Create Release Notes for 8.0 releases

[pramodk]

For major release 8.0 release, we need to create detailed release notes similar to below format Once done here, we can update #1221

---

Release Date : 30-04-2021

What's New

• Dynamic selection of legacy vs modern units using HOC/Python API (default : modern)
• Faster reaction-diffusion support
• Initial GPU support using integration of CoreNEURON
• Binary installer for new Apple M1 platform
• Binary wheel distribution for Python 3.9 and Python 2.7
• Release of NMODL version 0.3 (available as python wheel)
• Versioned documentation available via nrn.readthedocs.io
• CMake as a primary build system for NEURON and Interviews

Breaking Changes

• h.Section now interprets positional arguments as name, cell. Previously positional arguments were interpreted in the other order. (Calling it with keyword arguments is unchanged.)
• For 3d reaction-diffusion simulations, the voxelization and segment mapping algorithms have been adjusted, especially around the soma. Voxel indices and sometimes counts will change from previous versions.

Deprecations

• Five functions in the neuron module: neuron.init, neuron.run, neuron.psection, neuron.xopen, and neuron.quit.
• Autotools build is deprecated and will be removed in the next release. Use CMake instead.
• Python 2 and Python 3.5 support is deprecated and will be removed in the next release. Use Python >= 3.6

Bug Fixes

For the complete list of bug fixes, see the list on the GitHub here.

Improvements / Other Changes

• Allow for two point (single section) SWC somas
• GitHub Actions and Azure as primary CI systems. Travis CI removed.
• GitHub Releases provides full source tarballs, binary installers and python wheels.
• Improved testing and CI infrastructure including GPUs
• nrn-build-ci repository test nightly builds for Ubuntu 18.04, Ubuntu 20.04, Fedora 32, Fedora 33, CentOS7, CentOS8, Debian Buster (10) and macOS 10.15 platforms.
• Improved integration of CoreNEURON
• Support for recent numpy version
• Various build improvements on Linux, MacOS and HPC platforms
• Documentation from various repositories is consolidated under nrn repository
• New releases via Spack and Easybuild package managers
• Fix deadlock when compiling NEURON with AVX-512
• Add backward-cpp for better backtraces

Upgrade Steps

Existing models should work without any changes. In order to upgrade NEURON version you can:

• Use python wheels provided for Linux or Mac OS platform
• Use binary installer provided for windows
• Install from source, preferably using CMake build system
• For new version, it's always a good idea to start over from scratch with nrnivmodl (deleting existing directory like x86_64)

See Installation section under nrn.readthedocs.io/. In the very rare case that numerical differences exist, check selection of legacy vs modern units.

Contributors

See the list of contributors on respective GitHub projects:

• NEURON : https://github.com/neuronsimulator/nrn/graphs/contributors
• CoreNEURON : https://github.com/BlueBrain/CoreNeuron/graphs/contributors
• NMODL : https://github.com/BlueBrain/nmodl/graphs/contributors

Feedback / Help

• Software related issues should be reported on the GitHub : https://github.com/neuronsimulator/nrn/issues/new/choose
• For developing models and any scientific questions, see NEURON forum : https://www.neuron.yale.edu/phpBB/
• If you want to participate / contribute to the development of NEURON, you can join monthly developers meeting : https://github.com/neuronsimulator/nrn/wiki

[pramodk]

@nrnhines @ramcdougal @alexsavulescu @adamjhn : we can start populating this ticket directly for release notes? we can directly edit the above comment if it's convenient. For the bug fixes we can get list from commit history in https://github.com/neuronsimulator/nrn/pull/1171 but we need to write highlights / Breaking Changes / Deprecations aspects explicitly.

[nrnhines]

Useful issue as I don't fully know the answers to any of the questions off the top of my head:)

[pramodk]

@nrnhines : I think based on the commits being cherry picked in https://github.com/neuronsimulator/nrn/pull/1171, we should be able to list down the changes. I will start updating few tomorrow.

[alexsavulescu]

Actually we need to list all changes from 7.8.2, since 8.0a is a pre-release. once we merge #1171 I will provide a list here.

