Unable to import PHATE using M3 silicon chip

[nickli91]

Describe the bug
Unable to import PHATE after successful installation on M3 chip. I already have it working with the same version on python using the same installation method on an intel chip

To Reproduce
!pip install phate (in jupyter notebook) returns:
Collecting phate
Using cached phate-1.0.11-py3-none-any.whl.metadata (6.1 kB)
Requirement already satisfied: numpy>=1.16.0 in /Users/nick/.local/lib/python3.11/site-packages (from phate) (1.26.4)
Requirement already satisfied: scipy>=1.1.0 in /Users/nick/.local/lib/python3.11/site-packages (from phate) (1.12.0)
Requirement already satisfied: scikit-learn>=0.20.0 in /Users/nick/.local/lib/python3.11/site-packages (from phate) (1.4.1.post1)
Requirement already satisfied: future in /Users/nick/.local/lib/python3.11/site-packages (from phate) (1.0.0)
Requirement already satisfied: tasklogger>=1.2 in /Users/nick/.local/lib/python3.11/site-packages (from phate) (1.2.0)
Requirement already satisfied: graphtools>=1.5.3 in /Users/nick/.local/lib/python3.11/site-packages (from phate) (1.5.3)
Requirement already satisfied: scprep>=0.11.1 in /Users/nick/.local/lib/python3.11/site-packages (from phate) (1.2.3)
Requirement already satisfied: Deprecated in /Users/nick/.local/lib/python3.11/site-packages (from phate) (1.2.14)
Requirement already satisfied: s-gd2>=1.8.1 in /Users/nick/.local/lib/python3.11/site-packages (from phate) (1.8.1)
Requirement already satisfied: matplotlib>=3.0 in /Users/nick/.local/lib/python3.11/site-packages (from phate) (3.8.3)
Requirement already satisfied: pygsp>=0.5.1 in /Users/nick/.local/lib/python3.11/site-packages (from graphtools>=1.5.3->phate) (0.5.1)
Requirement already satisfied: contourpy>=1.0.1 in /Users/nick/.local/lib/python3.11/site-packages (from matplotlib>=3.0->phate) (1.2.0)
Requirement already satisfied: cycler>=0.10 in /Users/nick/.local/lib/python3.11/site-packages (from matplotlib>=3.0->phate) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in /Users/nick/.local/lib/python3.11/site-packages (from matplotlib>=3.0->phate) (4.49.0)
Requirement already satisfied: kiwisolver>=1.3.1 in /Users/nick/.local/lib/python3.11/site-packages (from matplotlib>=3.0->phate) (1.4.5)
Requirement already satisfied: packaging>=20.0 in /Users/nick/.local/lib/python3.11/site-packages (from matplotlib>=3.0->phate) (24.2)
Requirement already satisfied: pillow>=8 in /Users/nick/.local/lib/python3.11/site-packages (from matplotlib>=3.0->phate) (10.2.0)
Requirement already satisfied: pyparsing>=2.3.1 in /Users/nick/.local/lib/python3.11/site-packages (from matplotlib>=3.0->phate) (3.1.1)
Requirement already satisfied: python-dateutil>=2.7 in /Users/nick/.local/lib/python3.11/site-packages (from matplotlib>=3.0->phate) (2.8.2)
Requirement already satisfied: joblib>=1.2.0 in /Users/nick/.local/lib/python3.11/site-packages (from scikit-learn>=0.20.0->phate) (1.3.2)
Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/nick/.local/lib/python3.11/site-packages (from scikit-learn>=0.20.0->phate) (3.3.0)
Requirement already satisfied: decorator>=4.3.0 in /Users/nick/.local/lib/python3.11/site-packages (from scprep>=0.11.1->phate) (5.1.1)
Requirement already satisfied: pandas<2.1,>=0.25 in /Users/nick/.local/lib/python3.11/site-packages (from scprep>=0.11.1->phate) (2.0.3)
Requirement already satisfied: wrapt<2,>=1.10 in /Users/nick/.local/lib/python3.11/site-packages (from Deprecated->phate) (1.16.0)
Requirement already satisfied: pytz>=2020.1 in /Users/nick/.local/lib/python3.11/site-packages (from pandas<2.1,>=0.25->scprep>=0.11.1->phate) (2024.1)
Requirement already satisfied: tzdata>=2022.1 in /Users/nick/.local/lib/python3.11/site-packages (from pandas<2.1,>=0.25->scprep>=0.11.1->phate) (2024.1)
Requirement already satisfied: six>=1.5 in /Users/nick/.local/lib/python3.11/site-packages (from python-dateutil>=2.7->matplotlib>=3.0->phate) (1.16.0)
Using cached phate-1.0.11-py3-none-any.whl (23 kB)
Installing collected packages: phate
Successfully installed phate-1.0.11

Expected behavior
Phate to be successfully imported as it looks like a successful installation

