Zephyr utils #261

mahdiehmalekian · 2025-03-13T01:14:18Z

coordinate_systems.py : Contains namedtuples for Zephyr and Cartesian coordinates and the conversion functions between the two
plane_shift.py : Contains the class for displacement of nodes in the Cartesian plane.
node_edge.py: Contains the class for edge, edge of a Zephyr graph (which checks whether the edge exists in a perfect yield Zephyr graph), and the node of a Zephyr graph
qfloor.py: Contains the class for working with a tile (subset of nodes) in quotient Zephyr. Also contains the class for putting the tiles together in a number of rows and columns
survey.py: Contains the class for taking a survey of a Zephyr graph compared to a perfect-yield Zephyr graph on the same grid and tile size
The test suite contains the tests for these modules.

…flag to ZEdge

thisac

Thanks for the hard work @mahdiehmalekian. Had a first pass through node_edge. Will come back to it again, and the other files, in a future review soon.

minorminer/utils/zephyr/__init__.py

minorminer/utils/zephyr/node_edge.py

Co-authored-by: Theodor Isacsson <[email protected]>

thisac

Had another review round. Haven't checked the tests yet (will do that next).

A couple of overall comments and suggestions:

qfloor.py contains a couple of methods without or with incomplete docstrings.
Code in docstrings should have double back-ticks (``), and wherever possible, it's nice (but not mandatory) to have cross-references to classes and methods, etc. See here.
A couple of places I'd recommend adding a new line after returns and around for-loop-blocks, try-excepts, after raises and after returns, to make it a bit more legible.

minorminer/utils/zephyr/__init__.py

minorminer/utils/zephyr/node_edge.py

minorminer/utils/zephyr/qfloor.py

Co-authored-by: Theodor Isacsson <[email protected]>

Co-authored-by: Radomir Stevanovic <[email protected]>

randomir review implementation Co-authored-by: Radomir Stevanovic <[email protected]>

thisac review code suggestions Co-authored-by: Theodor Isacsson <[email protected]>

…anch with testing derived from TilingComposite

…nsibility

Co-authored-by: Radomir Stevanovic <[email protected]>

### New Features - Allow lattice type and lattice dimensions to be passed as options for `find_sublattice_embeddings()`. See [\dwavesystems#266](dwavesystems#266). ### Bug Fixes - Fix `find_sublattice_embeddings()` to not produce non-disjoint embeddings when `use_tile_embedding=True` is set. See [\dwavesystems#265](dwavesystems#265).

) * Added support for colorings in Glasgow subgraph solver * updated Glasgow to latest version (with patches for c++17 support) * new parameters for subgraph.find_subgraph * as_embedding=True will produce a dict with tuple values * node_labels to be respected by GSS, node labels must match * edge_labels as with node_labels; directed edge labels match

* removed kwargs handling in favor for explicit arguments (issue dwavesystems#255) * added injectivity parameter to support noninjective and locally-injective homomorphisms * fix isolated nodes issue dwavesystems#254 and add injectivity options * support random seeds (issue dwavesystems#243)

* added ability to interrupt find_subgraph via ctrl-c

randomir

Very well written code and super useful utils! Thank you, @mahdiehmalekian!

My feedback is mostly about code/docs style (for consistency with Ocean) and coding best practices.

In terms of interface/API, I would simplify ZNode by defining neighbor generators only, also removing membership test functions.

randomir · 2025-12-11T13:44:06Z

tests/utils/zephyr/test_coordinate_systems.py

+        xyks = [(0, 1), (1, 0, None), (12, -3)]
+        ccoords = [CartesianCoord(*xyk) for xyk in xyks]
+        for ccoord in ccoords:
+            cartesian_to_zephyr(ccoord=ccoord)


I would fold the two *_runs tests with the parameterized ones, but if you want to keep them as smoke tests, I recommend at least testing the returned type:

Suggested change

cartesian_to_zephyr(ccoord=ccoord)

self.assertIsInstance(cartesian_to_zephyr(ccoord=ccoord), ZephyrCoord)

randomir · 2025-12-11T13:44:39Z

tests/utils/zephyr/test_coordinate_systems.py

+        uwkjzs = [(0, 2, 4, 1, 5), (1, 3, 3, 0, 0), (1, 2, None, 1, 5)]
+        zcoords = [ZephyrCoord(*uwkjz) for uwkjz in uwkjzs]
+        for zcoord in zcoords:
+            zephyr_to_cartesian(zcoord=zcoord)


Same comment as above:

Suggested change

zephyr_to_cartesian(zcoord=zcoord)

self.assertIsInstance(zephyr_to_cartesian(zcoord=zcoord), CartesianCoord)

randomir · 2025-12-11T13:48:30Z

minorminer/utils/zephyr/plane_shift.py

+        x (int): The displacement in the x-direction of a Cartesian coordinate.
+        y (int): The displacement in the y-direction of a Cartesian coordinate.


