Add connected components to retworkx-core #595

enavarro51 · 2022-04-26T09:18:24Z

This PR adds the connected_components and number_connected_components functions to retworkx-core. Needs a release note and maybe further tests and docs.

mtreinish

This is a good start, thanks for doing this. I know this is still in progress, but I left a few inline comments all 3 functions need the same changes I think. Also it'd be good if we deleted the retworkx crate's version of these functions and just updated the python interface to call the retworkx-core version you're adding here.

retworkx-core/src/connectivity/conn_components.rs

coveralls · 2022-04-26T12:12:39Z

Pull Request Test Coverage Report for Build 2360696828

67 of 67 (100.0%) changed or added relevant lines in 2 files are covered.
3 unchanged lines in 2 files lost coverage.
Overall coverage increased (+0.01%) to 97.086%

Files with Coverage Reduction	New Missed Lines	%
retworkx-core/src/min_scored.rs	1	59.09%
src/shortest_path/all_pairs_dijkstra.rs	2	98.54%

Totals
Change from base Build 2333052804:	0.01%
Covered Lines:	12196
Relevant Lines:	12562

💛 - Coveralls

enavarro51 · 2022-04-26T21:03:36Z

@mtreinish Remaining is,

Add tests to docs
Release note
Remove retworkx's crate version of these functions and update python interface to point to retworkx-core version.

…workx into core_connected_components

georgios-ts

With current trait restrictions we can't really remove retworkx's crate version of these functions since they also work for directed StableGraphs.

retworkx-core/src/connectivity/conn_components.rs

georgios-ts · 2022-04-27T06:51:31Z

retworkx-core/src/connectivity/conn_components.rs

+///
+/// :param Graph graph: The input graph to find the number of connected
+///     components for.
+///
+/// :return: The number of connected components.
+/// :rtype: usize


Suggested change

///

/// :param Graph graph: The input graph to find the number of connected

/// components for.

///

/// :return: The number of connected components.

/// :rtype: usize

retworkx-core/src/connectivity/conn_components.rs

retworkx-core/src/connectivity/mod.rs

retworkx-core/src/connectivity/test_connectivity.rs

enavarro51 · 2022-04-27T13:55:21Z

With current trait restrictions we can't really remove retworkx's crate version of these functions since they also work for directed StableGraphs.

Can you elaborate on this for me? What are the trait restrictions? Thanks.

georgios-ts · 2022-04-27T16:11:13Z

Can you elaborate on this for me? What are the trait restrictions? Thanks.

@enavarro51
The input graph in retworkx-core must implement G: GraphProp<EdgeType = Undirected> but in retworkx we're calling connected_components https://github.com/Qiskit/retworkx/blob/main/src/connectivity/mod.rs#L329-L331
with a directed StableGraph as input which does not implement the above trait.

and remove retworkx/src/connectivity/conn_components.rs and modify retworkx/src/connectivity/mod.rs to point to retworkx/retworkx-core/src/connectivity/conn_components.rs

enavarro51 · 2022-05-01T21:56:14Z

This latest version should resolve all the open review issues here. The following changes have been made,

Remove the retworkx/src/connectivity/conn_components.rs file and change the mod.rs file in that directory to point to retworkx/retworkx-core/src/connectivity/conn_components.rs.
Change the 3 functions in retworkx-core/src/connectivity/conn_components.rs to work with either directed or undirected graphs.
Set up 3 layers of testing for the retworkx-core rust code. The first is doc-string tests. The second is tests within the module where a function is defined. The last is a new retworkx-core/tests directory, where more complex integration tests can be placed. Running cargo test within the retworkx-core directory will run all 3 types of tests.

…workx into core_connected_components

georgios-ts · 2022-05-02T10:34:05Z

retworkx-core/src/connectivity/conn_components.rs

+    stack.push_front(start);
+
+    while let Some(node) = stack.pop_front() {
+        for succ in graph.neighbors(node) {


It's not as simple as dropping GraphProp<EdgeType = Undirected> restriction. It will give wrong output for directed graphs since the algorithm that finds the weakly connected components of a directed graph must visit the neighbors of a node in both directions (incoming and outgoing).

For example the following fails (ideally our retworkx tests should have caught this):

import retworkx graph = retworkx.PyDiGraph() graph.add_nodes_from(range(4)) graph.add_edges_from_no_data([ (3, 2), (2, 1), (1, 0) ]) comps = retworkx.weakly_connected_components(graph) # Graph is weakly connected, so it should have just one component assert len(comps) == 1

There are some ways to fix this:

We can keep the old retworkx version and restrict GraphProp<EdgeType = Undirected> in order to accept only undirected graphs in retworkx-core, or

We can restrict G: IntoNeighborsDirected and:

Suggested change

for succ in graph.neighbors(node) {

for succ in graph

.neighbors_directed(node, Outgoing)

.chain(graph.neighbors_directed(node, Incoming))

{

mtreinish

Overall this LGTM now, thanks for sticking with it and making the updates. I just have a few small nits inline but once those are fixed I think we're good to go on this. @georgios-ts might want to take another look too before we merge though

mtreinish · 2022-05-19T21:18:29Z

retworkx-core/src/connectivity/conn_components.rs

+///
+/// * `graph` - The graph object to run the algorithm on
+/// * `node` - The node index to find the connected nodes for
+/// * `graph.visit_map()` - The visit map for the graph


Suggested change

/// * `graph.visit_map()` - The visit map for the graph

/// * `discovered` - The visit map for the graph

Done in d5e5def.

mtreinish · 2022-05-19T21:19:51Z

retworkx-core/src/connectivity/conn_components.rs

+use petgraph::{Incoming, Outgoing};
+
+/// Given an graph, a node in the graph, and a visit_map,
+/// return the set of nodes connected to the given node.


