V2: Add all notebooks to test

[hwpang]

Description

Currently when a notebook test fails, CI doesn't complain. I will work on debugging this in this PR.

Example / Current workflow

n/a

Bugfix / Desired workflow

n/a

Questions

n/a

Relevant issues

#798

Checklist

• linted with flake8?
• (if appropriate) unit tests added?

[shihchengli]

Is there any update for this PR? I looked at the test results, and it seems this CI would work. There are two notebooks that failed to run. One seems due to an outdated import, and the other one failed because of a matplotlib import error. Can you install this package in the CI when running the tests on those examples? We can wait for #834 to be merged and run the tests again.

[hwpang]

With the -v verbose tag, I was able to make the notebook test fails CI. After adding all the notebooks to CI, there are some bugs found.

mpnn_fingerprints notebook is now failing as it uses matplotlib, but chemprop env doesn't come with matplotlib. @shihchengli What do you think we should do? Should we add matplotlib to chemprop env? Or should we remove the plotting examples?

extra_features_from_featurizer notebook is also now failing due to cannot import name 'MoleculeFeaturizer' from 'chemprop.featurizers' error. I assumed that it intends to import SimpleMoleculeMolGraphFeaturizer, so I changed that. However, after fixing that, now the notebook fails with the following error during initialization of the MorganFingerprintMoleculeFeaturizer. @kevingreenman @KnathanM do you two know how to fix this?

mf = MorganFingerprintMoleculeFeaturizer()
morgan = mf(utils.make_mol(smis[0], keep_h=False, add_h=False))
morgan.shape, morgan
>>>
TypeError                                 Traceback (most recent call last)
Cell In[8], [line 1](vscode-notebook-cell:?execution_count=8&line=1)
----> [1](vscode-notebook-cell:?execution_count=8&line=1) mf = MorganFingerprintMoleculeFeaturizer()
      [2](vscode-notebook-cell:?execution_count=8&line=2) morgan = mf(utils.make_mol(smis[0], keep_h=False, add_h=False))
      [3](vscode-notebook-cell:?execution_count=8&line=3) morgan.shape, morgan

File <string>:6, in __init__(self, atom_featurizer, bond_featurizer, extra_atom_fdim, extra_bond_fdim, fp_size)

TypeError: MorganFingerprintMoleculeFeaturizer.__post_init__() takes 1 positional argument but 3 were given