Xopt integration by roussel-ryan · Pull Request #318 · bluesky/blop

roussel-ryan · 2026-06-04T19:57:35Z

This pull request adds support for integrating the Xopt optimization library into blop, introducing a new agent, optimizer, and mapping utilities, along with comprehensive tests for these components. The changes enable users to use Xopt Generator objects within the existing framework, and ensure robust mapping and interaction between the framework's abstractions and Xopt's API.

This PR should serve as a starting point for discussing Xopt integration into blop or bluesky-adaptive (bluesky/bluesky-adaptive#61).

The most important changes are:

Xopt Integration:

Added XoptAgent, XoptOptimizer, and build_vocs to the codebase, providing a new agent and optimizer that wrap Xopt generators and a utility for mapping framework abstractions to Xopt's VOCS format (src/blop/xopt/agent.py, src/blop/xopt/optimizer.py, src/blop/xopt/mapping.py, src/blop/xopt/__init__.py). [1] [2]
Made the new Xopt components available at the top-level API by importing them in src/blop/__init__.py and adding them to __all__. [1] [2]

Dependency Management:

Added xopt as an optional dependency in pyproject.toml to enable Xopt-based optimization.

Testing and Validation:

Added comprehensive tests for the Xopt agent (test_agent.py), optimizer (test_optimizer.py), and VOCS mapping (test_mapping.py), covering initialization, suggestion, ingestion, checkpointing, constraint handling, and error cases. [1] [2] [3]

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Checkmarx found the following issues in this Pull Request

#	Severity	Issue	Source File / Package	Checkmarx Insight
1		Deserialization_of_Untrusted_Data	src/blop/xopt/optimizer.py: 49	details The serialized object stream processed in in the file /src/blop/xopt/optimizer.py at line 49 is deserialized by load in the file /src/blop/xopt/o... `ID: rrz2NO86clojLL1mHn8JwmtiXOE%3D` Attack Vector

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roussel-ryan · 2026-06-05T14:35:53Z

Note: after discussion, I will refactor this PR to not do automatic conversion to VOCS parlance and just pass the generator object to an optimizer

roussel-ryan · 2026-06-05T15:50:10Z

@thopkins32 so it looks like we need to make a decision since the more recent versions of botorch (.v0.17.0) require python >=3.11 meaning that Xopt does the same, how do you think we should resolve this? I could potentially re-enable support 3.10, but only if this is something you all think is necessary

thopkins32 · 2026-06-05T17:28:48Z

@roussel-ryan I will open a separate issue to remove Python 3.10 support, feel free to do that in this PR for now to unblock

whs92 · 2026-06-06T08:46:15Z

Can you give a quick overview of the advantages of using Xopt over AX? Why might I use one or the other? Or is there just an existing community using Xopt that we want to serve?

roussel-ryan · 2026-06-07T18:08:28Z

Hi, there are several advantages to using Xopt over Ax for blop, primarily due to our focus on R&D towards accelerator / beam physics, however we do not intend to replace Ax completely. Some of the reasons:

Xopt supports other optimization algorithms that can be used for online operation / optimization including Simplex, RCDS, Extremum Seeking, Genetic algorithms, and multiple variants of BO (most based on botorch, just as Ax is). We will shortly be adding methods for Reinforcement Learning and algorithms provided by scipy minimize
We have added features to BO that are not included out of the box in Ax as it is currently implemented in blop, including first class support for trust region BO, time-dependent / contextual BO, multi-fidelity BO, interpolated measurements etc. (see https://journals.aps.org/prab/abstract/10.1103/PhysRevAccelBeams.27.084801)
Xopt is wrapped by Badger https://github.com/xopt-org/Badger which provides a GUI interface for running optimization in control rooms. Utilizing Xopt generators in blop takes a step forward for creating a GUI that works for blop
The same algorithms provided by Xopt used in online control via blop can be easily applied towards simulations and arbitrary problems, improving consistent use of algorithms across problems for users

Finally, supporting Xopt in blop more closely connects R&D efforts in accelerators and photon beamlines, allowing developments in one field to benefit the other. This PR is motivated by discussions this past week at the DSSI workshop for autonomous beamline control at BNL with @thopkins32 @tacaswell @mrakitin and others

whs92 · 2026-06-08T13:18:47Z

@roussel-ryan I am particularly interested in adding context to optimization. Thanks for your explanation.

roussel-ryan · 2026-06-08T14:41:25Z

Good to hear, please keep an eye on xopt-org/Xopt#425 which should be in the next release

whs92 · 2026-06-08T14:55:20Z

As far as I know adding additional observations for context was already supported by the earlier pre-AX version of blop. Whatever we come up with, blop should abstract away the differences (if they exist) between the different back ends so that if I want to provide context (or anything else) I shouldn't care whether I am talking to AX or XopT in the background.