[alexsavulescu]

Sorry for the big list, but this is the best place to leverage GitHub commits via keywords. So wrt 7.8.2 and 8.0-cherries :

git log --pretty=format:"%h , %ar : %s" 7.8.2..8.0-cherries

• [ ] 355fd6cd , 3 minutes ago : introduce docs/changelog.md (#1221)
• [ ] d294f259 , 19 minutes ago : NEURON_MODULE_OPTIONS env variable to pass in options to ivoc_main (#602)
• [ ] e2a0acc7 , 16 hours ago : bugfix: Fixes a 1D/3D voxelization problem where frusta are outside the 3D grid. (#1227)
• [ ] 6f00bc38 , 20 hours ago : oc regexp -> increase ESIZE to 256 (#1225)
• [ ] 1ef12594 , 25 hours ago : inform users Python3.5 will be dropped (#1224)
• [ ] 27bc04c9 , 2 days ago : Update CoreNEURON to 1.0 release (#1222)
• [ ] 743c7242 , 2 days ago : fix import in setup.py if wheel package is not installed (#1223)
• [ ] b04f9ea4 , 9 hours ago : bugfix: allow NodeList to access extracellular nodes. (#1214)
• [ ] ba37698e , 2 days ago : nrnversion(i) can appear multiple times in an arg list. (#1212)
• [ ] 74654303 , 2 days ago : Update INSTALL instructions with Python2 update for 8.0 release (#1210)
• [ ] ab38f8e1 , 2 days ago : When HocObject deleted desire prompt deletion of wrapped HOC Object. (#1209)
• [ ] c2cb51a4 , 2 days ago : Check if source value is a number or pointer for rxd node flux. (#1204)
• [ ] ac50f6ec , 3 days ago : SpacePlot occasionally segfaults on Windows. (#1198)
• [ ] 9b68fc10 , 3 days ago : Add help - about menu option (#1206)
• [ ] df5d9d97 , 3 days ago : Documentation CI: always update and upgrade before installing (#1208)
• [ ] fa3af46d , 3 days ago : Update CoreNeuron for various fix (#1207)
• [ ] 9ffa7b86 , 4 days ago : documentation: HocCommand (#1199)
• [ ] 60913ec2 , 5 days ago : Removing travis CI configuration (#1197)
• [ ] e4e41880 , 7 days ago : Link CONTRIBUTING.md from README (#1195)
• [ ] 55412e09 , 7 days ago : Update FAQ with instructions (#1194)
• [ ] 98bd692e , 7 days ago : Updated CONTRIBUTING.md with Python guidelines (#1191)
• [ ] eb8d038e , 7 days ago : Add python2 wheel support (#1173)
• [ ] 63cc2ed5 , 8 days ago : docs fix: PlotShape.plot supports plotly as of 7.8 (#1193)
• [ ] 71767e69 , 9 days ago : Updated hclass's all attribute (#1188)
• [ ] a5339cec , 10 days ago : bugfix: Setting extracellular diffusion coefficients. (#1186)
• [ ] f10c8af2 , 10 days ago : Add NRN_NMODL_CXX_FLAGS to facilitate cross compilation (#1174)
• [ ] 64a88e96 , 10 days ago : Reworked the neuron.hclass3 module (#1096)
• [ ] b83407d8 , 10 days ago : Use official auditwheel for RPATH handling (#1182)
• [ ] b4957cad , 10 days ago : Revert "Temporarily call brew update to unblock CI (#1163)" (#1183)
• [ ] f0b324ae , 11 days ago : Fix fast_imem struct initialization to 0 (#1181)
• [ ] d8153dc5 , 11 days ago : fix for recent numpy (#1075)
• [ ] 7390759a , 12 days ago : Make status printout less Makefile-specific. (#1180)
• [ ] 9ac8a44c , 12 days ago : Update documentation and CoreNEURON submodule (#1176)
• [ ] b6fc6176 , 12 days ago : Make custom installation command errors fatal. (#1179)
• [ ] 270afcac , 12 days ago : bugfix: Stop rxd 3d keeping sections alive and give an error if nseg changes after voxelization (#1103)
• [ ] 99d5f92e , 13 days ago : Fix VecPlayContinuous direct mode error with multiple threads. (#1155)
• [ ] ce028ed1 , 13 days ago : Use MPI_LIB_NRN_PATH for linux platform (#1172)
• [ ] b4ef7a68 , 13 days ago : fix old-style build
• [ ] 5ca85f48 , 13 days ago : Set CRAYPE_LINK_TYPE=dynamic on Cray systems. (#1170)
