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ndarray.base: Assignment to a read-only property #3690

Closed
rth opened this issue Jun 17, 2020 · 1 comment · Fixed by scikit-learn/scikit-learn#17627
Closed

ndarray.base: Assignment to a read-only property #3690

rth opened this issue Jun 17, 2020 · 1 comment · Fixed by scikit-learn/scikit-learn#17627

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@rth
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rth commented Jun 17, 2020 •
edited
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While trying to build scikit-learn with cython 3.0a5, numpy 1.18.1, Python 3.8 (ref scikit-learn/scikit-learn#17102) I get a few errors about narray.base being a read-only property,

Error compiling Cython file:
------------------------------------------------------------
...
        arr = PyArray_NewFromDescr(<PyTypeObject *> np.ndarray,
                                   CELL_DTYPE, 1, shape,
                                   strides, <void*> self.cells,
                                   np.NPY_DEFAULT, None)
        Py_INCREF(self)
        arr.base = <PyObject*> self
          ^
------------------------------------------------------------

sklearn/neighbors/_quad_tree.pyx:576:11: Assignment to a read-only property
Error compiling Cython file:
------------------------------------------------------------
...
        cdef np.ndarray arr
        arr = np.PyArray_SimpleNewFromData(3, shape, np.NPY_DOUBLE, self.value)
        Py_INCREF(self)
        arr.base = <PyObject*> self
------------------------------------------------------------

sklearn/tree/_tree.pyx:1100:11: Assignment to a read-only property

This seems to be related to the discussion in #3521 (comment) and generally to #3573.

If setting ndarray.base is now not supported, what is the recommended workaround?
@rth
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Author

rth commented Jun 17, 2020

Using PyArray_SetBaseObject explicitly instead seems to work. Closing.

@rth rth closed this as completed Jun 17, 2020
@rth rth mentioned this issue Jun 17, 2020
Merged
orbeckst added a commit to MDAnalysis/mdanalysis that referenced this issue Oct 16, 2020
@orbeckst
compile Cython extensions with Cython >= 3.0
5e6fc69 
- fix #2988
- Do not any longer use deprecated NumPy API.
- requires Cython >= 3.0 (tested locally with 3.0a6)
- fixed direct ndarray.base access (using cython/cython#3690 (comment) )
@orbeckst orbeckst mentioned this issue Oct 16, 2020
Closed
4 tasks
This was referenced Apr 26, 2023
Closed
Merged
@akaszynski akaszynski mentioned this issue May 7, 2023
Merged
andthum added a commit to andthum/mdtools that referenced this issue Jul 19, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
68c34a2 
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.
```
@Prajwal-Prathiksh Prajwal-Prathiksh mentioned this issue Jul 19, 2023
Closed
andthum added a commit to andthum/mdtools that referenced this issue Jul 20, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
c2956d8 
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/lintf2_ether_ana_postproc that referenced this issue Jul 20, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
3d42e58 
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/lintf2_ether_ana_postproc that referenced this issue Jul 20, 2023
@andthum
[pyproject.toml]: Limit Maximum MDAnalysis Version to <2.1
ad81571 
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
andthum added a commit to andthum/lintf2_ether_ana_postproc that referenced this issue Jul 20, 2023
@andthum
[pyproject.toml]: Limit Maximum MDAnalysis Version to <2.1
1623bee 
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
```
andthum added a commit to andthum/transfer_Li that referenced this issue Jul 20, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
4c52543 
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/transfer_Li that referenced this issue Jul 20, 2023
@andthum
[pyproject.toml]: Limit Maximum MDAnalysis Version to <2.1
152adf7 
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
```
andthum added a commit to andthum/lintf2_ether_ana_postproc that referenced this issue Jul 24, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
621459a 
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/lintf2_ether_ana_postproc that referenced this issue Jul 24, 2023
@andthum
[pyproject.toml]: Limit Maximum MDAnalysis Version to <2.1
ffe7fd9 
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
```
andthum added a commit to andthum/mdtools that referenced this issue Jul 24, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
5ad4501 
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 that referenced this issue Jul 25, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
fb857ca 
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 that referenced this issue Jul 26, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
563f8ee 
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 that referenced this issue Jul 26, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
d5a89df 
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 that referenced this issue Jul 26, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
37f6392 
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 that referenced this issue Jul 26, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
f9410a4 
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 that referenced this issue Jul 26, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
9757cb0 
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 that referenced this issue Jul 28, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
deb65c8 
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 that referenced this issue Aug 2, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
6f77579 
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 that referenced this issue Aug 2, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
1aedfbb 
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 that referenced this issue Aug 2, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
f051837 
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 that referenced this issue Aug 4, 2023
@andthum
[tests.yml]: Install Cython and Numpy Before MDAnalysis
04d8145 
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.
```
This was referenced Oct 13, 2023
Merged
Merged
andthum added a commit to andthum/mdtools that referenced this issue Jul 19, 2024
@andthum
[codeql-analysis.yml]: Update
993cf2a 
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).
andthum added a commit to andthum/lintf2_ether_ana_postproc that referenced this issue Jul 19, 2024
@andthum
[codeql-analysis.yml]: Update
a267d3c 
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).
andthum added a commit to andthum/lintf2_ether_ana_postproc that referenced this issue Jul 19, 2024
@andthum
[codeql-analysis.yml]: Update
c4a3a74 
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).
andthum added a commit to andthum/transfer_Li that referenced this issue Jul 19, 2024
@andthum
[codeql-analysis.yml]: Update
13e2f40 
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).
This was referenced Jul 22, 2024
Closed
Closed
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MNT Fix build with Cython 3.0a5 rth/scikit-learn
1 participant
@rth