Adding commit-interactions

NEWS.md

@@ -2,6 +2,18 @@
 
 # coronet – Changelog
 
+## unversioned
+
+### 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) as well as tests for these features (PR #252, eeba7e29932bc973513c963fb9e716e9230d570f, 8bb39f4df39b49dfaff8f19feb6db5e5fbd81fac, 54b6f655248720436af116fe72521f9cb0348429, 7a5497aaf9114017d1b3b9b68b6cccd7ca8ac114, 7b8585f87675795822c07230192d6454de31dcc7, ef725407bf8818c8fff96ea6f343338b7162cbe0)
+- Add commit-interaction networks that can be created with `create.author.network` and `create.artifact.network` if the `artifact.relation` and `author.relation` is configured to be `commit.interaction` (PR #252, d82857fbebd1111bb16588a4223bb24a8dcd07de, 329d97ec3de36a9e1bcadc0c7a53c1d92e8b481c) as well as tests for these features (PR #252, 07e7ed744209b0251217fa8f7f35d9b9875face2, 7068cfa10d993dcae3f5e3f76f8cafa99fa8b350)
+- Add helper function for prefixing function names with file names in `util-read.R` (PR #252, f8ea987b138173cf0509c7910e0572d8ee1b3f1f)
+
+### Changed/Improved
+
+### Fixed
+
 ## 4.4
 
 ### Announcement

README.md

@@ -142,6 +142,8 @@ Alternatively, you can run `Rscript install.R` to install the packages.
 - `jsonlite`: For parsing the issue data
 - `rTensor`: For calculating EDCPTD centrality
 - `Matrix`: For sparse matrix representation of large adjacency matrices
+- `fastmap`: For fast implementation of a map
+- `purrr`: For fast implementtion of a mapping function
 
 ### Submodule
 
@@ -264,6 +266,11 @@ Relations determine which information is used to construct edges among the verti
     * For artifact networks (configured via `artifact.relation` in the [`NetworkConf`](#networkconf)), source-code artifacts are connected when they reference each other (i.e., one artifact calls a function contained in the other artifact).
     * For bipartite networks (configured via `artifact.relation` in the [`NetworkConf`](#networkconf)), authors get linked to all source-code artifacts they have changed in their respective commits (same as for the relation `cochange`).
 
+- `commit.interaction`
+    * For author networks (configured via `author.relation` in the [`NetworkConf`](#networkconf)), authors who contribute to interacting commits are connected with an edge.
+    * For artifact networks (configured via `artifact.relation` in the [`NetworkConf`](#networkconf)), artifacts are connected when there is an interaction between two commits that occur in the artifacts.
+    * This relation does not apply for bipartite networks.
+
 #### Edge-construction algorithms for author networks
 
 When constructing author networks, we use events in time (i.e., commits, e-mails, issue events) to model interactions among authors on the same artifact as edges. Therefore, we group the events on artifacts, based on the configured relation (see the [previous section](#relations)).
@@ -597,6 +604,12 @@ There is no way to update the entries, except for the revision-based parameters.
 - `custom.event.timestamps.locked`:
     * Lock custom event timestamps to prevent them from being read if empty or not yet present when calling the getter.
     * [`TRUE`, *`FALSE`*]
+- `commit.interactions`:
+    * Allow construction of author and artifact networks using commit-interaction data
+    * [`TRUE`, *`FALSE`*]
+- `commit.interactions.filter.global`:
+    * Filter out entries from commit interaction data that are not matched to a specific function or file
+    * [*`TRUE`*, `FALSE`]
 
 ### NetworkConf
 

install.R

@@ -19,6 +19,7 @@
 ## Copyright 2020-2023 by Thomas Bock <[email protected]>
 ## Copyright 2019 by Anselm Fehnker <[email protected]>
 ## Copyright 2021 by Christian Hechtl <[email protected]>
+## Copyright 2024 by Leo Sendelbach <[email protected]>
 ## All Rights Reserved.
 ##
 ## Adapted from https://github.com/siemens/codeface/blob/be382e9171fb91b4aa99b99b09b2ef64a6dba0d5/packages.r
@@ -44,7 +45,9 @@ packages = c(
     "viridis",
     "jsonlite",
     "rTensor",
-    "Matrix"
+    "Matrix",
+    "fastmap",
+    "purrr"
 )
 
 

tests/README.md

@@ -16,6 +16,7 @@ We have two test projects you can use when writing your tests:
      * Commit messages
      * Pasta
      * Synchronicity
+     * Commit interactions
      * Custom event timestamps in `custom-events.list`
      * Revisions
 2. - Casestudy: `test_empty`

tests/codeface-data/results/testing/test_proximity/proximity/commit-interactions.yaml

