Sync with Recursion remote

[lohedges]

This PR synchronises with changes from the Recursion remote.

[lohedges]

Seeing failed tests on various platforms (unexpected ones, i.e. not related to CI issue or missing Sire packages):

FAILED tests/IO/test_file_cache.py::test_file_cache_mol_nums - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Parameters/test_parameters.py::test_molecule_rename - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Parameters/test_parameters.py::test_acdoctor - Failed: DID NOT RAISE <class 'BioSimSpace._Exceptions._exceptions.ParameterisationError'>
FAILED tests/Sandpit/Exscientia/IO/test_file_cache.py::test_file_cache_mol_nums - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Sandpit/Exscientia/Parameters/test_parameters.py::test_molecule_rename - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Sandpit/Exscientia/Parameters/test_parameters.py::test_acdoctor - Failed: DID NOT RAISE <class 'BioSimSpace.Sandpit.Exscientia._Exceptions._exceptions.ParameterisationError'>
FAILED tests/Sandpit/Exscientia/Process/test_restart.py::test_process[Production-system-True] - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Sandpit/Exscientia/Process/test_restart.py::test_process[Production-system-False] - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Sandpit/Exscientia/Process/test_restart.py::test_process[Production-system_vel-True] - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Sandpit/Exscientia/Process/test_restart.py::test_process[Production-system_vel-False] - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Sandpit/Exscientia/Process/test_restart.py::test_process[Production-system_vel0-True] - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Sandpit/Exscientia/Process/test_restart.py::test_process[Production-system_vel0-False] - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Sandpit/Exscientia/Process/test_restart.py::test_process[Equilibration-system-True] - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Sandpit/Exscientia/Process/test_restart.py::test_process[Equilibration-system-False] - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Sandpit/Exscientia/Process/test_restart.py::test_process[Equilibration-system_vel-True] - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Sandpit/Exscientia/Process/test_restart.py::test_process[Equilibration-system_vel-False] - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Sandpit/Exscientia/Process/test_restart.py::test_process[Equilibration-system_vel0-True] - ValueError: could not convert string to float: 'Need both input and output files and formats.'
FAILED tests/Sandpit/Exscientia/Process/test_restart.py::test_process[Equilibration-system_vel0-False] - ValueError: could not convert string to float: 'Need both input and output files and formats.'
...

As always, this isn't reproducible locally. Will see if I can recreate the exact environment.

[lohedges]

Having looked back at the CI, these errors also appeared in #398, so they aren't unique to this PR.

[lohedges]

Ah, this is an issue with the updated ambertools package since antechamber no longer reports a version so the following code fails:

    version = float(string.split(":")[0])

I'll wrap this in a try/except block.

[lohedges]

I decided to just remove the version check since openff now automatically pulls in a pinned version of ambertools anyway. The original code was written when we just used the base openff packages and allowed the use of an external ambertools specified via AMBERHOME, which could be incompatible.

[lohedges]

This has fixed the ValueError exceptions reported above, but I'm still seeing the following error on Linux Python 3.10 and macOS Python 3.11:

   @pytest.mark.skipif(
        has_antechamber is False or has_tleap is False,
        reason="Requires AmberTools/antechamber and tLEaP to be installed.",
    )
    def test_acdoctor():
        """
        Test that parameterising negatively charged molecules works when acdoctor
        is disabled.
        """
    
        # Load the molecule.
        mol = BSS.IO.readMolecules(f"{url}/negative_charge.sdf")[0]
    
        # Make sure parameterisation fails when acdoctor is enabled.
>       with pytest.raises(BSS._Exceptions.ParameterisationError):
E       Failed: DID NOT RAISE <class 'BioSimSpace._Exceptions._exceptions.ParameterisationError'>

I assume that antechamber has been updated so that acdoctor is no longer required. It's annoying that this is platform dependent. It appears that older Python variants have newer versions on ambertools:

Linux Python 3.10 (fails):

ambertools:                       24.8-cuda_None_nompi_py310h1ac786c_100 conda-forge         

Linux Python 3.11 (works):

    ambertools:                       23.6-cuda_None_nompi_py311h4a53416_105 conda-forge         

Not sure if I should just pin ambertools for now (other issues have been reported elsewhere for other dependencies) or just skip the test for now. Annoyingly, as the other error has shown there's no way to determine the version of antechamber so we can't conditionally change the xfail based on the version.

[lohedges]

sander does report the version information, so maybe we could use that as a proxy, i.e.:

sander -v
sander: Version 24.0

[lohedges]

Bah, that works locally in a conda environment with ambertools23 and 24, but doesn't work in the CI since sander doesn't report any version info either. I'll just skip the test for now.