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Cannot import phate: numpy version? #136

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haoqichen20 opened this issue Apr 22, 2023 · 1 comment
Open

Cannot import phate: numpy version? #136

haoqichen20 opened this issue Apr 22, 2023 · 1 comment
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@haoqichen20
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Describe the bug
Cannot import phate.

To Reproduce
(in python jupyter notebook)
!pip install phate
import phate

Expected behavior
Package should import into jupyter notebook.

Actual behavior
I got the following error:

ModuleNotFoundError Traceback (most recent call last)
~/miniconda3/envs/cmapPy3/lib/python3.9/site-packages/s_gd2/swig/layout.py in swig_import_helper()
16 try:
---> 17 return importlib.import_module(mname)
18 except ImportError:

~/miniconda3/envs/cmapPy3/lib/python3.9/importlib/init.py in import_module(name, package)
126 level += 1
--> 127 return _bootstrap._gcd_import(name[level:], package, level)
128

~/miniconda3/envs/cmapPy3/lib/python3.9/importlib/_bootstrap.py in _gcd_import(name, package, level)

~/miniconda3/envs/cmapPy3/lib/python3.9/importlib/_bootstrap.py in find_and_load(name, import)

~/miniconda3/envs/cmapPy3/lib/python3.9/importlib/_bootstrap.py in find_and_load_unlocked(name, import)

ModuleNotFoundError: No module named 's_gd2.swig._layout'

During handling of the above exception, another exception occurred:

RuntimeError Traceback (most recent call last)
RuntimeError: module compiled against API version 0x10 but this version of numpy is 0xe
Output exceeds the size limit. Open the full output data in a text editor---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
~/miniconda3/envs/cmapPy3/lib/python3.9/site-packages/s_gd2/swig/layout.py in swig_import_helper()
16 try:
---> 17 return importlib.import_module(mname)
18 except ImportError:

~/miniconda3/envs/cmapPy3/lib/python3.9/importlib/init.py in import_module(name, package)
126 level += 1
--> 127 return _bootstrap._gcd_import(name[level:], package, level)
128

~/miniconda3/envs/cmapPy3/lib/python3.9/importlib/_bootstrap.py in _gcd_import(name, package, level)

~/miniconda3/envs/cmapPy3/lib/python3.9/importlib/_bootstrap.py in find_and_load(name, import)

~/miniconda3/envs/cmapPy3/lib/python3.9/importlib/_bootstrap.py in find_and_load_unlocked(name, import)

ModuleNotFoundError: No module named 's_gd2.swig._layout'

During handling of the above exception, another exception occurred:

ImportError Traceback (most recent call last)
/var/folders/0j/3rpkx73963xd8ccxcbdqqv680000gp/T/ipykernel_8752/3609115909.py in
10 from sklearn.neighbors import kneighbors_graph
...
--> 127 return _bootstrap._gcd_import(name[level:], package, level)
128
129

ImportError: numpy.core.multiarray failed to import

System information:

Output of phate.__version__:

Since it cannot be imported, I run pip list instead, and the version is 1.0.10

Output of pd.show_versions():

INSTALLED VERSIONS
------------------
commit           : f00ed8f47020034e752baf0250483053340971b0
python           : 3.9.5.final.0
python-bits      : 64
OS               : Darwin
OS-release       : 22.4.0
Version          : Darwin Kernel Version 22.4.0: Mon Mar  6 21:00:17 PST 2023; root:xnu-8796.101.5~3/RELEASE_X86_64
machine          : x86_64
processor        : i386
byteorder        : little
LC_ALL           : None
LANG             : en_US.UTF-8
LOCALE           : en_US.UTF-8

pandas           : 1.3.0
numpy            : 1.20.3
pytz             : 2021.1
dateutil         : 2.8.2
pip              : 21.2.4
setuptools       : 52.0.0.post20210125
Cython           : None
pytest           : None
hypothesis       : None
sphinx           : None
blosc            : None
feather          : None
xlsxwriter       : None
lxml.etree       : None
html5lib         : None
pymysql          : None
psycopg2         : None
jinja2           : 3.0.1
IPython          : 7.26.0
pandas_datareader: None
bs4              : None
bottleneck       : 1.3.2
fsspec           : None
fastparquet      : None
gcsfs            : None
matplotlib       : 3.3.4
numexpr          : 2.7.3
odfpy            : None
openpyxl         : 3.0.7
pandas_gbq       : None
pyarrow          : None
pyxlsb           : None
s3fs             : None
scipy            : 1.7.0
sqlalchemy       : None
tables           : None
tabulate         : None
xarray           : None
xlrd             : 2.0.1
xlwt             : None
numba            : None

