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Another experiment with some CI fixes for jelic/8.2-py313#3352

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nrnhines merged 28 commits into
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hines/8.2-py313-exper2
Mar 24, 2025
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Another experiment with some CI fixes for jelic/8.2-py313#3352
nrnhines merged 28 commits into
release/8.2from
hines/8.2-py313-exper2

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@nrnhines

@nrnhines nrnhines commented Mar 19, 2025 •
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At starting point, jelic/8.2-py313 #3319 has only two CI failures. Is that still the case.

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

nrnhines and others added 20 commits January 24, 2025 00:25
@nrnhines nrnhines changed the base branch from master to release/8.2 March 19, 2025 10:56
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✔️ 9e48b5f -> Azure artifacts URL

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✔️ dd4c9f6 -> Azure artifacts URL

@nrnhines nrnhines force-pushed the hines/8.2-py313-exper2 branch from c9b6647 to 54c25d2 Compare March 19, 2025 13:23
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✔️ 54c25d2 -> Azure artifacts URL

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✔️ ade3f83 -> Azure artifacts URL

@nrnhines nrnhines force-pushed the hines/8.2-py313-exper2 branch 8 times, most recently from dad36d7 to 0d5047f Compare March 19, 2025 23:58
@nrnhines nrnhines force-pushed the hines/8.2-py313-exper2 branch from 0d5047f to 590c084 Compare March 20, 2025 10:19
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✔️ 590c084 -> Azure artifacts URL

@nrnhines nrnhines requested a review from JCGoran March 20, 2025 11:59
@nrnhines

nrnhines commented Mar 20, 2025

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@JCGoran I think is a good stopping point for this PR. A few details remain before starting a 8.2.7 tag but I'd like those to be separate from this. Please review.

JCGoran
JCGoran approved these changes Mar 20, 2025
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Comment thread docs/changelog.md
nrnhines added 2 commits March 21, 2025 10:16
@nrnhines
Fix thread sanitizer leak when launching Python 3.13 and using from n…
0438b75 
…euron import h, gui. (#3243)

* nrnpython_finalize can only cleanup and Py_Finalize from MainThread

* save stdin terminal settings on import hoc and restore on h.quit()
@nrnhines
On h.quit() terminal settings are same as when neuron.hoc was importe…
58f8a94 
…d. (#3259)


* Print tcgetatt/tcsetattr error messages only if STDIN is a tty.
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✔️ 58f8a94 -> Azure artifacts URL

@nrnhines nrnhines force-pushed the hines/8.2-py313-exper2 branch from 162870e to 011f13b Compare March 22, 2025 19:30
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codecov Bot commented Mar 23, 2025 •
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Codecov Report

Attention: Patch coverage is 68.29268% with 13 lines in your changes missing coverage. Please review.

Project coverage is 46.58%. Comparing base (a8cd8f5) to head (76a2a98).
Report is 13 commits behind head on release/8.2.

❗ Current head 76a2a98 differs from pull request most recent head 6d27c90

Please upload reports for the commit 6d27c90 to get more accurate results.

Files with missing lines Patch % Lines
share/lib/python/neuron/gui.py 64.70% 6 Missing ⚠️
share/lib/python/neuron/__init__.py 80.00% 1 Missing ⚠️
share/lib/python/neuron/rxd/node.py 66.66% 1 Missing ⚠️
share/lib/python/neuron/rxd/rxd.py 66.66% 1 Missing ⚠️
share/lib/python/neuron/tests/test_neuron.py 0.00% 1 Missing ⚠️
share/lib/python/neuron/tests/test_rxd.py 0.00% 1 Missing ⚠️
share/lib/python/neuron/tests/test_vector.py 0.00% 1 Missing ⚠️
src/oc/hoc.cpp 75.00% 1 Missing ⚠️
Additional details and impacted files 
@@             Coverage Diff              @@
##           release/8.2    #3352   +/-   ##
============================================
  Coverage        46.58%   46.58%           
============================================
  Files              527      527           
  Lines           119282   119298   +16     
============================================
+ Hits             55565    55576   +11     
- Misses           63717    63722    +5

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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@nrnhines nrnhines force-pushed the hines/8.2-py313-exper2 branch 2 times, most recently from ccf2227 to 58f8a94 Compare March 23, 2025 20:04
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sonarqubecloud Bot commented Mar 24, 2025

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Quality Gate Passed Quality Gate passed

Issues
3 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
2.3% Duplication on New Code

See analysis details on SonarQube Cloud

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✔️ 6d27c90 -> Azure artifacts URL

@nrnhines nrnhines merged commit 4de5671 into release/8.2 Mar 24, 2025
@nrnhines nrnhines deleted the hines/8.2-py313-exper2 branch March 24, 2025 12:42
This was referenced Mar 24, 2025
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@JCGoran JCGoran mentioned this pull request Apr 11, 2025
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