Version v3.2

NEWS.md

@@ -1,6 +1,43 @@
 # codeface-extraction-r – Changelog
 
 
+## 3.2
+
+### Added
+- Handling of multiple relations for all types of networks (#98, #15, #11, PR #115)
+    - Allow several entries for the entries `author.relation` and `artifact.relation` in the `NetworkConf` (2f1b4d9b0d6a629163a6dd3111b20930e15fcc13)
+    - Add the mandatory edge attribute `relation` representing `author.relation` or `artifact.relation`, respectively, for all types of networks (2f1b4d9b0d6a629163a6dd3111b20930e15fcc13)
+    - Return data for several relations in `get.bipartite.relation` (2f1b4d9b0d6a629163a6dd3111b20930e15fcc13)
+    - Retain one edge for each available value of edge attribute `relation` during network simplification (021ac8b88e9a181364a51e89807df55cb741ed44)
+    - Add new tests and adapt existing ones (784c417c50eb1de5d0143908a390ead6ba22dbbf, 7ad49c4ad937c9a6c7398a45179e25d5d5c03faa, be6ee8cd48dc7692e02b7f1c512870591300fa8a)
+- Add the mandatory vertex attribute `kind` describing the actual vertex kind (7c628fb93eb21f280c7d9da66680f817e107fa24, 784c417c50eb1de5d0143908a390ead6ba22dbbf)
+- Respect new vertex and edge attributes in plot functions (b55d3e84a5f9b122dacd0ee52784d930f22d1f4b)
+- Possibility to merge networks with function `merge.networks` (2f1b4d9b0d6a629163a6dd3111b20930e15fcc13)
+- Possibility to merge edge and vertex lists with function `merge.network.data` (2f1b4d9b0d6a629163a6dd3111b20930e15fcc13)
+- Add function `create.empty.edge.list` (2f1b4d9b0d6a629163a6dd3111b20930e15fcc13)
+- Possibility to contract imperfect ranges in the end (#104, 8ebcf20b0aba0cb82dcd7e1d1b95e261a866d04e)
+- Add method `ProjectData$equals` (#116, 00df306a3e6dbdeb81ddc116e88a4854b07afe72)
+- Add author classification by hierarchy to the core-peripheral module (8139f34fd809d6750064514a549024df4cbf5863)
+
+### Changed/Improved
+- Remove the mandatory vertex attribute `artifact.type` due to inconsistent use ()
+- Remove the mandatory vertex attribute `id` from artifact vertices due to inconsistent use (7ad49c4ad937c9a6c7398a45179e25d5d5c03faa)
+- Streamline edge attribute `artifact.type` for uniformity ()
+- Use color palette 'viridis' for plotting for better flexibility  (f190ca130a15a82e5eed836e9ffc53b8a34aac20)
+- Edge width in network plots now depends on edge weight, i.e., `width = 0.3 + 0.5 * log(weight)` (d791df8e2c41314f86c36b3af566141e7713f46c)
+- Split function `construct.network.from.list` into the two functions `construct.edge.list.from.key.value.list` and `construct.network.from.edge.list` (2f1b4d9b0d6a629163a6dd3111b20930e15fcc13)
+- Handle data for more than one relation in function `add.edges.for.bipartite.relation` (2f1b4d9b0d6a629163a6dd3111b20930e15fcc13)
+- Retain one edge for each available value of edge attribute `relation` during network simplification (021ac8b88e9a181364a51e89807df55cb741ed44)
+- Read also lines from the PaStA data without the `message.id` being mapped to a `commit.hash` (992ddf8d582a7a023f000b4fc57f9ff85a7f38f6)
+- Add column `revision.set.id` to PaStA data to indicate which e-mails are concerned with the same patch (992ddf8d582a7a023f000b4fc57f9ff85a7f38f6)
+- Add PaStA data to the unfiltered commit data if configured (70d9b8bd4cb16636086ca7ab90e817b89844f172)
+
+### Fixed
+- Check whether a given object to the `ProjectConf` setter in the `ProjectData` class really is a object of type `ProjectConf` (ab00c962e164428df2d59de7292eed3c3b1352aa)
+- The method for eigenvector centrality now properly considers whether the network is directed or not (c0277c36e4ff45cfbb421317a42b6ea8736afe53)
+- Fix a bug that caused errors when the core classification within a core-periphery classification is empty (c0277c36e4ff45cfbb421317a42b6ea8736afe53)
+
+
 ## 3.1.2
 
