Fails to install from pip

[kma-code]

I'm trying to install under MacOS 26.3 in a Python 3.11 env.
Using pip 26.0.1 and running pip install pyspike, I get:

Collecting pyspike
  Using cached pyspike-0.8.0.tar.gz (1.1 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy in /Users/km/owncloud/Projects Neuro/cortical_osci_error_coding/osciVenv/lib/python3.11/site-packages (from pyspike) (1.26.4)
Building wheels for collected packages: pyspike
  Building wheel for pyspike (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for pyspike (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [152 lines of output]
      /private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead.
      !!
      
              ********************************************************************************
              Usage of dash-separated 'description-file' will not be supported in future
              versions. Please use the underscore name 'description_file' instead.
              (Affected: pyspike).
      
              Available configuration options are listed in:
              https://setuptools.pypa.io/en/latest/userguide/declarative_config.html
      
              This deprecation is overdue, please update your project and remove deprecated
              calls to avoid build errors in the future.
      
              See https://github.com/pypa/setuptools/discussions/5011 for details.
              ********************************************************************************
      
      !!
        opt = self._enforce_underscore(opt, section)
      /private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
      !!
      
              ********************************************************************************
              Please consider removing the following classifiers in favor of a SPDX license expression:
      
              License :: OSI Approved :: BSD License
      
              See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
              ********************************************************************************
      
