update notebooks: switch from enums to codable concepts

[turbomam]

started like this:

pipenv install
pipenv run jupyter notebook

environemnt has

• crdch-model 1.1.3

https://pypi.org/project/crdch-model/1.1.5/ was the latest when this comment was written

Pipfile asks for crdch-model = "*". Maybe I should clear my Pipfile.lock and pip cache to force a later version

pipenv --rm

Removing virtualenv (/home/mark/.local/share/virtualenvs/example-data-8chtNU61)…

rm Pipfile.lock 
pip cache purge

Files removed: 98

pipenv install

Creating a virtualenv for this project… Using /usr/bin/python3 (3.8.10) to create virtualenv… ... Pipfile.lock not found, creating…

OK, have crdch-model 1.1.5 now. But didn't we say that this project depends on 3.9?

[turbomam]

working on GDC to CCDH conversion.ipynb first

whole notebook already runs to completion!

Ahh... it was still importing the model from the filesystem from ccdh import ccdhmodel as ccdh

---

Switch to import crdch_model as ccdh. Can still print ccdh.Specimen.__doc__ but not ccdh.EnumCCDHSpecimenSpecimenType.__doc__ due to expected change in modelling.

[turbomam]

Does this repo still need these directories now that the crdch model is being obtained from PyPI?

• ccdh
• crdc-h-model

I moved their contents into keep subdirectories.

[turbomam]

Would like to install black but

Warning: Your dependencies could not be resolved. You likely have a mismatch in your sub-dependencies. You can use $ pipenv install --skip-lock to bypass this mechanism, then run $ pipenv graph to inspect the situation. Could not find a version that matches black Tried: 18.3a0, 18.3a0, 18.3a1, 18.3a1, 18.3a2, 18.3a2, 18.3a3, 18.3a3, 18.3a4, 18.3a4, 18.4a0, 18.4a0, 18.4a1, 18.4a1, 18.4a2, 18.4a2, 18.4a3, 18.4a3, 18.4a4, 18.4a4, 18.5b0, 18.5b0, 18.5b1, 18.5b1, 18.6b0, 18.6b0, 18.6b1, 18.6b1, 18.6b2, 18.6b2, 18.6b3, 18.6b3, 18.6b4, 18.6b4, 18.9b0, 18.9b0, 19.3b0, 19.3b0, 19.10b0, 19.10b0, 20.8b0, 20.8b1, 21.4b0, 21.4b0, 21.4b1, 21.4b1, 21.4b2, 21.4b2, 21.5b0, 21.5b0, 21.5b1, 21.5b1, 21.5b2, 21.5b2, 21.6b0, 21.6b0, 21.7b0, 21.7b0, 21.8b0, 21.8b0, 21.9b0, 21.9b0

[jooho-lee-kim]

I followed your setup instruction on using pipenv to run jupyter notebook. I would be helpful to add pipenv instruction on README.md on root? I went back and forth starting and stoping Jupyter notebook.

When I launch jupyter notebook on pipenv, I was not able to execute cells on notebook because of the following error. ModuleNotFoundError: No module named 'appnope'

But the terminology service lookups worked when I ran jupyter notebook without using pipenv.