I'd probably also mention here that this is in breadth first order and treating all edges as undirected.

Done in d5e5def.

mtreinish · 2022-05-19T21:22:27Z

src/connectivity/mod.rs

+    let return_value: Vec<HashSet<usize>> = connectivity::connected_components(&graph.graph)
+        .into_iter()
+        .map(|res_map| res_map.into_iter().map(|x| x.index()).collect())
+        .collect();
+    return_value


It'll probably be optimized away by the compiler but we don't need the return_value variable:

Suggested change

let return_value: Vec<HashSet<usize>> = connectivity::connected_components(&graph.graph)

.into_iter()

.map(|res_map| res_map.into_iter().map(|x| x.index()).collect())

.collect();

return_value

connectivity::connected_components(&graph.graph)

.into_iter()

.map(|res_map| res_map.into_iter().map(|x| x.index()).collect())

.collect()

Done in d5e5def.

mtreinish · 2022-05-19T21:23:27Z

src/connectivity/mod.rs

+    let return_value: HashSet<usize> =
+        connectivity::bfs_undirected(&graph.graph, node, &mut graph.graph.visit_map())
+            .into_iter()
+            .map(|x| x.index())
+            .collect();
+    Ok(return_value)


Suggested change

let return_value: HashSet<usize> =

connectivity::bfs_undirected(&graph.graph, node, &mut graph.graph.visit_map())

.into_iter()

.map(|x| x.index())

.collect();

Ok(return_value)

Ok(connectivity::bfs_undirected(&graph.graph, node, &mut graph.graph.visit_map())

.into_iter()

.map(|x| x.index())

.collect())

Done in d5e5def.

mtreinish · 2022-05-19T21:23:45Z

src/connectivity/mod.rs

+    let return_value: Vec<HashSet<usize>> = connectivity::connected_components(&graph.graph)
+        .into_iter()
+        .map(|res_map| res_map.into_iter().map(|x| x.index()).collect())
+        .collect();
+    return_value


Done in d5e5def.

enavarro51 added 5 commits April 23, 2022 15:27

add connected_components to core

d409a07

Adjust Graph use

e117caf

Complete retworkx-core conn_components and add test

76324fb

Add test_connectivity.rs

bb74b5e

Finish tests for connected components in core

6fe44e5

mtreinish reviewed Apr 26, 2022

View reviewed changes

enavarro51 added 2 commits April 26, 2022 13:55

Finish conver to GraphBase

48eb720

Merge branch 'main' into core_connected_components

91bee3a

enavarro51 added 3 commits April 26, 2022 15:30

Convert return from usize to NodeId

cb53f6a

Fmt

66975aa

Merge branch 'core_connected_components' of github.com:enavarro51/ret…

16e3e2a

…workx into core_connected_components

georgios-ts reviewed Apr 27, 2022

View reviewed changes

enavarro51 added 3 commits April 27, 2022 07:33

Fix tests and traits

e46c0f6

Merge branch 'main' into core_connected_components

36ddb69

Make bfs non-pub

17bb73a

enavarro51 added 4 commits April 29, 2022 16:43

Finish doc tests and set up core test dir

af5b5ff

Add full testing for connected components

a31dc82

and remove retworkx/src/connectivity/conn_components.rs and modify retworkx/src/connectivity/mod.rs to point to retworkx/retworkx-core/src/connectivity/conn_components.rs

Release note

f3a7562

Merge branch 'main' into core_connected_components

a5c8058

enavarro51 added 2 commits May 1, 2022 15:24

Lint

93cbad5

Merge branch 'core_connected_components' of github.com:enavarro51/ret…

82950c5

…workx into core_connected_components

georgios-ts reviewed May 2, 2022

View reviewed changes

enavarro51 mentioned this pull request May 2, 2022

Move more connected components functions to retworkx-core #602

Open

enavarro51 added 2 commits May 9, 2022 12:45

Add weakly directed test

dde263e

Use neighbors_directed

6bf462b

enavarro51 added 3 commits May 14, 2022 13:24

Merge branch 'main' into core_connected_components

7c79cdb

Cleanup

7200124

Lint

914ab22

enavarro51 changed the title ~~[WIP] Add connected components to retworkx-core~~ Add connected components to retworkx-core May 16, 2022

mtreinish approved these changes May 19, 2022

View reviewed changes

enavarro51 added 2 commits May 20, 2022 14:09

Docs and clean up

d5e5def

Merge branch 'main' into core_connected_components

6d029d5

georgios-ts added the automerge Queue a approved PR for merging label May 23, 2022

mergify bot merged commit 0c253be into Qiskit:main May 23, 2022

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Add connected components to retworkx-core #595

Add connected components to retworkx-core #595

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	/// * `graph.visit_map()` - The visit map for the graph
	/// * `discovered` - The visit map for the graph

Add connected components to retworkx-core #595

Add connected components to retworkx-core #595

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