• [ ] d35b7ab0 , 13 days ago : Use coding-conventions helper; accelerate build. (#1150)
• [ ] e2e6fe25 , 13 days ago : CMake Python2: check for pathlib for documentation generation (#1157)
• [ ] f1ee4dbf , 13 days ago : Fix deprecation of importing directly abc from collections (#1168)
• [ ] 36c57687 , 13 days ago : Remove dependency on wheel<0.35 (#1161)
• [ ] 23fc73bb , 13 days ago : Create x86_64 (or arch) folder under install prefix (#1167)
• [ ] 76fbc011 , 13 days ago : import3d_gui bugfix for HOC classes and top-level (#1159)
• [ ] 25096fef , 2 weeks ago : Temporarily call brew update to unblock CI (#1163)
• [ ] beb5b49a , 2 weeks ago : Fix rxd atexit error in windows. (#1156)
• [ ] 5799edc6 , 2 weeks ago : RxD 3D fix for dendrites voxels inside the soma. (#1149)
• [ ] 12d35a9a , 2 weeks ago : fix copyright date (used to say 2019) (#1148)
• [ ] bc88d21d , 3 weeks ago : RxD 3D support for importing multiple morphologies and for moving imported morphologies. (#1147)
• [ ] 2a84b83c , 3 weeks ago : Add tests from issue #119 (#1146)
• [ ] 85d82691 , 3 weeks ago : Allow for two point (single section) SWC somas (#1144)
• [ ] b0caff92 , 3 weeks ago : Docs updates (#1145)
• [ ] a38e0684 , 3 weeks ago : bugfix: for rxd 1D/3D hybrid example. (#1116)
• [ ] 2438223a , 3 weeks ago : Move MPIEXEC_NAME setting to top-level cmake (#1141)
• [ ] e350c8ef , 3 weeks ago : Re-enable build parallelism in CI. (#1142)
• [ ] 16e398bd , 3 weeks ago : Make rxd test tolerance configurable. (#1137)
• [ ] a15d8b66 , 4 weeks ago : Exp except (#1136)
• [ ] 63c2f3c1 , 4 weeks ago : Enable coreneuron_modtests::datareturn_py on GPU. (#1132)
• [ ] 8af2974a , 4 weeks ago : correct Node3D location to from the corner to the centre of the voxel. (#1114)
• [ ] 424b6e58 , 4 weeks ago : Add an option to allow higher resolution calculation of surface areas. (#1127)
• [ ] 9478631f , 4 weeks ago : Enable more tests in GPU builds. (#1122)
• [ ] 0b0469c0 , 4 weeks ago : bugfix: Use soma outline for 3d voxelization. (#1126)
• [ ] ce4c3f33 , 5 weeks ago : Ste cover (#1125)
• [ ] e50f5796 , 5 weeks ago : deprecation warnings (#1079)
• [ ] 4db3b961 , 5 weeks ago : Update vector.rst (#1124)
• [ ] 535fbe4e , 5 weeks ago : Fixed FindCython when detected Cython produces error exit code (#1113)
• [ ] 865b21af , 5 weeks ago : Fix RX3D compilation with NVHPC. (#1119)
• [ ] a75e0aba , 5 weeks ago : rxd bugfix: lost a function call 2 months ago (#1117)
• [ ] f2e8281f , 5 weeks ago : Simpler set-up for live debugging (#1111)
• [ ] d4de2a97 , 5 weeks ago : bugfix: Check species id before deleting atolscale. (#1106)
• [ ] 88e0e42e , 5 weeks ago : Fix linking against external CoreNEURON libraries. (#1107)
• [ ] b571df76 , 5 weeks ago : Add python 2 deprecation warning in CMake and Autotools (#1108)
• [ ] 26b5bb02 , 5 weeks ago : Azure + GHA : use VM Image msys2 (#1110)
• [ ] cadaf07c , 5 weeks ago : documentation: information about Object* types (#1102)
• [ ] 017e3688 , 5 weeks ago : StateTransitionEvent pointer not updated. (#1101)
• [ ] bd214597 , 5 weeks ago : notify autotools will be dropped in the next release (post 8.0) (#1067)
• [ ] 74c51ba1 , 5 weeks ago : rxd select 3d, cleaner error handling, docstr fix (#1089)
• [ ] 8276759b , 5 weeks ago : bugfix: Fix for rxd 3D species loading initial values from neuron. (#1087)
• [ ] 70387c51 , 5 weeks ago : bugfix: Stop calling h.ion_region for all species. (#1077)
• [ ] f107ff9a , 6 weeks ago : bugfix: Stop rxd.Region keeping sections alive when they go out of scope. (#1072)
