Python packaging for PyNEST-NG #33
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…n run_examples.sh
…rsion to 3.8.post0.dev4
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Hi @steffengraber! Thanks for this PR and apologies for taking weeks before looking at it. I have tried the pip install and that worked very nicely on my macOS 15.5 (arm64) system. I could also run all non-MPI tests with
pytest --ignore=$PyTestDir/mpi --ignore=$PyTestDir/sli2py_mpi $PyTestDir
where PyTestDir points to .../testsuite/pytests under the site_packages/nest directory.
Building with MPI did not quite work. NEST built, but the CMake output did not even show a search for OpenMPI and NEST then built nicely without MPI. One problem I had was that my zsh shell did not like the line
python3 -m pip install -v --force-reinstall --check-build-dependencies --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ --config-settings=cmake.define.with-mpi="ON" --no-binary pynest-ng pynest-ng[mpi]
I had to put the final pynest-ng[mpi] in quotes to make this run. Could that have caused the problem?
What are the SKBUILD switches in the CMake files about? Probably a dumb question ...
You also mentioned that some secrets needed adjustment before merging. Do you mean merging this branch into my branch or the eventual merge into NEST master?
| "Bug Tracker" = "https://github.com/nest/nest-simulator/issues" | ||
| Changelog = "https://nest-simulator.readthedocs.io/en/stable/whats_new/index.html" | ||
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| [tool.scikit-build] |
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I use a program called "Scikit-build-core" to help me package pynest-ng. "It provides a bridge between CMake and the Python build system, allowing you to make Python modules with CMake." https://scikit-build-core.readthedocs.io/en/latest/
The scikit tag here marks some definitions for the build process.
| ] | ||
| dependencies = [ | ||
| "numpy", | ||
| "pynest-api", |
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Maybe add pytest, so one can easily run the testsuite after installation?
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Pytest has been added as a dependency.
pyproject.toml
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| NEST_SRC_DIR=${PWD} | ||
| if [ $AUDITWHEEL_POLICY == "musllinux_1_2" ] | ||
| then | ||
| apk add git readline readline-dev libc6-compat gsl gsl-dev ncurses ncurses-dev wget bzip2 hdf5 cmake |
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For PyNEST-NG, we should no longer need readline and readline-dev.
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👍 Readline has been removed.
Maybe a Mac thing?
For Phyton packaging, some installation paths need to be adjusted. The SKBUILB switch recognizes that a build is being performed with Scikit-build-core and the corresponding changes can be made.
Both. In order for CI to perform the upload to testpypi or later to pypi, a token must be set as an environment variable. |
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Pull request automatically marked stale! |
2 participants
Key changes:
Python packaging
CI Workflow
CMake Files
Before merging, the project name and deployment secrets need to be adjusted.
The Python package may be tested in a Docker container:
docker run -it --rm --name test ubuntu:24.04 bashInstall Dependencies and Create an Python venv
Intalll from https://test.pypi.org/project/pynest-ng/
python3 -m pip --no-cache-dir install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ pynest-ng python3 -c "import nest; nest.help()"Rebuild with MPI
Install and Build from GitHub Repository
python3 -m pip install -v --force-reinstall git+https://{GITHUB_TOKEN}@github.com/steffengraber/nest-simulator.git@hep_pynest-ng python3 -c "import nest; nest.help()"