Merge pull request #264 from MaLoefUDS/dev

Fix igraph deprecation warnings as well as a bug in issue network construction

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

.github/workflows/pull_request.yml

@@ -11,7 +11,7 @@
 ## with this program; if not, write to the Free Software Foundation, Inc.,
 ## 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 ##
-## Copyright 2023-2024 by Maximilian Löffler <s8maloef@cs.uni-saarland.de>
+## Copyright 2023-2024 by Maximilian Löffler <s8maloef@stud.uni-saarland.de>
 ## Copyright 2024 by Thomas Bock <bockthom@cs.uni-saarland.de>
 ## All Rights Reserved.
 
@@ -37,7 +37,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        r-version: ['3.6', '4.0', '4.1', '4.2', '4.3', 'latest']
+        r-version: ['4.0', '4.1', '4.2', '4.3', '4.4', 'latest']
 
     steps:
       - name: Checkout Repo

NEWS.md

@@ -11,12 +11,18 @@
 - Add helper function for prefixing function names with file names in `util-read.R` (PR #252, f8ea987b138173cf0509c7910e0572d8ee1b3f1f)
 - Add line-based code coverage reports into CI pipeline. Coverage reports are generated by `coverage.R` (PR #262, 10cac49d005e87c3964cc61711e7f5acef749626, b3b9f4ac7a9911bd00293c68fac88e0f9033bdfb, c815d18dc6266d620a7a145493417b87ac08679e, e8093525fdaf46e54f2f7fcc6358ca7892e795e5, 32d04823e2007c63d2a43ce59bea3057327c19a7)
 - Add the possibility to split data time-based by multiple data sources (PR #261, 1088395f46b84028c8d7c463ca86b5dc38500c26, e1f79fc9e40cd6f41c946be42db364b2101cfe10, 0bb187fec0fd801d7634bf8d5180525770f6ab0b, 371a97ac6ebf3de4fe9360dea79d62e2ed3ef585)
+- Add tests for uncovered functionality in `util-misc.R` and `util-networks.R` (PR #264, ff30f3238b1bf2539280d0d055a5d925c197c271, af80551d0615a49b86e45ff596bd75941ee88f91)
 
 ### Changed/Improved
 
+- 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, 0df9d5bf6bafbb5d440f4c47db4ec901cf11f037)
+- Deprecate support for R version 3.6 (PR #264, c8e6f45111e487fadbe7f0a13c7595eb23f3af6e, fb3f5474259d4a88f4ff545691cca9d1ccde90e3)
+- Explicitly add R version 4.4 to the CI test pipeline (c8e6f45111e487fadbe7f0a13c7595eb23f3af6e)
+
 ### Fixed
 
-- Ensure the correct installation of a compatible `Matrix` version for R 3.6 (PR #262, cb1cf42b2136f35b7e85239d36d5f91ff05d8cd7)
+- Fix the creation of edgelists for issue-based artifact-networks by correctly iterating over the issue data (PR #264, 321d85043112971c04998249c14a0677a32c9004)
 
 ## 4.4
 

README.md

@@ -59,14 +59,14 @@ While using the package, we require the following infrastructure.
 
 #### [`R`](https://www.r-project.org/)
 
-Minimum requirement is `R` version `3.4.4`. Hence, later `R` versions also work. (Earlier `R` versions beginning from version `3.3.1` on should also work, but some packages are not available any more for these versions, so we do not test them any more in our CI pipeline.)
+Minimum requirement is `R` version `4.0.5`. Hence, later `R` versions also work. (Earlier `R` versions beginning from version `3.3.1` on should also work, but some packages are not available any more for these versions, so we do not test them any more in our CI pipeline.)
 
-We currently *recommend* `R` version `4.1.1` or `3.6.3` for reliability reasons and `packrat` compatibility, but also later `R` versions should work (and are tested using our CI script).
+We currently *recommend* `R` version `4.1.1` or `4.3.0` for reliability reasons and `packrat` compatibility, but also later `R` versions should work (and are tested using our CI script).
 