@@ -0,0 +1,55 @@
+scope:        REGION
+result-map:
+  test_function:
+    demangled-name:   test_function
+    file:             test3.c
+    num-instructions: 30
+    insts:
+      - base-hash:
+          region:         45620620587549
+          function:       test_function
+          commit:         1143db502761379c2bfcecc2007fc34282e7ee61
+          repository:     test-repo
+        interacting-hashes:
+          - region:         87546092348456
+            commit:         5a5ec9675e98187e1e92561e1888aa6f04faa338
+            repository:     test-repo
+        amount:         2
+    callees:
+      - test_callee
+    commits:
+      - commit:         3383d8e5561dfc6fb2b65e0a194df94ccb5e08af
+        repository:     test-repo
+  test2:
+    demangled-name:   test2
+    file:             test2.c
+    num-instructions: 26
+    insts:
+      - base-hash:
+          region:         50956672345141
+          commit:         3a0ed78458b3976243db6829f63eba3eead26774
+          repository:     test-repo
+        interacting-hashes:
+          - region:          98750276234511
+            commit:          0a1a5c523d835459c42f33e863623138555e2526
+            repository:      test-repo
+        amount:          1
+      - base-hash:
+          region:         67230588834344
+          commit:         0a1a5c523d835459c42f33e863623138555e2526
+          repository:     test-repo
+        interacting-hashes:
+          - region:          33295067820043
+            function:        test2
+            commit:          418d1dc4929ad1df251d2aeb833dd45757b04a6f
+            repository:      test-repo
+          - region:          20194653678423
+            function:        test2
+            commit:          d01921773fae4bed8186b0aa411d6a2f7a6626e6
+            repository:      test-repo
+        amount:          3
+    callees:
+      - test_callee
+    commits:
+      - commit:         3383d8e5561dfc6fb2b65e0a194df94ccb5e08af
+        repository:     test-repo

tests/test-data.R

@@ -20,6 +20,7 @@
 ## Copyright 2021 by Mirabdulla Yusifli <[email protected]>
 ## Copyright 2022 by Jonathan Baumann <[email protected]>
 ## Copyright 2023 by Maximilian Löffler <[email protected]>
+## Copyright 2024 by Leo Sendelbach <[email protected]>
 ## All Rights Reserved.
 
 
@@ -98,6 +99,13 @@ test_that("Compare two ProjectData objects on empty data", {
     proj.data.two$set.project.conf.entry("commit.messages", "message")
     proj.data.two$get.commit.messages()
     expect_true(proj.data.one$equals(proj.data.two), "Two identical ProjectData objects (commit.messages).")
+
+    proj.data.one$set.project.conf.entry("commit.interactions", TRUE)
+    proj.data.one$get.commit.interactions()
+    expect_false(proj.data.one$equals(proj.data.two), "Two non-identical ProjectData objects (commit.interactions).")
+    proj.data.two$set.project.conf.entry("commit.interactions", TRUE)
+    proj.data.two$get.commit.interactions()
+    expect_true(proj.data.one$equals(proj.data.two), "Two identical ProjectData objects (commit.interactions).")
 })
 
 test_that("Compare two ProjectData objects on non-empty data", {
@@ -511,3 +519,78 @@ test_that("Create RangeData objects from Codeface ranges and check data path", {
 