Additional context
I'm installing phate into an existing environment. Below is the full output of pip list

Package Version

appnope 0.1.2
argon2-cffi 20.1.0
async-generator 1.10
attrs 21.2.0
backcall 0.2.0
biopython 1.78
bleach 4.0.0
Bottleneck 1.3.2
cached-property 1.5.2
certifi 2021.5.30
cffi 1.14.6
chardet 4.0.0
charset-normalizer 2.0.3
cmapPy 4.0.1
cycler 0.10.0
debugpy 1.4.1
decorator 5.0.9
defusedxml 0.7.1
Deprecated 1.2.13
entrypoints 0.3
et-xmlfile 1.1.0
future 0.18.3
gmpy2 2.0.8
graphtools 1.5.3
h5py 3.2.1
idna 3.2
importlib-metadata 3.10.0
ipykernel 6.2.0
ipython 7.26.0
ipython-genutils 0.2.0
ipywidgets 7.6.3
jdcal 1.4.1
jedi 0.18.0
Jinja2 3.0.1
joblib 1.2.0
jsonschema 3.2.0
jupyter 1.0.0
jupyter-client 6.1.12
jupyter-console 6.4.0
jupyter-core 4.7.1
jupyterlab-pygments 0.1.2
jupyterlab-widgets 1.0.0
jupyterthemes 0.20.0
kiwisolver 1.3.1
lesscpy 0.15.0
MarkupSafe 2.0.1
matplotlib 3.3.4
matplotlib-inline 0.1.2
mistune 0.8.4
mkl-fft 1.3.0
mkl-random 1.2.2
mkl-service 2.4.0
mpmath 1.2.1
MultiscaleEMD 1.1.1
nbclient 0.5.3
nbconvert 6.1.0
nbformat 5.1.3
nest-asyncio 1.5.1
networkx 2.5
notebook 6.4.3
numexpr 2.7.3
numpy 1.24.2
olefile 0.46
openpyxl 3.0.7
packaging 21.0
pandas 1.3.0
pandocfilters 1.4.3
parso 0.8.2
patsy 0.5.1
pexpect 4.8.0
phate 1.0.10
pickleshare 0.7.5
Pillow 8.3.1
pip 21.2.4
ply 3.11
POT 0.9.0
prometheus-client 0.11.0
prompt-toolkit 3.0.17
ptyprocess 0.7.0
pycparser 2.20
Pygments 2.10.0
PyGSP 0.5.1
pyparsing 2.4.7
pyrsistent 0.18.0
python-dateutil 2.8.2
python-igraph 0.9.6
pytz 2021.1
pyzmq 22.2.1
qtconsole 5.1.0
QtPy 1.10.0
requests 2.26.0
s-gd2 1.8.1
scikit-learn 1.2.2
scipy 1.10.1
scprep 1.2.2
seaborn 0.11.1
Send2Trash 1.5.0
setuptools 52.0.0.post20210125
sip 4.19.13
six 1.16.0
snakeviz 2.1.1
statsmodels 0.12.2
sympy 1.8
tasklogger 1.2.0
terminado 0.9.4
testpath 0.5.0
texttable 1.6.4
threadpoolctl 2.2.0
tornado 6.1
tqdm 4.62.2
traitlets 5.0.5
urllib3 1.26.6
wcwidth 0.2.5
webencodings 0.5.1
wheel 0.37.0
widgetsnbextension 3.5.1
wrapt 1.15.0
xlrd 2.0.1
zipp 3.5.0
@scottgigante
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scottgigante commented Apr 28, 2023 via email

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