 #### [`packrat`](http://rstudio.github.io/packrat/) (recommended)
 
 The local package manager of `R` enables the user to store all needed `R` packages for this repository inside the repository itself.
-All `R` tools and IDEs should provide a  more sophisticated interface for the interaction with `packrat`([RStudio](https://www.rstudio.com/) does).
+All `R` tools and IDEs should provide a more sophisticated interface for the interaction with `packrat`([RStudio](https://www.rstudio.com/) does).
 
 #### Folder structure of the input data
 
@@ -141,9 +141,9 @@ Alternatively, you can run `Rscript install.R` to install the packages.
 - `viridis`: For plotting of networks with nice colors
 - `jsonlite`: For parsing the issue data
 - `rTensor`: For calculating EDCPTD centrality
-- `Matrix`: For sparse matrix representation of large adjacency matrices
+- `Matrix`: For sparse matrix representation of large adjacency matrices (package version `1.3.0` or higher is mandatory)
 - `fastmap`: For fast implementation of a map
-- `purrr`: For fast implementtion of a mapping function
+- `purrr`: For fast implementation of a mapping function
 
 ### Submodule
 
@@ -574,7 +574,7 @@ There is no way to update the entries, except for the revision-based parameters.
     * [*`TRUE`*, `FALSE`]
 - `issues.from.source`
     * Choose from which sources the issue data on disk is read in. Multiple sources can be chosen.
-    * [*`github`, `jira`*]
+    * [*`github`*, `jira`]
 - `issues.locked`
     * Lock issues to prevent them from being read if not yet present when calling the getter.
     * [`TRUE`, *`FALSE`*]

install.R

@@ -78,9 +78,7 @@ if (length(p) > 0) {
     Matrix.version = installed.packages()[rownames(installed.packages()) == "Matrix", "Version"]
     if (compareVersion(Matrix.version, "1.3.0") == -1) {
         print("WARNING: Matrix version 1.3.0 or higher is necessary for using coronet. Re-install package Matrix...")
-        #install.packages("Matrix", dependencies = NA, verbose = TRUE, quiet = TRUE)
-        matrix.1.3.4.url = "https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.3-4.tar.gz"
-        install.packages(matrix.1.3.4.url, repos = NULL, dependencies = NA, verbose = TRUE, quiet = TRUE)
+        install.packages("Matrix", dependencies = NA, verbose = TRUE, quiet = TRUE)
         Matrix.version = installed.packages()[rownames(installed.packages()) == "Matrix", "Version"]
         if (compareVersion(Matrix.version, "1.3.0") == -1) {
             print("WARNING: Re-installation of package Matrix did not end up in the necessary package version.")

showcase.R

@@ -407,7 +407,7 @@ plot.print.network(g, labels = TRUE)
 lay = matrix(c(  20, 179, 693, 552, 956, 1091, 124, 317, 516, 615, 803, 1038,
                 245, 175, 255, 185, 253, 225,   73,   8,  75,   0,  96,   86),
              nrow = 12, byrow = FALSE) # for sample graph
-g = igraph::set.graph.attribute(g, "layout", lay)
+g = igraph::set_graph_attr(g, "layout", lay)
 plot.print.network(g, labels = TRUE)
 
 ## get the plot object and modify it before plotting

tests/test-core-peripheral.R

@@ -17,7 +17,7 @@
 ## Copyright 2022 by Thomas Bock <bockthom@cs.uni-saarland.de>
 ## Copyright 2019 by Christian Hechtl <hechtl@fim.uni-passau.de>
 ## Copyright 2021 by Christian Hechtl <hechtl@cs.uni-saarland.de>
-## Copyright 2023 by Maximilian Löffler <s8maloef@stud.uni-saarland.de>
+## Copyright 2023-2024 by Maximilian Löffler <s8maloef@stud.uni-saarland.de>
 ## All Rights Reserved.
 
