magic - Githubissues

Describe the bug Magic not working

To Reproduce Standalone code to reproduce the error

Expected behavior A clear and concise description of what you expected to happen.

Actual behavior Please include the full traceback of any errors

System information:

Output of magic.__version__:

If you are running MAGIC in R or Python, please run magic.__version__ and paste the results here.

You can do this with `python -c 'import magic; print(magic.__version__)'`

 python -c 'import magic'
/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/numpy/__init__.py:143: UserWarning: mkl-service package failed to import, therefore Intel(R) MKL initialization ensuring its correct out-of-the box operation under condition when Gnu OpenMP had already been loaded by Python process is not assured. Please install mkl-service package, see http://github.com/IntelPython/mkl-service
  from . import _distributor_init
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/magic/__init__.py", line 1, in <module>
    from .magic import MAGIC
  File "/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/magic/magic.py", line 9, in <module>
    from . import utils
  File "/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/magic/utils.py", line 1, in <module>
    from scipy import sparse
  File "/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/scipy/__init__.py", line 67, in <module>
    from numpy import show_config as show_numpy_config
  File "/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/numpy/__init__.py", line 326, in <module>
    **import mkl
ModuleNotFoundError: No module named 'mkl'**

Output of pd.show_versions():

``` If you are running MAGIC in R or Python, please run pd.show_versions() and paste the results here. /Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/numpy/__init__.py:143: UserWarning: mkl-service package failed to import, therefore Intel(R) MKL initialization ensuring its correct out-of-the box operation under condition when Gnu OpenMP had already been loaded by Python process is not assured. Please install mkl-service package, see http://github.com/IntelPython/mkl-service from . import _distributor_init Traceback (most recent call last): File "", line 1, in File "/Users/abhaykanodia/opt/anaconda3/lib/python3.9/site-packages/pandas/__init__.py", line 16, in raise ImportError( ImportError: Unable to import required dependencies: **numpy: No module named 'mkl'** > reticulate::py_module_available("magic") [1] FALSE > reticulate::py_available() [1] TRUE > reticulate::import("magic") Error in py_module_import(module, convert = convert) : ModuleNotFoundError: No module named 'magic' In Terminal pip3 install magic-impute Requirement already satisfied: magic-impute in ./opt/anaconda3/lib/python3.9/site-packages (3.0.0) Requirement already satisfied: scipy>=1.1.0 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (1.7.1) Requirement already satisfied: scikit-learn>=0.19.1 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (0.24.2) Requirement already satisfied: graphtools>=1.4.0 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (1.5.2) Requirement already satisfied: tasklogger>=1.0.0 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (1.1.2) Requirement already satisfied: matplotlib in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (3.4.3) Requirement already satisfied: future in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (0.18.2) Requirement already satisfied: numpy>=1.14.0 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (1.20.3) Requirement already satisfied: pandas>=0.25 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (1.3.4) Requirement already satisfied: scprep>=1.0 in ./opt/anaconda3/lib/python3.9/site-packages (from magic-impute) (1.1.0) Requirement already satisfied: pygsp>=0.5.1 in ./opt/anaconda3/lib/python3.9/site-packages (from graphtools>=1.4.0->magic-impute) (0.5.1) Requirement already satisfied: Deprecated in ./opt/anaconda3/lib/python3.9/site-packages (from graphtools>=1.4.0->magic-impute) (1.2.13) Requirement already satisfied: python-dateutil>=2.7.3 in ./opt/anaconda3/lib/python3.9/site-packages (from pandas>=0.25->magic-impute) (2.8.2) Requirement already satisfied: pytz>=2017.3 in ./opt/anaconda3/lib/python3.9/site-packages (from pandas>=0.25->magic-impute) (2021.3) Requirement already satisfied: six>=1.5 in ./opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.7.3->pandas>=0.25->magic-impute) (1.16.0) Requirement already satisfied: joblib>=0.11 in ./opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.19.1->magic-impute) (1.1.0) Requirement already satisfied: threadpoolctl>=2.0.0 in ./opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.19.1->magic-impute) (2.2.0) Requirement already satisfied: packaging in ./opt/anaconda3/lib/python3.9/site-packages (from scprep>=1.0->magic-impute) (21.0) Requirement already satisfied: decorator>=4.3.0 in ./opt/anaconda3/lib/python3.9/site-packages (from scprep>=1.0->magic-impute) (5.1.0) Requirement already satisfied: wrapt<2,>=1.10 in ./opt/anaconda3/lib/python3.9/site-packages (from Deprecated->graphtools>=1.4.0->magic-impute) (1.12.1) Requirement already satisfied: kiwisolver>=1.0.1 in ./opt/anaconda3/lib/python3.9/site-packages (from matplotlib->magic-impute) (1.3.1) Requirement already satisfied: cycler>=0.10 in ./opt/anaconda3/lib/python3.9/site-packages (from matplotlib->magic-impute) (0.10.0) Requirement already satisfied: pillow>=6.2.0 in ./opt/anaconda3/lib/python3.9/site-packages (from matplotlib->magic-impute) (8.4.0) Requirement already satisfied: pyparsing>=2.2.1 in ./opt/anaconda3/lib/python3.9/site-packages (from matplotlib->magic-impute) (3.0.4)

KrishnaswamyLab / MAGIC

magic #201