add sanitize arg in read_sdf

[Ishan-Kumar2]

Checklist:

• Add tests to cover the fixed bug(s) or the new introduced feature(s) (not needed).
• Added a news entry.
  • copy news/TEMPLATE.rst to news/my-feature-or-branch.rst) and edit it.

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[hadim]

Thank you @Ishan-Kumar2 for your contribution!

@maclandrol do you think it's usefull to propagate strictParsing as well?

[maclandrol]

@maclandrol do you think it's usefull to propagate strictParsing as well?

Aside from not validating the SDF definition, I am struggling to see use cases where strictParsing!=True would be useful.

^ On second thought, yes.

[Ishan-Kumar2]

Thanks for the feedback @maclandrol and @hadim
I have added the strictParsing arg and used the dm function for santisation.

I just checked that the sanitize_mol is causing the output to have a different address as the original molecule. This causes the GetPropsAsDict() function to not work and hence some of the tests fail. Is there a fix through which we can keep the old addresses?

[hadim]

Good catches, the props are lost during sanitize_mol. You could use dm.copy_mol_props or dm.set_mol_props.

[hadim]

I will let @maclandrol doing a last review and it should be fine.

Tests are failing because of the conflict in the doc dependencies not related to this PR. I just fixed it on master. @Ishan-Kumar2 can you rebase this PR on master and check whether the tests are passing or not?

[maclandrol]

See comment on sanitize_mol. Otherwise lgtm

[maclandrol]

Thanks @Ishan-Kumar2 for the awesome contribution !

[hadim]

Thanks for your contribution!!!