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@heplesser heplesser commented Nov 30, 2025

This PR replaces #3510 because that PR had grown to 458 files due to some git mix-up. There is the original description:

This code was written by me [@Helveg] with a lot of initial enthusiasm for pytest during a hackathon experimenting with best patterns for pytest, and it completely missed its mark for providing an easy reusable simulation fixture. I've removed it in favor of straightforward, less complex, much more readable test code.

The tests included here map to SLI tests as follows. The tests were ported first at an earlier point in time and then revised @Helveg in June 2025 and are now re-revised. The original SLI tests covered by the PR were in NEST-3.2:

Helveg and others added 13 commits June 25, 2025 10:34
* remove trailing spaces

* set haveMPI4py to 'False' if NEST was compiled without MPI

* Check that NEST is installed with MPI support and mpi4py is available

* Check that NEST is installed with MPI support and mpi4py is available

* load MPI module

* fix code style violations

* check that NEST is installed with MPI support and mpi4py is available

* check that NEST is installed with MPI support and mpi4py is available

* fix typo in workflow

* revert quoting in github expression syntax

* added diffs from developers without pre-commit

* Bump actions/cache from 4.2.3 to 4.2.4

Bumps [actions/cache](https://github.com/actions/cache) from 4.2.3 to 4.2.4.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](actions/cache@5a3ec84...0400d5f)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-version: 4.2.4
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump actions/checkout from 4.2.2 to 5.0.0

Bumps [actions/checkout](https://github.com/actions/checkout) from 4.2.2 to 5.0.0.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@11bd719...08c6903)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: 5.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump github/codeql-action from 3.29.2 to 3.29.9

Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.2 to 3.29.9.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](github/codeql-action@181d5ee...df55935)

---
updated-dependencies:
- dependency-name: github/codeql-action
  dependency-version: 3.29.9
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* add test

* change ampltiude

* black

* black

* black

* flake8

* flake8

* rm original test

* Bump actions/setup-python from 4.7.0 to 5.6.0

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.0 to 5.6.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.0...a26af69)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: 5.6.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* Update testsuite/pytests/sli2py_neurons/test_iaf_psc_exp_ps_lossless.py

Co-authored-by: Hans Ekkehard Plesser <[email protected]>

* parameterize test, single file

* improve network model text, add links

* Update doc/htmldoc/models/index.rst

* Bump actions/dependency-review-action from 4.7.1 to 4.7.2

Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.7.1 to 4.7.2.
- [Release notes](https://github.com/actions/dependency-review-action/releases)
- [Commits](actions/dependency-review-action@da24556...bc41886)

---
updated-dependencies:
- dependency-name: actions/dependency-review-action
  dependency-version: 4.7.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump github/codeql-action from 3.29.9 to 3.29.10

Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.9 to 3.29.10.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](github/codeql-action@df55935...96f518a)

---
updated-dependencies:
- dependency-name: github/codeql-action
  dependency-version: 3.29.10
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump actions/checkout from 4.1.1 to 5.0.0

Bumps [actions/checkout](https://github.com/actions/checkout) from 4.1.1 to 5.0.0.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v4.1.1...08c6903)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: 5.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* remove Potjans from examples

* update links, add intersphinx to pd14

* update network index page

* Bump github/codeql-action from 3.29.10 to 3.29.11

Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.10 to 3.29.11.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](github/codeql-action@96f518a...3c3833e)

---
updated-dependencies:
- dependency-name: github/codeql-action
  dependency-version: 3.29.11
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Properly delete proxy nodes on finalization.

* Use unique_ptr to pass SecondaryEvents to functions to avoid memory leaks.

Co-authored-by: med-ayssar <[email protected]>

* Update-cycle monitoring now thread-safe

* Ensure that testsuite detects missing test results

* Ensure all found tests are run and phases with zero results detected

* Detect missing tests based on hard-coded minimal numbers

* Temporarily show summary invocation

* Fix bugs in shell code

* Adjust required test counts to account for missing python and missing threads

* Fix typo.

Co-authored-by: Pooja Babu <[email protected]>

* Fix indentation

* Temporarily active debug output for Music tests

* Remove quotes that broke musictests

* Remove debug output and add comment

* Bump step-security/harden-runner from 2.13.0 to 2.13.1

Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.13.0 to 2.13.1.
- [Release notes](https://github.com/step-security/harden-runner/releases)
- [Commits](step-security/harden-runner@ec9f2d5...f4a75cf)

---
updated-dependencies:
- dependency-name: step-security/harden-runner
  dependency-version: 2.13.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Add doxygen comment for method.

