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srmnitc / pyiron-apt

Use paraprobe and python together
MIT License
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problem on executing notebook after installation #2

Open mdforti opened 1 year ago

mdforti commented 1 year ago

I am making a fresh install of paraprobe and composition space from conda with this command:

conda create -p /AnacondaEnvironments/paraprove-compositionspace -c conda-forge paraprobe compositionspace

then, I try to execute this notebook:

https://github.com/srmnitc/pyiron-apt/blob/main/paraprobe/workflow_paraprobe.ipynb

I get the same error as in the linked one, regarding missing jupyterlab_h5web, which works after installing manually with pip.

Then I get errors regarding missing modules:

ModuleNotFoundError Traceback (most recent call last) Cell In[2], line 1 ----> 1 from paraprobe_parmsetup.tools.transcoder_guru import ParmsetupTranscoder 2 from paraprobe_parmsetup.tools.ranger_guru import ParmsetupRanger 3 from paraprobe_parmsetup.tools.surfacer_guru import ParmsetupSurfacer

File /scratch/AnacondaEnvironments/paraprove-compositionspace/lib/python3.10/site-packages/paraprobe_parmsetup/tools/transcoder_guru.py:10 1 """ 2 //##MK::GPLV3. 3 4 Python class to be used in Jupyter notebooks for creating 5 HDF5 configuration files for paraprobe-transcoder 6 """ 8 import numpy as np ---> 10 from paraprobe_parmsetup.utils.numerics import TOOLS_IN_TOOLBOX 12 from paraprobe_parmsetup.utils.hashing import get_file_hashvalue 14 from paraprobe_parmsetup.utils.nodeinfo import NodeInfo

ModuleNotFoundError: No module named 'paraprobe_parmsetup.utils'

which is solved by modifying the pointed lines to:

from paraprobe_parmsetup.tools.utils.numerics import TOOLS_IN_TOOLBOX

is this a versioning problem or should I make an issue in paraprobe gitlab ?

Best regards,

srmnitc commented 1 year ago

This should be fixed in the latest release of paraprobe.

srmnitc commented 1 year ago

I can confirm this has been fixed in the latest conda release

mdforti commented 1 year ago

this is partially fixed:

jupyterlab_h5web needs to be installed manually using pip

pyiron needs to be installed manually using conda from conda-forge.

but then trying to use the notebook:

https://github.com/mdforti/pyiron-apt/blob/failing_run/paraprobe_pyiron/workflow_paraprobe_pyiron.ipynb

fails with the shown error, probably due to missing config?

srmnitc commented 1 year ago

I had not pushed some local commits, should be okay now.