Move reference data from test_rxd.py to rxd_data.json. #3143

adamjhn · 2024-10-24T14:04:57Z

Added --save flag to regenerate test data.

Also added a --save flag to regenerate the data.

nrnhines

Are you sure the json file is appearing in the installed module?
I was working on this as well (using from neuron.tests.utils.checkresult import Chk) and can't figure out so far how to install the json file

share/lib/python/neuron/tests/test_rxd.py

nrnhines

It appears that the following can be used to install the json file

$ git diff setup.py
diff --git a/setup.py b/setup.py
index ba0922b27..05e8ca67e 100644
--- a/setup.py
+++ b/setup.py
@@ -500,7 +500,7 @@ def setup_package():
         name=package_name,
         package_dir={"": NRN_PY_ROOT},
         packages=py_packages,
-        package_data={"neuron": ["*.dat"]},
+        package_data={"neuron": ["*.dat", "tests/*.json"]},
         ext_modules=extensions,
         scripts=[
             os.path.join(NRN_PY_SCRIPTS, f)

I don't know if that is the best solution. I did not check a wheel build.

azure-pipelines · 2024-10-24T17:15:30Z

✔️ e3c4a1f -> Azure artifacts URL

adamjhn · 2024-10-24T17:22:28Z

It appears that the following can be used to install the json file

$ git diff setup.py
diff --git a/setup.py b/setup.py
index ba0922b27..05e8ca67e 100644
--- a/setup.py
+++ b/setup.py
@@ -500,7 +500,7 @@ def setup_package():
         name=package_name,
         package_dir={"": NRN_PY_ROOT},
         packages=py_packages,
-        package_data={"neuron": ["*.dat"]},
+        package_data={"neuron": ["*.dat", "tests/*.json"]},
         ext_modules=extensions,
         scripts=[
             os.path.join(NRN_PY_SCRIPTS, f)

I don't know if that is the best solution. I did not check a wheel build.

Looks like that worked. Thanks

src/nrnpython/CMakeLists.txt

share/lib/python/neuron/tests/rxd_data.json

sonarqubecloud · 2024-10-24T18:08:20Z

Quality Gate passed

Issues
1 New issue
0 Accepted issues

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

See analysis details on SonarCloud

azure-pipelines · 2024-10-24T18:23:37Z

✔️ 77f0c6b -> Azure artifacts URL

bbpbuildbot · 2024-10-24T19:10:10Z

pramodk · 2024-10-25T05:32:13Z

@adamjhn @nrnhines : I didn’t check error details but just want to point out that wheel testing is failing : https://app.circleci.com/pipelines/github/neuronsimulator/nrn/9439/workflows/419f7eb5-d63d-4b07-87d4-b7b9ca39f9e5/jobs/4667/parallel-runs/0/steps/0-104

nrnhines · 2024-10-25T11:29:06Z

@pramodk
Interesting. I just installed neuron-nightly for python3.12 and the ./env/lib/python3.12/site-packages/neuron/tests/test_rxd.json is present. But I do get an error for python -c 'import neuron;neuron.test_rxd()' for each of the 4 subprocesses.

$ python -c 'import neuron;neuron.test_rxd()'
test_ecs_diffusion_fixed_step (neuron.tests.test_rxd.RxDTestCase.test_ecs_diffusion_fixed_step) ... 
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.1.2 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "<string>", line 1, in <module>
  File "/home/hines/.pyenv/versions/3.12.4/lib/python3.12/multiprocessing/spawn.py", line 122, in spawn_main
...
  File "/home/hines/neuron/nrn/build/install/lib/python/neuron/rxd/geometry3d/surface.py", line 1, in <module>
    from . import ctng

Don't know what it means for the CI failure but downgrading numpy on my virtual environment fixed the issue.

$ pip install "numpy<2.0.0"

$ python -c 'import neuron;neuron.test_rxd()'
test_ecs_diffusion_fixed_step (neuron.tests.test_rxd.RxDTestCase.test_ecs_diffusion_fixed_step) ... ok
test_ecs_diffusion_variable_step_coarse (neuron.tests.test_rxd.RxDTestCase.test_ecs_diffusion_variable_step_coarse) ... ok
test_ecs_diffusion_variable_step_fine (neuron.tests.test_rxd.RxDTestCase.test_ecs_diffusion_variable_step_fine) ... ok
test_rxd (neuron.tests.test_rxd.RxDTestCase.test_rxd) ... ok

----------------------------------------------------------------------
Ran 4 tests in 4.026s

OK

The CI failure seems to be for python3.11. With a virtual environment for 3.11.8 and pip install neuron-nightly
I'm getting

~/tmp$ python -c 'import neuron;neuron.test_rxd()'
test_ecs_diffusion_fixed_step (neuron.tests.test_rxd.RxDTestCase.test_ecs_diffusion_fixed_step) ... ok
test_ecs_diffusion_variable_step_coarse (neuron.tests.test_rxd.RxDTestCase.test_ecs_diffusion_variable_step_coarse) ... ok
test_ecs_diffusion_variable_step_fine (neuron.tests.test_rxd.RxDTestCase.test_ecs_diffusion_variable_step_fine) ... ok
test_rxd (neuron.tests.test_rxd.RxDTestCase.test_rxd) ... ok

----------------------------------------------------------------------
Ran 4 tests in 4.610s

