Codecov Report

Attention: Patch coverage is 35.29412% with 11 lines in your changes are missing coverage. Please review.

Project coverage is 67.20%. Comparing base (63053bd) to head (350c964).
Report is 2 commits behind head on master.

@@            Coverage Diff             @@
##           master    #2255      +/-   ##
==========================================
- Coverage   67.20%   67.20%   -0.01%     
==========================================
  Files         564      564              
  Lines      104267   104281      +14     
==========================================
+ Hits        70073    70078       +5     
- Misses      34194    34203       +9     

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✔️ 7da1dbb -> Azure artifacts URL

Logfiles from GitLab pipeline #105816 (⛔) have been uploaded here!

Status and direct links:

* [✅](https://bbpgitlab.epfl.ch/hpc/cellular/nrn/-/jobs/581438) [mac_m1_cmake_build: [cmake, ON, OFF, OFF, address]](https://gist.githubusercontent.com/bbpbuildbot/4220f59c833ab74c08dfc6afcaa467ba/raw/bb817c61fa372630759dd62415d916635f7e53b9/mac-m1-cmake-build-cmake-on-off-off-address.txt)

* [⛔](https://bbpgitlab.epfl.ch/hpc/cellular/nrn/-/jobs/581439) [spack_setup](https://gist.githubusercontent.com/bbpbuildbot/4220f59c833ab74c08dfc6afcaa467ba/raw/de0b5b407d02fcb26860fce797086b9f5a34a6a9/spack-setup.txt)

Just to say we have some internal updates ongoing at the moment, so everything except the M1 build in the gitlab pipeline will most likely fail for the next 1+ days...

I've rebased the PR on top of setup-py-the-one-and-only. That should go in soon (waiting for BBP CI updates before merging, all in line)

✔️ 7da1dbb -> Azure artifacts URL

The reason I changed the base branch to master is so I could get a working setup.exe artifact for use by Michele in his course.
(some of the students have Windows 11). (I wasn't able to find an artifact when the base branch was setup-py-the-one-and-only.)
Anyway, it was ok to switch back because I now do have the artifact.

The fix for nrniv -python introduces problems as serious as what it was intended to fix. Apparently, Py_BytesMain calls Py_Finalize before returning and that causes a segfault during nrniv cleanup even before I get to a second Py_Finalize

Program received signal SIGSEGV, Segmentation fault.
PyThreadState_New (interp=0x0) at Python/pystate.c:684

Maybe the fix is just as simple as avoiding all Py calls after return from Py_BytesMain, but my reading further suggests it is completely unexpected by Python developers that one would even do Py calls or Py_Initialize before calling Py_BytesMain ( https://bugs.python.org/issue34008 ) so maybe it is prudent to avoid that as a replacement for PyRun_InteractiveLoop.

I'd like to keep PyRun_InteractiveLoop but the problem is that I cannot find a way to get a FILE* from python given a file descriptor. Note that

PyObject *PyFile_FromFd(int fd, const char *name, const char *mode, int buffering, const char *encoding, const char *errors, const char *newline, int closefd)

does not return FILE*

Edit: Hmm. Looks like it may suffice to just call Py_Initialize() after return from Py_BytesMain. Further testing needed.

✔️ 40d6321 -> Azure artifacts URL

Is failing test:neuron:nmodl:nvhpc:omp:legacy
something we need to worry about? Did I recently ask this question in another PR? Well, something similar
#2598 (comment)
but I guess not since this failing CI mentions.

95% tests passed, 17 tests failed out of 373

Some (all?) of those seem to be out of memory issues. Can we restart just the test:neuron:nmodl:nvhpc:omp:legacy ?

✔️ e046d04 -> Azure artifacts URL

✔️ 9700129 -> Azure artifacts URL

✔️ b1a657e -> Azure artifacts URL

✔️ f87173f -> Azure artifacts URL

Quality Gate passed

Issues
3 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

✔️ 350c964 -> Azure artifacts URL

Logfiles from GitLab pipeline #206770 (:white_check_mark:) have been uploaded here!

Status and direct links:

• ✅ mac_m1_cmake_build: [cmake, ON, OFF, OFF, address]
• ✅ spack_setup
• ✅ build:nmodl
• ✅ build:neuron:nmodl:intel:legacy
• ✅ build:neuron:nmodl:intel:shared
• ✅ build:neuron:nmodl:nvhpc:acc:legacy
• ✅ build:neuron:nmodl:nvhpc:acc:shared
• ✅ build:neuron:nmodl:nvhpc:omp:legacy
• ✅ build:neuron:nmodl:nvhpc:omp
• ✅ test:neuron:nmodl:intel:legacy
• ✅ test:neuron:nmodl:intel:shared
• ✅ test:neuron:nmodl:nvhpc:acc:legacy
• ✅ test:neuron:nmodl:nvhpc:acc:shared
• ✅ test:neuron:nmodl:nvhpc:omp:legacy
• ✅ test:neuron:nmodl:nvhpc:omp

@neuroman314 @ramcdougal I think this PR is ready to merge. But it would be good to try it out (on a windows machine) to verify that https://github.com/neuronsimulator/nrn/actions/runs/8786668302/ works in the context of the upcoming June course.
For windows 11, I have verified that launching python, nrniv, and nrniv -python from a bash and powershell terminal work with respect to

from neuron import h, gui
g = h.Graph()
del g # the graph should be closed without crashing
# NEURONMainMenu/File/Quit works

Note that on my windows 11 virtualbox guest, there is no readline when launchng python12 but readline works properly with nrniv and nrniv -python

I have not tested with windows10.
edit
I tested with windows10 and the above installer works properly. Note that it was somewhat painful to install as extracting the above zip file (to get the exe) caused the windows virus defender to complain and the exe would be removed after a few seconds. I had to

Turn off Defender antivirus protection in Windows Security
Select Start and type "Windows Security" to search for that app.
Select the Windows Security app from the search results, go to Virus & threat protection, and under Virus & threat protection settings select Manage settings.
Switch Real-time protection to Off.

Also the name of the file nrn-nightly-AMD64.exe does not indicate the version. But these issues are out of scope of this PR and can be considered later.