roussel-ryan · 2026-06-08T15:11:48Z

Based on previous discussions, we wanted to try to keep the Ax/Xopt interfaces separate (see previous comments above) and not include a translation layer to unify the interfaces to the user. I think we should discuss this further, but it may be a good initial step to get Xopt support capability integrated into blop first and then work on improving the user interface. I want to hear other folks opinions on the matter

roussel-ryan · 2026-06-08T15:52:31Z

I've addressed all the issues on my side, I didn't make any changes to tutorials/xrt-kb-mirrors.md so I think that might be an issue that you all want to work on

thopkins32

Initial review done. I'll follow up with a more in-depth one after I get clarification on one point.

thopkins32 · 2026-06-08T19:36:52Z

+        self._next_id = 0
+        self._params_by_id: dict[int | str, dict[str, Any]] = {}
+        self._seed_state_from_existing_data()


Looking at the Xopt docs, is the data frame index of self._generator.data something we can use instead of doing ID tracking in Blop? I don't want to duplicate state tracking here if Xopt already has a mechanism for this.

The reason we have an ID associated with every suggestion is that when we evaluate multiple points in a single optimizer iteration (e.g., RE(optimize(..., n_points=5))) we may have a more optimal sampling route than the default order provided by the optimizer. Bluesky always emits events in the order they were collected (and we cache this reordering information in the Bluesky metadata). Therefore, to match Bluesky's event/collection order with the optimizer suggestion order, we need to track IDs for each suggestion.

I would keep the ID tracking in Blop, certainly for now, but going forward as well. I think Xopt may adopt a more formal ID tracking formalism. Certainly we shouldn't hold up this PR to decide this IMO

thopkins32 · 2026-06-08T19:41:38Z

Also, I merged the change removing Python 3.10 support if you would like to rebase or merge main into this branch.

roussel-ryan

add tutorial (see https://github.com/bluesky/blop/blob/main/docs/source/tutorials/xrt-kb-mirrors.md)

roussel-ryan · 2026-07-20T14:28:15Z

@whs92 just as a followup the most recent version of Xopt (3.2.0) now supports contextual BO (see https://xopt.xopt.org/examples/single_objective_bayes_opt/contextual_bo/ for an example)

