[WIP] quickrun result error inspection command

[dwhswenson]

Clean version of #491. Repeating description from that:

This adds an inspect-result command to the CLI, which takes a result JSON file and outputs some basic information on each unit.

The information included here can definitely be expanded later (timings, possibly more details on simulation parameters, etc). But I thought it was most urgent to get error messages out.

Here's an example output from an edge that had a NaN failure:

$ openfe inspect-result easy_rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json
This edge was a SUCCESS.
This edge consists of 4 units.

Unit ProtocolUnitResult-e8e4c380537f4bfd89639cf52b8a8b95 ran successfully.

Unit ProtocolUnitFailure-4c981804da4c40b198d7fc310401c755 failed with an error:
SimulationNaNError: Propagating replica 1 at state 1 resulted in a NaN!
The state of the system and integrator before the error were saved in results/easy_rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent/shared_RelativeHybridTopologyProtocolUnit-60df96a488094f63978880d19487d299_attempt_0/nan-error-logs
Traceback (most recent call last):
  File "/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/multistate/multistatesampler.py", line 1326, in _propagate_replica
    mcmc_move.apply(thermodynamic_state, sampler_state, context_cache=self.sampler_context_cache)
  File "/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/mcmc.py", line 1151, in apply
    super(LangevinDynamicsMove, self).apply(thermodynamic_state, sampler_state,
  File "/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/mcmc.py", line 755, in apply
    raise IntegratorMoveError(err_msg, self, context)
openmmtools.mcmc.IntegratorMoveError: Potential energy is NaN after 20 attempts of integration with move LangevinDynamicsMove

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/gufe/protocols/protocolunit.py", line 308, in execute
    outputs = self._execute(context, **inputs)
  File "/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openfe/protocols/openmm_rfe/equil_rfe_methods.py", line 674, in _execute
    outputs = self.run(scratch_basepath=ctx.scratch, shared_basepath=ctx.shared)
  File "/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openfe/protocols/openmm_rfe/equil_rfe_methods.py", line 617, in run
    sampler.equilibrate(int(equil_steps / mc_steps))  # type: ignore
  File "/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/multistate/multistatesampler.py", line 696, in equilibrate
    self._propagate_replicas()
  File "/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/utils/utils.py", line 95, in _wrapper
    return func(*args, **kwargs)
  File "/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/multistate/multistatesampler.py", line 1299, in _propagate_replicas
    propagated_states, replica_ids = mpiplus.distribute(self._propagate_replica, range(self.n_replicas),
  File "/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/mpiplus/mpiplus.py", line 523, in distribute
    all_results = [task(job_args, *other_args, **kwargs) for job_args in distributed_args]
  File "/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/mpiplus/mpiplus.py", line 523, in <listcomp>
    all_results = [task(job_args, *other_args, **kwargs) for job_args in distributed_args]
  File "/lila/home/henrym3/micromamba/envs/openfe-0.10.1/lib/python3.10/site-packages/openmmtools/multistate/multistatesampler.py", line 1337, in _propagate_replica
    raise SimulationNaNError(message)
openmmtools.multistate.utils.SimulationNaNError: Propagating replica 1 at state 1 resulted in a NaN!
The state of the system and integrator before the error were saved in results/easy_rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent/shared_RelativeHybridTopologyProtocolUnit-60df96a488094f63978880d19487d299_attempt_0/nan-error-logs


Unit ProtocolUnitResult-3be6df093b0e4f61ad443dc966595621 ran successfully.

Unit ProtocolUnitResult-5ea0dbdc7ee94e86a547f66e421adb95 ran successfully.

Still needs tests, so that'll come after review comments on output.

[codecov]

Codecov Report

Attention: 22 lines in your changes are missing coverage. Please review.

Comparison is base (5f4cc01) 91.40% compared to head (9700c71) 91.19%.
Report is 1 commits behind head on main.

Files	Patch %	Lines
openfecli/commands/inspect_result.py	31.25%	22 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #492      +/-   ##
==========================================
- Coverage   91.40%   91.19%   -0.22%     
==========================================
  Files         132      133       +1     
  Lines        9109     9141      +32     
==========================================
+ Hits         8326     8336      +10     
- Misses        783      805      +22     

Flag	Coverage Δ
fast-tests	91.19% <31.25%> (-0.22%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[RiesBen]

Hi this is a neat idea!
is is possible to throw in a regex for files and directly geht a summary for multiple edges as well?

[pep8speaks]

Hello @dwhswenson! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file openfecli/commands/inspect_result.py:

Line 7:1: E302 expected 2 blank lines, found 1
Line 19:1: E302 expected 2 blank lines, found 1
Line 45:1: E305 expected 2 blank lines after class or function definition, found 1