Fix typos and styling. #226

qwriter · 2023-02-03T21:20:38Z

Copyedit for clarity.
Add reference documentation for the following methods because they were not being generated:

chimera_node_placer_2d
draw_chimera_embedding
draw_chimera_yield
draw_pegasus_yield
zephyr_node_placer_2d

Copyedit for clarity. Add reference documentation for the following methods because they were not being generated: chimera_node_placer_2d draw_chimera_embedding draw_chimera_yield draw_pegasus_yield zephyr_node_placer_2d

docs/reference/drawing.rst

arcondello · 2023-02-03T21:24:17Z

dwave_networkx/drawing/chimera_layout.py

-       with the exception of the `pos` parameter which is not used by this
-       function. If `linear_biases` or `quadratic_biases` are provided,
-       any provided `node_color` or `edge_color` arguments are ignored.
+       Parameters in :func:`~networkx.drawing.nx_pylab.draw_networkx`, except for the ``pos`` parameter.


Does it work with the simpler path networkx.draw_networkx, it will be less fragile to changes in structure than networkx.drawing.nx_pylab.draw_networkx.

I don't think so. @JoelPasvolsky?

Also don't think so, networkx.drawing.nx_pylab.draw_networkx reference/generated/networkx.drawing.nx_pylab.draw_networkx.html#networkx.drawing.nx_pylab.draw_networkx is the only draw_networkx under py:function in the NetworkX objects.inv file that I see

JoelPasvolsky

@qwriter, I looked at the Chimera updates and made some general comments at are applicable to the other files as well. I can do a 2nd full round later

JoelPasvolsky · 2023-02-07T15:37:36Z

dwave_networkx/drawing/chimera_layout.py

@@ -28,33 +28,34 @@


 def chimera_layout(G, scale=1., center=None, dim=2):
-    """Positions the nodes of graph G in a Chimera cross topology.
+    """Position the nodes of graph ``G`` in a Chimera cross topology.


@arcondello, If I remember correctly, we made dwave-networkx an exception to the Python PEP style of using the imperative to conform with the networkx style instead.

JoelPasvolsky · 2023-02-07T15:45:52Z

dwave_networkx/drawing/chimera_layout.py


    scale : float (default 1.)
-        Scale factor. When scale = 1,  all positions fit within [0, 1]
+        Scale factor. If ``scale = 1``, then all positions fit within [0, 1]


This is fine, but you can reduce the amount of formatted text with something like "When scale is 1, all positions" (also removes the unneeded "then". It's worth keeping formatted text to a minimum, looks nicer

JoelPasvolsky · 2023-02-07T15:48:53Z

dwave_networkx/drawing/chimera_layout.py

        on the x-axis and [-1, 0] on the y-axis.

    center : None or array (default None)
        Coordinates of the top left corner.

    dim : int (default 2)
-        Number of dimensions. When dim > 2, all extra dimensions are
+        Number of dimensions. If ``dim > 2``, then all extra dimensions are


Can drop the "then". (Applied elsewhere too)
An alternative to consider (less formatted text): "For dim greater than 2, all extra ..."

Isn't the mathematical symbols more succinct and audience appropriate?

Similar to this comment, weigh additional formatting versus succinctness of math instead of text. I find it most helpful to look at the rendered HTML for the section to feel if it's starting to look checkerboardish.

I looked at the HTML and I think it looks okay.

It's also a bit hard in API docs not to have a lot of syntax highlighting; it's just the nature of API docs.

JoelPasvolsky · 2023-02-07T17:57:50Z

dwave_networkx/drawing/chimera_layout.py


-    If `linear_biases` and/or `quadratic_biases` are provided, these
-    are visualized on the plot.
+    Linear and quadratic biases are visualized on the plot as specified


Suggested change

Linear and quadratic biases are visualized on the plot as specified

Linear and quadratic biases are visualized on the plot if specified

The new wording of the intro makes it seem mandatory

JoelPasvolsky · 2023-02-07T18:02:48Z

dwave_networkx/drawing/chimera_layout.py

+        A dict of biases associated with each node in ``G`` and of
+        the form ``{node: bias, ...}``. Each bias is numeric.