commit 39b6afc Merge: 2441457 9bcc903 Author: MTakahashi-KWH <60798296+MTakahashi-KWH@users.noreply.github.com> Date: Thu Jul 23 12:37:56 2026 -0400 Merge pull request bluesky#331 from bluesky/contributing Add CONTRIBUTING.md commit 9bcc903 Author: thomashopkins32 <thopkins1@bnl.gov> Date: Thu Jul 23 10:40:12 2026 -0400 pre-commit commit 2b68d8a Author: thomashopkins32 <thopkins1@bnl.gov> Date: Thu Jul 23 10:39:51 2026 -0400 Updated Review and Merge Policy; Types of Changes section commit 2441457 Author: josephhanrahan <79729091+josephhanrahan@users.noreply.github.com> Date: Wed Jul 22 14:36:00 2026 -0400 move queueserver_agent testcases to new test module (bluesky#332) commit 1fee80a Author: thomashopkins32 <thopkins1@bnl.gov> Date: Wed Jul 22 14:07:09 2026 -0400 Add CONTRIBUTING.md commit c2332cf Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Wed Jul 22 13:38:41 2026 -0400 Set checkpoint path after init on Ax agent and optimizer (bluesky#327) commit 0a75969 Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Wed Jul 22 13:34:21 2026 -0400 Add checkpointing to queueserver runner (bluesky#328) * Add checkpointing to queueserver runner * Add checkpoint_interval argument to QueueserverAgent.run commit 70468ab Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Thu Jul 16 15:43:52 2026 -0400 Final edits before v1.0 release (bluesky#324) * Cleaned up all docstrings and other misc items * Add release history for v1.0.0 * Add deployments page * Add docs on callbacks * Update timepix3 description commit 9e0f135 Author: Ryan Roussel <rroussel@slac.stanford.edu> Date: Thu Jul 9 11:36:34 2026 -0700 Xopt integration (bluesky#318) * initial commit * add tests * Update test_optimizer.py * linting * linting * inline comments * refactor code to only define an XoptOptimizer class * linting * solving pre-commit issues * change code to native xopt vocs methods * remove python 3.10 * linting * Update test_optimizer.py * add tests for coverage * Update pyproject.toml * linting * create RunEngine test and random initial point generation * remove fixed parameters in favor of VOCS constants * utilize pydantic serialization, fix ingest append/insert issues * code simplification /modernization * additional code simplification * linting * Update xrt-kb-mirrors.md * Update src/blop/__init__.py * Update src/blop/__init__.py --------- Co-authored-by: Thomas Hopkins <thomashopkins000@gmail.com> commit 1406049 Merge: 697ca51 7e3d7c3 Author: MTakahashi-KWH <60798296+MTakahashi-KWH@users.noreply.github.com> Date: Mon Jul 6 11:10:50 2026 -0400 Merge pull request bluesky#323 from bluesky/Explanation_docs Explanation passages to go into depth about user responsible components commit 7e3d7c3 Author: MTakahashi-KWH <60798296+MTakahashi-KWH@users.noreply.github.com> Date: Mon Jul 6 10:31:25 2026 -0400 Update docs/source/explanations/evaluation-function.rst dropping highly contextual sidenote Co-authored-by: Thomas Hopkins <thopkins1@bnl.gov> commit aa83a24 Author: MTakahashi-KWH <60798296+MTakahashi-KWH@users.noreply.github.com> Date: Mon Jul 6 10:23:14 2026 -0400 Update docs/source/explanations/evaluation-function.rst Yeah, I had this in to personally disambiguate between bluesky document driven and run end uid event driven processing. But, given that i explicitly stated uid this is a bit of a muddying reference. Co-authored-by: Thomas Hopkins <thopkins1@bnl.gov> commit 13d14e0 Author: Rhys Takahashi <19mt01@gmail.com> Date: Mon Jun 29 13:46:40 2026 -0400 impl fixed suggested by J Moylan commit 7b8db61 Author: Rhys Takahashi <19mt01@gmail.com> Date: Mon Jun 29 12:38:02 2026 -0400 added explanation passages to go into more depth about user responsible components commit 697ca51 Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Mon Jun 8 15:40:36 2026 -0400 Update & Rework Dependencies (bluesky#321) * Update & rework dependencies * Update docs with dependencies * Add 'all' extra; Rename 'qs' to 'queueserver'; Add extras table to installation docs commit 90a01fa Author: Will Smith <ecgatt.ws@gmail.com> Date: Mon Jun 8 20:26:02 2026 +0200 Start queueserver listener in runner init (bluesky#316) * Start queueserver listener in runner init * Ignore unrelated Blop documents in queueserver listener * ruff formatting * removed redundant start_doc_filter * moved correlation id check bcack into _process_acquisition method * corrected pytest to match previous check on ignoring other blop runs * ruff linting for queueserver.py2 commit 7af7cc1 Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Thu May 28 14:58:46 2026 -0400 Replace ZMQ address argument with RemoteDispatcher for queueserver integration (bluesky#308) commit df10ad6 Author: MTakahashi-KWH <60798296+MTakahashi-KWH@users.noreply.github.com> Date: Thu May 28 12:04:02 2026 -0400 version bump (bluesky#315) commit 2ddab57 Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Tue May 26 12:51:28 2026 -0400 XRT KB mirror tutorial improvements (bluesky#311) * Fix z-coordinate of toroid * Minimize fwhm; track intensity and ensure > 10000 * Removed checking optimization health section; Reduced BO iterations to 10 from 20 * Fix best parameters returned by Ax commit fb28042 Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Mon May 25 09:00:52 2026 -0400 Stop publishing docs on scheduled workflow (bluesky#310) commit 69d1ff7 Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Sun May 24 11:56:33 2026 -0400 Document that queueserver integration is experimental (bluesky#309)