 ### Changed/Improved

README.md

@@ -43,6 +43,7 @@ When selecting a version to work with, you should consider the following points:
 - `ggraph`: For plotting of networks (needs `udunits2` system library, e.g., `libudunits2-dev` on Ubuntu!)
 - `markovchain`: For core/peripheral transition probabilities
 - `lubridate`: For convenient date conversion and parsing
+- `viridis`: For plotting of networks with nice colours
 
 
 ## How-To
@@ -214,7 +215,7 @@ Updates to the parameters can be done by calling `NetworkConf$update.variables(.
 **Note**: Default values are shown in *italics*.
 
 - `author.relation`
-  * The relation among authors, encoded as edges in an author network
+  * The relation(s) among authors, encoded as edges in an author network
   * **Note**: The  author--artifact relation in bipartite and multi networks is configured by `artifact.relation`!
   * possible values: [*`"mail"`*, `"cochange"`, `"issue"`]
 - `author.directed`
@@ -228,7 +229,7 @@ Updates to the parameters can be done by calling `NetworkConf$update.variables(.
   * Remove all authors from an author network (including bipartite and multi networks) who are not present in an author network constructed with `artifact.relation` as relation, i.e., all authors that have no biparite relations in a bipartite/multi network are removed.
   * [`TRUE`, *`FALSE`*]
 - `artifact.relation`
-  * The relation among artifacts, encoded as edges in an artifact network
+  * The relation(s) among artifacts, encoded as edges in an artifact network
   * **Note**: This relation configures also the author--artifact relation in bipartite and multi networks!
   * possible values: [*`"cochange"`*, `"callgraph"`, `"mail"`, `"issue"`]
 - `artifact.directed`
@@ -239,13 +240,14 @@ Updates to the parameters can be done by calling `NetworkConf$update.variables(.
   * The list of edge-attribute names and information
   * a subset of the following as a single vector:
        - timestamp information: *`"date"`*, `"date.offset"`
+       - general information: *`"artifact.type"`*
        - author information: `"author.name"`, `"author.email"`
        - committer information: `"committer.date"`, `"committer.name"`, `"committer.email"`
        - e-mail information: *`"message.id"`*, *`"thread"`*, `"subject"`
-       - commit information: *`"hash"`*, *`"file"`*, *`"artifact.type"`*, *`"artifact"`*, `"changed.files"`, `"added.lines"`, `"deleted.lines"`, `"diff.size"`, `"artifact.diff.size"`, `"synchronicity"`
+       - commit information: *`"hash"`*, *`"file"`*, *`"artifact"`*, `"changed.files"`, `"added.lines"`, `"deleted.lines"`, `"diff.size"`, `"artifact.diff.size"`, `"synchronicity"`
        - PaStA information: `"pasta"`,
        - issue information: *`"issue.id"`*, *`"event.name"`*, `"issue.state"`, `"creation.date"`, `"closing.date"`, `"is.pull.request"`
-  * **Note**: `"date"` is always included as this information is needed for several parts of the library, e.g., time-based splitting.
+  * **Note**: `"date"` and `"artifact.type"` are always included as this information is needed for several parts of the library, e.g., time-based splitting.
   * **Note**: For each type of network that can be built, only the applicable part of the given vector of names is respected.
   * **Note**: For the edge attributes `"pasta"` and `"synchronicity"`, the project configuration's parameters `pasta` and `synchronicity` need to be set to `TRUE`, respectively (see below).
 - `simplify`
@@ -267,6 +269,22 @@ You can also update the `NetworkConf` object at any time by calling `NetworkBuil
 For more examples, please look in the file `showcase.R`.
 
