update notebooks: switch from enums to codable concepts #27

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1. turbomam

   self-assigned this

   on Oct 21, 2021
2. turbomam commented on Oct 21, 2021

   

   turbomam

   on Oct 21, 2021

   Last edited by turbomam

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   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?
3. turbomam commented on Oct 21, 2021

   

   turbomam

   on Oct 21, 2021

   Last edited by turbomam

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   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.
4. turbomam commented on Oct 21, 2021

   

   turbomam

   on Oct 21, 2021

   Last edited by turbomam

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   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.
5. turbomam commented on Oct 21, 2021

   

   turbomam

   on Oct 21, 2021

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   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
6. jooho-lee-kim commented on Oct 21, 2021

   

   jooho-lee-kim

   on Oct 21, 2021

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   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.
7. gaurav

   added this to the Build a complete Example Data Workflow (Phase 3, Quarter 4, 2021) milestone on Nov 4, 2021