commit 0dfa3f2 Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Tue Jul 28 13:10:14 2026 -0400 Use proper autostart API for queueserver (bluesky#326) * Add temp raw prefix * Add sleeps * Autostart the queue properly * Fix merge issue commit 39b6afc Merge: 2441457 9bcc903 Author: MTakahashi-KWH <60798296+MTakahashi-KWH@users.noreply.github.com> Date: Thu Jul 23 12:37:56 2026 -0400 Merge pull request bluesky#331 from bluesky/contributing Add CONTRIBUTING.md commit 9bcc903 Author: thomashopkins32 <thopkins1@bnl.gov> Date: Thu Jul 23 10:40:12 2026 -0400 pre-commit commit 2b68d8a Author: thomashopkins32 <thopkins1@bnl.gov> Date: Thu Jul 23 10:39:51 2026 -0400 Updated Review and Merge Policy; Types of Changes section commit 2441457 Author: josephhanrahan <79729091+josephhanrahan@users.noreply.github.com> Date: Wed Jul 22 14:36:00 2026 -0400 move queueserver_agent testcases to new test module (bluesky#332) commit 1fee80a Author: thomashopkins32 <thopkins1@bnl.gov> Date: Wed Jul 22 14:07:09 2026 -0400 Add CONTRIBUTING.md commit c2332cf Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Wed Jul 22 13:38:41 2026 -0400 Set checkpoint path after init on Ax agent and optimizer (bluesky#327) commit 0a75969 Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Wed Jul 22 13:34:21 2026 -0400 Add checkpointing to queueserver runner (bluesky#328) * Add checkpointing to queueserver runner * Add checkpoint_interval argument to QueueserverAgent.run commit 70468ab Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Thu Jul 16 15:43:52 2026 -0400 Final edits before v1.0 release (bluesky#324) * Cleaned up all docstrings and other misc items * Add release history for v1.0.0 * Add deployments page * Add docs on callbacks * Update timepix3 description commit 9e0f135 Author: Ryan Roussel <rroussel@slac.stanford.edu> Date: Thu Jul 9 11:36:34 2026 -0700 Xopt integration (bluesky#318) * initial commit * add tests * Update test_optimizer.py * linting * linting * inline comments * refactor code to only define an XoptOptimizer class * linting * solving pre-commit issues * change code to native xopt vocs methods * remove python 3.10 * linting * Update test_optimizer.py * add tests for coverage * Update pyproject.toml * linting * create RunEngine test and random initial point generation * remove fixed parameters in favor of VOCS constants * utilize pydantic serialization, fix ingest append/insert issues * code simplification /modernization * additional code simplification * linting * Update xrt-kb-mirrors.md * Update src/blop/__init__.py * Update src/blop/__init__.py --------- Co-authored-by: Thomas Hopkins <thomashopkins000@gmail.com> commit 1406049 Merge: 697ca51 7e3d7c3 Author: MTakahashi-KWH <60798296+MTakahashi-KWH@users.noreply.github.com> Date: Mon Jul 6 11:10:50 2026 -0400 Merge pull request bluesky#323 from bluesky/Explanation_docs Explanation passages to go into depth about user responsible components commit 7e3d7c3 Author: MTakahashi-KWH <60798296+MTakahashi-KWH@users.noreply.github.com> Date: Mon Jul 6 10:31:25 2026 -0400 Update docs/source/explanations/evaluation-function.rst dropping highly contextual sidenote Co-authored-by: Thomas Hopkins <thopkins1@bnl.gov> commit aa83a24 Author: MTakahashi-KWH <60798296+MTakahashi-KWH@users.noreply.github.com> Date: Mon Jul 6 10:23:14 2026 -0400 Update docs/source/explanations/evaluation-function.rst Yeah, I had this in to personally disambiguate between bluesky document driven and run end uid event driven processing. But, given that i explicitly stated uid this is a bit of a muddying reference. Co-authored-by: Thomas Hopkins <thopkins1@bnl.gov> commit 13d14e0 Author: Rhys Takahashi <19mt01@gmail.com> Date: Mon Jun 29 13:46:40 2026 -0400 impl fixed suggested by J Moylan commit 7b8db61 Author: Rhys Takahashi <19mt01@gmail.com> Date: Mon Jun 29 12:38:02 2026 -0400 added explanation passages to go into more depth about user responsible components commit 697ca51 Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Mon Jun 8 15:40:36 2026 -0400 Update & Rework Dependencies (bluesky#321) * Update & rework dependencies * Update docs with dependencies * Add 'all' extra; Rename 'qs' to 'queueserver'; Add extras table to installation docs commit 90a01fa Author: Will Smith <ecgatt.ws@gmail.com> Date: Mon Jun 8 20:26:02 2026 +0200 Start queueserver listener in runner init (bluesky#316) * Start queueserver listener in runner init * Ignore unrelated Blop documents in queueserver listener * ruff formatting * removed redundant start_doc_filter * moved correlation id check bcack into _process_acquisition method * corrected pytest to match previous check on ignoring other blop runs * ruff linting for queueserver.py2 commit 7af7cc1 Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Thu May 28 14:58:46 2026 -0400 Replace ZMQ address argument with RemoteDispatcher for queueserver integration (bluesky#308) commit df10ad6 Author: MTakahashi-KWH <60798296+MTakahashi-KWH@users.noreply.github.com> Date: Thu May 28 12:04:02 2026 -0400 version bump (bluesky#315) commit 2ddab57 Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Tue May 26 12:51:28 2026 -0400 XRT KB mirror tutorial improvements (bluesky#311) * Fix z-coordinate of toroid * Minimize fwhm; track intensity and ensure > 10000 * Removed checking optimization health section; Reduced BO iterations to 10 from 20 * Fix best parameters returned by Ax commit fb28042 Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Mon May 25 09:00:52 2026 -0400 Stop publishing docs on scheduled workflow (bluesky#310) commit 69d1ff7 Author: Thomas Hopkins <thopkins1@bnl.gov> Date: Sun May 24 11:56:33 2026 -0400 Document that queueserver integration is experimental (bluesky#309)

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