Import fails

[janosh]

Trying to import automatminer fails with IndexError: list index out of range. Tested locally and on Google Colab, same behavior.

Full stack trace

----> 2 import automatminer as amm

/usr/local/Caskroom/miniconda/base/envs/default/lib/python3.6/site-packages/automatminer/__init__.py in 
      1 from automatminer.automl import SinglePipelineAdaptor, TPOTAdaptor  # noqa
----> 2 from automatminer.featurization import AutoFeaturizer  # noqa
      3 from automatminer.pipeline import MatPipe  # noqa
      4 from automatminer.preprocessing import DataCleaner, FeatureReducer  # noqa
      5 from automatminer.presets import get_preset_config  # noqa

/usr/local/Caskroom/miniconda/base/envs/default/lib/python3.6/site-packages/automatminer/featurization/__init__.py in 
----> 1 from .core import AutoFeaturizer  # noqa

/usr/local/Caskroom/miniconda/base/envs/default/lib/python3.6/site-packages/automatminer/featurization/core.py in 
     25 from automatminer.utils.pkg import check_fitted, set_fitted
     26 from automatminer.base import DFTransformer
---> 27 from automatminer.featurization.sets import (
     28     CompositionFeaturizers,
     29     StructureFeaturizers,

/usr/local/Caskroom/miniconda/base/envs/default/lib/python3.6/site-packages/automatminer/featurization/sets.py in 
      8 """
      9 import matminer.featurizers.composition as cf
---> 10 import matminer.featurizers.structure as sf
     11 import matminer.featurizers.dos as dosf
     12 import matminer.featurizers.bandstructure as bf

/usr/local/Caskroom/miniconda/base/envs/default/lib/python3.6/site-packages/matminer/featurizers/structure.py in 
     34 
     35 from matminer.featurizers.base import BaseFeaturizer
---> 36 from matminer.featurizers.site import OPSiteFingerprint, \
     37     CoordinationNumber, LocalPropertyDifference, CrystalNNFingerprint, \
     38     AverageBondAngle, AverageBondLength

/usr/local/Caskroom/miniconda/base/envs/default/lib/python3.6/site-packages/matminer/featurizers/site.py in 
   1668 
   1669 # TODO: Figure out whether to take NN-counting method as an option (see VoronoiFingerprint)
-> 1670 class LocalPropertyDifference(BaseFeaturizer):
   1671     """
   1672     Differences in elemental properties between site and its neighboring sites.

/usr/local/Caskroom/miniconda/base/envs/default/lib/python3.6/site-packages/matminer/featurizers/site.py in LocalPropertyDifference()
   1693     """
   1694 
-> 1695     def __init__(self, data_source=MagpieData(), weight='area',
   1696                  properties=('Electronegativity',), signed=False):
   1697         """ Initialize the featurizer

/usr/local/Caskroom/miniconda/base/envs/default/lib/python3.6/site-packages/matminer/utils/data.py in __init__(self)
    213                                           lines[atomic_no - 1].split()]
    214                         else:
--> 215                             prop_value = float(lines[atomic_no - 1])
    216                     except ValueError:
    217                         prop_value = float("NaN")

IndexError: list index out of range

[janosh]

Happens with pip install automatminer==1.0.2.20191110 as well.

[utf]

Can you try updating matminer?

This should have been fixed in hackingmaterials/matminer#452

[ardunn]

Hey Janosh, Which version of matminer and pymatgen are you using? Amm hasn’t been updated to work with the newest matminer yet. If you are looking for a config that works, use the requirements.txt and make sure the versions match Thanks, Alex

…

On Tue, Jun 2, 2020 at 10:49 AM Alex Ganose ***@***.***> wrote: Can you try updating matminer? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#306 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYDHS2MQGR6SIYQOHLRHI3RUU3BVANCNFSM4NQ4QAPA> .

[janosh]

pip install scikit-learn==0.22.2 did the trick.