Errors while running SimpleExample.ipynb

[somyagr]

Hi mentors,
Even after installing all the dependencies by running pip install . , I am getting many errors while running SimpleExample.ipynb in jupyter notebook like "No module named 'onnx' ". After installing onnx by pip command, I got the next error "No module named 'modelspec' " and since then there have been a lot of errors. Please tell me if I'm going wrong or I'll have to install these modules like this only.
Thanks in advance.

[pgleeson]

@somyagr What OS are you using and have you set up a virtual environment? Can you paste here the output of pip list?

[somyagr]

I am using Ubuntu 20.04, yes I have set up a virtual environment.

(MDF-env) HP-348-G4:~/MDF$ pip list
Package Version

---

airspeed 0.5.19
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
asttokens 2.0.5
attrs 21.4.0
autograd 1.3
backcall 0.2.0
beautifulsoup4 4.10.0
bleach 4.1.0
bokeh 2.4.2
boltons 21.0.0
cachetools 5.0.0
cattrs 1.10.0
cffi 1.15.0
click 8.1.0
cloudpickle 2.0.0
colorama 0.4.4
commonmark 0.9.1
cycler 0.11.0
Cython 0.29.28
dask 2022.3.0
debugpy 1.6.0
decorator 4.4.2
defusedxml 0.7.1
dill 0.3.4
distributed 2022.3.0
docstring-parser 0.13
elfi 0.8.2
entrypoints 0.4
executing 0.8.3
face 20.1.1
fsspec 2022.2.0
future 0.18.2
glom 22.1.0
GPy 1.10.0
graph-scheduler 1.0.0
graphviz 0.16
grpcio 1.42.0
grpcio-tools 1.42.0
h5py 3.6.0
HeapDict 1.0.1
importlib-resources 5.6.0
ipykernel 6.10.0
ipyparallel 8.2.0
ipython 8.2.0
ipython-genutils 0.2.0
ipywidgets 7.7.0
jedi 0.18.1
Jinja2 3.1.1
joblib 1.1.0
jsonschema 4.4.0
jupyter 1.0.0
jupyter-client 7.2.0
jupyter-console 6.4.3
jupyter-core 4.9.2
jupyterlab-pygments 0.1.2
jupyterlab-widgets 1.1.0
kiwisolver 1.4.2
leabra-psyneulink 0.3.2
libNeuroML 0.3.1
llvmlite 0.37.0
locket 0.2.1
lxml 4.8.0
MarkupSafe 2.1.1
matplotlib 3.3.3
matplotlib-inline 0.1.3
mistune 0.8.4
modeci-mdf 0.3.3
modelspec 0.2.1
mpmath 1.2.1
msgpack 1.0.3
nbclient 0.5.13
nbconvert 6.4.5
nbformat 5.2.0
nest-asyncio 1.5.4
networkx 2.5.1
neuromllite 0.4.3
notebook 6.4.10
numpy 1.20.2
onnx 1.9.0
onnxconverter-common 1.8.1
onnxruntime 1.7.0
packaging 21.3
pandocfilters 1.5.0
paramz 0.9.5
parso 0.8.3
partd 1.2.0
pexpect 4.8.0
pickleshare 0.7.5
Pillow 8.4.0
Pint 0.17
pip 22.0.4
prometheus-client 0.13.1
prompt-toolkit 3.0.28
protobuf 3.19.4
psutil 5.9.0
psyneulink 0.10.0.0
ptyprocess 0.7.0
pure-eval 0.2.2
pycparser 2.21
Pygments 2.11.2
PyLEMS 0.5.9
pyNeuroML 0.5.20
pyparsing 2.4.7
pyrsistent 0.18.1
python-dateutil 2.8.2
PyYAML 6.0
pyzmq 22.3.0
qtconsole 5.3.0
QtPy 2.0.1
rich 10.12.0
scikit-learn 1.0.2
scipy 1.8.0
Send2Trash 1.8.0
setuptools 52.0.0
six 1.16.0
skl2onnx 1.8.0
sortedcontainers 2.4.0
soupsieve 2.3.1
stack-data 0.2.0
sympy 1.8
tabulate 0.8.9
tblib 1.7.0
terminado 0.13.3
testpath 0.6.0
threadpoolctl 3.1.0
toolz 0.11.2
toposort 1.7
torch 1.8.0
tornado 6.1
tqdm 4.63.1
traitlets 5.1.1
typecheck-decorator 1.2
typing_extensions 4.1.1
wcwidth 0.2.5
webencodings 0.5.1
wheel 0.36.2
widgetsnbextension 3.6.0
zict 2.1.0
zipp 3.7.0

[sanjayankur31]

Are you running the jupyter notebook in the virtualenv you created and installed the packages in?

[pgleeson]

Try creating a new notebook and typing !pip list into the first cell and make sure that the package list is the same as you get at the command line.

[somyagr]

@sanjayankur31 yes I'm running the jupyter notebook in the virtual environment only,
@pgleeson I've verified, the list is the same at both the places

[pgleeson]

Sorry @somyagr, not sure what else to suggest... If the pip list is stating that onnx is installed, but running the notebook complains that it's not, it's an inconsistency.

All I could suggest is making a new virtual env (or use conda to manage a fresh environment), test that the examples at https://github.com/ModECI/MDF/tree/main/examples/MDF all run fine at the command line, make sure you're using executables inside the env, e.g run which jupyter-notebook, and try the notebook again.

[somyagr]

@pgleeson Sorry to disturb you again for this issue, please help me out if you have any alternative.
I've installed modelspec through pip but I'm getting No module named 'modelspec.BaseTypes' error. Version of modelspec installed currently is 0.2.3.
I've tried uninstalling it and reinstalling via pip3 but that makes no difference.
It seems the problem is not with installing modelspec, but with the BaseTypes associated with it.
If anyone else has gone through this error please help me out.

[pgleeson]

@somyagr I would strongly recommend using conda and make a new virtual environment, basing it on python 3.9, as that's the best tested. Then install MDF, from the development branch, as that has the latest updates. It should pick up the relevant dependencies from there, inlcuding modelspec.