In Ocean, we follow Google Python Style Guide, and omit types from docstrings when they are type-annotated. Here, and elsewhere in this PR.

randomir · 2025-12-11T16:44:49Z

minorminer/utils/zephyr/plane_shift.py

+        Returns:
+            PlaneShift: The displacement in CartesianCoord by self followed by other.
+        """
+        if type(self) != type(other):


By using isinstance, you support PlaneShift subclasses for other:

Suggested change

if type(self) != type(other):

if not isinstance(other, PlaneShift):

randomir · 2025-12-11T16:52:03Z

minorminer/utils/zephyr/plane_shift.py

+
+from __future__ import annotations
+
+from typing import Iterator


Deprecated in favor of:

Suggested change

from typing import Iterator

from collections.abc import Iterator

randomir · 2025-12-11T18:49:21Z

minorminer/utils/zephyr/node_edge.py

+            for cc in self.odd_neighbors_generator(where=where):
+                yield cc
+
+    def neighbors(


What's the reason to include both the generators for all kinds of neighbors, and then redundant functions that return a set?

I would remove _generator suffix from the generators, and keep only those.

randomir · 2025-12-11T18:53:32Z

minorminer/utils/zephyr/node_edge.py

+        for nbr in self.internal_neighbors_generator(where=where):
+            if other == nbr:
+                return True
+        return False


This, and the similar 3 other functions feel redundant as they can be replaced with:

Suggested change

for nbr in self.internal_neighbors_generator(where=where):

if other == nbr:

return True

return False

return other in self.internal_neighbors_generator(where=where)

randomir · 2025-12-11T18:56:50Z

minorminer/utils/zephyr/node_edge.py

+        self,
+        nbr_kind: EdgeKind | Iterable[EdgeKind] | None = None,
+        where: Callable[[CartesianCoord | ZephyrCoord], bool] = lambda coord: True,
+    ) -> list[ZEdge]:


Why not make this function a generator?

randomir · 2025-12-11T18:59:25Z

minorminer/utils/zephyr/node_edge.py

+        return self._ccoord == other._ccoord
+
+
+    def __gt__(self, other: ZNode) -> bool:


Instead of manually defining all comparison methods, use @functools.total_ordering.

randomir · 2025-12-11T19:01:54Z

tests/utils/zephyr/test_node_edge.py

+        ]
+    )
+    def test_degree(self, xy, m, nbr_kind, a, b) -> None:
+            for t in [None, 1, 4, 6]:


check indent

Initial commit

4c7a75a

mahdiehmalekian changed the title ~~Initial commit~~ Zephyr utils Mar 13, 2025

Mahdieh Malekian added 4 commits March 13, 2025 11:15

Reformat

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Reformat

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Allow Edge input to be any type, not just int + Add check_edge_valid …

