Merge pull request #274 from maxloeffler/dev

Change default representation of edge attributes from vectors to lists & other miscellaneous adjustments

Reviewed-by: Thomas Bock <bockthom@cs.uni-saarland.de>

NEWS.md

@@ -4,6 +4,10 @@
 
 ## unversioned
 
+### Announcement
+
+- Coronet is not compatible with `igraph` versions below 2.1.0 anymore. This is due to the simultaneous deprecation of `subgraph.edges` and the introduction of the replacement for it, `subgraph_from_edges`, in igraph version 2.1.0.
+
 ### Added
 
 - Add commit-interaction data and add functions `read.commit.interactions` for reading, as well as `get.commit.interactions`, `set.commit.interactions` and utility functions for working with commit-interaction data (PR #252, d82857fbebd1111bb16588a4223bb24a8dcd07de, b4fd2a29c9b5fd561b1106c6febb54a32b0085ab, fd0aa05f824b93545ae8e05833b95b3bd9809286, bca35760eb0aac86c04923f2d534b2d8cece204e, PR #263, 849123a8b7d898fbb1343745ecffc1f6000c9367, 3fb7437b68950303916b62984fa449732c70353e, 170bc66eb779d7cf2ab504db7c3f4ec483103838) as well as tests for these features (PR #252, eeba7e29932bc973513c963fb9e716e9230d570f, 8bb39f4df39b49dfaff8f19feb6db5e5fbd81fac, 54b6f655248720436af116fe72521f9cb0348429, 7a5497aaf9114017d1b3b9b68b6cccd7ca8ac114, 7b8585f87675795822c07230192d6454de31dcc7, ef725407bf8818c8fff96ea6f343338b7162cbe0,)
@@ -18,16 +22,21 @@
 
 ### Changed/Improved
 
+- **Breaking Change**: Change the default representation of edge attributes from vectors to lists. This change is necessary for the interplay of coronet networks with certain `igraph` functionality since igraph version 2.1.0 (PR #274, 1c35d1fa2548deb297dbfa5e2b07fce31962c5b7, eda30b838369ec46376812298a3ea8159eec5789, 0c6b2eba79b37f8ef2af7ffc41d86f1f307581bf, 44c7b72e3234cb332bb2713fb408c124e67255d9, 7303eabef6a78198575fe5bdfc02813fde3d3974, 0c27012641d24e19e5fa037406b480034c93f1aa)
 - Change the default value for the `issues.from.source` configuration parameter. Instead of reading JIRA and GitHub issues together, which was the previous default, the new default value causes only GitHub issue data to be read. To restore the previous default behavior and read data from both issue sources, this now needs to be manually configured when needed. (PR #264, 5ff83c364f6bfc1e6ff95e9c5f1087e031c48a5d, 8c8080cb9caf115f19d9f145ad6e6c108b131a67, 8bcbc81db521877908d2e5c2989082ed672f2a3b)
-- Replace deprecated `igraph` functions by their preferred alternatives (PR #264, PR #268, 0df9d5bf6bafbb5d440f4c47db4ec901cf11f037, 7ac840d287a862eff61b1a84e194a4cba399f9e5)
+- Replace deprecated `igraph` functions by their preferred alternatives (PR #264, PR #268, PR #274, 0df9d5bf6bafbb5d440f4c47db4ec901cf11f037, 7ac840d287a862eff61b1a84e194a4cba399f9e5, e3617b8c6b21fb4242c1d392124813501069ca84, 4b0d5221dd56bb3c9ddf196f67719d4f503d9b61)
 - Deprecate support for R version 3.6 (PR #264, c8e6f45111e487fadbe7f0a13c7595eb23f3af6e, fb3f5474259d4a88f4ff545691cca9d1ccde90e3)
 - Explicitly add R version 4.4 to the CI test pipeline (c8e6f45111e487fadbe7f0a13c7595eb23f3af6e)
 - Refactor function `construct.edge.list.from.key.value.list` to be more readable (PR #263, 05c3bc09cb1d396fd59c34a88030cdca58fd04dd)
+- Update necessary `igraph` version to 2.1.0 in `README.md` (PR #274, 6c3bcd1a2366d0d3a176d9fde95b8356b0158da3)
 
