Unable to Run Demo ("Syntax Error")

[gracegliu]

I have motion mapper installed in a fresh Python 3.6.13 environment. It mostly installed correctly, I ran into some errors during the setup process which meant that I had to install numba and scikit-learn manually, and I can't seem to install h5py 2.1 in the Python 3.6 environment.

I am unable to run the demo, and I receive this error when I do.

(mmapper) C:\Users\AhmariLab\MotionMapperPy>python demo/demo.py
Traceback (most recent call last):
  File "demo/demo.py", line 9, in <module>
    import motionmapperpy as mmpy
  File "<frozen importlib._bootstrap>", line 971, in _find_and_load
  File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 656, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 626, in _load_backward_compatible
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\motionmapperpy-1.0-py3.6.egg\motionmapperpy\__init__.py", line 3, in <module>
  File "<frozen importlib._bootstrap>", line 971, in _find_and_load
  File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 656, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 626, in _load_backward_compatible
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\motionmapperpy-1.0-py3.6.egg\motionmapperpy\motionmapper.py", line 9, in <module>
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\sklearn\__init__.py", line 82, in <module>
    from .base import clone
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\sklearn\base.py", line 17, in <module>
    from .utils import _IS_32BIT
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\sklearn\utils\__init__.py", line 23, in <module>
    from .class_weight import compute_class_weight, compute_sample_weight
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\sklearn\utils\class_weight.py", line 7, in <module>
    from .validation import _deprecate_positional_args
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\sklearn\utils\validation.py", line 22, in <module>
    import joblib
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\joblib\__init__.py", line 120, in <module>
    from .parallel import Parallel
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\joblib\parallel.py", line 26, in <module>
    from ._parallel_backends import (FallbackToBackend, MultiprocessingBackend,
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\joblib\_parallel_backends.py", line 17, in <module>
    from .pool import MemmappingPool
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\joblib\pool.py", line 31, in <module>
    from ._memmapping_reducer import get_memmapping_reducers
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\joblib\_memmapping_reducer.py", line 37, in <module>
    from .externals.loky.backend import resource_tracker
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\joblib\externals\loky\__init__.py", line 12, in <module>
    from .backend.reduction import set_loky_pickler
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\joblib\externals\loky\backend\reduction.py", line 125, in <module>
    from joblib.externals import cloudpickle  # noqa: F401
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\joblib\externals\cloudpickle\__init__.py", line 4, in <module>
    from .cloudpickle import *  # noqa
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\joblib\externals\cloudpickle\cloudpickle.py", line 63, in <module>
    import typing_extensions as _typing_extensions
  File "C:\Users\AhmariLab\anaconda3\envs\mmapper\lib\site-packages\typing_extensions-4.12.2-py3.6.egg\typing_extensions.py", line 1039
    def TypedDict(typename, fields=_marker, /, *, total=True, closed=False, **kwargs):
                                            ^
SyntaxError: invalid syntax

Here is the pip list:

cached-property    1.5.2
certifi            2021.5.30
colorama           0.4.6
cycler             0.11.0
decorator          4.4.2
easydict           1.13
h5py               3.1.0
hdf5storage        0.1.19
imageio            2.15.0
importlib_metadata 8.5.0
joblib             1.0.1
kiwisolver         1.3.1
llvmlite           0.36.0
matplotlib         3.3.4
mkl-fft            1.3.0
mkl-random         1.1.1
mkl-service        2.3.0
motionmapperpy     1.0
networkx           2.5.1
numba              0.53.1
numpy              1.19.5
Pillow             8.4.0
pip                21.2.2
pynndescent        0.5.13
pyparsing          3.1.4
python-dateutil    2.9.0.post0
PyWavelets         1.1.1
scikit-image       0.17.2
scikit-learn       0.24.2
scipy              1.5.4
setuptools         58.0.4
six                1.17.0
threadpoolctl      2.2.0
tifffile           2020.9.3
tqdm               4.67.1
typing_extensions  4.12.2
umap-learn         0.5.7
wheel              0.37.1
wincertstore       0.2
zipp               3.21.0

Thank you!

[kanishkbjain]

Hi Grace,

Could you check if the error persist if you upgrade to Python 3.8 or 3.9? A lot of packages now have backward compatibility issue with python 3.6, I'm guessing upgrading python will solve the issue. I'm able to run the demo notebook on google colab with Python 3.10.

Please let me know if this doesn't resolve it!

Best,
Kanishk