forward declare procedure kernels in generated GPU code by @noraabiakar in #1787
• modcc: exit solvers early if errors encountered. by @noraabiakar in #1755
• Fix cmake configuration of out-of-core fmt library by @bcumming in #1796
• Bug fix: properly partition networks containing one-sided gap-junction connections by @noraabiakar in #1774
• Remove footgun: Catalogue Lifetimes by @thorstenhater in #1807

New Contributors

• @kanzl made their first contribution in #1635
• @max9901 made their first contribution in #1670
• @boeschf made their first contribution in #1769

Full Changelog: v0.5.2...v0.6