a394ead

…flag to ZEdge

Turn off check_edge_valid flag for _edges attribute in ZSurvey

cdeeff8

thisac reviewed Apr 2, 2025

View reviewed changes

Mahdieh Malekian and others added 18 commits April 4, 2025 11:07

Correct header

e6eca6d

Add NodeKind and EdgeKind and adjust; Add document

20b79d0

Reformat

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Explicitly return None

fd78154

Simplify, Add space

9f7e5ab

Clarify arguments

13a29b4

Co-authored-by: Theodor Isacsson <[email protected]>

Capitalize

a15e92b

Co-authored-by: Theodor Isacsson <[email protected]>

Update minorminer/utils/zephyr/node_edge.py

94e85be

Co-authored-by: Theodor Isacsson <[email protected]>

Update minorminer/utils/zephyr/node_edge.py

904a4a3

Co-authored-by: Theodor Isacsson <[email protected]>

Update minorminer/utils/zephyr/node_edge.py

bb8afc9

Co-authored-by: Theodor Isacsson <[email protected]>

Update minorminer/utils/zephyr/node_edge.py

0f4a1bd

Co-authored-by: Theodor Isacsson <[email protected]>

Update minorminer/utils/zephyr/node_edge.py

c53380d

Co-authored-by: Theodor Isacsson <[email protected]>

Clarify documentation, set shape in init

974489c

Add doc to EdgeKind, NodeKind, clarify doc re. direction, Change name

70d84ed

Edit document

03765f1

Change nbr_kind argument type

edfde0f

Add edge_kind to ZEdge

7a8da7e

Disable changing znodes of QuoTile, change Dim to Dim_2D

f525e25

thisac reviewed Apr 30, 2025

View reviewed changes

mahdiehmalekian and others added 4 commits April 30, 2025 09:37

Update minorminer/utils/zephyr/node_edge.py

d496bfc

Co-authored-by: Theodor Isacsson <[email protected]>

Update minorminer/utils/zephyr/node_edge.py

b415ad3

Co-authored-by: Theodor Isacsson <[email protected]>

Update minorminer/utils/zephyr/node_edge.py

bd461a4

Co-authored-by: Theodor Isacsson <[email protected]>

Update minorminer/utils/zephyr/node_edge.py

4a1f63d

Co-authored-by: Theodor Isacsson <[email protected]>

jackraymond and others added 29 commits November 14, 2025 11:31

Correct variable names in fallover function

a35eefa

random review: Update minorminer/utils/parallel_embeddings.py

045ba05

Co-authored-by: Radomir Stevanovic <[email protected]>

Apply suggestions from code review

554fe4b

randomir review implementation Co-authored-by: Radomir Stevanovic <[email protected]>

Implement randomir review recommendations

e3b8de0

Add test of array_to_embeddings

7eeaf45

Delete redundant failover code

685a068

Apply suggestions from code review

5c21048

thisac review code suggestions Co-authored-by: Theodor Isacsson <[email protected]>

implement thisac review

a62934c

Remove obsolete doxygen configuration

db8b95c

Release 0.2.18

219fcf4

Bugfix: replace full graph by local decimated graph for use tiling br…

92e227a

…anch with testing derived from TilingComposite

Minor changes to docstrings and defaulting for compatibility/comprehe…

9ed506a

…nsibility

implement review changes to docstrings

4c5515b

Allow dwave_networkx to be passed as kwargs rather than in T

19dff7b

Bugfix: remove None test for required List argument

8af6832

Apply suggestions from code review

6a06776

Co-authored-by: Radomir Stevanovic <[email protected]>

Fix Optional type hinting, fix handling of T=None code and tests

4db164e

Add Python 3.14 and remove 3.9 support

72067f2

Set default start method for multiprocessing to 'fork'

449c067

Bump release to 0.2.20

52a897a

Update releasenote entry to fix reno parsing

4860b34

Add keyboard interrupts for subgraph.find_subgraph (dwavesystems#275)

1c088d6

* added ability to interrupt find_subgraph via ctrl-c

Increment version for release

8223301

Include utils.zephyr in packages

c14b7da

Apply suggestions from code review

d8c9790

Merge remote-tracking branch 'upstream' into zephyr-utils

8912073

randomir reviewed Dec 11, 2025

View reviewed changes

	cartesian_to_zephyr(ccoord=ccoord)
	self.assertIsInstance(cartesian_to_zephyr(ccoord=ccoord), ZephyrCoord)

	zephyr_to_cartesian(zcoord=zcoord)
	self.assertIsInstance(zephyr_to_cartesian(zcoord=zcoord), CartesianCoord)

		x (int): The displacement in the x-direction of a Cartesian coordinate.
		y (int): The displacement in the y-direction of a Cartesian coordinate.

	if type(self) != type(other):
	if not isinstance(other, PlaneShift):


		from __future__ import annotations

		from typing import Iterator

	from typing import Iterator
	from collections.abc import Iterator

		return self._ccoord == other._ccoord


		def __gt__(self, other: ZNode) -> bool:

Zephyr utils #261

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Zephyr utils #261

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mahdiehmalekian commented Mar 13, 2025 •

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