• [ ] 9f4b878b , 6 weeks ago : test_direct.py : revert v check to tolerance check (#1073)
• [ ] b5824cf7 , 6 weeks ago : avoid basename -s (#1074)
• [ ] c99a1ef9 , 6 weeks ago : Updated several rxd tutorials (#1061)
• [ ] e8fa58cd , 6 weeks ago : HOC push_section(python_section_name) does not work. (#1070)
• [ ] 160c8ea2 , 6 weeks ago : Disable docs-only PRs filters for the time being #1063 (#1068)
• [ ] 9537ba54 , 6 weeks ago : Test for rxd extracellular initialization #1062. (#1069)
• [ ] 05a0c2dd , 6 weeks ago : bugfix: rxd initialization problem where a section is added after ecs initiation. (#1062)
• [ ] 4796c3bd , 7 weeks ago : Partrans cover (#1051)
• [ ] aa43da45 , 7 weeks ago : Improve support for external CoreNEURON. (#1056)
• [ ] 71eedecd , 7 weeks ago : Fix the build issues and tests on Apple M1 (#1053)
• [ ] d9259118 , 7 weeks ago : Skip Azure pipeline for docs-only PRs (#1050)
• [ ] 47213792 , 7 weeks ago : Skip GHA CIs for docs-only PRs (#1049)
• [ ] 050113ed , 7 weeks ago : separate docs build from CI (#1035)
• [ ] 7c6d045a , 8 weeks ago : psection displays up-to-date diameters (#1048)
• [ ] 35d2d725 , 8 weeks ago : Re-enable tests fixed upstream in CoreNEURON. (#1046)
• [ ] 172b4916 , 8 weeks ago : quickfix for sphinx autodoc on RTD (#1043)
• [ ] dbbb308b , 8 weeks ago : Fix sphinx autodoc (#1041)
• [ ] b778f8b2 , 8 weeks ago : Gaperr (#1010)
• [ ] ef9310b1 , 8 weeks ago : two more rxd tutorials converted (#1038)
• [ ] 8ce26c84 , 8 weeks ago : Updated rxd example on initial conditions and parameters (#1036)
• [ ] 8e52d11c , 8 weeks ago : Notarize (#952)
• [ ] c46e2c5d , 8 weeks ago : Missing include that defines USE_PYTHON (#1032)
• [ ] 14e41270 , 8 weeks ago : Beginning a "Developer Builds" topic under BUILDING. (#1031)
• [ ] e8dba744 , 9 weeks ago : move INSTALL.md to docs (#1024)
• [ ] c6c1e517 , 9 weeks ago : Add tests from external testcorenrn repository (#1019)
• [ ] 65c295b1 , 9 weeks ago : Update GPU-specific CoreNEURON documentation. (#1022)
• [ ] 3c924a59 , 9 weeks ago : generic switch{hoc<->python} in sphinx (#1021)
• [ ] 7f1be7ea , 9 weeks ago : Support for building sub-models using pc.nrncore_write(path, append) (#964)
• [ ] 762cfc87 , 9 weeks ago : more Vector API tests + missing column tests (#1003)
• [ ] 68f47794 , 9 weeks ago : Updated coreneuron submodule (#1020)
• [ ] e8ad5d7a , 9 weeks ago : Recommend to install Python deps through pip (#1018)
• [ ] 0b969aa4 , 9 weeks ago : Use nrn_add_test*() helpers in more places. (#1011)
• [ ] 2bbd3925 , 9 weeks ago : help menu now links to readthedocs (#1013)
• [ ] 5870dcfc , 9 weeks ago : h.hh docstring now language-agnostic (#1009)
• [ ] d1b0c4b6 , 9 weeks ago : Add support for different geometries on different sections of the same region. (#1000)
• [ ] ac6ab1b6 , 9 weeks ago : Add external ringtest to CTest suite (#997)
• [ ] 3e3f4b8d , 10 weeks ago : help_dat.dat automatic handling (#998)
• [ ] cf3a61f0 , 10 weeks ago : Remove ICC/Clang unsupported ignore warnings (#996)
• [ ] bdbee64c , 2 months ago : Mac m1 (#992)
• [ ] 8001ba83 , 2 months ago : Add readthedocs.io setup for documentation (#968)
• [ ] 51d5c757 , 3 months ago : fix coverage.yml issue (#963)
• [ ] f1ed21c7 , 3 months ago : Code coverage setup - codecov.io (#962)
• [ ] 6164f383 , 3 months ago : bring up neuron for docs build
• [ ] 99480eef , 3 months ago : add notebooks execution + adapt CI add single parse_rst.py + update docs paths
• [ ] c339f350 , 3 months ago : Add 'docs/hoc/' from commit '590f1bc0bd97814b6681c4771fac255d2fe25b51'