Suggested change

A dict of biases associated with each node in ``G`` and of

the form ``{node: bias, ...}``. Each bias is numeric.

Linear biases for all nodes of ``G``, as a dict of form ``{node: bias, ...}``,

where ``bias`` is numeric.

We prefer to start the description with what the parameter means ("linear biases") rather than the data type ("dict"). The above is more consistent with our docs

Also applies elsewhere below

JoelPasvolsky · 2023-02-07T18:10:39Z

dwave_networkx/drawing/chimera_layout.py

-    If interaction_edges is not None, then only display the couplers in that
-    list.  If embedded_graph is not None, the only display the couplers between
-    chains with intended couplings according to embedded_graph.
+    If the ``interaction_edges`` parameter is not None, then only display the couplers in that


Do we need this intro paragraph? Why can't this all be specified in the descriptions of the parameters themselves? The intro should be to point out general, crucial, or unintuitive aspects of the function

JoelPasvolsky · 2023-02-07T18:13:32Z

dwave_networkx/drawing/chimera_layout.py

+        Graph which contains all keys of the ``emb`` parameter as nodes. If specified, then
+        the edges of ``G`` will be considered interactions if and only if they
+        exist between two chains of the ``emb`` parameter and if their keys are connected by
+        an edge in the ``embedded_graph`` parameter.


Perhaps it is helpful to use a "the x parameter" for the first usage to call attention that the formatted text is params listed and described here, but three uses adds text with decreasing marginal utility

JoelPasvolsky · 2023-02-07T18:14:38Z

dwave_networkx/drawing/chimera_layout.py


    interaction_edges : list (optional, default None)
-        A list of edges which will be used as interactions.
+        List of edges which will be used as interactions.


Suggested change

List of edges which will be used as interactions.

Interactions as a list of edges.

JoelPasvolsky · 2023-02-07T18:17:28Z

dwave_networkx/drawing/chimera_layout.py

-        in chains, and edges which are neither chain edges nor interactions.
-        If unused_color is None, these nodes and edges will not be shown at all.
+        Color to use for graph ``G``'s nodes that are not part of
+        chains and edges that are neither chain edges nor interactions.


Ambiguous phrasing: it's unclear whether it is saying "part of chains and edges that are" or "... and edges that are"

JoelPasvolsky · 2023-02-07T18:17:51Z

dwave_networkx/drawing/chimera_layout.py

-        If unused_color is None, these nodes and edges will not be shown at all.
+        Color to use for graph ``G``'s nodes that are not part of
+        chains and edges that are neither chain edges nor interactions.
+        If None, then these nodes and edges will not be shown.


Another reminder that you can drop all these "then"s

qwriter · 2023-03-13T21:31:48Z

dwave_networkx/drawing/chimera_layout.py

@@ -28,33 +28,34 @@


 def chimera_layout(G, scale=1., center=None, dim=2):
-    """Positions the nodes of graph G in a Chimera cross topology.


wrt this comment, could we delete the phrase "in a Chimera cross topology"?

This function creates a Chimera layout that can then be plotted. It could have potentially realized the layout in different ways, in particular, the cross and column layouts shown here. The modifier "in a Chimera cross topology" is saying that the function selected to implement the cross layout.
"topology" is not the best word choice because it's used for the QPU connectivity (i.e. Chimera structure). So the info is needed but needs improved phrasing.

"in a Chimera cross layout"?

Might be okay or perhaps something like, "Positions a graph's nodes in a Chimera layout with unit cells as crosses."
Kelly uses "cross configuration" in Pegasus but I'm not sure that's clear to most users.

Looking at the HTML rendering, it seems to me that the modifier "with unit cells as crosses" is given too much importance at the top-level by being in the one-line descriptions. For someone looking for Chimera graph functions, what's important at the top level is that function chimera_layout "Positions the nodes of a graph in a Chimera layout."
If we provided column-layout too, it would make sense to specify at the top level the cross/column info. We just have the one option, so I'm inclined to put that in a separate, next line.