      !!
        self._finalize_license_expression()
      running bdist_wheel
      running build
      running build_py
      creating build/lib.macosx-10.9-universal2-cpython-311/pyspike
      copying pyspike/spike_distance.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike
      copying pyspike/DiscreteFunc.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike
      copying pyspike/spikes.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike
      copying pyspike/PieceWiseConstFunc.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike
      copying pyspike/generic.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike
      copying pyspike/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike
      copying pyspike/PieceWiseLinFunc.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike
      copying pyspike/isi_lengths.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike
      copying pyspike/psth.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike
      copying pyspike/spike_directionality.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike
      copying pyspike/spike_sync.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike
      copying pyspike/SpikeTrain.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike
      copying pyspike/isi_distance.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike
      creating build/lib.macosx-10.9-universal2-cpython-311/test
      copying test/test_distance.py -> build/lib.macosx-10.9-universal2-cpython-311/test
      copying test/test_MRTS.py -> build/lib.macosx-10.9-universal2-cpython-311/test
      copying test/test_reconcile.py -> build/lib.macosx-10.9-universal2-cpython-311/test
      copying test/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/test
      copying test/test_sync_filter.py -> build/lib.macosx-10.9-universal2-cpython-311/test
      copying test/test_save_load.py -> build/lib.macosx-10.9-universal2-cpython-311/test
      copying test/test_directionality.py -> build/lib.macosx-10.9-universal2-cpython-311/test
      copying test/test_spikes.py -> build/lib.macosx-10.9-universal2-cpython-311/test
      copying test/test_function.py -> build/lib.macosx-10.9-universal2-cpython-311/test
      copying test/test_generic_interfaces.py -> build/lib.macosx-10.9-universal2-cpython-311/test
      copying test/test_auto_thresh.py -> build/lib.macosx-10.9-universal2-cpython-311/test
      copying test/test_empty.py -> build/lib.macosx-10.9-universal2-cpython-311/test
      creating build/lib.macosx-10.9-universal2-cpython-311/pyspike/cython
      copying pyspike/cython/__init__.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike/cython
      copying pyspike/cython/python_backend.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike/cython
      copying pyspike/cython/directionality_python_backend.py -> build/lib.macosx-10.9-universal2-cpython-311/pyspike/cython
      copying pyspike/cython/cython_add.c -> build/lib.macosx-10.9-universal2-cpython-311/pyspike/cython
      copying pyspike/cython/cython_profiles.c -> build/lib.macosx-10.9-universal2-cpython-311/pyspike/cython
      copying pyspike/cython/cython_get_tau.c -> build/lib.macosx-10.9-universal2-cpython-311/pyspike/cython
      copying pyspike/cython/cython_distances.c -> build/lib.macosx-10.9-universal2-cpython-311/pyspike/cython
      copying pyspike/cython/cython_directionality.c -> build/lib.macosx-10.9-universal2-cpython-311/pyspike/cython
      copying pyspike/cython/cython_simulated_annealing.c -> build/lib.macosx-10.9-universal2-cpython-311/pyspike/cython
      running build_ext
      building 'pyspike.cython.cython_add' extension
      Traceback (most recent call last):
        File "/Users/km/owncloud/Projects Neuro/cortical_osci_error_coding/osciVenv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
          main()
        File "/Users/km/owncloud/Projects Neuro/cortical_osci_error_coding/osciVenv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs"])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/Users/km/owncloud/Projects Neuro/cortical_osci_error_coding/osciVenv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel
          return _build_backend().build_wheel(
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 441, in build_wheel
          return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 429, in _build
          return self._build_with_temp_dir(
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 410, in _build_with_temp_dir
          self.run_setup()
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 520, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 317, in run_setup
          exec(code, locals())
        File "<string>", line 84, in <module>
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/__init__.py", line 117, in setup
          return distutils.core.setup(**attrs)  # type: ignore[return-value]
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 186, in setup
          return run_commands(dist)
                 ^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
          dist.run_commands()
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1000, in run_commands
          self.run_command(cmd)
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 1107, in run_command
          super().run_command(command)
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1019, in run_command
          cmd_obj.run()
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/command/bdist_wheel.py", line 370, in run
          self.run_command("build")
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 341, in run_command
          self.distribution.run_command(command)
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 1107, in run_command
          super().run_command(command)
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1019, in run_command
          cmd_obj.run()
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 135, in run
          self.run_command(cmd_name)
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 341, in run_command
          self.distribution.run_command(command)
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 1107, in run_command
          super().run_command(command)
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1019, in run_command
          cmd_obj.run()
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/command/build_ext.py", line 97, in run
          _build_ext.run(self)
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 367, in run
          self.build_extensions()
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 483, in build_extensions
          self._build_extensions_serial()
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 509, in _build_extensions_serial
          self.build_extension(ext)
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/command/build_ext.py", line 262, in build_extension
          _build_ext.build_extension(self, ext)
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build_ext.py", line 564, in build_extension
          objects = self.compiler.compile(
                    ^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/compilers/C/base.py", line 638, in compile
          macros, objects, extra_postargs, pp_opts, build = self._setup_compile(
                                                            ^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/compilers/C/base.py", line 388, in _setup_compile
          pp_opts = gen_preprocess_options(macros, incdirs)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/compilers/C/base.py", line 1347, in gen_preprocess_options
          pp_opts.extend(f"-I{dir}" for dir in include_dirs)
        File "/private/var/folders/zb/q43ry99x69g19b1w0cyrrr700000gn/T/pip-build-env-yfyri06v/overlay/lib/python3.11/site-packages/setuptools/_distutils/compilers/C/base.py", line 1347, in <genexpr>
          pp_opts.extend(f"-I{dir}" for dir in include_dirs)
                         ^^^^^^^^^^
        File "<string>", line 27, in __str__
      ModuleNotFoundError: No module named 'numpy'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pyspike
Failed to build pyspike
error: failed-wheel-build-for-install

× Failed to build installable wheels for some pyproject.toml based projects
╰─> pyspike

[guymatz]

Same results on MacOS 26.4.1, pip 26.0.1, python 3.14

[SaeedTaghavi]

@kma-code @guymatz
I ran into the same issue on Python 3.12 and also tried 3.11. What ended up working for me was using Python 3.10 with numpy<2. Here's the full process:
1. Install Python 3.10 and its dev headers (if not already available)
On Ubuntu/Debian/(I used ubuntu wsl2):

sudo apt install software-properties-common
sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt update
sudo apt install python3.10 python3.10-venv python3.10-dev

2. Create and activate a virtual environment

python3.10 -m venv my-pyspike
source my-pyspike/bin/activate

3. Pin numpy to 1.x before installing pyspike

The bundled .c files were compiled against numpy 1.x, and numpy 2.0 removed some internal structs they depend on (e.g. PyArray_Descr.subarray), causing the build to fail even on Python 3.10 if you have a newer numpy.

pip install "numpy<2"
pip install pyspike

That's it — import pyspike should work after that. The core issue is that the pre-generated Cython .c files bundled in the 0.8.0 release are out of date and incompatible with both newer Python versions and numpy 2.x. It seems these build errors are tied to legacy Cython artifacts; re-generating them would be a great way to support users on modern distributions.