• [ ] 672a4988 , 3 months ago : Add 'docs/python/' from commit '4b2d220e7dc8d1f233d738399b631fbd8d859e9f'
• [ ] 5fd6203d , 3 months ago : Add 'docs/rxd-tutorials/' from commit 'bd256fa592c964d62d2c51bf81320e822907d581'
• [ ] 58a6f193 , 3 months ago : Add 'docs/tutorials/' from commit 'a5661a04ca6804aef66b83cd6ddef08efddcf1a7'
• [ ] ee384618 , 3 months ago : git rm docs/{tutorials, rxd-tutorials, py_doc, new_doc}
• [ ] 39c7a582 , 3 months ago : Update coreneuron to latest release/1.0 (#958)
• [ ] 050934a5 , 3 months ago : Fix compilation if git signatures shown by default (#955)
• [ ] b34f80d2 , 3 months ago : neuron-ci.yml:cmake:launch rxdtests/run_all.py (#863)
• [ ] c95603b9 , 3 months ago : Add compatibility workaround for Spack's Python (#953)
• [ ] b4afa7d3 , 3 months ago : In one place $python_path did not replace $p. (#954)
• [ ] 39213d67 , 3 months ago : Update CoreNEURON documentation (#950)
• [ ] 12791513 , 3 months ago : Fix for a problem with anisotropic extracellular diffusion, found by @alexsavulescu. (#946)
• [ ] d9b44b18 , 3 months ago : Add missing image for INSTALL.md (#940)
• [ ] 4f4a36ce , 3 months ago : ParallelContext.cell(...) segfault if gid maps not allocated. (#938)
• [ ] 4d677f16 , 3 months ago : Update README.md and INSTALL.md (#780)
• [ ] e557383b , 3 months ago : Fix pip bootstrapping with Python 3.5 (#939)
• [ ] 8e107421 , 3 months ago : Update test for better code coverage and bufix with the gid (#937)
• [ ] 6dab8201 , 3 months ago : rxd: can now check if a node is IN region; resolves #876 (#881)
• [ ] f6f39158 , 3 months ago : Root point not a soma requires special handling. (#936)
• [ ] 6d31448e , 3 months ago : Fix an rxd reaction problem where regions with different number of sections are grouped together. (#922)
• [ ] d4d40461 , 3 months ago : Dynamic number of extracellular layers. (#926)
• [ ] 3a9e3d19 , 3 months ago : Add CoreNEURON 1.0a tag for preparation of 8.0a release (#930)
• [ ] 6198541c , 3 months ago : Fixswc (#907)
• [ ] 3f1f7316 , 3 months ago : Support for using file transfer mode via coreneuron embedded module (#927)
• [ ] b6dcfc42 , 3 months ago : Fix docs building issue and update README (#925)
• [ ] f8ac042b , 3 months ago : GHA manual release: fix git clone (#920)
• [ ] 4480215c , 3 months ago : Follow changes in Homebrew 2.7.0 CLI. (#916)
• [ ] 09c525dd , 3 months ago : Added CoreNEURON documentation in docs (#912)
• [ ] 9c315a90 , 3 months ago : nrnivmodl fix default to original compiler (#910)
• [ ] e46dc723 , 3 months ago : add test for Vector api (#914)
• [ ] cf00a44f , 3 months ago : ignore 0 length sections for recommending dx (#911)
• [ ] 79961f6e , 4 months ago : Fix rxd initialization problem with gui thread. (#908)
• [ ] 8024ddc4 , 4 months ago : Python nrn.Section.cell() changed from no to weak reference. (#905)
• [ ] 42c86837 , 4 months ago : Update coreneuron with nmodl and improve sub-modules cloning (#878)
• [ ] 1aeef03e , 4 months ago : Fix rxd ScalableBorder geometry to handle truncated cones. (#880)
• [ ] 7cbe5da6 , 4 months ago : Fix double arch/arch directory (x86_64/x86_64) (#904)
• [ ] ef65470e , 4 months ago : Update 3D voxelization. (#892)
• [ ] e56456a6 , 4 months ago : Fix deadlock when compiling with AVX-512 (#901)
• [ ] a0487c0c , 4 months ago : GHA: tests fail but CI is green (#896)
• [ ] 80e01ecd , 4 months ago : h.Section(name='name', cell=cell) arg order is now name, cell. (#897)
• [ ] 8b0218b5 , 4 months ago : Inform users 8.0 release is last one to support autotools (#819)
• [ ] 9e12ff33 , 4 months ago : Iontransfer (#883)