 ### Fixed
 
 - Fix the creation of edgelists for issue-based artifact-networks by correctly iterating over the issue data (PR #264, 321d85043112971c04998249c14a0677a32c9004)
 - Fix a bug in `extract.timestamps` that occurs when the first `data.source` contains empty data and that leads to a return value of type numeric which should be POSIXct (PR #270, 10696e4cf4ae92371917ed8ccaec2b0183da145c, 646c01a42ad8decfbc9040030e790e51cb65cffd)
+- Fix `read.commit.interactions` by explicitly considering non-existent commit interactions (PR #274, f591528a0f1f11b1a4390949ab770f3f74a766f9)
+- Add range information to network-splits when splitting a network using `split.network.time.based.by.ranges`. This effect also propagates into `split.networks.time.based` (PR #274, 87911ade231c44b93be194a1d6734f7de043a4af)
+- Adjust `metrics.scale.freeness` and `metrics.is.scale.free` functions to be compatible with both older and newer igraph versions (PR #274, 4b0d5221dd56bb3c9ddf196f67719d4f503d9b61)
 
 ## 4.4
 

README.md

@@ -125,7 +125,7 @@ Alternatively, you can run `Rscript install.R` to install the packages.
 
 - `yaml`: To read YAML configuration files (i.e., Codeface configuration files)
 - `R6`: For proper classes
-- `igraph`: For the construction of networks (package version `1.3.0` or higher is recommended)
+- `igraph`: For the construction of networks (package version `2.1.0` or higher is required)
 - `plyr`: For the `dlply` splitting-function and `rbind.fill`
 - `parallel`: For parallelization
 - `logging`: Logging

showcase.R

@@ -404,7 +404,7 @@ plot.network(g.simplified)
 
 ## construct sample network for plotting
 g = get.sample.network()
-g = igraph::as.directed(g, mode = "arbitrary")
+g = igraph::as_directed(g, mode = "arbitrary")
 g = g + igraph::edges("A6", "A5", type = TYPE.EDGES.INTRA, weight = 2,
                       relation = "callgraph", artifact.type = "Feature")
 g = simplify.network(g)

tests/test-networks-artifact.R

@@ -57,6 +57,7 @@ test_that("Network construction of the undirected artifact-cochange network", {
     )
     ## 3) build expected network
     network.expected = igraph::graph_from_data_frame(edges, directed = FALSE, vertices = vertices)
+    network.expected = convert.edge.attributes.to.list(network.expected)
 
 
     ##
@@ -158,6 +159,7 @@ patrick::with_parameters_test_that("Network construction of an issue-based artif
 
     ## build expected network
     network.expected = igraph::graph_from_data_frame(edges, directed = test.directed, vertices = vertices)
+    network.expected = convert.edge.attributes.to.list(network.expected)
 
     ## build network
     network.built = network.builder$get.artifact.network()
@@ -207,6 +209,7 @@ patrick::with_parameters_test_that("Network construction of an empty 'comments-o
 
     ## build expected network
     network.expected = igraph::graph_from_data_frame(edges, directed = test.directed, vertices = vertices)
+    network.expected = convert.edge.attributes.to.list(network.expected)
 
     ## test
     assert.networks.equal(network.built, network.expected)
@@ -258,6 +261,7 @@ patrick::with_parameters_test_that("Network construction with commit-interaction
         relation = c("commit.interaction", "commit.interaction", "commit.interaction", "commit.interaction")
         )
     network = igraph::graph_from_data_frame(edges, directed = test.directed, vertices = vertices)
+    network = convert.edge.attributes.to.list(network)
 
     expect_true(igraph::identical_graphs(network.built, network))
 }, patrick::cases(
@@ -308,6 +312,7 @@ patrick::with_parameters_test_that("Network construction with commit-interaction
         relation = c("commit.interaction", "commit.interaction", "commit.interaction", "commit.interaction")
         )
     network = igraph::graph_from_data_frame(edges, directed = test.directed, vertices = vertices)
+    network = convert.edge.attributes.to.list(network)
 
     expect_true(igraph::identical_graphs(network.built, network))
 }, patrick::cases(

tests/test-networks-author.R

@@ -232,6 +232,7 @@ test_that("Network construction of the undirected author-cochange network", {
     )
     ## 3) build expected network
     network.expected = igraph::graph_from_data_frame(data, directed = FALSE, vertices = authors)
+    network.expected = convert.edge.attributes.to.list(network.expected)
 
 
     ##
@@ -316,6 +317,7 @@ test_that("Network construction of the undirected but temorally ordered author-c
 
     ## build expected network
     network.expected = igraph::graph_from_data_frame(data, directed = FALSE, vertices = authors)
+    network.expected = convert.edge.attributes.to.list(network.expected)
 
     expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -357,6 +359,7 @@ test_that("Network construction of the directed author-cochange network", {
 