Actual behavior
import phate (in jupyter notebook)
ModuleNotFoundError Traceback (most recent call last)
File ~/.local/lib/python3.11/site-packages/s_gd2/swig/layout.py:17, in swig_import_helper()
16 try:
---> 17 return importlib.import_module(mname)
18 except ImportError:

File ~/anaconda3/envs/new/lib/python3.11/importlib/init.py:126, in import_module(name, package)
125 level += 1
--> 126 return _bootstrap._gcd_import(name[level:], package, level)

File :1204, in _gcd_import(name, package, level)

File :1176, in find_and_load(name, import)

File :1140, 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)
Cell In[1], line 1
----> 1 import phate

File ~/anaconda3/envs/new/lib/python3.11/site-packages/phate/init.py:3
1 from future import absolute_import
----> 3 from .phate import PHATE
4 import phate.tree
5 import phate.io

File ~/anaconda3/envs/new/lib/python3.11/site-packages/phate/phate.py:19
15 import tasklogger
17 import matplotlib.pyplot as plt
---> 19 from . import utils, vne, mds
21 try:
22 import anndata

File ~/anaconda3/envs/new/lib/python3.11/site-packages/phate/mds.py:14
12 import tasklogger
13 import scprep
---> 14 import s_gd2
16 _logger = tasklogger.get_tasklogger("graphtools")
19 # Fast classical MDS using random svd

File ~/.local/lib/python3.11/site-packages/s_gd2/init.py:1
----> 1 from .s_gd2 import *
2 from .version import version

File ~/.local/lib/python3.11/site-packages/s_gd2/s_gd2.py:1
----> 1 from .swig import layout as cpp
2 import numpy as np
4 all = [
5 "layout",
6 "layout_convergent",
(...)
11 "draw_png",
12 ]

File ~/.local/lib/python3.11/site-packages/s_gd2/swig/layout.py:21
18 except ImportError:
19 return importlib.import_module("_layout")
---> 21 _layout = swig_import_helper()
22 del swig_import_helper
23 elif _swig_python_version_info >= (2, 6, 0):

File ~/.local/lib/python3.11/site-packages/s_gd2/swig/layout.py:19, in swig_import_helper()
17 return importlib.import_module(mname)
18 except ImportError:
---> 19 return importlib.import_module("_layout")

File ~/anaconda3/envs/new/lib/python3.11/importlib/init.py:126, in import_module(name, package)
124 break
125 level += 1
--> 126 return _bootstrap._gcd_import(name[level:], package, level)

ImportError: dlopen(/Users/nick/.local/lib/python3.11/site-packages/_layout.cpython-311-darwin.so, 0x0002): tried: '/Users/nick/.local/lib/python3.11/site-packages/_layout.cpython-311-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/nick/.local/lib/python3.11/site-packages/_layout.cpython-311-darwin.so' (no such file), '/Users/nick/.local/lib/python3.11/site-packages/_layout.cpython-311-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64'))

System information:

Output of phate.__version__:

Please run phate.__version__ and paste the results here.

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

I am unable to import phate, but the version installed seems to be phate-1.0.11

Output of pd.show_versions():

INSTALLED VERSIONS

commit : 0f437949513225922d851e9581723d82120684a6
python : 3.11.11.final.0
python-bits : 64
OS : Darwin
OS-release : 24.1.0
Version : Darwin Kernel Version 24.1.0: Thu Oct 10 21:05:23 PDT 2024; root:xnu-11215.41.3~2/RELEASE_ARM64_T6031
machine : arm64
processor : arm
byteorder : little
LC_ALL : en_US.UTF-8
LANG : en_US.UTF-8
LOCALE : en_US.UTF-8

pandas : 2.0.3
numpy : 1.26.4
pytz : 2024.1
dateutil : 2.8.2
setuptools : 75.1.0
pip : 24.2
Cython : None
pytest : None
hypothesis : None
sphinx : None
blosc : None
feather : None
xlsxwriter : None
lxml.etree : None
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 3.1.4
IPython : 8.30.0
pandas_datareader: None
bs4 : 4.12.3
bottleneck : None
brotli : 1.0.9
fastparquet : None
fsspec : None
gcsfs : None
matplotlib : 3.8.3
numba : None
numexpr : None
odfpy : None
openpyxl : None
pandas_gbq : None
pyarrow : None
pyreadstat : None
pyxlsb : None
s3fs : None
scipy : 1.12.0
snappy : None
sqlalchemy : None
tables : None
tabulate : None
xarray : None
xlrd : None
zstandard : None
tzdata : 2024.1
qtpy : None
pyqt5 : None

Please run pd.show_versions() and paste the results here.

You can do this with `python -c 'import pandas as pd; pd.show_versions()'`

Additional context
Would appreciate any help in this matter.

Kind regards,

Nick