 
@@ -37,6 +37,7 @@ if (!dir.exists(CF.DATA)) CF.DATA = file.path(".", "tests", "codeface-data")
 
 ## Prepare global setting
 proj.conf = ProjectConf$new(CF.DATA, CF.SELECTION.PROCESS, CASESTUDY, ARTIFACT)
+proj.conf$update.value("issues.from.source", c("jira", "github"))
 proj.conf$update.value("issues.only.comments", FALSE)
 proj.data = ProjectData$new(proj.conf)
 
@@ -301,7 +302,7 @@ test_that("Core classification of cochange author networks with vertices but no
     ## create network with one author and no edges
     authors = data.frame(author.name = "A", kind = TYPE.AUTHOR, type = TYPE.AUTHOR)
     edges = create.empty.edge.list()
-    network = igraph::graph.data.frame(edges, directed = TRUE, vertices = authors)
+    network = igraph::graph_from_data_frame(edges, directed = TRUE, vertices = authors)
 
     ## classify the authors into core/peripheral
     classification = get.author.class.by.type(network, type = "network.eigen")
@@ -311,7 +312,7 @@ test_that("Core classification of cochange author networks with vertices but no
     ## create network with several authors and no edges
     authors = data.frame(author.name = LETTERS[1:5], kind = TYPE.AUTHOR, type = TYPE.AUTHOR)
     edges = create.empty.edge.list()
-    network = igraph::graph.data.frame(edges, directed = TRUE, vertices = authors)
+    network = igraph::graph_from_data_frame(edges, directed = TRUE, vertices = authors)
 
     ## classify the authors into core/peripheral
     classification = get.author.class.by.type(network, type = "network.eigen")

tests/test-data.R

@@ -402,6 +402,7 @@ test_that("Filter bots from commit data", {
 
 test_that("Filter bots from issue data", {
     proj.conf = ProjectConf$new(CF.DATA, CF.SELECTION.PROCESS, CASESTUDY, ARTIFACT)
+    proj.conf$update.value("issues.from.source", c("jira", "github"))
     proj.conf$update.value("filter.bots", TRUE)
     ## disable all other filterings
     proj.conf$update.value("issues.only.comments", FALSE)

tests/test-misc.R

@@ -19,6 +19,35 @@
 ## All Rights Reserved.
 
 
+## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
+## Network data ------------------------------------------------------------
+
+test_that("Get edgelist augmented with timestamps", {
+
+    ## construct network
+    edges = list(list("A", "A"), list("D", "C"), list("C", "A"), list("B", "C"))
+    timestamps = c("2016-12-07 15:30:02", "2016-08-07 15:37:02", "2016-07-12 15:59:25", "2016-07-12 15:59:59")
+    network =
+        igraph::make_empty_graph(n = 0, directed = TRUE) +
+        igraph::vertices("A", "B", "C", "D") +
+        igraph::edges(edges, relation = "mail", date = timestamps)
+
+
+    ## get edgelist augmented with timestamps
+    edgelist = get.edgelist.with.timestamps(network)
+
+    ## check correctness
+    expect_equal(names(edgelist), c("from", "to", "date"))
+    expect_equal(nrow(edgelist), 4)
+    lapply(1:4, function(i) {
+        actual = edgelist[i, ]
+        expect_equal(actual[["from"]], edges[[i]][[1]])
+        expect_equal(actual[["to"]], edges[[i]][[2]])
+        expect_equal(actual[["date"]], timestamps[i])
+    })
+})
+
+
 ## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
 ## Parameter verification --------------------------------------------------
 

tests/test-networks-artifact.R

@@ -56,7 +56,7 @@ test_that("Network construction of the undirected artifact-cochange network", {
         relation = "cochange"
     )
     ## 3) build expected network
-    network.expected = igraph::graph.data.frame(edges, directed = FALSE, vertices = vertices)
+    network.expected = igraph::graph_from_data_frame(edges, directed = FALSE, vertices = vertices)
 
 
     ##
@@ -147,6 +147,7 @@ patrick::with_parameters_test_that("Network construction of an issue-based artif
 
     ## configurations
     proj.conf = ProjectConf$new(CF.DATA, CF.SELECTION.PROCESS, CASESTUDY, ARTIFACT)
+    proj.conf$update.value("issues.from.source", c("jira", "github"))
     proj.conf$update.value("issues.only.comments", FALSE)
     net.conf = NetworkConf$new()
     net.conf$update.values(updated.values = list(artifact.relation = "issue", artifact.directed = test.directed))
@@ -156,7 +157,7 @@ patrick::with_parameters_test_that("Network construction of an issue-based artif
     network.builder = NetworkBuilder$new(project.data = proj.data, network.conf = net.conf)
 