* Backport atomic from pynest-ng to avoid data race

* Move update of thread-local node data out of set_target() and into serial location; rename methods and variables.

* Revert "Backport atomic from pynest-ng to avoid data race" because it introduces a new data race.

This reverts commit c4ed2c4.

* Fix typo

* Remove unused function

* Switch to auto or size_t instead of decltype.

* add whatsnew

* typo

* update text

* Update doc/htmldoc/whats_new/v3.9/index.rst

Co-authored-by: Hans Ekkehard Plesser <[email protected]>

* Update doc/htmldoc/whats_new/v3.9/index.rst

Co-authored-by: Hans Ekkehard Plesser <[email protected]>

* Started simplifying stopwatch

* Simplified stopwatch implementation and fixed bugs

* Fix problems and tidy up code

* Update nestkernel/stopwatch_impl.h

Co-authored-by: Hans Ekkehard Plesser <[email protected]>

* Fix nest-server

* Update benchmark plots for documentation

* Update description

* Add website with correct benchmark results of NEST 3.8

* Fix naming

* Apply suggestions from code review

* Update doc/htmldoc/benchmark_results.rst

* Update doc/htmldoc/previous_benchmark_results.rst

Co-authored-by: jessica-mitchell <[email protected]>

* Add error description

* Update doc/htmldoc/previous_benchmark_results.rst

* Improve test for GetNodes()

* Made test_GetNodes MPI-safe

* Fix various bugs in GetNodes

* Fixes for backport from ng to master

* Make tests safe if NEST was built without threads

* Fix backport

* Check local_only also for no-match case.

Co-authored-by: med-ayssar <[email protected]>

* Bump actions/stale from 9.1.0 to 10.1.0

Bumps [actions/stale](https://github.com/actions/stale) from 9.1.0 to 10.1.0.
- [Release notes](https://github.com/actions/stale/releases)
- [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md)
- [Commits](actions/stale@5bef64f...5f858e3)

---
updated-dependencies:
- dependency-name: actions/stale
  dependency-version: 10.1.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* bump version

* Bump actions/dependency-review-action from 4.7.2 to 4.8.1

Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.7.2 to 4.8.1.
- [Release notes](https://github.com/actions/dependency-review-action/releases)
- [Commits](actions/dependency-review-action@bc41886...40c09b7)

---
updated-dependencies:
- dependency-name: actions/dependency-review-action
  dependency-version: 4.8.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump github/codeql-action from 3.29.11 to 4.30.9

Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.11 to 4.30.9.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](github/codeql-action@3c3833e...16140ae)

---
updated-dependencies:
- dependency-name: github/codeql-action
  dependency-version: 4.30.9
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump actions/setup-python from 5.6.0 to 6.0.0

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.6.0 to 6.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@a26af69...e797f83)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: 6.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump peter-evans/repository-dispatch from 3.0.0 to 4.0.0

Bumps [peter-evans/repository-dispatch](https://github.com/peter-evans/repository-dispatch) from 3.0.0 to 4.0.0.
- [Release notes](https://github.com/peter-evans/repository-dispatch/releases)
- [Commits](peter-evans/repository-dispatch@ff45666...5fc4efd)

---
updated-dependencies:
- dependency-name: peter-evans/repository-dispatch
  dependency-version: 4.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump ossf/scorecard-action from 2.4.2 to 2.4.3

Bumps [ossf/scorecard-action](https://github.com/ossf/scorecard-action) from 2.4.2 to 2.4.3.
- [Release notes](https://github.com/ossf/scorecard-action/releases)
- [Changelog](https://github.com/ossf/scorecard-action/blob/main/RELEASE.md)
- [Commits](ossf/scorecard-action@05b42c6...4eaacf0)

---
updated-dependencies:
- dependency-name: ossf/scorecard-action
  dependency-version: 2.4.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump actions/cache from 4.2.4 to 4.3.0

Bumps [actions/cache](https://github.com/actions/cache) from 4.2.4 to 4.3.0.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](actions/cache@0400d5f...0057852)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-version: 4.3.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump psf/black from 25.1.0 to 25.9.0

Bumps [psf/black](https://github.com/psf/black) from 25.1.0 to 25.9.0.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@8a737e7...af0ba72)

---
updated-dependencies:
- dependency-name: psf/black
  dependency-version: 25.9.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump actions/upload-artifact from 4.6.2 to 5.0.0

Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4.6.2 to 5.0.0.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](actions/upload-artifact@ea165f8...330a01c)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-version: 5.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* Bump github/codeql-action from 4.30.9 to 4.31.1

Bumps [github/codeql-action](https://github.com/github/codeql-action) from 4.30.9 to 4.31.1.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](github/codeql-action@16140ae...5fe9434)

---
updated-dependencies:
- dependency-name: github/codeql-action
  dependency-version: 4.31.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* add note in docs about how to use volume transmitter during network setup

* Add suggestion for future code improvement.

