Add support for openff-nagl for generation of partial charges

[lohedges]

This PR adds support for using openff-nagl to generate partial charges during parameterisation. Rather than adding openff-nagl as a hard dependency, I decided to check for availability at runtime and selectively use it if available. The user can choose to disable NAGL when calling an OpenFF parameterisation function using use_nagl=False, in which case it will use AmberTools. To activate the feature, a user should only need to install openff-nagl-base and openff-nagl-models on top of the base BioSimSpace environment. Thankfully these are pinned against specific versions of openff-toolkit, so we should always be able to resolve a compatible environment. (The full openff-nagl package pulls in over 2GB of dependencies, so it is desirable to exclude it if it's not absolutely necessary.)

• 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

[lohedges]

All CI has started failing with:

Run conda mambabuild -c conda-forge -c openbiosim/label/dev /home/runner/work/biosimspace/biosimspace/biosimspace/recipes/biosimspace
Traceback (most recent call last):
  File "/home/runner/miniconda3/envs/bss_build/bin/conda-mambabuild", line 6, in <module>
    from boa.cli.mambabuild import main
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/boa/cli/mambabuild.py", line 21, in <module>
    from boa.core.solver import MambaSolver
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/boa/core/solver.py", line 7, in <module>
    from boltons.setutils import IndexedSet
ModuleNotFoundError: No module named 'boltons'

Looks like boa is missing a dependency. Bah.

[lohedges]

Okay, manually adding boltons to our CI dependencies didn't fix things:

Traceback (most recent call last):
  File "/home/runner/miniconda3/envs/bss_build/bin/conda-mambabuild", line 10, in <module>
    sys.exit(main())
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/boa/cli/mambabuild.py", line 301, in main
    call_conda_build(action, config)
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/boa/cli/mambabuild.py", line 273, in call_conda_build
    result = api.build(
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/conda_build/api.py", line 253, in build
    return build_tree(
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/conda_build/build.py", line 3799, in build_tree
    packages_from_this = build(
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/conda_build/build.py", line 2469, in build
    output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)])
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/conda_build/render.py", line 923, in expand_outputs
    for output_dict, m in deepcopy(_m).get_output_metadata_set(
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/conda_build/metadata.py", line 2565, in get_output_metadata_set
    conda_packages = finalize_outputs_pass(
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/conda_build/metadata.py", line 909, in finalize_outputs_pass
    fm = finalize_metadata(
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/conda_build/render.py", line 637, in finalize_metadata
    build_unsat, host_unsat = add_upstream_pins(
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/conda_build/render.py", line 452, in add_upstream_pins
    build_deps, build_unsat, extra_run_specs_from_build = _read_upstream_pin_files(
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/conda_build/render.py", line 431, in _read_upstream_pin_files
    deps, actions, unsat = get_env_dependencies(
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/conda_build/render.py", line 151, in get_env_dependencies
    actions = environ.get_install_actions(
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/boa/cli/mambabuild.py", line 180, in mamba_get_install_actions
    link_precs = mamba_get_package_records(
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/boa/cli/mambabuild.py", line 142, in mamba_get_package_records
    _, link_precs = solver.solve_for_unlink_link_precs(_specs, prefix)
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/boa/core/solver.py", line 252, in solve_for_unlink_link_precs
    return to_unlink_link_precs(
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/boa/core/solver.py", line 87, in to_unlink_link_precs
    unlink_precs, link_precs = diff_for_unlink_link_precs(
  File "/home/runner/miniconda3/envs/bss_build/lib/python3.9/site-packages/conda/core/solve.py", line 1152, in diff_for_unlink_link_precs
    assert isinstance(final_precs, IndexedSet)
AssertionError

Presumably boa is broken, or incompatible with the version of conda / conda-bulild. I'll leave until tomorrow. (Fingers crossed it will be magically fixed overnight.)

[lohedges]

It's a sad day when the solution to conda hell is now broken.

[chryswoods]

This looks good. I like that we don't depend on nagl_models being installed, and that we check at runtime. This is a pattern I am increasingly using in sire. R has a concept of "suggests" with run-time checking for dependencies which is similar.

Good spot that the miniconda-setup recipe has gone up a version. Thanks to this PR I've now bumped the version in sire.

The merge-base changed after approval.