     ## build expected network
-    network.expected = igraph::graph.data.frame(edges, directed = test.directed, vertices = vertices)
+    network.expected = igraph::graph_from_data_frame(edges, directed = test.directed, vertices = vertices)
 
     ## build network
     network.built = network.builder$get.artifact.network()
@@ -176,6 +177,7 @@ patrick::with_parameters_test_that("Network construction of an empty 'comments-o
 
     ## configurations
     proj.conf = ProjectConf$new(CF.DATA, CF.SELECTION.PROCESS, CASESTUDY, ARTIFACT)
+    proj.conf$update.value("issues.from.source", c("jira", "github"))
     net.conf = NetworkConf$new()
     net.conf$update.values(updated.values = list(artifact.relation = "issue", artifact.directed = test.directed))
 
@@ -204,7 +206,7 @@ patrick::with_parameters_test_that("Network construction of an empty 'comments-o
     )
 
     ## build expected network
-    network.expected = igraph::graph.data.frame(edges, directed = test.directed, vertices = vertices)
+    network.expected = igraph::graph_from_data_frame(edges, directed = test.directed, vertices = vertices)
 
     ## test
     assert.networks.equal(network.built, network.expected)
@@ -254,7 +256,7 @@ patrick::with_parameters_test_that("Network construction with commit-interaction
         type = c(TYPE.EDGES.INTRA, TYPE.EDGES.INTRA, TYPE.EDGES.INTRA, TYPE.EDGES.INTRA),
         relation = c("commit.interaction", "commit.interaction", "commit.interaction", "commit.interaction")
         )
-    network = igraph::graph.data.frame(edges, directed = test.directed, vertices = vertices)
+    network = igraph::graph_from_data_frame(edges, directed = test.directed, vertices = vertices)
 
     expect_true(igraph::identical_graphs(network.built, network))
 }, patrick::cases(
@@ -303,7 +305,7 @@ patrick::with_parameters_test_that("Network construction with commit-interaction
         type = c(TYPE.EDGES.INTRA, TYPE.EDGES.INTRA, TYPE.EDGES.INTRA, TYPE.EDGES.INTRA),
         relation = c("commit.interaction", "commit.interaction", "commit.interaction", "commit.interaction")
         )
-    network = igraph::graph.data.frame(edges, directed = test.directed, vertices = vertices)
+    network = igraph::graph_from_data_frame(edges, directed = test.directed, vertices = vertices)
 
     expect_true(igraph::identical_graphs(network.built, network))
 }, patrick::cases(

tests/test-networks-author.R

@@ -147,6 +147,7 @@ test_that("Amount of authors (author.all.authors, author.only.committers).", {
 
                 ## configurations
                 proj.conf = ProjectConf$new(CF.DATA, CF.SELECTION.PROCESS, CASESTUDY, ARTIFACT)
+                proj.conf$update.value("issues.from.source", c("jira", "github"))
                 proj.conf$update.value("commits.filter.base.artifact", FALSE)
                 proj.conf$update.value("commits.filter.untracked.files", TRUE)
                 net.conf = NetworkConf$new()
@@ -230,7 +231,7 @@ test_that("Network construction of the undirected author-cochange network", {
                       relation = "cochange"
     )
     ## 3) build expected network
-    network.expected = igraph::graph.data.frame(data, directed = FALSE, vertices = authors)
+    network.expected = igraph::graph_from_data_frame(data, directed = FALSE, vertices = authors)
 
 
     ##
@@ -314,7 +315,7 @@ test_that("Network construction of the undirected but temorally ordered author-c
     )
 
     ## build expected network
-    network.expected = igraph::graph.data.frame(data, directed = FALSE, vertices = authors)
+    network.expected = igraph::graph_from_data_frame(data, directed = FALSE, vertices = authors)
 
     expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -355,7 +356,7 @@ test_that("Network construction of the directed author-cochange network", {
     )
 
