Feature web (a.k.a. BioSimSpace 2023.0.0)

[chryswoods]

This is the update of BioSimSpace that is compatible with Sire 2023.0.0.

The changes are minimal, i.e. updating to using the new (PEP8) module names of sire (but not the PEP8 function names - hence why sire.use_mixed_api() is used).

The other changes are to the build system. This now mirrors sire's updated build system. This supports building Windows packages, plus gives more control over the dependency relationship between BioSimSpace and Sire.

This won't pass its tests until Sire 2023.0.0 is available.

[lohedges]

Okay, I've made a few edits to remove some redundant imports and tidy some comments. One thing that I've noticed is that a search with no results now raises a ValueError, rather than giving an empty SelectResult, i.e. one with zero results. There are a few places in BioSimSpace where we perform a search then check that search.nResults() == 0. I'll need to go through and replace these with appropriate try/except blocks.

(The new behaviour makes more sense to me, since it is good to know that a search is empty/invalid immediately.)

[lohedges]

Bah, it turns out that the behaviour is inconsistent, i.e. it sometimes returns an empty search if the string is valid but there is no result, but sometimes returns a ValueError. For example:

# Search for an unknown element.
system.search("element Z")

ValueError: 'Invalid search query: 'element Z' : SireMol::parse_error: Failed to parse any of the selection 'element Z'. (call sire.error.get_last_error_details() for more info)

# Search for a valid element, using an invalid property map.
system.search("element H", property_map={"element" : "cheese"})

ValueError: 'Invalid search query: 'element H' : 'Nothing matched the search.'

# Now the same thing on the first molecule in the system.

# Search for an invalid element.
molecule.search("element Z")
# Same error as before.
ValueError: 'Invalid search query: 'element Z' (SireMol::parse_error: Failed to parse any of the selection 'element Z'. (call sire.error.get_last_error_details() for more info))

# Search for a valid element, using an invalid property map.
molecule.search("element H", property_map={"element" : "cheese"})

# No error, rather an empty result is returned.
<BioSimSpace.SearchResult: nResults=0>

I'll try to figure out why this is, since we need the behaviour to be consistent.

[lohedges]

Ah, this is because BioSimSpace._SireWrappers.Molecule.search() returns an empty result when the search fails, whereas the other wrappers raise the exception:

        try:
            # Query the Sire molecule.
            search_result = query(self._sire_object, property_map)
        except KeyError:
            # Nothing matched - return an empty result
            search_result = _SireMol.SelectorMol()

I'll change this for consistency.

[lohedges]

Okay, I've needed to make quite a few edits to handle the new search functionality. However, it looks like the existing searches used to find atoms when applying different types of restraint (using system.getRestraintAtoms()) are no longer valid. I'll need to work out why this is, then adapt the search strings to whatever the equivalent is for Sire 2023.0.0. (I'll also add some tests so that validate the various restraint search terms that we allow.)

(Definitely highlighting a lack of unit tests in certain areas where functionality was blasted out for a workshop.)

[lohedges]

This is now fixed. There were some issues with formatting for combining searches via a logical and. We also no longer need to do searches like atoms in ... since atoms are returned by default.