Add dependency to env variables

[nadja-mansurov]

Description

Add "rdkit" to fix failed test

Todos

Notable points that this PR has either accomplished or will accomplish.

• [ ] TODO 1

Questions

• [ ] Question1

Status

• [ ] Ready to go

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[dominiquesydow]

Hi @nadja-mansurov,

Thanks for starting to clean up here :) This notebook is so far only a playground for me - code will be moved to the package in the next few day. Happy that you already took a look!

Could you change the base branch to dominiquesydow:view-2d? That way we can clean up view-2d bit by bit and I can start to move the dev code from the notebook into the actual package.

If you would like to get the last failed test running, you could do:

EDITED (previous version used flake8 instead of flake8-nb):

cd path/to/dynophores/folder
black-nb -l 99 docs/tutorials/explore_view2d.ipynb  # Format code
flake8-nb --config setup.cfg docs/tutorials/explore_view2d.ipynb  # Find e.g. lint errors

But I can also do these fixes after I merged your PR into dominiquesydow:view-2d - as you prefer.

[codecov-io]

Codecov Report

Merging #18 (02e4a8d) into master (7d03017) will not change coverage. The diff coverage is n/a.

[dominiquesydow]

I am happy to take over the flake8 errors - I get many "line too long" errors.

(dyno) dominique@carbon: ~/Documents/GitHub/dynophores on view-2d
$ flake8 --config setup.cfg docs/tutorials/explore_view2d.ipynb
docs/tutorials/explore_view2d.ipynb:23:100: E501 line too long (121 > 99 characters)
docs/tutorials/explore_view2d.ipynb:54:100: E501 line too long (491 > 99 characters)
docs/tutorials/explore_view2d.ipynb:55:100: E501 line too long (132 > 99 characters)
docs/tutorials/explore_view2d.ipynb:57:100: E501 line too long (369 > 99 characters)
docs/tutorials/explore_view2d.ipynb:58:100: E501 line too long (132 > 99 characters)
docs/tutorials/explore_view2d.ipynb:60:100: E501 line too long (375 > 99 characters)
docs/tutorials/explore_view2d.ipynb:61:100: E501 line too long (132 > 99 characters)
docs/tutorials/explore_view2d.ipynb:113:100: E501 line too long (16536 > 99 characters)
docs/tutorials/explore_view2d.ipynb:174:100: E501 line too long (12508 > 99 characters)
docs/tutorials/explore_view2d.ipynb:206:100: E501 line too long (15352 > 99 characters)
docs/tutorials/explore_view2d.ipynb:271:100: E501 line too long (139 > 99 characters)
docs/tutorials/explore_view2d.ipynb:382:100: E501 line too long (124 > 99 characters)
docs/tutorials/explore_view2d.ipynb:431:100: E501 line too long (52756 > 99 characters)

[dominiquesydow]

We can for sure merge this into dominiquesydow:view-2d with failing linter - and I fix it there. Let me know what you prefer.

[dominiquesydow]

Interesting! Failed again with docs/tutorials/explore_view2d.ipynb#In[7]:5:22: F541 f-string is missing placeholders. I do not have that - maybe because of Mac/Linux?

[nadja-mansurov]

@dominiquesydow I changed the base-branch, could you try to fix it in your branch, please? I guess, it shouldn't be a problem caused by OS, but I can't be sure

[dominiquesydow]

Excellent, thanks! Merging now!

[dominiquesydow]

Quick folllow-up: We were searching for the f-string problem in the wrong cell: docs/tutorials/explore_view2d.ipynb#In[7]:5:22: F541 f-string is missing placeholders Cell 7 had an f-string with a string only (no placeholders). Sorry for not spotting this right away! Fixed in #17 now.