     ## build expected network
     network.expected = igraph::graph_from_data_frame(data, directed = TRUE, vertices = authors)
+    network.expected = convert.edge.attributes.to.list(network.expected)
 
     expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -403,6 +406,7 @@ test_that("Network construction of the directed author-cochange network without
 
     ## build expected network
     network.expected = igraph::graph_from_data_frame(data, directed = TRUE, vertices = authors)
+    network.expected = convert.edge.attributes.to.list(network.expected)
 
     expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -431,25 +435,26 @@ test_that("Network construction of the undirected simplified author-cochange net
     date.attr = igraph::edge_attr(network.built, "date")
     date.conversion.function = ifelse(all(sapply(date.attr, lubridate::is.POSIXct)),
                                       get.date.from.unix.timestamp, identity)
+    date.conversion.function = get.date.from.unix.timestamp
 
     ## edge attributes
     data = data.frame(
         from = c("Björn", "Olaf", "Olaf", "Karl"),
         to = c("Olaf", "Karl", "Thomas", "Thomas"),
-        date = I(list(date.conversion.function(c(1468339139, 1468339245)),
-                      date.conversion.function(c(1468339541, 1468339570)),
-                      date.conversion.function(c(1468339541, 1468339592)),
-                      date.conversion.function(c(1468339570, 1468339592)))),
-        artifact.type = I(list(c("Feature", "Feature"), c("Feature", "Feature"), c("Feature", "Feature"),
-                               c("Feature", "Feature"))),
+        date = I(list(as.list(date.conversion.function(c(1468339139, 1468339245))),
+                      as.list(date.conversion.function(c(1468339541, 1468339570))),
+                      as.list(date.conversion.function(c(1468339541, 1468339592))),
+                      as.list(date.conversion.function(c(1468339570, 1468339592))))),
+        artifact.type = I(list(list("Feature", "Feature"), list("Feature", "Feature"), list("Feature", "Feature"),
+                               list("Feature", "Feature"))),
         hash = I(list(
-            c("72c8dd25d3dd6d18f46e2b26a5f5b1e2e8dc28d0", "5a5ec9675e98187e1e92561e1888aa6f04faa338"),
-            c("3a0ed78458b3976243db6829f63eba3eead26774", "1143db502761379c2bfcecc2007fc34282e7ee61"),
-            c("3a0ed78458b3976243db6829f63eba3eead26774", "0a1a5c523d835459c42f33e863623138555e2526"),
-            c("1143db502761379c2bfcecc2007fc34282e7ee61", "0a1a5c523d835459c42f33e863623138555e2526"))),
-        file = I(list(c("test.c", "test.c"), c("test2.c", "test3.c"), c("test2.c", "test2.c"), c("test3.c", "test2.c"))),
-        artifact = I(list(c("A", "A"), c("Base_Feature", "Base_Feature"), c("Base_Feature", "Base_Feature"),
-                          c("Base_Feature", "Base_Feature"))),
+            list("72c8dd25d3dd6d18f46e2b26a5f5b1e2e8dc28d0", "5a5ec9675e98187e1e92561e1888aa6f04faa338"),
+            list("3a0ed78458b3976243db6829f63eba3eead26774", "1143db502761379c2bfcecc2007fc34282e7ee61"),
+            list("3a0ed78458b3976243db6829f63eba3eead26774", "0a1a5c523d835459c42f33e863623138555e2526"),
+            list("1143db502761379c2bfcecc2007fc34282e7ee61", "0a1a5c523d835459c42f33e863623138555e2526"))),
+        file = I(list(list("test.c", "test.c"), list("test2.c", "test3.c"), list("test2.c", "test2.c"), list("test3.c", "test2.c"))),
+        artifact = I(list(list("A", "A"), list("Base_Feature", "Base_Feature"), list("Base_Feature", "Base_Feature"),
+                          list("Base_Feature", "Base_Feature"))),
         weight = 2,
         type = TYPE.EDGES.INTRA,
         relation = "cochange"
@@ -589,6 +594,7 @@ test_that("Network construction of the undirected author-issue network with all
 
     ## build expected network
     network.expected = igraph::graph_from_data_frame(edges, directed = FALSE, vertices = vertices)
+    network.expected = convert.edge.attributes.to.list(network.expected)
 
     expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -649,6 +655,7 @@ test_that("Network construction of the undirected author-issue network with just
 