     expect_identical(range.paths, expected.paths, "RangeData data paths")
 })
+
+test_that("Compare two ProjectData Objects with commit.interactions", {
+    ## configuration object for the datapath
+    proj.conf = ProjectConf$new(CF.DATA, CF.SELECTION.PROCESS, CASESTUDY, "file")
+    proj.conf$update.value("commit.interactions", TRUE)
+    proj.conf$update.value("commits.filter.untracked.files", FALSE)
+    proj.conf$update.value("commits.filter.base.artifact", FALSE)
+    proj.conf$update.value("commit.interactions.filter.global", FALSE)
+
+    proj.data.one = ProjectData$new(project.conf = proj.conf)
+    proj.data.two = proj.data.one$clone(deep = TRUE)
+
+    ## test if the project data is equal and the commit interactions are as well
+    expect_equal(proj.data.one$get.commit.interactions(), proj.data.two$get.commit.interactions())
+    expect_true(proj.data.one$equals(proj.data.two))
+
+    ## change commit interactions of one project data and assert that equality check fails
+    proj.data.two$set.commit.interactions(create.empty.commit.interaction.list())
+    expect_false(proj.data.one$equals(proj.data.two))
+
+    ## change commit data in one to test if commit-interactions are correctly updated
+    ## call get.commit.interactions() once to restore read interactions
+    proj.data.two$get.commit.interactions()
+
+    ## change commits in one project data
+    commit.data = proj.data.one$get.commits()
+    commit.data[["hash"]][[5]] = 1
+    proj.data.one$set.commits(commit.data)
+
+    ## use isTRUE to compress result of all.equal into a single boolean
+    expect_false(isTRUE(all.equal(proj.data.one$get.commit.interactions(),
+                                  proj.data.two$get.commit.interactions())))
+
+    ## The data frame should still have 4 entries:
+    expect_true(nrow(proj.data.one$get.commit.interactions()) == 4)
+    ## after cleanup is called, the data frame should only have 3 entries:
+    proj.data.one$cleanup.commit.interactions()
+    expect_true(nrow(proj.data.one$get.commit.interactions()) == 3)
+
+    ## set commit list of one project data to empty and test that last
+    ## two rows of result data frame are empty
+    proj.data.two$set.commits(create.empty.commits.list())
+
+    ## create empty data frame of correct size
+    commit.interactions.data.expected = data.frame(matrix(nrow = 4, ncol = 8))
+    ## assure that the correct type is used
+    for(i in seq_len(8)) {
+        commit.interactions.data.expected[[i]] = as.character(commit.interactions.data.expected[[i]])
+    }
+    ## set everything except for authors as expected
+    colnames(commit.interactions.data.expected) = c("commit.hash", "base.hash", "func", "file",
+                                                    "base.func", "base.file", "base.author",
+                                                    "interacting.author")
+    commit.interactions.data.expected[["commit.hash"]] =
+                                                        c("0a1a5c523d835459c42f33e863623138555e2526",
+                                                        "418d1dc4929ad1df251d2aeb833dd45757b04a6f",
+                                                        "5a5ec9675e98187e1e92561e1888aa6f04faa338",
+                                                        "d01921773fae4bed8186b0aa411d6a2f7a6626e6")
+    commit.interactions.data.expected[["base.hash"]] =
+                                                      c("3a0ed78458b3976243db6829f63eba3eead26774",
+                                                        "0a1a5c523d835459c42f33e863623138555e2526",
+                                                        "1143db502761379c2bfcecc2007fc34282e7ee61",
+                                                        "0a1a5c523d835459c42f33e863623138555e2526")
+    commit.interactions.data.expected[["func"]] = c("GLOBAL", "test2.c::test2", "GLOBAL", "test2.c::test2")
+    commit.interactions.data.expected[["file"]] = c("GLOBAL", "test2.c", "GLOBAL", "test2.c")
+    commit.interactions.data.expected[["base.func"]] = c("test2.c::test2", "test2.c::test2",
+                                                         "test3.c::test_function", "test2.c::test2")
+    commit.interactions.data.expected[["base.file"]] = c("test2.c", "test2.c", "test3.c", "test2.c")
+
+    expect_equal(proj.data.two$get.commit.interactions(), commit.interactions.data.expected)
+
+    ## reactivate filtering of commit interactions
+    proj.data.two$set.project.conf.entry("commit.interactions.filter.global", TRUE)
+    expect_true(nrow(proj.data.two$get.commit.interactions()) == 2)
+})