• [ ] c4518043 , 4 months ago : detect dx errors at time of Region creation (#887)
• [ ] 63983fa7 , 4 months ago : remove unused share/lib/hoc/rcs.{hoc,iv} (#882)
• [ ] 8764dc47 , 4 months ago : remove FISHER ifdefs (#879)
• [ ] 35ed3973 , 4 months ago : Fix nrnivmodl -coreneuron : mod files not copied to $CPU (#875)
• [ ] 4753484d , 4 months ago : GHA: Manual workflow to create releases (#871)
• [ ] aa3a6703 , 4 months ago : GHA:NEURON:CMake: fix compiler settings + glitch (#867)
• [ ] aad5228f , 5 months ago : Autotools default NRN_RX3D_OPT_LEVEL=2 (#865)
• [ ] a1a40744 , 5 months ago : Fix typo in mac pkg build script. (#864)
• [ ] b051a885 , 5 months ago : GHA CIs: setup build for 'release/' branches (#861)
• [ ] 1569af3f , 5 months ago : Add a warning and avoid errors when a region does not have any sections. (#747)
• [ ] 9f9c998e , 5 months ago : GHA: upload artifact: nrn-nightly-AMD64.exe (#858)
• [ ] 41ec0b29 , 5 months ago : nrnivmodl under cmake no longer uses symbolic links. (#850)
• [ ] 564ae67c , 5 months ago : Dblunits (#853)
• [ ] a8e0a9c6 , 5 months ago : nsis curl cmd: set retries + remove resume option (#857)
• [ ] 210611a2 , 5 months ago : Windows CIs: use curl to get NSIS 3.05 (#856)
• [ ] 894edb64 , 5 months ago : Build modlunit and nocmodl with debug flags. (#852)
• [ ] e6334e55 , 5 months ago : nrnversion fails when not in git (#831)
• [ ] 12f644bc , 5 months ago : Documentation deployment with GitHub Actions (#849)
• [ ] da2acc56 , 5 months ago : Github Actions - NEURON CI (#848)
• [ ] 879baf24 , 5 months ago : Fix/newobj error (#833)
• [ ] c0720406 , 5 months ago : Fix compilation issue with latest PGI compiler (#832)
• [ ] d87f34ba , 5 months ago : For mac pgk -DNRN_ENABLE_INTERNAL_READLINE=ON (#841)
• [ ] 83026212 , 5 months ago : Enable Python 3.9 manylinux1 wheel (#838)
• [ ] 961dd9b4 , 5 months ago : fix issue #836 (#837)
• [ ] 0491235c , 5 months ago : Add timeout for Windows Github Actions CI (#835)
• [ ] 68ae1999 , 5 months ago : macos wheel for Python3.9 (#834)
• [ ] e68a6901 , 5 months ago : Windows anaconda3 2020 without path. Figure out the python path. (#824)
• [ ] 20c2d56a , 5 months ago : Use early version of cmake for CI. (#812)
• [ ] a03d70ea , 5 months ago : Windows Installer Test via Github Actions (#822)
• [ ] 22a6f400 , 5 months ago : Remove hasattr check for _voltage_dependent in rates and reactions to avoid unnecessary recursion. (#813)
• [ ] 3cbcaf0b , 5 months ago : fix azure test installer task + make it more robust (#821)
• [ ] 8f2aaaa9 , 6 months ago : nrniv -python windows gui event loop not started (#817)
• [ ] 6e841386 , 6 months ago : Update coreneuron to the last version (#818)
• [ ] 9552a684 , 6 months ago : Windows does not have dlfcn.h (#811)
• [ ] 2387a2b9 , 6 months ago : travis quickly return for Azure CI changes (#809)
• [ ] 36983d1f , 6 months ago : Publish windows installer as artifact on Azure CI (#808)
• [ ] 140f046b , 6 months ago : Test modlunit (#794)
• [ ] cccff146 , 6 months ago : nhost_world() does not have to be a multiple of the subworld size. (#803)
• [ ] 94147e59 , 6 months ago : Check consistency of units selection for NEURON and CoreNEURON. (#793)
• [ ] cc845032 , 6 months ago : CMake option to toggle new/legacy for dynamic units (#805)
• [ ] 8a0c5e3c , 6 months ago : Wheel distribution compiles cython files with -O2 despite long compil… (#798)
• [ ] f6105de7 , 6 months ago : Use early numpy wheel for each neuron wheel. (#801)
• [ ] ebe86051 , 6 months ago : contributing points to neuron development topics (#804)