OK
(env) hines@hines-ThinkStation-P5:~/tmp$ python
Python 3.11.8 (main, Jul 14 2024, 15:22:56) [GCC 13.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.__version__
'2.1.2'
>>>

JCGoran · 2024-11-01T09:55:23Z

Here's a reproducer dockerfile:

FROM ubuntu:22.04
RUN apt-get update && apt-get install -y python3-venv python3-pip wget
# get one of the "broken" wheels for Python 3.10 (they are not on PyPI since CI failed)
# taken from:
# https://app.circleci.com/pipelines/github/neuronsimulator/nrn/9439/workflows/419f7eb5-d63d-4b07-87d4-b7b9ca39f9e5/jobs/4668/artifacts
RUN wget 'https://output.circle-artifacts.com/output/job/76a56ccb-419e-4952-8784-6ea2a95cf62a/artifacts/0/artifacts/NEURON_nightly-9.0a1.dev380-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl'
RUN python3 -m venv env
RUN env/bin/python -m pip install NEURON*.whl
RUN env/bin/python -c 'import neuron; neuron.test_rxd()'

Build using docker build -t reproducer --platform linux/arm64 . The build will fail with exactly the issue as in the CI, namely:

test_ecs_diffusion_fixed_step (neuron.tests.test_rxd.RxDTestCase) ... ok
test_ecs_diffusion_variable_step_coarse (neuron.tests.test_rxd.RxDTestCase) ... FAIL
test_ecs_diffusion_variable_step_fine (neuron.tests.test_rxd.RxDTestCase) ... FAIL
test_rxd (neuron.tests.test_rxd.RxDTestCase) ... ok

======================================================================
FAIL: test_ecs_diffusion_variable_step_coarse (neuron.tests.test_rxd.RxDTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/env/lib/python3.10/site-packages/neuron/tests/test_rxd.py", line 163, in test_ecs_diffusion_variable_step_coarse
    assert p.exitcode == 0
AssertionError

======================================================================
FAIL: test_ecs_diffusion_variable_step_fine (neuron.tests.test_rxd.RxDTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/env/lib/python3.10/site-packages/neuron/tests/test_rxd.py", line 170, in test_ecs_diffusion_variable_step_fine
    assert p.exitcode == 0
AssertionError

----------------------------------------------------------------------
Ran 4 tests in 16.973s

FAILED (failures=2)

Note that if your underlying platform is x86_64, you need to install QEMU support using:

docker run --rm --privileged multiarch/qemu-user-static --reset -p yes

nrnhines · 2024-11-01T15:39:49Z

Just for a permanent record... Thanks @JCGoran ! Because of many false starts some of the below may not be needed. Please edit if some details are misleading.

sudo apt update

sudo apt install docker.io
sudo systemctl start docker
docker run --rm --privileged docker.io/multiarch/qemu-user-static --reset -p yes
docker run -ti --rm --platform linux/arm64 docker.io/ubuntu:22.04 /bin/bash

JCGoran · 2024-11-01T16:11:48Z

Looks like a similar issue occurs on MacOS as well, at least on arm64: https://github.com/neuronsimulator/nrn/actions/runs/11632330511/job/32395225512?pr=3168#step:7:285

For context, I tried setting up the CI so we can have nightly/release wheels on MacOS on arm, here's the CI file: https://github.com/neuronsimulator/nrn/actions/runs/11632330511/workflow?pr=3168 (Python 3.9 had the same error, and I assume the others would as well if I could figure out how to not cancel the workflow jobs if one of them fail).

This reverts commit f8e94c5.

adamjhn added 2 commits October 24, 2024 09:58

Move reference data from test_rxd.py to rxd_data.json.

895d4e7

Also added a --save flag to regenerate the data.

Removed unused argument.

c155dff

adamjhn added the rxd reaction-diffusion label Oct 24, 2024

nrnhines reviewed Oct 24, 2024

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Set trival_ecs tests to use sys.exit.

aceb963

nrnhines reviewed Oct 24, 2024

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adamjhn added 2 commits October 24, 2024 12:23

Add *.json to include rxd_data.json in build.

ad860ed

Add "test/*.json" to package_data in setup.py.

e3c4a1f

nrnhines approved these changes Oct 24, 2024

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adamjhn and others added 3 commits October 24, 2024 13:48

Rename rxd_data.json to test_rxd.json

2cb8477

Revert change to CMakeLists.txt.

5999786

Merge branch 'master' into rxd_test_update

77f0c6b

nrnhines merged commit f8e94c5 into master Oct 24, 2024
34 of 35 checks passed

nrnhines deleted the rxd_test_update branch October 24, 2024 18:59

nrnhines restored the rxd_test_update branch October 25, 2024 10:50

JCGoran mentioned this pull request Nov 1, 2024

NEURON 9.0 release #3137

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JCGoran added a commit that referenced this pull request Nov 3, 2024

Revert "Move reference data from test_rxd.py to test_rxd.json. (#3143)"

d652b41

This reverts commit f8e94c5.

This was referenced Nov 6, 2024

Skip RXD tests on ARM #3177

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Fix RXD failures on ARM #3179

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Move reference data from test_rxd.py to rxd_data.json. #3143

Move reference data from test_rxd.py to rxd_data.json. #3143

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Move reference data from test_rxd.py to rxd_data.json. #3143

Move reference data from test_rxd.py to rxd_data.json. #3143

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