tests/test-networks-artifact.R

@@ -212,3 +212,101 @@ patrick::with_parameters_test_that("Network construction of an empty 'comments-o
     "directed: FALSE" = list(test.directed = FALSE),
     "directed: TRUE" = list(test.directed = TRUE)
 ))
+
+patrick::with_parameters_test_that("Network construction with commit-interactions as relation, artifact type 'file'", {
+    ## configuration object for the datapath
+    proj.conf = ProjectConf$new(CF.DATA, CF.SELECTION.PROCESS, CASESTUDY, "file")
+    proj.conf$update.value("commit.interactions", TRUE)
+    proj.conf$update.value("commits.filter.untracked.files", FALSE)
+    proj.conf$update.value("commits.filter.base.artifact", FALSE)
+    proj.conf$update.value("commit.interactions.filter.global", FALSE)
+    proj.data = ProjectData$new(project.conf = proj.conf)
+
+    net.conf = NetworkConf$new()
+    net.conf$update.values(updated.values = list(artifact.relation = "commit.interaction",
+                                                 artifact.directed = test.directed))
+
+    network.builder = NetworkBuilder$new(project.data = proj.data, network.conf = net.conf)
+    network.built = network.builder$get.artifact.network()
+    ## build the expected nbetwork
+    vertices = data.frame(
+        name = c("test2.c", "test3.c", "GLOBAL"),
+        kind = "File",
+        type = TYPE.ARTIFACT
+        )
+    edges = data.frame(
+        from = c("GLOBAL", "test2.c", "GLOBAL", "test2.c"),
+        to = c("test2.c", "test2.c", "test3.c", "test2.c"),
+        func = c("GLOBAL", "test2.c::test2", "GLOBAL", "test2.c::test2"),
+        hash = c("0a1a5c523d835459c42f33e863623138555e2526",
+                 "418d1dc4929ad1df251d2aeb833dd45757b04a6f",
+                 "5a5ec9675e98187e1e92561e1888aa6f04faa338",
+                 "d01921773fae4bed8186b0aa411d6a2f7a6626e6"),
+        base.hash = c("3a0ed78458b3976243db6829f63eba3eead26774",
+                      "0a1a5c523d835459c42f33e863623138555e2526",
+                      "1143db502761379c2bfcecc2007fc34282e7ee61",
+                      "0a1a5c523d835459c42f33e863623138555e2526"),
+        base.func = c("test2.c::test2", "test2.c::test2",
+                      "test3.c::test_function", "test2.c::test2"),
+        base.author = c("Olaf", "Thomas", "Karl", "Thomas"),
+        interacting.author = c("Thomas", "Karl", "Olaf", "Thomas"),
+        weight = c(1, 1, 1, 1),
+        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)
+
+    expect_true(igraph::identical_graphs(network.built, network))
+}, patrick::cases(
+    "directed: FALSE" = list(test.directed = FALSE),
+    "directed: TRUE" = list(test.directed = TRUE)
+))
+
+patrick::with_parameters_test_that("Network construction with commit-interactions as relation, artifact type 'function'", {
+    ## configuration object for the datapath
+    proj.conf = ProjectConf$new(CF.DATA, CF.SELECTION.PROCESS, CASESTUDY, "function")
+    proj.conf$update.value("commit.interactions", TRUE)
+    proj.conf$update.value("commits.filter.untracked.files", FALSE)
+    proj.conf$update.value("commits.filter.base.artifact", FALSE)
+    proj.conf$update.value("commit.interactions.filter.global", FALSE)
+    proj.data = ProjectData$new(project.conf = proj.conf)
+
+    net.conf = NetworkConf$new()
+    net.conf$update.values(updated.values = list(artifact.relation = "commit.interaction",
+                                                 artifact.directed = test.directed))
+
+    network.builder = NetworkBuilder$new(project.data = proj.data, network.conf = net.conf)
+    network.built = network.builder$get.artifact.network()
+    ## build the expected network
+    vertices = data.frame(
+        name = c("test2.c::test2", "test3.c::test_function", "GLOBAL"),
+        kind = "Function",
+        type = TYPE.ARTIFACT
+        )
+    edges = data.frame(
+        from = c("GLOBAL", "test2.c::test2", "GLOBAL", "test2.c::test2"),
+        to = c("test2.c::test2", "test2.c::test2",
+               "test3.c::test_function", "test2.c::test2"),
+        hash = c("0a1a5c523d835459c42f33e863623138555e2526",
+                 "418d1dc4929ad1df251d2aeb833dd45757b04a6f",
+                 "5a5ec9675e98187e1e92561e1888aa6f04faa338",
+                 "d01921773fae4bed8186b0aa411d6a2f7a6626e6"),
+        file = c("GLOBAL", "test2.c", "GLOBAL", "test2.c"),
+        base.hash = c("3a0ed78458b3976243db6829f63eba3eead26774",
+                      "0a1a5c523d835459c42f33e863623138555e2526",
+                      "1143db502761379c2bfcecc2007fc34282e7ee61",
+                      "0a1a5c523d835459c42f33e863623138555e2526"),
+        base.file = c("test2.c", "test2.c", "test3.c", "test2.c"),
+        base.author = c("Olaf", "Thomas", "Karl", "Thomas"),
+        interacting.author = c("Thomas", "Karl", "Olaf", "Thomas"),
+        weight = c(1, 1, 1, 1),
+        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)
+
+    expect_true(igraph::identical_graphs(network.built, network))
+}, patrick::cases(
+    "directed: FALSE" = list(test.directed = FALSE),
+    "directed: TRUE" = list(test.directed = TRUE)
+))