CMakeLists.txt | 6 5 + 1 - 0 !
1 file changed, 5 insertions(+), 1 deletion(-)

 [patch] find packaged hpc coding conventions

src/nrniv/nrnpy.cpp | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 [patch] find libnrnpython3

CMakeLists.txt | 5 3 + 2 - 0 !
bin/CMakeLists.txt | 14 7 + 7 - 0 !
2 files changed, 10 insertions(+), 9 deletions(-)

 [patch] fix paths

.circleci/config.yml | 6 4 + 2 - 0 !
.github/workflows/coverage.yml | 4 2 + 2 - 0 !
.github/workflows/neuron-ci.yml | 13 7 + 6 - 0 !
.readthedocs.yml | 27 24 + 3 - 0 !
azure-pipelines.yml | 17 15 + 2 - 0 !
bldnrnmacpkgcmake.sh | 25 17 + 8 - 0 !
ci/azure-win-installer-upload.yml | 2 1 + 1 - 0 !
ci/win_build_cmake.sh | 9 5 + 4 - 0 !
ci/win_download_deps.cmd | 3 1 + 2 - 0 !
ci/win_install_deps.cmd | 27 11 + 16 - 0 !
ci/win_test_installer.cmd | 20 17 + 3 - 0 !
ci/win_test_installer_wo_rxd.cmd | 5 2 + 3 - 0 !
docs/changelog.md | 5 5 + 0 - 0 !
docs/conda_environment.yml | 2 1 + 1 - 0 !
docs/conf.py | 40 29 + 11 - 0 !
docs/docs_requirements.txt | 5 3 + 2 - 0 !
docs/domains/hocdomain.py | 1 0 + 1 - 0 !
docs/index.rst | 2 1 + 1 - 0 !
docs/install/install_instructions.md | 2 1 + 1 - 0 !
docs/install/mac_pkg.md | 2 1 + 1 - 0 !
docs/parse_rst.py | 1 0 + 1 - 0 !
nrn_requirements.txt | 4 2 + 2 - 0 !
packaging/python/build_requirements.txt | 2 1 + 1 - 0 !
packaging/python/build_wheels.bash | 11 6 + 5 - 0 !
packaging/python/oldest_numpy_requirements.txt | 8 8 + 0 - 0 !
packaging/python/test_requirements.txt | 2 2 + 0 - 0 !
packaging/python/test_wheels.sh | 21 15 + 6 - 0 !
setup.py | 23 19 + 4 - 0 !
share/lib/python/neuron/__init__.py | 11 11 + 0 - 0 !
share/lib/python/neuron/doc.py | 2 0 + 2 - 0 !
share/lib/python/neuron/gui.py | 38 24 + 14 - 0 !
share/lib/python/neuron/rxd/geometry3d/FullJoinMorph.py | 2 0 + 2 - 0 !
share/lib/python/neuron/rxd/geometry3d/GeneralizedVoxelization.py | 5 3 + 2 - 0 !
share/lib/python/neuron/rxd/geometry3d/surfaces.pyx | 4 1 + 3 - 0 !
share/lib/python/neuron/rxd/gui.py | 3 3 + 0 - 0 !
share/lib/python/neuron/rxd/node.py | 6 3 + 3 - 0 !
share/lib/python/neuron/rxd/region.py | 1 0 + 1 - 0 !
share/lib/python/neuron/rxd/rxd.py | 17 7 + 10 - 0 !
share/lib/python/neuron/rxd/section1d.py | 2 1 + 1 - 0 !
share/lib/python/neuron/rxd/species.py | 17 8 + 9 - 0 !
share/lib/python/neuron/rxdtests/tests/3d/circadian_rhythm.py | 1 1 + 0 - 0 !
share/lib/python/neuron/rxdtests/tests/hh.py | 1 1 + 0 - 0 !
share/lib/python/neuron/rxdtests/tests/hh_cvode.py | 1 1 + 0 - 0 !
share/lib/python/neuron/rxdtests/tests/hh_param.py | 1 1 + 0 - 0 !
share/lib/python/neuron/rxdtests/tests/hh_param_cvode.py | 1 1 + 0 - 0 !
share/lib/python/neuron/tests/test_all.py | 2 0 + 2 - 0 !
share/lib/python/neuron/tests/test_neuron.py | 5 1 + 4 - 0 !
share/lib/python/neuron/tests/test_rxd.py | 3 1 + 2 - 0 !
share/lib/python/neuron/tests/test_vector.py | 5 1 + 4 - 0 !
src/nrniv/glinerec.cpp | 1 0 + 1 - 0 !
src/nrnpython/CMakeLists.txt | 3 3 + 0 - 0 !
src/nrnpython/inithoc.cpp | 44 41 + 3 - 0 !
src/nrnpython/nrnpy_hoc.cpp | 5 4 + 1 - 0 !
src/nrnpython/nrnpython.cpp | 7 7 + 0 - 0 !
src/oc/fileio.cpp | 2 1 + 1 - 0 !
src/oc/hoc.cpp | 14 7 + 7 - 0 !
src/oc/redef.h | 1 0 + 1 - 0 !
test/cover/checkresult.py | 1 1 + 0 - 0 !
test/cover/test_netcvode.py | 1 1 + 0 - 0 !
test/gjtests/test_par_gj.py | 4 0 + 4 - 0 !
test/parallel_tests/test_bas.py | 1 0 + 1 - 0 !
test/pynrn/test_fast_imem.py | 1 0 + 1 - 0 !
test/pynrn/test_hoc_po.py | 1 1 + 0 - 0 !
test/pynrn/test_nrnste.py | 1 0 + 1 - 0 !
test/pynrn/test_partrans.py | 2 1 + 1 - 0 !
test/pynrn/test_template_err.py | 1 0 + 1 - 0 !
test/rxd/3d/test_soma_outlines.py | 2 1 + 1 - 0 !
test/rxd/conftest.py | 6 4 + 2 - 0 !
68 files changed, 341 insertions(+), 174 deletions(-)

