Problem with pyspike installation #82
Description
Good morning!
Sorry for the inconvenience but I am finding some difficulties to install the PySpike package with pip I get the following error message:
`Collecting pyspike
Using cached pyspike-0.8.0.tar.gz (1.1 MB)
Preparing metadata (pyproject.toml) ... Requirement already satisfied: numpy in /home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages (from pyspike) (2.2.4)
Building wheels for collected packages: pyspike
Building wheel for pyspike (pyproject.toml) ... error: subprocess-exited-with-error
× Building wheel for pyspike (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [190 lines of output]
/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/dist.py:493: SetuptoolsDeprecationWarning: Invalid dash-separated options
!!
********************************************************************************
Usage of dash-separated 'description-file' will not be supported in future
versions. Please use the underscore name 'description_file' instead.
This deprecation is overdue, please update your project and remove deprecated
calls to avoid build errors in the future.
See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
********************************************************************************
!!
opt = self.warn_dash_deprecation(opt, section)
running bdist_wheel
running build
running build_py
creating build/lib.linux-x86_64-cpython-313/test
copying test/test_save_load.py -> build/lib.linux-x86_64-cpython-313/test
copying test/test_sync_filter.py -> build/lib.linux-x86_64-cpython-313/test
copying test/test_reconcile.py -> build/lib.linux-x86_64-cpython-313/test
copying test/test_auto_thresh.py -> build/lib.linux-x86_64-cpython-313/test
copying test/test_directionality.py -> build/lib.linux-x86_64-cpython-313/test
copying test/__init__.py -> build/lib.linux-x86_64-cpython-313/test
copying test/test_spikes.py -> build/lib.linux-x86_64-cpython-313/test
copying test/test_distance.py -> build/lib.linux-x86_64-cpython-313/test
copying test/test_MRTS.py -> build/lib.linux-x86_64-cpython-313/test
copying test/test_empty.py -> build/lib.linux-x86_64-cpython-313/test
copying test/test_function.py -> build/lib.linux-x86_64-cpython-313/test
copying test/test_generic_interfaces.py -> build/lib.linux-x86_64-cpython-313/test
creating build/lib.linux-x86_64-cpython-313/pyspike
copying pyspike/PieceWiseConstFunc.py -> build/lib.linux-x86_64-cpython-313/pyspike
copying pyspike/DiscreteFunc.py -> build/lib.linux-x86_64-cpython-313/pyspike
copying pyspike/spikes.py -> build/lib.linux-x86_64-cpython-313/pyspike
copying pyspike/spike_distance.py -> build/lib.linux-x86_64-cpython-313/pyspike
copying pyspike/spike_sync.py -> build/lib.linux-x86_64-cpython-313/pyspike
copying pyspike/isi_distance.py -> build/lib.linux-x86_64-cpython-313/pyspike
copying pyspike/spike_directionality.py -> build/lib.linux-x86_64-cpython-313/pyspike
copying pyspike/__init__.py -> build/lib.linux-x86_64-cpython-313/pyspike
copying pyspike/isi_lengths.py -> build/lib.linux-x86_64-cpython-313/pyspike
copying pyspike/generic.py -> build/lib.linux-x86_64-cpython-313/pyspike
copying pyspike/psth.py -> build/lib.linux-x86_64-cpython-313/pyspike
copying pyspike/SpikeTrain.py -> build/lib.linux-x86_64-cpython-313/pyspike
copying pyspike/PieceWiseLinFunc.py -> build/lib.linux-x86_64-cpython-313/pyspike
creating build/lib.linux-x86_64-cpython-313/pyspike/cython
copying pyspike/cython/python_backend.py -> build/lib.linux-x86_64-cpython-313/pyspike/cython
copying pyspike/cython/__init__.py -> build/lib.linux-x86_64-cpython-313/pyspike/cython
copying pyspike/cython/directionality_python_backend.py -> build/lib.linux-x86_64-cpython-313/pyspike/cython
copying pyspike/cython/cython_add.c -> build/lib.linux-x86_64-cpython-313/pyspike/cython
copying pyspike/cython/cython_profiles.c -> build/lib.linux-x86_64-cpython-313/pyspike/cython
copying pyspike/cython/cython_get_tau.c -> build/lib.linux-x86_64-cpython-313/pyspike/cython
copying pyspike/cython/cython_distances.c -> build/lib.linux-x86_64-cpython-313/pyspike/cython
copying pyspike/cython/cython_directionality.c -> build/lib.linux-x86_64-cpython-313/pyspike/cython
copying pyspike/cython/cython_simulated_annealing.c -> build/lib.linux-x86_64-cpython-313/pyspike/cython
running build_ext
Traceback (most recent call last):
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
main()
~~~~^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
json_out["return_val"] = hook(**hook_input["kwargs"])
~~~~^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel
return _build_backend().build_wheel(
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
wheel_directory, config_settings, metadata_directory
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/build_meta.py", line 438, in build_wheel
return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/build_meta.py", line 426, in _build
return self._build_with_temp_dir(
~~~~~~~~~~~~~~~~~~~~~~~~~^
cmd,
^^^^
...<3 lines>...
