Add Eriks updates: experimental state-space-setting framework; lots of little fixes

enielse commented 10 months ago

A number of accumulated minor fixes along with one experimental feature to allow setting a model member's state space labels. This updates modelmember.py, composedop.py, and embeddedop.py and is an experimental feature that hasn't been fully tested yet. In particular, caches of representation objects will need to be cleared in the forward simulator and/or model to get the approach to work robustly.

Aside from this, the main fixes are:

computes initial score of forced germs before beginning germ selection iterations so the routine will just exit if the forced germs are amplificationally complete.
fixes a Label renaming bug, mostly likely to be encountered when renaming a gate in a Circuit.
fixes to MongoDB serialization related to serializing strings and circuits.
adds verbosity argument to ConfidenceRegionFactory.project_hessian
adds ability to specify gaugeopt_suite=None to indicate no gauge optimization should be performed when constructing GST and model test protocol objects.
when constructing computing reference values for 1D wildcard error, adds fallback to use the trace distance in place of the diamond distance if the latter computation fails.
fixes a few minor things in the reports: guards Gram matrix failure, argument ordering fix related to constructing a report with wildcard error.
adds additional include directories in setup.py when building cython extensions. I think these are needed to build on some platforms, maybe M1 macs (?).

sserita commented 10 months ago

Thanks for the quick PR @enielse!

sserita commented 9 months ago

Hi Bas,

No worries, this branch will be staying up for now. I’ll urge to migrate over to pygsti 0.9.12 when it makes sense as it includes these bugfixes and many more, but I realize that is a process for many of our users.

I’ll also mention that at some point this branch will likely just be active in a fork of pyGSTi, but exactly what that looks like is TBD in the near future as we reorganize how we manage the repository.

-- Stefan K. Seritan

From: Bas Nijholt @.> Date: Wednesday, December 13, 2023 at 10:30 AM To: sandialabs/pyGSTi @.> Cc: Seritan, Stefan Kelley @.>, State change @.> Subject: [EXTERNAL] Re: [sandialabs/pyGSTi] Add Eriks updates: experimental state-space-setting framework; lots of little fixes (PR #375)

Would it be possible to leave to branch up for a little while? We've internally pinned some stuff to this branch and not all of that broke 😭

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sandialabs / pyGSTi

Add Eriks updates: experimental state-space-setting framework; lots of little fixes #375