Downloading sub packages for analysis

[ghost]

I am a begineer to machine learning and pymatgen. I am trying to use the analysis feature on pymatgen but I keep getting an Import error. Below is the code I am using. I have found out there are numerous subpackages that contain analysis. I am struggling to download these packages, is there a way to download packages for analysis?

from pymatgen.analysis.adsorption import plot_slab
from matplotlib import pyplot as plt

[janosh]

Your import

from pymatgen.analysis.adsorption import plot_slab

should work if pymatgen was installed correctly.

You'll probably have to post more details to get help. How did you install pymatgen (pip install pymatgen)? What's the error message?

[ghost]

Yes I installed pymatgen using (pip install pymatgen). Below is the error message that it gives me.

ImportError Traceback (most recent call last)
Input In [59], in <cell line: 1>()
----> 1 from pymatgen.analysis.adsorption import plot_slab
2 from matplotlib import pyplot as plt
3 get_ipython().run_line_magic('matplotlib', 'inline')

File ~/opt/anaconda3/envs/py39/lib/python3.9/site-packages/pymatgen/analysis/adsorption.py:13, in
10 import os
12 import numpy as np
---> 13 from matplotlib import patches
14 from matplotlib.path import Path
15 from monty.serialization import loadfn

File ~/opt/anaconda3/envs/py39/lib/python3.9/site-packages/matplotlib/init.py:109, in
105 from packaging.version import parse as parse_version
107 # cbook must import matplotlib only within function
108 # definitions, so it is safe to import from it here.
--> 109 from . import _api, _version, cbook, docstring, rcsetup
110 from matplotlib.cbook import MatplotlibDeprecationWarning, sanitize_sequence
111 from matplotlib.cbook import mplDeprecation # deprecated

File ~/opt/anaconda3/envs/py39/lib/python3.9/site-packages/matplotlib/rcsetup.py:27, in
25 from matplotlib import _api, cbook
26 from matplotlib.cbook import ls_mapper
---> 27 from matplotlib.colors import Colormap, is_color_like
28 from matplotlib.fontconfig_pattern import parse_fontconfig_pattern
29 from matplotlib._enums import JoinStyle, CapStyle

File ~/opt/anaconda3/envs/py39/lib/python3.9/site-packages/matplotlib/colors.py:51, in
49 from numbers import Number
50 import re
---> 51 from PIL import Image
52 from PIL.PngImagePlugin import PngInfo
54 import matplotlib as mpl

File ~/opt/anaconda3/envs/py39/lib/python3.9/site-packages/PIL/Image.py:132, in
123 MAX_IMAGE_PIXELS = int(1024 * 1024 * 1024 // 4 // 3)
126 try:
127 # If the _imaging C module is not present, Pillow will not load.
128 # Note that other modules should not refer to _imaging directly;
129 # import Image and use the Image.core variable instead.
130 # Also note that Image.core is not a publicly documented interface,
131 # and should be considered private and subject to change.
--> 132 from . import _imaging as core
134 if version != getattr(core, "PILLOW_VERSION", None):
135 raise ImportError(
136 "The _imaging extension was built for another version of Pillow or PIL:\n"
137 f"Core version: {getattr(core, 'PILLOW_VERSION', None)}\n"
138 f"Pillow version: {version}"
139 )

ImportError: dlopen(/Users/jasonpereira/opt/anaconda3/envs/py39/lib/python3.9/site-packages/PIL/_imaging.cpython-39-darwin.so, 2): Symbol not found: ____chkstk_darwin
Referenced from: /Users/jasonpereira/opt/anaconda3/envs/py39/lib/python3.9/site-packages/PIL/.dylibs/libtiff.5.dylib (which was built for Mac OS X 11.0)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/jasonpereira/opt/anaconda3/envs/py39/lib/python3.9/site-packages/PIL/.dylibs/libtiff.5.dylib### ###

[janosh]

Your import error is raised by PIL, not pymatgen. I would try reinstalling or installing different versions.

This seems related.