self._arbitrary_args(config_settings),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/build_meta.py", line 407, in _build_with_temp_dir
self.run_setup()
~~~~~~~~~~~~~~^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/build_meta.py", line 522, in run_setup
super().run_setup(setup_script=setup_script)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/build_meta.py", line 320, in run_setup
exec(code, locals())
~~~~^^^^^^^^^^^^^^^^
File "<string>", line 84, in <module>
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/__init__.py", line 117, in setup
return distutils.core.setup(**attrs)
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/_distutils/core.py", line 186, in setup
return run_commands(dist)
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
dist.run_commands()
~~~~~~~~~~~~~~~~~^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 983, in run_commands
self.run_command(cmd)
~~~~~~~~~~~~~~~~^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
super().run_command(command)
~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
cmd_obj.run()
~~~~~~~~~~~^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/command/bdist_wheel.py", line 369, in run
self.run_command("build")
~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/_distutils/cmd.py", line 339, in run_command
self.distribution.run_command(command)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
super().run_command(command)
~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
cmd_obj.run()
~~~~~~~~~~~^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/_distutils/command/build.py", line 136, in run
self.run_command(cmd_name)
~~~~~~~~~~~~~~~~^^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/_distutils/cmd.py", line 339, in run_command
self.distribution.run_command(command)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
super().run_command(command)
~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
cmd_obj.run()
~~~~~~~~~~~^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/_distutils/command/build_ext.py", line 365, in run
self.build_extensions()
~~~~~~~~~~~~~~~~~~~~~^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/_distutils/command/build_ext.py", line 481, in build_extensions
self._build_extensions_serial()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/setuptools/_distutils/command/build_ext.py", line 507, in _build_extensions_serial
self.build_extension(ext)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/Cython/Distutils/build_ext.py", line 130, in build_extension
new_ext = cythonize(
~~~~~~~~~^
ext,force=self.force, quiet=self.verbose == 0, **options
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)[0]
^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/Cython/Build/Dependencies.py", line 1010, in cythonize
module_list, module_metadata = create_extension_list(
~~~~~~~~~~~~~~~~~~~~~^
module_list,
^^^^^^^^^^^^
...<4 lines>...
language=language,
^^^^^^^^^^^^^^^^^^
aliases=aliases)
^^^^^^^^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/Cython/Build/Dependencies.py", line 859, in create_extension_list
kwds = deps.distutils_info(file, aliases, base).values
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/Cython/Build/Dependencies.py", line 707, in distutils_info
return (self.transitive_merge(filename, self.distutils_info0, DistutilsInfo.merge)
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/Cython/Build/Dependencies.py", line 716, in transitive_merge
return self.transitive_merge_helper(
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
node, extract, merge, seen, {}, self.cimported_files)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/Cython/Build/Dependencies.py", line 728, in transitive_merge_helper
for next in outgoing(node):
~~~~~~~~^^^^^^
File "Cython/Utils.py", line 129, in Cython.Utils.cached_method.wrapper
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/Cython/Build/Dependencies.py", line 629, in cimported_files
pxd_file = self.find_pxd(module, filename)
File "Cython/Utils.py", line 129, in Cython.Utils.cached_method.wrapper
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/Cython/Build/Dependencies.py", line 610, in find_pxd
pxd = self.context.find_pxd_file(relative, source_file_path=filename)
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/Cython/Compiler/Main.py", line 281, in find_pxd_file
pxd = self.search_include_directories(
qualified_name, suffix=".pxd", source_pos=pos, sys_path=sys_path, source_file_path=source_file_path)
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/Cython/Compiler/Main.py", line 309, in search_include_directories
return search_include_directories(
include_dirs, qualified_name, suffix or "", source_pos, include, source_file_path)
File "Cython/Utils.py", line 90, in Cython.Utils.cached_function.wrapper
File "/home/gabricasa/anaconda3/envs/brian2/lib/python3.13/site-packages/Cython/Compiler/Main.py", line 703, in search_include_directories
path = os.path.join(dirname, dotted_filename)
File "<frozen posixpath>", line 77, in join
TypeError: expected str, bytes or os.PathLike object, not numpy_include
[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 to build installable wheels for some pyproject.toml based projects (pyspike)`
I am currently using the version 2.2.4 of numpy in the conda env where I would like to install PySpyke.
Thank in advance for the information and wish you a good day.