[SaeedTaghavi]

Installing PySpike on Python 3.12

Environment:

• Python 3.12.3
• pip 24.x
• Ubuntu (WSL2)

---

Problem

Installing pyspike via pip fails on Python 3.12 in two distinct ways.

Attempt 1 — standard install:

pip install pyspike

Fails during the build with ModuleNotFoundError: No module named 'numpy' even after numpy is installed. This is a build isolation issue: pip creates a temporary isolated environment to compile the Cython extensions, and numpy is not visible inside it because pyspike does not declare numpy as a build-time dependency in pyproject.toml.

Attempt 2 — with --no-build-isolation:

pip install pyspike --no-build-isolation

Fails with dozens of C compiler errors such as:

• 'PyLongObject' has no member named 'ob_digit'
• '_PyErr_StackItem' has no member named 'exc_type'
• 'PyThreadState' has no member named 'curexc_type'
• 'PyArray_Descr' has no member named 'subarray'

The root cause is that the pre-generated .c files bundled in the pyspike 0.8.0 release were produced by an old version of Cython that is incompatible with Python 3.12's updated internal C API.

---

Solution

Clone the repository and regenerate the Cython .c files using a modern version of Cython, then install in editable mode:

# 1. Create and activate a virtual environment
python3 -m venv my-pyspike
source my-pyspike/bin/activate

# 2. Install build dependencies
pip install numpy cython setuptools

# 3. Clone the repo
git clone https://github.com/mariomulansky/PySpike.git
cd PySpike

# 4. Regenerate the C extensions from source
cython pyspike/cython/*.pyx

# 5. Install in editable mode
pip install -e . --no-build-isolation

Two additional fixes were needed in pyspike/__init__.py:

Fix 1: pkg_resources is not available in newer setuptools environments. Replace the version-detection block (lines 38–56) with the modern importlib.metadata equivalent:

# Before
# define the __version__ following
# http://stackoverflow.com/questions/17583443
from pkg_resources import get_distribution, DistributionNotFound
import os.path

try:
    _dist = get_distribution('pyspike')
    # Normalize case for Windows systems
    dist_loc = os.path.normcase(_dist.location)
    here = os.path.normcase(__file__)
    if not here.startswith(os.path.join(dist_loc, 'pyspike')):
        # not installed, but there is another version that *is*
        raise DistributionNotFound
except DistributionNotFound:
    __version__ = 'Please install this project with setup.py'
else:
    __version__ = _dist.version

disable_backend_warning = False

...

# After
# define the __version__ following
# http://stackoverflow.com/questions/17583443
from importlib.metadata import version, PackageNotFoundError
 
try:
    __version__ = version('pyspike')
except PackageNotFoundError:
    __version__ = 'Please install this project with setup.py'

disable_backend_warning = False

importlib.metadata is part of the Python standard library since 3.8 and requires no extra dependencies.
That's it — import pyspike should work after that.

[SaeedTaghavi]

@kma-code @guymatz
I've been working on a fix for this and opened a pull request: [#85]

The changes include regenerating the Cython .c files using a modern Cython version, adding a pyproject.toml to properly declare build dependencies, and replacing pkg_resources with importlib.metadata. This should make installation work out of the box on Python 3.11, 3.12, and future versions without pinning numpy.

In the meantime, if anyone wants to try it before it lands in the official release, you can install directly from my fork:

pip install git+https://github.com/SaeedTaghavi/PySpike.git@fix/python312-compatibility

Tested on Python 3.12.3 with numpy 2.4.4 on Ubuntu WSL2.

[kma-code]

@SaeedTaghavi I've installed your fork, and your fix solved the issue using Python 3.11 with pip 26.0.1 and numpy 1.26.4. Thanks so much!

[guymatz]

@SaeedTaghavi Well done! I hope you and your loved ones are safe & well.

Perhaps this is not the right place to discuss this, but do you folks think the approach taken in this package is still the best way to go about burst detection? I'm wondering if there any more modern approaches that might be better . . . perhaps using Machine Learning?

[SaeedTaghavi]

@guymatz Thanks for your kind words!
Regarding your question on burst detection: I haven't actually used or tested that specific section of the package yet, so I'm not familiar with the current best practices or potential ML-based alternatives. I specifically needed to use the SPIKE-distance section, so I focused on figuring out how to get the package installed and working on my machine and Python version.