JoelPasvolsky

Comments on the Chimera functions so far. Will get to the Pegasus & Zephyr later

JoelPasvolsky · 2023-03-15T14:31:35Z

docs/reference/drawing.rst

@@ -4,12 +4,12 @@
 Drawing
 *******

-Tools to visualize topologies of D-Wave QPUs and weighted graph problems on them.
+Tools to visualize topologies of D-Wave QPUs and weighted :term:`graph` problems on them.

 .. currentmodule:: dwave_networkx

 .. note:: Some functionality requires `NumPy <https://scipy.org>`_ and/or


"requires NumPy <https://scipy.org>_ and/or" --> both dwave-networkx's dependencies, dimod and networkx, have NumPy as a dependency. Is there any chance dwave-networkx users won't have NumPy? @arcondello

Hmm. We don't have it as a full dependency so theoretically NetworkX and dimod could drop their dependencies on it. That said, making it a full dependency seems reasonable to me.

Would this be a future enhancement? Do I need to update this sentence?

JoelPasvolsky · 2023-03-15T14:41:28Z

dwave_networkx/drawing/chimera_layout.py

@@ -28,33 +28,34 @@


 def chimera_layout(G, scale=1., center=None, dim=2):
-    """Positions the nodes of graph G in a Chimera cross topology.


Looking at the HTML rendering, it seems to me that the modifier "with unit cells as crosses" is given too much importance at the top-level by being in the one-line descriptions. For someone looking for Chimera graph functions, what's important at the top level is that function chimera_layout "Positions the nodes of a graph in a Chimera layout."
If we provided column-layout too, it would make sense to specify at the top level the cross/column info. We just have the one option, so I'm inclined to put that in a separate, next line.

JoelPasvolsky · 2023-03-15T14:47:02Z

docs/reference/drawing.rst


-	Graph H (blue) overlaid on a Chimera unit cell (red nodes and black edges).
+    Graph H (blue) overlaid on a Chimera unit cell (red nodes and black edges).


Missing :code:`` (or backtic) for the H.
Here's a good place to unobtrusively point out that this Chimera unit cell is rendered in cross layout (because we refer to that in the functions but don't show cross versus column to really clarify that [which we don't do because column drawing is not supported])

JoelPasvolsky · 2023-03-15T14:49:06Z

dwave_networkx/drawing/chimera_layout.py

@@ -28,33 +28,34 @@


 def chimera_layout(G, scale=1., center=None, dim=2):
-    """Positions the nodes of graph G in a Chimera cross topology.
+    """Positions the nodes of graph ``G`` in a Chimera layout with unit cells as crosses.

    NumPy (https://scipy.org) is required for this function.


Same question about NumPy as in drawing.rst

JoelPasvolsky · 2023-03-15T14:52:59Z

dwave_networkx/drawing/chimera_layout.py

        on the x-axis and [-1, 0] on the y-axis.

    center : None or array (default None)
        Coordinates of the top left corner.

    dim : int (default 2)
-        Number of dimensions. When dim > 2, all extra dimensions are
+        Number of dimensions. If ``dim`` > 2, all extra dimensions are
        set to 0.

    Returns
    -------
    xy_coords : function


JoelPasvolsky · 2023-03-15T15:04:54Z

dwave_networkx/drawing/chimera_layout.py

-        If overlapped_embedding is True, then chains in emb may overlap (contain
-        the same vertices in G), and the drawing will display these overlaps as
+        If True, chains in the ``emb`` parameter may overlap (contain
+        the same vertices in ``G``), and the drawing will display these overlaps as


"the drawing will display these overlaps" --> "the drawing displays these overlaps"

JoelPasvolsky · 2023-03-15T15:06:18Z

dwave_networkx/drawing/chimera_layout.py

-       function. If `linear_biases` or `quadratic_biases` are provided,
-       any provided `node_color` or `edge_color` arguments are ignored.
+       Parameters in :func:`~networkx.drawing.nx_pylab.draw_networkx`, except for the ``pos`` parameter.
+       If the ``linear_biases`` or ``quadratic_biases`` parameters are specified,


"If the linear_biases or quadratic_biases parameters are specified" --> This function does not have linear_biases or quadratic_biases parameters, at least in the above descriptions.

