NEURON 8.0.1 release #1603
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NEURON 8.0.1 release #1603
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* avoid relying on %errolevel% and make failure consistent to testing
* revert temporary fix done for CI to pass
* Avoid CMake v3.20 issue with NVHPC dependencies.
Without this fix then CMake v3.20.{0..2} does not correctly track
include dependencies with the Ninja build system. CMake issue #22168.
* Bump CoreNEURON commit to include CoreNeuron#543.
* fixes parsing issue for Sphinx >= 4.0 * initial splitting is done at `id` level * old logic preserved
* Update __init__.py * resolve clashes when `hoc` folders are found in path * docs conf.py - drop `hoc` clash workaround
* Add missing dependency of `hoc_module` on `rxd_cython_generated` * This declares that src/nrnpython/setup.py depends on generated .cpp files such as share/lib/python/neuron/rxd/geometry3d/graphicsPrimitives.cpp and fixes build errors.
* show external shared libraries that the wheel depends on * linux: auditwheel show * macos: delocate-listdeps * useful for debugging (since repair happens in docker image)
* add HOC domain hacked from Sphinx Python domain @ v.4.4.0 * adjust HOC documentation for HOC domain * update jumptable handling (docs/translators/html2.py)
* Python 3.10 wheels for Linux and Mac OS * Windows Installer has Python 3.10 support * universal2 tag is replaced with x86_64 (see build_wheels.bash)
* liblto_plugin-0.dll not available anymore * * temporarily disable rxd testing ( ci/win_test_installer.cmd <-> ci/win_test_installer_wo_rxd.cmd) * see #1522
* single requirements file across CIs: `nrn_requirements.txt` * env variables for python versions
* newer pip is stricter with the `file:` URI syntax
* use `bash` since we launch a bash script * fixes #1590
* Add getters/setters to neuron.coreneuron 'module'. * Collections.Callable is deprecated. * Code cleanup
* manual cherry-pick
* yet another attempt: run the the test in two steps * 1st step -> launch association.hoc here and test the output in another step * 2nd step -> check association.hoc output after we've launched 1step in previous CI step * goto error when nsis download fails * update `association.hoc` file opening logic
* launch association.hoc again if `association.hoc.out` not found
* Make rxd.Species keep corresponding SpeciesOnRegion alive. * Add comment.
* bugfix: Windows fix for 3D and hybrid rxd reaction. * Try running the old rxdtests. * Avoid using matplotlib in rxdtests. * Avoid using matplotlib in rxd wave1d tests. * Avoid using matplotlib in rxdtests. * Delete PlotShape in rxdtests to avoid timeouts. * Delete PlotShape in rxdtests to avoid timeouts.
* manual cherry-pick
* (global) include paths added by cmake could contain unnecessary/undesirable MPI library headers for dynamic mpi library (see #1566) * in order to have preference for corresponding MPI library headers, prepend mpi include path so that those paths are added first. See: #1566 (comment) fixes #1566
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Codecov Report
@@ Coverage Diff @@
## release/8.0 #1603 +/- ##
===============================================
+ Coverage 32.01% 32.09% +0.07%
===============================================
Files 572 572
Lines 109500 109527 +27
===============================================
+ Hits 35059 35153 +94
+ Misses 74441 74374 -67
Continue to review full report at Codecov.
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* since it has been officially removed from VMs
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* all other jobs will be shipped from manylinux1
Closed
* in mitigation of #1560 * related to: pypa/setuptools#2936
alexsavulescu
requested review from
ramcdougal,
adamjhn,
nrnhines and
olupton
and removed request for
ramcdougal
* add 8.0.1 realease info * make some adjustments to the sidebar
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Last call before the release. I will assume everyone happy with the changelog :) |
iomaganaris
approved these changes
Jan 28, 2022
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NEURON 8.0.1 release
Changelog
8.0.1
Release Date : 28-01-2022
What's New
Bug Fixes
For the complete list of bug fixes, see the list in GitHub PR #1603
Improvements / Other Changes
ReadTheDocs sneak peak
Activated ReadTheDocs for this branch to make sure it works:
Commits going into 8.0.1
via:
git log --pretty=format:"%h : %s" 8.0.0..8.0.1-cherriesc7ab135 : temporarily pin setuptools to <59.7.0 (#1561)
34467f7 : catch2: bump to v2.13.7 (#1521)
a95032b : Python3.10 available only in the manylinux2014 wheel * all other jobs will be shipped from manylinux1
6bbc6e9 : disable VM testing for Python3.5 * since it has been officially removed from VMs
e6bc984 : Prepend MPI include paths in case of dynamic MPI build (#1585)
df7622a : fix rxd
8086790 : Fix rxdmath problem with abs (#1545)
d525c36 : bugfix: rxd missing surface area in voxels on grid boundaries. (#1471)
acbd432 : Fix rxd initialization of extracellular species. (#1326)
e32092a : Fix rxd.re_init so that it loads values from NEURON into rxd nodes. (#1310)
0042fcc : bugfix: Windows fix for 3D and hybrid rxd reaction. (#1319)
d2b1879 : Make rxd.Species keep the corresponding SpeciesOnRegion alive. (#1270)
7a05520 : bugfix: Uninitialized memory for particular rxd reaction currents. (#1254)
e631cfe : split manylinux wheels between manylinux1 and manylinux14
157f42b : Windows CI: add hoc association test mitigation strategy (#1445)
568c9c3 : WinCI: new strategy for hoc file association test (#1395)
9428175 : NEURON can dynamically link to Python3.10 (#1558)
c455158 : Refactor neuron.coreneuron for Python 3.10.x (#1528)
9601b95 : nrnversion_h: Use
bashinstead of$ENV{SHELL}(#1591)729ee57 : CondaEnvironment: get rid of
file:URI syntax (#1392)cfe69b4 : use manylinux1 docker tag for Linux wheels
00b8ba0 : more robust python requirements management
d8322f8 : liblto_plugin-0.dll not available anymore (#1551)
8252822 : Add support for Python 3.10 (#1562)
acde642 : Sphinx HOC Domain workaround (#1588)
9d831c9 : build_wheels: more logging (#1295)
dedb06a : Add missing build dependency of hoc_module. (#1277)
7ec004e : init.py relative import for HOC - PEP328 (#1267)
fd9f9e0 : docs html2py - improve jump table links parsing (#1273)
c2f39ea : Support NVHPC compiler with CMake v3.20. (#1266)
b91db0e : CMake: pytest-cov is now optional (#1250)
c9b6fb9 : fixed links for HOC Interpreter doc; resolves #1104 (#1244)
74831f7 : documentation CI: avoid apt-get update & upgrade (#1238)
c80b194 : Win CIs: exit with code 1 since %errorlevel% may be off (#1239)
ab83f43 : Use full repo when building windows installer (#1232) (#1233)
d956d8c : windows CI: add python3.9 (#1230) (#1231)