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MDAnalysis / mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.
https://mdanalysis.org
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Type Hints for Analysis Classes #3463

Open PicoCentauri opened 3 years ago

PicoCentauri commented 3 years ago

Is your feature request related to a problem?

With the first version of the CLI released, we now would like to support more Analysis classes. This is especially limited to classes taking lists as parameters as the InterRDF_s

https://github.com/MDAnalysis/mdanalysis/blob/735abb8c76d71e1dc8197d73ee6f5d1845634914/package/MDAnalysis/analysis/rdf.py#L429-L447

where ags is a list of AtomGroups. For building the CLI we have to know the variable type. For example, what is the type of the list elements. The current implementation does not allow this. To overcome this issue we could introduce type hints as they were discussed in issues previously.

Describe the solution you'd like

Adding type hints to the Analysis classes. Type hints can be easily extracted using the typing module

typing.get_type_hints(InterRDF_s.__init__)

Describe alternatives you've considered

Be more precise in the docstring about parameter types. Similar to type hints but only (or maybe additionally) in the docstring.

orbeckst commented 3 years ago

From which version of Python onwards is type hinting supported?

How does this fit into the current roadmap/NEP29 ?

cc @IAlibay

lilyminium commented 3 years ago

3.5, I think 3.7 is when it got a lot better, and numpy.typing is only supported from 1.20.0 onwards, which is IIRC 3.7+.

IAlibay commented 3 years ago

So 2.1.0 is going to be 3.7+ but according to NEP29, we don't drop 1.19 until June 2022 (see: https://numpy.org/neps/nep-0029-deprecation_policy.html#drop-schedule).

I would be in favour of waiting until we can fully use numpy's typing functionality (rather than implementing something now and then redoing it later). That being said, if bits of the API can start to be typed without hurting other bits then that's fine (as long as we keep detailed notes of the process and what needs doing!)

ALescoulie commented 2 years ago

Is this something we can work on now now? I think this would be a great feature for ease of use and avoiding strange errors.

IAlibay commented 2 years ago

Is this something we can work on now now? I think this would be a great feature for ease of use and avoiding strange errors.

I believe this is at least part of a propose GSoC project. Due to clashes regarding this it would be best to avoid at this point in time.

1krishnasharma commented 2 years ago

Hi, this is my first time with open source, I want to do Type hinting in this project. An example of my work is below. Example:- python code for addition function ->

def add_numbers(num1, num2): return num1 + num2 print(add_numbers(3, 5)) # 8

->type hinted code >

def add_number( int : num1 , int : num2) -> int : return num1+num2; print(add_numbers(3, 5)) # 8

Please tell me how can I start with the project

orbeckst commented 2 years ago

@1krishnasharma for questions about projects and Outreachy/GSOC please ask on the developer mailing list. Examples of how you would apply type hinting to MDAnalysis would go in your proposal/application.