     ## build expected network
-    network.expected = igraph::graph.data.frame(data, directed = TRUE, vertices = authors)
+    network.expected = igraph::graph_from_data_frame(data, directed = TRUE, vertices = authors)
 
     expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -401,7 +402,7 @@ test_that("Network construction of the directed author-cochange network without
     )
 
     ## build expected network
-    network.expected = igraph::graph.data.frame(data, directed = TRUE, vertices = authors)
+    network.expected = igraph::graph_from_data_frame(data, directed = TRUE, vertices = authors)
 
     expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -427,7 +428,7 @@ test_that("Network construction of the undirected simplified author-cochange net
                          type = TYPE.AUTHOR)
 
     ## make test independent of igraph version
-    date.attr = igraph::get.edge.attribute(network.built, "date")
+    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)
 
@@ -462,7 +463,7 @@ test_that("Network construction of the undirected simplified author-cochange net
     data[["artifact"]] = unclass(data[["artifact"]])
 
     ## build expected network
-    network.expected = igraph::graph.data.frame(data, directed = FALSE, vertices = authors)
+    network.expected = igraph::graph_from_data_frame(data, directed = FALSE, vertices = authors)
 
     expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -472,6 +473,7 @@ test_that("Network construction of the undirected author-issue network with all
 
     ## configurations
     proj.conf = ProjectConf$new(CF.DATA, CF.SELECTION.PROCESS, CASESTUDY, ARTIFACT)
+    proj.conf$update.value("issues.from.source", c("jira", "github"))
     proj.conf$update.value("commits.filter.base.artifact", FALSE)
     proj.conf$update.value("issues.only.comments", FALSE)
     net.conf = NetworkConf$new()
@@ -586,7 +588,7 @@ test_that("Network construction of the undirected author-issue network with all
             )
 
     ## build expected network
-    network.expected = igraph::graph.data.frame(edges, directed = FALSE, vertices = vertices)
+    network.expected = igraph::graph_from_data_frame(edges, directed = FALSE, vertices = vertices)
 
     expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -595,6 +597,7 @@ test_that("Network construction of the undirected author-issue network with just
 
     ## configurations
     proj.conf = ProjectConf$new(CF.DATA, CF.SELECTION.PROCESS, CASESTUDY, ARTIFACT)
+    proj.conf$update.value("issues.from.source", c("jira", "github"))
     proj.conf$update.value("commits.filter.base.artifact", FALSE)
     net.conf = NetworkConf$new()
     net.conf$update.values(updated.values = list(author.relation = "issue"))
@@ -645,7 +648,7 @@ test_that("Network construction of the undirected author-issue network with just
                        relation = "issue")
 
     ## build expected network
-    network.expected = igraph::graph.data.frame(edges, directed = FALSE, vertices = vertices)
+    network.expected = igraph::graph_from_data_frame(edges, directed = FALSE, vertices = vertices)
 
     expect_true(igraph::identical_graphs(network.built, network.expected))
 })
@@ -673,7 +676,7 @@ test_that("Network construction with only untracked files (no edges expected)",
     ## build expected network (two vertices, no edges)
     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 = igraph::add_vertices(network.expected, nv = max(lengths(vertices)), attr = vertices)
 
     ## test
     expect_true(igraph::identical_graphs(network.built, network.expected))
@@ -721,10 +724,10 @@ patrick::with_parameters_test_that("Network construction with commit-interaction
         type = c(TYPE.EDGES.INTRA, TYPE.EDGES.INTRA, TYPE.EDGES.INTRA, TYPE.EDGES.INTRA),
         relation = c("commit.interaction", "commit.interaction", "commit.interaction", "commit.interaction")
         )
-    network = igraph::graph.data.frame(edges, directed = test.directed, vertices = vertices)
+    network = igraph::graph_from_data_frame(edges, directed = test.directed, vertices = vertices)
 
     expect_true(igraph::identical_graphs(network.built, network))
 }, patrick::cases(
     "directed: FALSE" = list(test.directed = FALSE),
     "directed: TRUE" = list(test.directed = TRUE)
-))
+))