     ## build expected network
     network.expected = igraph::graph_from_data_frame(edges, directed = FALSE, vertices = vertices)
+    network.expected = convert.edge.attributes.to.list(network.expected)
 
     expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -677,6 +684,7 @@ test_that("Network construction with only untracked files (no edges expected)",
     vertices = list(name = c("Karl", "Thomas"), kind = TYPE.AUTHOR, type = TYPE.AUTHOR)
     network.expected = create.empty.network(directed = FALSE, add.attributes = TRUE)
     network.expected = igraph::add_vertices(network.expected, nv = max(lengths(vertices)), attr = vertices)
+    network.expected = convert.edge.attributes.to.list(network.expected)
 
     ## test
     expect_true(igraph::identical_graphs(network.built, network.expected))
@@ -726,6 +734,7 @@ patrick::with_parameters_test_that("Network construction with commit-interaction
         relation = c("commit.interaction", "commit.interaction", "commit.interaction", "commit.interaction")
         )
     network = igraph::graph_from_data_frame(edges, directed = test.directed, vertices = vertices)
+    network = convert.edge.attributes.to.list(network)
 
     expect_true(igraph::identical_graphs(network.built, network))
 }, patrick::cases(

tests/test-networks-bipartite.R

@@ -84,6 +84,7 @@ test_that("Construction of the bipartite network for the feature artifact with a
     ## 3) construct expected network
     network.expected = igraph::graph_from_data_frame(network.expected.data, vertices = vertices,
                                                 directed = net.conf$get.value("author.directed"))
+    network.expected = convert.edge.attributes.to.list(network.expected)
 
     expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -137,6 +138,7 @@ test_that("Construction of the bipartite network for the file artifact with auth
               ## 3) construct expected network
               network.expected = igraph::graph_from_data_frame(network.expected.data, vertices = vertices,
                                                           directed = net.conf$get.value("author.directed"))
+              network.expected = convert.edge.attributes.to.list(network.expected)
 
               expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -189,6 +191,7 @@ test_that("Construction of the bipartite network for the function artifact with
               )
               ## 3) construct expected network
               network.expected = igraph::graph_from_data_frame(network.expected.data, directed = net.conf$get.value("author.directed"), vertices = vertices)
+              network.expected = convert.edge.attributes.to.list(network.expected)
 
               expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -240,6 +243,7 @@ test_that("Construction of the bipartite network for the featureexpression artif
               ## 3) construct expected network
               network.expected = igraph::graph_from_data_frame(network.expected.data, vertices = vertices,
                                                           directed = net.conf$get.value("author.directed"))
+              network.expected = convert.edge.attributes.to.list(network.expected)
 
               expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -309,6 +313,7 @@ test_that("Construction of the bipartite network for the feature artifact with a
               )
               ## 3) construct expected network
               network.expected = igraph::graph_from_data_frame(network.expected.data, directed = net.conf$get.value("author.directed"), vertices = vertices)
+              network.expected = convert.edge.attributes.to.list(network.expected)
 
               expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -362,6 +367,7 @@ test_that("Construction of the directed bipartite network for the feature artifa
               ## 3) construct expected network
               network.expected = igraph::graph_from_data_frame(network.expected.data, vertices = vertices,
                                                           directed = net.conf$get.value("author.directed"))
+              network.expected = convert.edge.attributes.to.list(network.expected)
 
               expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -415,6 +421,7 @@ test_that("Construction of the directed bipartite network for the file artifact
               ## 3) construct expected network
               network.expected = igraph::graph_from_data_frame(network.expected.data, vertices = vertices,
                                                           directed = net.conf$get.value("author.directed"))
+              network.expected = convert.edge.attributes.to.list(network.expected)
 
               expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -469,6 +476,7 @@ test_that("Construction of the directed bipartite network for the function artif
               ## 3) construct expected network
               network.expected = igraph::graph_from_data_frame(network.expected.data, vertices = vertices,
                                                           directed = net.conf$get.value("author.directed"))
+              network.expected = convert.edge.attributes.to.list(network.expected)
 
               expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -521,6 +529,7 @@ test_that("Construction of the directed bipartite network for the featureexpress
               ## 3) construct expected network
               network.expected = igraph::graph_from_data_frame(network.expected.data, vertices = vertices,
                                                           directed = net.conf$get.value("author.directed"))
+              network.expected = convert.edge.attributes.to.list(network.expected)
 
               expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -563,6 +572,7 @@ test_that("Network construction with only untracked files (no edges and artifact
                                                         directed = net.conf$get.value("author.directed"))
     ## 4) remove edge again
     network.expected = igraph::delete_edges(network.expected, 1)
+    network.expected = convert.edge.attributes.to.list(network.expected)
 
     ## test
     expect_true(igraph::identical_graphs(network.built, network.expected))