These were present in the original. Perhaps they are referring to the parameters in draw_chimera? Should we point to draw_chimera?

I suggest leaving this bit (for all three topographies) alone in this PR because I suspect the current functionality has problems that will be fixed by this PR. Currently, it seems to me that the node_color and edge_color params are not supported:

G = dnx.chimera_graph(2) embedding = {"N1": [0, 4, 5], "N2": [1, 6, 7]} dnx.draw_chimera_embedding(G, embedding, show_labels=True, node_color="r")

returns a TypeError: networkx.drawing.nx_pylab.draw() got multiple values for keyword argument 'node_color' error.

In any case the other PR and this change have conflicts so leaving it untouched will save Kelly work.

JoelPasvolsky · 2023-03-15T15:07:05Z

dwave_networkx/drawing/chimera_layout.py

    """
    draw_embedding(G, chimera_layout(G), *args, **kwargs)


 def draw_chimera_yield(G, **kwargs):
-    """Draws the given graph G with highlighted faults, according to layout.
+    """Draws the given graph ``G`` with highlighted faults.


"Draws the given graph G with highlighted faults" --> consistency: other one-line descriptions don't use "given"

JoelPasvolsky · 2023-03-15T15:07:42Z

dwave_networkx/drawing/chimera_layout.py

-        The color to use for nodes and edges of G which are not faults.
-        If unused_color is None, these nodes and edges will not be shown at all.
+        Color to use for graph ``G``'s nodes and edges which are not faults.
+        If None, these nodes and edges will not be shown.


"these nodes and edges will not be shown" --> "these nodes and edges are not shown"

JoelPasvolsky · 2023-03-15T15:08:53Z

dwave_networkx/drawing/chimera_layout.py

+       Parameters in :class:`.draw_networkx`, except for the ``pos`` parameter.
+       If the ``linear_biases`` or ``quadratic_biases`` parameters are specified,
+       the :func:`~networkx.drawing.nx_pylab.draw_networkx` ``node_color``
+       or ``edge_color`` parameters are ignored.


"If the linear_biases or quadratic_biases parameters are specified" --> This function does not have linear_biases or quadratic_biases parameters, at least in the above descriptions.

JoelPasvolsky

Comments on Pegasus functions

JoelPasvolsky · 2023-03-15T16:29:33Z

docs/reference/drawing.rst


-	Graph H (blue) overlaid on a small Pegasus lattice(yellow nodes and black edges).
+    Graph H (blue) overlaid on a small Pegasus lattice(yellow nodes and black edges).


Just for consistency we should probably :code:`` (backtick) the H

JoelPasvolsky · 2023-03-15T16:36:21Z

docs/reference/drawing.rst


-	Graph H (blue) overlaid on a small Pegasus lattice(yellow nodes and black edges).
+    Graph H (blue) overlaid on a small Pegasus lattice(yellow nodes and black edges).


Here is a good place to also point out that the layout is rendered in cross format to help users understand what "cross" refers to when used elsewhere (be a good result returned when someone searches "cross")

JoelPasvolsky · 2023-03-15T16:38:36Z

dwave_networkx/drawing/pegasus_layout.py

-        by an edge in this graph. If given, only couplers between chains
+        Graph that contains all keys of the ``emb`` parameter as nodes. If specified,
+        edges of ``G`` are considered interactions if and only if (1) they
+        exist between two chains of the emb parameter and (2) their keys are connected


"of the emb parameter" --> "of the emb parameter"

