Add Xopt and Optimas generator tests

[shuds13]

Add tests for these Xopt generators

Generator: Baysian (Expected Improvement)
Gen: https://github.com/xopt-org/Xopt/blob/generator_standard/xopt/generators/bayesian/expected_improvement.py

Xopt tests: https://github.com/xopt-org/Xopt/blob/generator_standard/xopt/tests/generators/bayesian/test_expected_improvement.py

Generator: Sequential (neldermead)
Gen: https://github.com/xopt-org/Xopt/blob/generator_standard/xopt/generators/sequential/neldermead.py

Xopt tests: https://github.com/xopt-org/Xopt/blob/generator_standard/xopt/tests/generators/sequential/test_neldermead.py

To check

• Xopt Expected Improvement test (with libE sim and with gest-api sim)
• Xopt Sequential (neldermead) test - Fixed self.future_state is None error
• Need to merge in Remove automapping #1622 into this branch - removing auto-conversions that we dont want.
• Also adding gest_api_wrapper sim func so xopt/gest-api style sims can be used directly
• Check for TODO notes
• Make sure xopt dependency in CI files (test or extra tests) and run full tests
• Add xopt generator notebook and tutorial in docs
• Enable pass-through of executor and user_specs to gest-api sim
• Add forces variant using xopt generator.

Deferred to #1634
- [ ] Currently fixing nworkers to batch_size. Change to run using test harness command line settings.
- [ ] Re-enable running of full tests (REG_TEST_LIST = "test_*.py") - currently only runs new tests.

Optimas generators

• GridSamplingGenerator based on Optimas test test_grid_sampling.py

Deferred to #1634
- [ ] Ax Generators (single/multi-fidelity / multitask). - Unexpected vars from suggest (not in H array).

Set GenSpecs / SimSpecs by vocs

This highlights need for GenSpecs/SimSpecs to be settable by vocs to prevent repetition. This should also use dtypes if they are set.

e.g.

    gen_specs = GenSpecs(
        generator=gen,
        batch_size=batch_size,
        vocs=vocs,
    )

For vocs settings:

• Add vocs option to GenSpecs
• Add vocs option to SimSpecs
• Make sure handles types correctly (from vocs objects - defaulting to float)
• Check does not result in bypassing any validation (currently none to bypass)
  - [ ] For libE gens with user specs it should set lb/ub from vocs also (defer Make set_fields_from_vocs set bounds when required. #1621)
• Make unit test for this feature.

Note that if generator.vocs storage of vocs was in the standard, we could take from the gen, and not even need to supply vocs here (better SSoT).

[shuds13]

On first run I get:

  File "/home/shudson/libensemble/libe_vocs_xopt_fixes/libensemble/utils/runners.py", line 54, in run
    return self._result(calc_in, Work["persis_info"], Work["libE_info"])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/shudson/libensemble/libe_vocs_xopt_fixes/libensemble/utils/runners.py", line 160, in _result
    return self._persistent_result(calc_in, persis_info, libE_info)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/shudson/libensemble/libe_vocs_xopt_fixes/libensemble/utils/runners.py", line 149, in _persistent_result
    self._get_initial_suggest(libE_info),
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/shudson/libensemble/libe_vocs_xopt_fixes/libensemble/utils/runners.py", line 136, in _get_initial_suggest
    H_out = self.gen.suggest(initial_batch)
            ^^^^^^^^^^^^^^^^
AttributeError: 'dict' object has no attribute 'suggest'

Looks like this is due to going via standard runner, while libE gest-api generators go via subclasses.

Fix: This was due to generator being converted to dictionary in libE (given that xopt gen is a pydantic model). I now restore the original in that case.

[codecov]

Codecov Report

❌ Patch coverage is 49.09091% with 56 lines in your changes missing coverage. Please review.
✅ Project coverage is 47.95%. Comparing base (41a4cbc) to head (589d8fb).
⚠️ Report is 52 commits behind head on experimental/jlnav_plus_shuds_asktell.

Files with missing lines	Patch %	Lines
libensemble/sim_funcs/gest_api_wrapper.py	0.00%	30 Missing ⚠️
libensemble/specs.py	71.42%	13 Missing and 7 partials ⚠️
libensemble/generators.py	0.00%	2 Missing ⚠️
libensemble/libE.py	0.00%	1 Missing and 1 partial ⚠️
libensemble/utils/runners.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@                            Coverage Diff                             @@
##           experimental/jlnav_plus_shuds_asktell    #1620       +/-   ##
==========================================================================
- Coverage                                  78.73%   47.95%   -30.78%     
==========================================================================
  Files                                         79       80        +1     
  Lines                                       7993     8079       +86     
  Branches                                    1196     1222       +26     
==========================================================================
- Hits                                        6293     3874     -2419     
- Misses                                      1481     3985     +2504     
- Partials                                     219      220        +1     

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[jlnav]

VOCS has a VOCS.output_names property that may be usable here. Perhaps VOCS could use an .input_names property too.