* Fix whitespace.

* Add empty line to comply with coding standards.

* Update models/stdp_dopamine_synapse.h

Co-authored-by: jessica-mitchell <[email protected]>

* Set expected SLI test file counts to 1 to facilitate SLI2Py sprint

* Broke one test function with multiple tests into multiple functions

* Add additional pytest marker to pyproject

* Connect array test for all_to_all

* Update testsuite/pytests/sli2py_regressions/test_ticket_710.py

* Update testsuite/pytests/sli2py_regressions/test_ticket_507.py

* Update testsuite/pytests/sli2py_regressions/test_ticket_433.py

* Update testsuite/pytests/sli2py_regressions/test_ticket_716.py

* Update testsuite/pytests/sli2py_regressions/test_ticket_737.py

Co-authored-by: jessica-mitchell <[email protected]>

* readd

* Make MPI test wrapper more robust when parametrizing with strings and functions

* Move test_connect_array_* tests from SLI to Py

* Adjust test to improved wrapper

* Fix Flake8 issues

* Convert non-thread-skipping from unittest to pytest

* Simplify tests to focus on connectivity generation.

* Remove test_get_nodes.sli, Python implementation already in place

* Port test_ginzburg_neuron from SLI to Py

* Fix line length

* Convert non-thread-skipping from unittest to pytest

* Add wrapper variant checking for identical results on all ranks

* Port test_global_rng from SLI to Py

* rm test 881

* Port mpitets/test_iaf_ring from SLI to Py and refactor in the process

* Turn off debug output

* port test using cursor

* Fix bug in GetLocalNodeCollection

* Port mpitests/test_localonly from SLI to Py

* Port mpitests/test_mip_generator to Python

* Delete sli version

* Make MPI test wrapper more robust when parametrizing with strings and functions

* Generalizd test to parameterized version covering almost all generator tests

* Fix copyright header

* Adjust test to improved wrapper

* Remove test_global_rng.sli to completed nest#3630

* Port test_multiple_synapses from SLI to Py

* Integrate one_to_one and pairwise_bernoulli cases into test_all_to_all and rename

* Include test_pp_psc_delta in test_generators and thus port from SLI to Py

* Add support for multimeter data and enforce tab-separated other.csv files

* Port test_rate_neurons_mpi from SLI to Py

* Ensure tests write tab-separated other.csv files

* Add support for multimeter data and enforce tab-separated other.csv files

* Ensure tests write tab-separated other.csv files

* Add support for test-specific assert functions

* Port tests for identical and individual spike trains from poisson generator from SLI to Py

* Fixed flake8 problems

* Remove test that has no meaningful function any more

* Port test ticket-955 from SLI to Py

* Turn off debug mode.

Co-authored-by: Jan Vogelsang <[email protected]>

* Remove test for default delay; handled by other tests today

* Simplified and integrated test

* Fix get_comparable_timesamples

* Add historic output comment

* Fixed typo in test

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Guido Trensch <[email protected]>
Co-authored-by: Dennis Terhorst <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Dennis Terhorst <[email protected]>
Co-authored-by: janskaar <[email protected]>
Co-authored-by: Jessica Mitchell <[email protected]>
Co-authored-by: jessica-mitchell <[email protected]>
Co-authored-by: med-ayssar <[email protected]>
Co-authored-by: Pooja Babu <[email protected]>
Co-authored-by: Jan Vogelsang <[email protected]>
Co-authored-by: Jan Vogelsang <[email protected]>
Co-authored-by: Sebastian Spreizer <[email protected]>
Co-authored-by: Melissa Lober <[email protected]>
Co-authored-by: Melissa Lober <[email protected]>
Co-authored-by: C.A.P. Linssen <[email protected]>
Co-authored-by: clinssen <[email protected]>
@heplesser heplesser requested a review from terhorstd December 1, 2025 18:50
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OK, this all looks okay to me now. Thanks for the nice discussion and the quick and thorough fixes.
🚀

@terhorstd terhorstd merged commit 7ab0c23 into nest:master Dec 2, 2025
53 of 54 checks passed
@github-project-automation github-project-automation bot moved this from In progress to Done in PyNEST-NG Dec 2, 2025
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3 participants