JoelPasvolsky · 2023-03-15T16:42:12Z

dwave_networkx/drawing/pegasus_layout.py

-       function. If ``linear_biases`` or ``quadratic_biases`` are provided,
-       any provided ``node_color`` or ``edge_color`` arguments are ignored.
+       Parameters in :func:`~networkx.drawing.nx_pylab.draw_networkx`, except for the ``pos`` parameter.
+       If the ``linear_biases`` or ``quadratic_biases`` parameters are specified,


same comment

JoelPasvolsky · 2023-03-15T16:43:13Z

dwave_networkx/drawing/pegasus_layout.py

    """
    crosses = kwargs.pop("crosses", False)
    draw_embedding(G, pegasus_layout(G, crosses=crosses), *args, **kwargs)

 def draw_pegasus_yield(G, **kwargs):
-    """Draws the given graph G with highlighted faults, according to layout.
+    """Draws the given graph ``G`` with highlighted faults.


same comment

JoelPasvolsky · 2023-03-15T16:44:07Z

dwave_networkx/drawing/pegasus_layout.py

-       function. If `linear_biases` or `quadratic_biases` are provided,
-       any provided `node_color` or `edge_color` arguments are ignored.
+       Parameters in :func:`~networkx.drawing.nx_pylab.draw_networkx`, except for the ``pos`` parameter.
+       If the ``linear_biases`` or ``quadratic_biases`` parameters are specified,


same comment

JoelPasvolsky · 2023-03-15T16:45:32Z

dwave_networkx/drawing/pegasus_layout.py

@@ -32,31 +32,31 @@


 def pegasus_layout(G, scale=1., center=None, dim=2, crosses=False):
-    """Positions the nodes of graph G in a Pegasus topology.
+    """Positions the nodes of graph ``G`` in a Pegasus topology.

    `NumPy <https://scipy.org>`_ is required for this function.


same handling as here

JoelPasvolsky · 2023-03-15T16:47:38Z

dwave_networkx/drawing/pegasus_layout.py

        set to 0.

    crosses: boolean (optional, default False)
        If True, :math:`K_{4,4}` subgraphs are shown in a cross
-        rather than L configuration.
+        rather than an L configuration.

    Returns
    -------
    xy_coords : function


Same comment

JoelPasvolsky

Comments on Zephyr functions

JoelPasvolsky · 2023-03-15T16:51:35Z

dwave_networkx/drawing/zephyr_layout.py

-        If given, only couplers between chains based on this graph are displayed.
+        Graph that contains all keys of the ``emb`` parameter as nodes. If specified,
+        the edges of ``G`` are considered interactions if and only if (1) they
+        exist between two chains of the emb parameter and (2) the keys of the


Suggested change

exist between two chains of the emb parameter and (2) the keys of the

exist between two chains of the ``emb`` parameter and (2) the keys of the

Adding a Suggested Change so you can see how you commit these without needing to edit yourself

JoelPasvolsky · 2023-03-15T16:53:28Z

dwave_networkx/drawing/zephyr_layout.py

-       are provided, any provided ``node_color`` or ``edge_color`` arguments are
-       ignored.
+       Parameters in :func:`~networkx.drawing.nx_pylab.draw_networkx`, except for the ``pos`` parameter.
+       If the ``linear_biases`` or ``quadratic_biases`` parameters are specified,


same comment

JoelPasvolsky · 2023-03-15T16:54:11Z

dwave_networkx/drawing/zephyr_layout.py

    """
    draw_embedding(G, zephyr_layout(G), *args, **kwargs)

 def draw_zephyr_yield(G, **kwargs):
-    """Draws the given graph G with highlighted faults, according to layout.
+    """Draws the given graph ``G`` with highlighted faults, according to the Zephyr layout.


same comment on "given"

JoelPasvolsky · 2023-03-15T16:55:13Z

dwave_networkx/drawing/zephyr_layout.py

-        The color to use for nodes and edges of G which are not faults.
-        If unused_color is None, these nodes and edges will not be shown at all.
+        Color to use for nodes and edges of ``G`` which are not faults.
+        If None, these nodes and edges will not be shown.


Suggested change

If None, these nodes and edges will not be shown.

If None, these nodes and edges are not shown.

