Expose sire.convert functionality

[lohedges]

This PR exposes the new functionality from sire.convert through the BioSimSpace.Convert sub-package. I have also wrapped functionality to create molecules from SMILES strings, and have exposed this on all wrapped Sire objects, i.e. so you can do things like system.smiles() to get a list of SMILES strings for all molecules in the system.

The PR also resolves some minor formatting issues and typos in the documentation, fixes issue #8, and adds support for reading remote trajectory files, as discussed here.

Note that this PR currently requires functionality from the feature_rdkit2 branch of Sire, so I will cancel CI until this is ready. (We will also need a new Sire release, so this PR can be built against that version upwards.) Alternatively I have workarounds that will allow it to work with the current Sire devel, which could be removed at a later date. (Although I would need to disable certain functionality on Windows.)

Checklist

• I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
• I confirm that I have added a test for any new functionality in this pull request: [y]
• I confirm that I have added documentation (e.g. a new tutorial page or detailed guide) for any new functionality in this pull request: [y]
• I confirm that I have permission to release this code under the GPL3 license: [y]

Suggested reviewers:

@chryswoods

[chryswoods]

This all looks good :-)

[lohedges]

Thanks. I'll wait until the Sire devel build is done, then merge. The only thing that I had thought of was adding convenience functions to some of the wrapped Sire objects so that you can do .toRDKit(), etc. Perhaps I can just bind these automatically at import time by checking what's available in BioSimSpace.Convert.

Oh, does you merge include a release bump, since this PR won't work with the original RDKit feature? It should pull in the most recent package, but who knows. Once there is a new release I can update the Sire requirement.

[chryswoods]

No, sorry, I didn't do a version bump. I'll remove the old packages from anaconda.org though, as I want to try and keep it so that we only have one latest devel package available. I agree it may lead to some breakage for people using those packages, but that is the price of living on the bleeding edge ;-)