• [ ] 5d9de72e , 6 months ago : Merge pull request #785: Add support for human-readable stacktraces
• [ ] 50414d8a , 6 months ago : Merge branch 'master' into enh/733
• [ ] eff5ee25 , 6 months ago : also run rxd tests for osx autotools job (#795)
• [ ] 45483fbf , 6 months ago : Added a few useful comments
• [ ] 26651ec0 , 6 months ago : Return type from -4 to 1
• [ ] a6404454 , 6 months ago : MPI_Abort if hoc_execerror from python and nhost > 1. (#796)
• [ ] 66630762 , 6 months ago : don't attempt to parse stacktrace on _WIN32
• [ ] a26f3e23 , 6 months ago : Merge branch 'master' into enh/733
• [ ] 14f0a76e , 6 months ago : Fixes and improvements thanks to @pramodk's comments
• [ ] ef5bc825 , 6 months ago : modlunit units.c space not allocated. (#792)
• [ ] 7254be1a , 6 months ago : find_library in FindPythonLibsNew.cmake needs prior unset of PYTHON_LIBRARY (#758)
• [ ] d4116fab , 6 months ago : Try to unref hoc object if constructor fails after Object* created. (#762)
• [ ] 69241d8c , 6 months ago : h.cas() calling chk_access cannot handle the possible hoc_execerror. (#773)
• [ ] af2ad864 , 6 months ago : Nrnunit assign (#790)
• [ ] d74533f7 , 6 months ago : Axon attach (#781)
• [ ] 49632400 , 6 months ago : Support for building NEURON on windows under Azure CI with installer (#572)
• [ ] 609e1d9a , 6 months ago : Simpler fixup of neurondemo libnrnmech.so for relative libnrniv.dylib (#787)
• [ ] 65393ef1 , 6 months ago : Binprog wheel (#765)
• [ ] c17998b9 , 6 months ago : Fix loop to conform to C standard
• [ ] 562fe509 , 6 months ago : Merge branch 'master' into enh/733
• [ ] 601ef334 , 6 months ago : Fixes in build system
• [ ] e6ea6cf8 , 6 months ago : Added backtrace line parsing for linux
• [ ] 623bdc40 , 6 months ago : Added back simple backtraces
• [ ] 40b3c357 , 6 months ago : Removed homegrown code
• [ ] 0b11dc7d , 6 months ago : Add backward-cpp for better backtraces
• [ ] ce417f76 , 6 months ago : Remove scipy from rxd tests. (#764)
• [ ] 86ce4171 , 6 months ago : One of the neurondemo examples unnecessarily assigned to FARADAY. (#783)
• [ ] 9f15e518 , 6 months ago : Print CMake version as part of CI build (#779)
• [ ] 6aff783a , 6 months ago : Dynam units (#746)
• [ ] 48287ca4 , 6 months ago : autotools: -with-paranrn: CXX loses the -std=c++11 flag. (#778)
• [ ] 8570e8e3 , 6 months ago : Update SCMGuide.md (#777)
• [ ] fc74b85d , 6 months ago : Avoid "NEURON model internal structures are out of date" error while running NEURON (#774)
• [ ] acdd898e , 7 months ago : Some PROP_PY_INDEX dependent fragments need #if USE_PYTHON wrapper. (#772)
• [ ] ea6e034c , 7 months ago : Update CoreNEURON submodule to latest release v0.22 (#766)
• [ ] 04fd8b47 , 7 months ago : Some usage doc info about NRN_ENABLE_TESTS. (#755)
• [ ] 5feec909 , 7 months ago : Fix error in rxd test when using python2. (#757)
• [ ] b3b29cc8 , 7 months ago : Fix some ctest errors. (#752)
• [ ] 42ff857b , 7 months ago : ${IV_DIR}/lib/cmake is place to find CMake configuration files. (#721)
• [ ] e1194ee2 , 7 months ago : sysconfig provenance requires major.minor in libpython name. (#744)
• [ ] 07ad326c , 7 months ago : Added C++ demangling
• [ ] b2125945 , 7 months ago : If a netcon_srcgid is negative, need to determine the thread. (#735)
• [ ] 1101017f , 7 months ago : bugfix: Distribute mulitcompartment reaction fluxes in MPI. (#728)
• [ ] a42fae5b , 7 months ago : _semi_compile raises Exception if bad state (#715)
• [ ] f560830c , 8 months ago : Set Python_ADDITIONAL_VERSIONS cmake property (#737)
