Initial implementation of checkpointing for GST. This initially implementation targets the GateSetTomography protocol specifically and future updates will add support for additional protocols. To support the checkpointing functionality a new generator function version of the iterative GST algorithm has been implemented to enable lazy evaluation. This commit also introduces a new ProtcolCheckpoint parent class and the GateSetTomographyCheckpoint class. Each protocol requires a somewhat different set of information to enable it to checkpoint properly during runtime, so the current vision is that each protocol will have a specialized checkpoint object associated with it.

Minor revision to restructure some of the control logic for the checkpointing.

An initial implementation of checkpointing for model testing. This really only saves intermediate objective function values, as that was all I identified that was either a) computationally worth checkpointing or b) safe to checkpoint given concerns about being independent of layout specific configuration details in resource alloc etc.

This commit adds an initial implementation of the StandardGSTCheckpointing object and it's use in the StandardGST protocol. Also includes a few bug fixes for the implementations of GateSetTomographyCheckpoint and ModelTestCheckpoint. The idea behind the implementation of the StandardGSTCheckpoint is to treat it as a container for some number of checkpoint objects for each of the sub-protocols run during StandardGST. To facilitate this I have also added a 'parent' attribute to the base ProtocolCheckpoint object to enable a link between child objects and their parents. This is primarily used at present to swap the child's write method with that of the parent's (which invokes the parent's serialization instead) when a parent checkpoint is present. Bugfixes were related to a mistake in using mutable objects as default kwarg values.

The old behavior for the modes argument is kind of wonky and doesn't have any analogues in the code that I can recall. This switches the argument to take either an iterable or a single string (i.e. for specifying a single-mode), and adds a deprecation warning about the comma-separated version.

Properly manage file access for MPI compatibility.

Updates the docstrings for new checkpointing functionality.

Adds in the plumbing for passing in checkpoint objects to the driver function based interface.

When this is set to True checkpoint objects are neither created nor written to disk. If there are values passed in for the checkpoint and checkpoint_path kwarg these are ignored entirely.

This adds some unit tests for the checkpointing functionality. Decided to add this to the drivers test package for simplicity. Only test we may want to revisit is for the StandardGSTCheckpoint, which uses log-likelihoods temporarily due to unexpected sign behavior with CPTPLND parameterized models. May also want to add tests for when checkpoints are disabled and such, but then that is already largely covered already. Also refactored a few other tests to bring them in line with the recent deprecations of comma-separated strings for modes on StandardGST.

Update tutorial notebooks to reflect new StandardGST syntax.

I was inadvertently using a method that is only in pathlib for 3.9+, switch to a call that is compatible with older versions.

Pretty sure this is a false positive in flake8, not sure why else there would be a syntax error...

Remove errant print statement from test file (which incidentally breaks on older versions of python).

I seem to have added this file by accident...

Add sections on checkpointing an its usage to the tutorials on GST and model testing protocols. Also makes a minor change to one of the unit tests that is inexplicably failing on older python versions.

Remove some of the disable_checkpointing flags I had added to the earlier parts of the of updated tutorials. I am still concerned we might run into file access collisions since we're running the notebook test suite with multiple processes, but I am more worried about accidentally shaping user behavior negatively. Most of our users will copy and paste directly from the tutorials and assume the disable_checkpointing flags are important/needed, and that is worse than weird testing behavior to debug.

Bugfix and refactoring for deprecated mode labels.

Fix minor typo in updated label

Refactor run_iterative_gst to use the new iterative_gst_generator generator function under the hood to avoid code duplication.

Add a new test for warmstarting of iterative_gst_generator.