 [patch] release/8.2 can use python 3.13 (#3352)

At starting point, jelic/8.2-py313 #3319 had only two CI failures.

Almost the entirety of this PR is to get 8.2 to pass CI.
In addition it supports Python3.13.
Bug fixes adopted from the master are
#3239 Launching nrniv -python with Python 3.13.0 does not allow use of gui.
#3259 On h.quit() terminal settings are same as when neuron.hoc was imported.
#3243 save stdin terminal settings on import hoc and restore on h.quit()
#3276 Python 3.13.1 broke [s for s in sl] where sl is a SectionList. Manual partial cherry-pick.

Other PR attempts at fixing CI failures that can be closed when this PR is merged, are #3329 #3325 #3319 #3317

Many of the CI fixes are backports from #3028 #3040 #3303 #3105 #3278

bldnrnmacpkgcmake.sh was updated. It isolates a change (avoid breaking CI) with -DNRN_MAC_PKG=ON

CMakeLists.txt | 2 2 + 0 - 0 !
bin/nrnivmodl_makefile_cmake.in | 4 2 + 2 - 0 !
cmake/CMakeListsNrnMech.cmake | 1 1 + 0 - 0 !
3 files changed, 5 insertions(+), 2 deletions(-)

 [patch] fedora gcc-15 fixes for release/8.2 (#3381)

* Update coreneuron to avoid can't find <cstdio> issue on Apple M1

src/ivoc/axis.h | 2 2 + 0 - 0 !
src/ivoc/epsprint.h | 2 2 + 0 - 0 !
src/ivoc/idraw.h | 2 2 + 0 - 0 !
src/ivoc/ivoc.h | 1 1 + 0 - 0 !
src/ivoc/ocbox.h | 2 2 + 0 - 0 !
src/ivoc/ocdeck.h | 2 2 + 0 - 0 !
src/ivoc/xmenu.h | 2 2 + 0 - 0 !
7 files changed, 13 insertions(+)

 [patch] fix missing std namespace usages

Unsure why this works upstream and fails here, potentially our
newer GCC version is more strict or there is some include-chain
upstream with patched vendored code that masks the issue there.
This needs further investigation.

setup.py | 5 4 + 1 - 0 !
1 file changed, 4 insertions(+), 1 deletion(-)

 [patch] don't fail python build when we are not in a git repo

We are building the Debian package not in a Git repo, so, allow us
to override the version number in the Debian packaging.