Adding a second Suggested Change so you can see how you can collect all such suggestion into a single commit

JoelPasvolsky · 2023-03-15T16:56:11Z

dwave_networkx/drawing/zephyr_layout.py

-       are provided, any provided ``node_color`` or ``edge_color`` arguments are
-       ignored.
+       Parameters in :func:`~networkx.drawing.nx_pylab.draw_networkx`, except for the ``pos`` parameter.
+       If the ``linear_biases`` or ``quadratic_biases`` parameters are specified,


same comment on linear_biases or quadratic_biases

JoelPasvolsky · 2023-03-15T16:57:13Z

dwave_networkx/drawing/zephyr_layout.py

@@ -31,25 +31,25 @@


 def zephyr_layout(G, scale=1., center=None, dim=2):
-    """Positions the nodes of graph G in a Zephyr topology.
+    """Positions the nodes of graph ``G`` in a Zephyr topology.

    `NumPy <https://scipy.org>`_ is required for this function.


same NumPy handling as here

JoelPasvolsky · 2023-03-15T16:58:53Z

dwave_networkx/drawing/zephyr_layout.py

        [0, 1] on the x-axis and [-1, 0] on the y-axis.

    center : None or array (default None)
        Coordinates of the top left corner.

    dim : int (default 2)
-        Number of dimensions. When dim > 2, all extra dimensions are
+        Number of dimensions. If ``dim`` > 2, all extra dimensions are
        set to 0.

    Returns
    -------
    xy_coords : function


same comment about Function

JoelPasvolsky

Plus remaining open comment from before

dwave_networkx/drawing/chimera_layout.py

Co-authored-by: Joel Pasvolsky <[email protected]>

…drawing

Fix typos and styling.

fcbd1a4

Copyedit for clarity. Add reference documentation for the following methods because they were not being generated: chimera_node_placer_2d draw_chimera_embedding draw_chimera_yield draw_pegasus_yield zephyr_node_placer_2d

arcondello reviewed Feb 3, 2023

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arcondello reviewed Feb 3, 2023

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JoelPasvolsky reviewed Feb 7, 2023

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qwriter commented Mar 13, 2023

View reviewed changes

Implement Joel and Alex C's feedback.

1ad8d98

JoelPasvolsky reviewed Mar 15, 2023

View reviewed changes

Implement Joel's feedback.

c164faa

JoelPasvolsky approved these changes Mar 16, 2023

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dwave_networkx/drawing/chimera_layout.py Outdated Show resolved Hide resolved

qwriter and others added 3 commits March 16, 2023 14:04

Update dwave_networkx/drawing/chimera_layout.py

373201e

Co-authored-by: Joel Pasvolsky <[email protected]>

Remove note about NumPy requirement.

54a54c0

Merge remote-tracking branch 'origin/copyedit_drawing' into copyedit_…

f02010d

…drawing

arcondello approved these changes Mar 20, 2023

View reviewed changes

arcondello merged commit 17a33a6 into dwavesystems:main Mar 20, 2023

	Linear and quadratic biases are visualized on the plot as specified
	Linear and quadratic biases are visualized on the plot if specified

		A dict of biases associated with each node in ``G`` and of
		the form ``{node: bias, ...}``. Each bias is numeric.

	List of edges which will be used as interactions.
	Interactions as a list of edges.

		@@ -28,33 +28,34 @@


		def chimera_layout(G, scale=1., center=None, dim=2):
		"""Positions the nodes of graph G in a Chimera cross topology.


		Graph H (blue) overlaid on a Chimera unit cell (red nodes and black edges).
		Graph H (blue) overlaid on a Chimera unit cell (red nodes and black edges).


		Graph H (blue) overlaid on a small Pegasus lattice(yellow nodes and black edges).
		Graph H (blue) overlaid on a small Pegasus lattice(yellow nodes and black edges).

	exist between two chains of the emb parameter and (2) the keys of the
	exist between two chains of the ``emb`` parameter and (2) the keys of the

	If None, these nodes and edges will not be shown.
	If None, these nodes and edges are not shown.

Fix typos and styling. #226

Fix typos and styling. #226

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qwriter commented Feb 3, 2023

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qwriter Mar 11, 2023 •

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