Nexus: Generate PySCF inputs without template

[mcbennet]

Proposed changes

This PR extends pyscf_input.py to allow template-less workflows. The user can now specify a calculation object with variables that contain information about the run, e.g.

scf = generate_pyscf(
    identifier = 'scf',                           # log output goes to scf.out
    path       = 'h2o_ae_hf',               # directory to run in
    job        = job(serial=True),          # pyscf must run serially         
    system     = system,
    mole       = obj(                             # used to make Mole() inputs
        basis    = 'ccpvtz',
        symmetry = True,
        verbose       = 5,
        ),
    calculation = obj(                          # used to specify run parameters
        method      = 'RHF',
        df_fitting  = True,
        max_cycle  = 200,
        level_shift  = 0.0,
        xc         = 'pbe',
        tol        = '1e-10',
        chkfile    = 'H2O.chk'
        ),
    save_qmc   = True ,
    )

What type(s) of changes does this code introduce?

• New feature

Does this introduce a breaking change?

• No. All nxs-test tests pass.

What systems has this change been tested on?

Laptop

Checklist

• This PR is up to date with current the current state of 'develop'
• N/A. Code added or changed in the PR has been clang-formatted
• This PR adds tests to cover any new code, or to catch a bug that is being fixed
• Documentation has been added (if appropriate)

[qmc-robot]

Can one of the admins verify this patch?

[jtkrogel]

Please add a unit test for input generation in tests/unit/test_pyscf_input.py, function test_generate. You should be able to just copy and then generalize an existing test, now including the calculation input and any others added.

[mcbennet]

Thank you, Jaron. Unit tests have been added and I have addressed all your comments above.

[jtkrogel]

LGTM

[ye-luo]

Test this please