MDA compilation crash with aarch64 #3374
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Looking at the logs a bit more, looks like an issue with GSD? I don't have an ARM machine on hand to test this unfortunately :( |
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Remembered I had access to a ThunderX2 machine. I can reproduce this issue: pip install cython==0.29.24 numpy==1.19.1 scipy==1.7.0
pip install --no-build-isolation hypothesis matplotlib pytest pytest-cov pytest-xdist tqdm threadpoolctl
git clone https://github.com/MDAnalysis/mdanalysis.git
cd mdanalysis/package
python setup.py installDetails |
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Appears to be fine with numpy>=1.19.2 Whilst it would be nice to hunt down for the exact cause here, given that aarch64 is somewhat experimental, I'd perfer just set the numpy lower bound to something a bit higher? (unless there are any objections) |
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MDAnalysis < 3.0 seems to require Cython < 2.0 for compilation (see also MDAnalysis/mdanalysis#4129 and MDAnalysis/mdanalysis#3374).
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MDAnalysis < 3.0 seems to require Cython < 1.0 for compilation (see also MDAnalysis/mdanalysis#4129 and MDAnalysis/mdanalysis#3374).
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MDAnalysis < 3.0 seems to require Cython < 1.0 for compilation (see also MDAnalysis/mdanalysis#4129, cython/cython#3690 and MDAnalysis/mdanalysis#3374). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires NumPy >= 1.16.0, even for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
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MDAnalysis < 3.0 seems to require Cython < 1.0 for compilation (see also MDAnalysis/mdanalysis#4129 and MDAnalysis/mdanalysis#3374).
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MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
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MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
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Decrease the maximum allowed MDAnalysis version from `<3.0` to `<2.1`, because higher MDAnalysis versions can cause issues during the compilation with Cython on Python 3.7. Perhaps somehow related to * MDAnalysis/mdanalysis#4129 * cython/cython#3690 * MDAnalysis/mdanalysis#3374
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Decrease the maximum allowed MDAnalysis version from `<3.0` to `<2.1`, because higher MDAnalysis versions causes issues during the compilation with Cython on Python 3.7. Perhaps somehow related to * MDAnalysis/mdanalysis#4129 * cython/cython#3690 * MDAnalysis/mdanalysis#3374 Error code when installing MDAnalysis 2.1.0 on Python 3.7 using Cython 0.29.36: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ```
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MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
andthum
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Decrease the maximum allowed MDAnalysis version from `<3.0` to `<2.1`, because higher MDAnalysis versions cause issues during the compilation with Cython on Python 3.7. Perhaps somehow related to * MDAnalysis/mdanalysis#4129 * cython/cython#3690 * MDAnalysis/mdanalysis#3374 Error code when installing MDAnalysis 2.1.0 on Python 3.7 using Cython 0.29.36: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ```
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MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
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Jul 24, 2023
Decrease the maximum allowed MDAnalysis version from `<3.0` to `<2.1`, because higher MDAnalysis versions causes issues during the compilation with Cython on Python 3.7. Perhaps somehow related to * MDAnalysis/mdanalysis#4129 * cython/cython#3690 * MDAnalysis/mdanalysis#3374 Error code when installing MDAnalysis 2.1.0 on Python 3.7 using Cython 0.29.36: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-zntq4dco/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ```
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Jul 24, 2023
MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
andthum
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Jul 25, 2023
MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
andthum
added a commit
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Jul 26, 2023
MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
andthum
added a commit
to andthum/mdtools
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Jul 26, 2023
MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
andthum
added a commit
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Jul 26, 2023
MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
andthum
added a commit
to andthum/mdtools
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Jul 26, 2023
MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
andthum
added a commit
to andthum/mdtools
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Jul 26, 2023
MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
andthum
added a commit
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Jul 28, 2023
MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
andthum
added a commit
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Aug 2, 2023
MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
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Aug 2, 2023
MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
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Aug 2, 2023
MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
andthum
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Aug 4, 2023
MDAnalysis `<3.0` requires Cython `<3.0` for compilation (see MDAnalysis/mdanalysis#4129 and cython/cython#3690). Otherwise, installing MDAnalysis via pip throws the following error: ``` shell Error compiling Cython file: ------------------------------------------------------------ ... array_wrapper = ArrayWrapper() array_wrapper.set_data(<void*> data_ptr, <int*> &dim[0], dim.size, data_type) cdef np.ndarray ndarray = np.array(array_wrapper, copy=False) # Assign our object to the 'base' of the ndarray object ndarray.base = <PyObject*> array_wrapper ^ ------------------------------------------------------------ MDAnalysis/lib/formats/cython_util.pyx:115:11: Assignment to a read-only property Traceback (most recent call last): File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module> main() File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/home/runner/.local/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 488, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 590, in <module> File "<string>", line 453, in extensions File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize cythonize_one(*args) File "/tmp/pip-build-env-uemocs7v/overlay/lib/python3.7/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: MDAnalysis/lib/formats/cython_util.pyx ``` Furthermore, MDAnalysis requires at leas NumPy `>=1.16.0`, but better Numpy `>=1.19.2` (see MDAnalysis/mdanalysis#3374 (comment)), for setup: ``` shell *** package "numpy" not found *** MDAnalysis requires a version of NumPy (>=1.16.0), even for setup. Please get it from http://numpy.scipy.org/ or install it through your package manager. ```
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Jul 19, 2024
Install python-dev-tools, Cython <3.0 and numpy >=1.19.2 before installing MDTools, because MDAnalysis requires NumPy >=1.19.2 for setup (see also MDAnalysis/mdanalysis#3374 (comment)) and MDAnalysis <3.0 requires Cython <3.0 (see MDAnalysis/mdanalysis#4129 and cython/cython#3690).
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Jul 19, 2024
Install python-dev-tools, Cython <3.0 and numpy >=1.19.2 before installing this project, because MDAnalysis requires NumPy >=1.19.2 for setup (see also MDAnalysis/mdanalysis#3374 (comment)) and MDAnalysis <3.0 requires Cython <3.0 (see MDAnalysis/mdanalysis#4129 and cython/cython#3690).
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Jul 19, 2024
Install python-dev-tools, Cython <3.0 and numpy >=1.19.2 before installing this project, because MDAnalysis requires NumPy >=1.19.2 for setup (see also MDAnalysis/mdanalysis#3374 (comment)) and MDAnalysis <3.0 requires Cython <3.0 (see MDAnalysis/mdanalysis#4129 and cython/cython#3690).
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Install python-dev-tools, Cython <3.0 and numpy >=1.19.2 before installing this project, because MDAnalysis requires NumPy >=1.19.2 for setup (see also MDAnalysis/mdanalysis#3374 (comment)) and MDAnalysis <3.0 requires Cython <3.0 (see MDAnalysis/mdanalysis#4129 and cython/cython#3690).
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For some reason our latest aarch64 builds are reproducibly failing on aarch64, see: https://travis-ci.com/github/MDAnalysis/mdanalysis/jobs/526646721#L1562-L1582
Issue seems to coincide with the release of cython 0.29.24.
@tylerjereddy sorry to bug you here, are you seeing anything similar upstream?
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