• [ ] 72ace5d5 , 8 months ago : Link cmake_doc/options.rst (#738)
• [ ] b3f0a081 , 8 months ago : Added conftest variable and fixed minor issues
• [ ] 5a765cee , 8 months ago : Allow signal handlers to print backtrace
• [ ] db707781 , 8 months ago : nrnbbcore_write code re-organisation (#722)
• [ ] 03400bfd , 8 months ago : Callback from CoreNEURON to help transfer data to NEURON. (#717)
• [ ] 19cb091f , 8 months ago : RangeVarPlot enhancements (#706)
• [ ] 1a7d97cc , 8 months ago : Avoid rare duplication of RangeVarPlot points due to recursion. (#720)
• [ ] 6f4ae452 , 8 months ago : CoreNEURON GPU build integration improvements (#707)
• [ ] 1759767c , 8 months ago : Avoid using xcrun on non-osx platforms (#710)
• [ ] d1ba5056 , 8 months ago : Test of FOR_NETCONS (#695)
• [ ] dbeb52b8 , 9 months ago : added info on how to get a Vect* argument
• [ ] b72c244d , 9 months ago : clarification about ref counts for nrnpy_po2ho
• [ ] b804df52 , 9 months ago : referencing and unrefrerencing NEURON objects
• [ ] da763654 , 9 months ago : temporary workaround since pep425tags no longer available from wheel 0.35 (#703)
• [ ] 7ab735f0 , 9 months ago : Sped up rxd tests by reducing model sizes and moved the test data into a submodule. (#701)
• [ ] 677b1da8 , 9 months ago : bugfix: Stop rxd keeping section alive and fix CVode/nseg change problem. (#693)
• [ ] 6d2aa059 , 9 months ago : Update CoreNEURON submodule to latest master (#696)
• [ ] f067494b , 9 months ago : catch if too many arguments to SectionList.append (#694)
• [ ] cbabda21 , 9 months ago : callback for returning spikes from CORENEURON (#692)
• [ ] 0681c0fd , 9 months ago : Cmakeuserdoc (#690)
• [ ] f2d96790 , 9 months ago : CMake - consolidate docs building target (#691)
• [ ] f6987100 , 9 months ago : Bug fix for library name extensions (#687)
• [ ] a77db57d , 9 months ago : ion style error (#685)
• [ ] 71eda9d8 , 9 months ago : Build error fix for Random123 on IBM Power9 system with PGI compiler (#684)
• [ ] 9a08d10a , 9 months ago : Look for corenrn_embedded_run instead of corenrn_version for CoreNEURON (#683)
• [ ] 9782fccb , 9 months ago : NRN_ENABLE_SHARED=OFF builds static library (for GPU support) (#682)
• [ ] ddf47c75 , 9 months ago : Avoid system directories into rpath (#681)
• [ ] 1f8b2f8b , 9 months ago : separate nbconvert target (#679)
• [ ] 78fd391f , 9 months ago : Fix warn (#678)
• [ ] bf3a292c , 9 months ago : Pointer can be dereferenced only if non-NULL. (#676)
• [ ] 7c567bad , 9 months ago : Adamjhn gridswarning (#675)
• [ ] 9641b2e4 , 9 months ago : re-introduce toplinks (cf html2.py) (#674)
• [ ] 3ea6c3d8 , 9 months ago : Skip stub libraries from OSX (#670)
• [ ] e341499e , 9 months ago : Observer list iteration bug when iteration removed items. (#666)

[nrnhines]

Very well done!

Dynamic selection of legacy vs modern units using HOC/Python API

Dynamic selection of legacy vs modern units using HOC/Python API (default modern) (or does that make the line too long?)

Existing models should work fine due backward compatibility

Existing models should work. In the very rare case that numerical differences exist, check ... Is a pointer to the document about how to select legacy units useful here? It is always a good idea to start over from scratch with nrnivmodl. Is dictionary order in later Python3 relevant to mention?

[pramodk]

Thank you Michael! I incorporated comments.

I didn't mention python3 dictionary aspects because we haven't changed anything default.