Remove nagl nbs from skipped notebooks

[lilyminium]

Opening this PR to see if the notebook rendering has been fixed. Related to openforcefield/openff-nagl#92

[github-actions]

This repository caches data generated from notebooks stored in other repositories in the _cookbook_data_* branches. Regenerating this cache takes about half an hour, so it is not done automatically in PRs. The current value of the cache from the main branch has been copied over to this PR's cache.

To regenerate the cache for this PR, create a comment on this PR consisting only of the string:

/regenerate-cache

[lilyminium]

/regenerate-cache

[github-actions]

A workflow has been dispatched to regenerate the cookbook cache for this PR.

• Run ID: 8374170234
• Triggering actor: github-actions[bot]
• Target branch: unskip-nagl-nbs
• Deployment branch: _cookbook_data_PR42

[Yoshanuikabundi]

The updated notebooks should need to be in a release on Conda Forge with a tag on GitHub before the cookbook can pick them up

[github-actions]

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

• Run ID: 8374170234
• Triggering actor: github-actions[bot]
• Target branch: unskip-nagl-nbs
• Deployment branch: _cookbook_data_PR42
• Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

[lilyminium]

Ah, thanks -- I just made a release with the docs fixes and am adding it to conda now, so hopefully it'll be live by tomorrow.

[Yoshanuikabundi]

/regenerate-cache

[github-actions]

A workflow has been dispatched to regenerate the cookbook cache for this PR.

• Run ID: 8383971298
• Triggering actor: github-actions[bot]
• Target branch: unskip-nagl-nbs
• Deployment branch: _cookbook_data_PR42

[github-actions]

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

• Run ID: 8383971298
• Triggering actor: github-actions[bot]
• Target branch: unskip-nagl-nbs
• Deployment branch: _cookbook_data_PR42
• Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

[lilyminium]

Ah... my examples CI is run with OpenEye, which might be why it works in NAGL and not here.

Would you consider adding OpenEye to the examples environment @Yoshanuikabundi or should I try to change examples to find a molecule that reliably works with AmberTools?

[lilyminium]

Although it looks like it's failing to generate charges for methane?! Edit: ok, that conformer is.... whacky

 ValueError: No registered toolkits can provide the capability "assign_partial_charges" for args "()" and kwargs "{'molecule': Molecule with name '' and SMILES '[H][C]([H])([H])[H]', 'partial_charge_method': 'am1-mulliken', 'use_conformers': [<Quantity([[ 6.25223582e+122 -1.86314103e+081  1.56369643e-096]
 [ 4.58367649e+225  3.07184515e+246 -1.82988079e-306]
 [-3.84059717e-237 -1.24119129e-267  9.87487490e+120]
 [-2.01772259e-030 -1.44408025e+199 -2.96194458e+131]
 [ 1.84149756e-157  3.19860209e+259 -6.10481269e+222]], 'angstrom')>], 'strict_n_conformers': False, 'normalize_partial_charges': True, '_cls': <class 'openff.toolkit.topology.molecule.Molecule'>}"
Available toolkits are: [ToolkitWrapper around The RDKit version 2023.03.3, ToolkitWrapper around AmberTools version 22.0, ToolkitWrapper around Built-in Toolkit version None]
 ToolkitWrapper around The RDKit version 2023.03.3 <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : partial_charge_method 'am1-mulliken' is not available from RDKitToolkitWrapper. Available charge methods are ['mmff94', 'gasteiger'] 
 ToolkitWrapper around AmberTools version 22.0 <class 'subprocess.CalledProcessError'> : Command '['antechamber', '-i', 'molecule.sdf', '-fi', 'sdf', '-o', 'charged.mol2', '-fo', 'mol2', '-pf', 'yes', '-dr', 'n', '-c', 'mul', '-nc', '0.0']' returned non-zero exit status 1.
 ToolkitWrapper around Built-in Toolkit version None <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : Partial charge method "am1-mulliken"" is not supported by the Built-in toolkit. Available charge methods are ['zeros', 'formal_charge']

[lilyminium]

/regenerate-cache

[github-actions]

A workflow has been dispatched to regenerate the cookbook cache for this PR.

• Run ID: 8384341730
• Triggering actor: github-actions[bot]
• Target branch: unskip-nagl-nbs
• Deployment branch: _cookbook_data_PR42

[github-actions]

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

• Run ID: 8384341730
• Triggering actor: github-actions[bot]
• Target branch: unskip-nagl-nbs
• Deployment branch: _cookbook_data_PR42
• Status: failure

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

[Yoshanuikabundi]

We'd really rather stick to freely available software in the examples environment - it's provided to users as the recommended way to run these notebooks and also used in Colab, and we want to make that process as smooth as possible. Sorry about that!

[lilyminium]

Makes sense -- I've removed it from my examples environment and made another release with a bug fix for RDKit.

[lilyminium]

/regenerate-cache

[github-actions]

A workflow has been dispatched to regenerate the cookbook cache for this PR.

• Run ID: 8390426520
• Triggering actor: github-actions[bot]
• Target branch: unskip-nagl-nbs
• Deployment branch: _cookbook_data_PR42

[github-actions]

A workflow dispatched to regenerate the cookbook cache for this PR has just finished.

• Run ID: 8390426520
• Triggering actor: github-actions[bot]
• Target branch: unskip-nagl-nbs
• Deployment branch: _cookbook_data_PR42
• Status: success

If the workflow was successful, changes will only be visible in the ReadTheDocs preview after it has been rebuilt.

[Yoshanuikabundi]

Awesome! Thanks for doing this so promptly!