smiles extra and decorator for rdkit functions #200
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| return func(*args, **kwargs) | ||
| return wrapper | ||
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| @requires_rdkit |
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this is not code that is actually used, right?
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yes, just as a reference for @boopthesnoot
alphabase/peptide/smiles.py
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| @functools.wraps(func) | ||
| def wrapper(*args, **kwargs): | ||
| try: | ||
| from rdkit import Chem |
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is there another option to find out that the package is there, without actually importing it? this would avoid the side effect of this decorator
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also, this will only work if the imports are done within the functions not for top-level imports, right?
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You could use importlib.util.find_spec("rdkit") is not None which still invokes the import machinery to some degree.
On the second point, I think there is no way around this.
If you have a module level import you will always fail during initialization.
Maybe it's possible with some heavy import magic but I'm not aware.
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okay, but can we then not just catch the import error in the smiles module, and change it to the user-friendly error message?
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Yes, I prefer to catch ImportError once this module is imported
extra_requirements/smiles.txt
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| @@ -0,0 +1 @@ | |||
| rdkit>=2024.3.3 | |||
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What is the connection between this PR and #199 |
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If smiles is imported in many other modules, i think it is better to place rdkit in the main requirement |
This allows to install rdkit only when the smiles extra is defined.
All RDKit dependent functions will give a meaningfull error message if called: