Merge branch '3.4' of https://github.com/tractor/tractor into 3.4

tractor · Feb 22, 2024 · 2a93c4d · 2a93c4d
2 parents 1754f5e + 48374cb
commit 2a93c4d
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Showing 3 changed files with 33 additions and 16 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -22,7 +22,7 @@ jobs:
 
     steps:
     - name: Check out code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         submodules: true
 
@@ -37,7 +37,7 @@ jobs:
 
     - name: Cache dependencies
       id: cache-deps
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: lib/R
         key: ${{ runner.os }}-deps-${{ matrix.R }}-${{ hashFiles('lib/*/DESCRIPTION') }}

diff --git a/tractor.graph/inst/tinytest/test-15-partition.R b/tractor.graph/inst/tinytest/test-15-partition.R
@@ -15,17 +15,25 @@ expect_true(all(t_partitioned$getVertexWeights() %in% 0:1))
 expect_equal_to_reference(modularityMatrix(graph), "modmat.rds")
 expect_true(modularity(t_partitioned) >= 0)
 expect_true(modularity(t_partitioned) <= 1)
-i_partitioned <- igraph::cluster_leading_eigen(as(graph, "igraph"))
-expect_equal(modularity(t_partitioned), igraph::modularity(i_partitioned), tolerance=1e-3)
+
+if (requireNamespace("igraph", quietly=TRUE))
+{
+    i_partitioned <- igraph::cluster_leading_eigen(as(graph, "igraph"))
+    expect_equal(modularity(t_partitioned), igraph::modularity(i_partitioned), tolerance=1e-3)
+}
 
 # Binarised version
 graph$binarise()
 t_partitioned <- partitionGraph(graph, method="modularity")
 expect_equal(t_partitioned$nCommunities(), 3L)
 expect_true(all(t_partitioned$getVertexWeights() %in% 0:1))
-i_partitioned <- igraph::cluster_leading_eigen(as(graph, "igraph"))
-expect_true(membershipMatches(t_partitioned$getVertexMemberships(), i_partitioned$membership))
-expect_equal(modularity(t_partitioned), igraph::modularity(i_partitioned))
+
+if (requireNamespace("igraph", quietly=TRUE))
+{
+    i_partitioned <- igraph::cluster_leading_eigen(as(graph, "igraph"))
+    expect_true(membershipMatches(t_partitioned$getVertexMemberships(), i_partitioned$membership))
+    expect_equal(modularity(t_partitioned), igraph::modularity(i_partitioned))
+}
 
 graph <- readGraphFile("graph")
 pn <- principalNetworks(graph)$graph$serialise()

diff --git a/tractor.graph/inst/tinytest/test-20-fuzz.R b/tractor.graph/inst/tinytest/test-20-fuzz.R
@@ -31,7 +31,21 @@ testMetricAgreement <- function (t_graph, i_graph = as(t_graph,"igraph"))
     i_density <- igraph::edge_density(i_graph, loops=t_graph$isSelfConnected())
     expect_equal(t_density, i_density, info=info)
 
+    # Some metrics are not supported by igraph for directed graphs
+    if (!t_graph$isDirected())
+    {
+        # Clustering coefficients
+        # igraph returns NaN when there are no triangles
+        i_clustering <- igraph::transitivity(i_graph, "barrat", isolates="zero")
+        expect_equal(clusteringCoefficients(t_graph,method="barrat"), i_clustering, info=info)
+
+        # Laplacian matrix
+        expect_equivalent(laplacianMatrix(t_graph), igraph::laplacian_matrix(i_graph,sparse=FALSE), info=info)
+    }
+
     # Convert weights to costs
+    # NB: this is needed only for quantities tested below, so timing of the
+    # inversion is significant
     if (t_graph$isWeighted())
         igraph::E(i_graph)$weight <- 1 / igraph::E(i_graph)$weight
 
@@ -50,23 +64,18 @@ testMetricAgreement <- function (t_graph, i_graph = as(t_graph,"igraph"))
     expect_equivalent(graphEfficiency(t_graph,type="global"), i_global_eff, info=info)
 
     # Some metrics are not supported by igraph for directed graphs
-    if(!t_graph$isDirected())
+    if (!t_graph$isDirected())
     {
-        # Clustering coefficients
-        # igraph returns NaN when there are no triangles
-        i_clustering <- igraph::transitivity(i_graph, "barrat", isolates="zero")
-        expect_equal(clusteringCoefficients(t_graph,method="barrat"), i_clustering, info=info)
-
         # Betweenness centrality
         t_bc <- structure(betweennessCentrality(t_graph$getAssociationMatrix()), dim=NULL)
         i_bc <- igraph::betweenness(i_graph)
         expect_equal(t_bc, 2*i_bc, info=info)
-
-        # Laplacian matrix
-        expect_equivalent(laplacianMatrix(t_graph), igraph::laplacian_matrix(i_graph,sparse=FALSE), info=info)
     }
 }
 
+if (!requireNamespace("igraph", quietly=TRUE))
+    exit_file("The \"igraph\" package is not available")
+
 # Random binary graph
 testMetricAgreement(randomGraph(10, M=20))