 
+###  Network properties
+
+- Mandatory vertex attributes
+  * *`"type"`*: [`"Author"`, `"Artifact"`]
+  * *`"kind"`*: [`"Author"`,`"File"`, `"Feature"`, `"Function"`, `"MailThread"`,
+  `"Issue"`,`"FeatureExpression"`]
+  * *`"name"`*
+
+- Mandatory edge attributes
+  * *`"type"`*: [`Unipartite`, `Bipartite`]
+  * *`"artifact.type"`*: [`"File"`, `"Feature"`, `"Function"`, `"Mail"`,
+  `"IssueEvent"`,`"FeatureExpression"`]
+  * *`"relation"`*: [`mail`, `cochange`, `issue`, `callgraph`] (from `artifact.relation` and `author.relation` attributes in the `NetworkConf` class)
+  * *`"date"`*
+
+
 ## File/Module overview
 
 - `util-init.R`

install.R

@@ -22,7 +22,7 @@
 ## to our needs.
 
 
-pacakges = c(
+packages = c(
     "yaml",
     "R6",
     "igraph",
@@ -34,7 +34,8 @@ pacakges = c(
     "ggplot2",
     "ggraph",
     "markovchain",
-    "lubridate"
+    "lubridate",
+    "viridis"
 )
 
 
@@ -47,7 +48,7 @@ filter.installed.packages = function(packageList)  {
 }
 
 
-p = filter.installed.packages(pacakges)
+p = filter.installed.packages(packages)
 if (length(p) > 0) {
     print(sprintf("Installing package '%s'.", p))
     install.packages(p, dependencies = TRUE, verbose = FALSE, quiet = FALSE)

showcase.R

@@ -49,10 +49,10 @@ CF.DATA = "/path/to/codeface-data" # path to codeface data
 CF.SELECTION.PROCESS = "threemonth" # releases, threemonth(, testing)
 
 CASESTUDY = "busybox"
-ARTIFACT = "feature" # function, feature, file, featureexpression
+ARTIFACT = "feature" # function, feature, file, featureexpression (only relevant for cochange)
 
-AUTHOR.RELATION = "mail" # mail, cochange
-ARTIFACT.RELATION = "cochange" # cochange, callgraph
+AUTHOR.RELATION = "mail" # mail, cochange, issue
+ARTIFACT.RELATION = "cochange" # cochange, callgraph, mail, issue
 
 
 ## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /

tests/codeface-data/results/testing/test_pasta/similar-mailbox → tests/codeface-data/results/testing/test_pasta/mbox-result

@@ -1,5 +1,5 @@
 <[email protected]> => 72c8dd25d3dd6d18f46e2b26a5f5b1e2e8dc28d0
 <[email protected]> => 5a5ec9675e98187e1e92561e1888aa6f04faa338
-<[email protected]> => 3a0ed78458b3976243db6829f63eba3eead26774
+<[email protected]>
 <[email protected]> <[email protected]> <[email protected]> => 1143db502761379c2bfcecc2007fc34282e7ee61
 <[email protected]> => 0a1a5c523d835459c42f33e863623138555e2526 72c8dd25d3dd6d18f46e2b26a5f5b1e2e8dc28d0

tests/test-data-cut.R

@@ -14,6 +14,7 @@
 ## Copyright 2017 by Christian Hechtl <[email protected]>
 ## Copyright 2017 by Felix Prasse <[email protected]>
 ## Copyright 2018 by Claus Hunsen <[email protected]>
+## Copyright 2018 by Barbara Eckl <[email protected]>
 ## All Rights Reserved.
 
 
@@ -68,7 +69,8 @@ test_that("Cut commit and mail data to same date range.", {
                                     date = get.date.from.string("2016-07-12 16:04:40"),
                                     date.offset = as.integer(c(100)),
                                     subject = c("Re: Fw: busybox 2 tab"),
-                                    thread = sprintf("<thread-%s>", c(9)))
+                                    thread = sprintf("<thread-%s>", c(9)),
+                                    artifact.type = "Mail")
 
     commit.data = x.data$get.data.cut.to.same.date(data.sources = data.sources)$get.commits()
     rownames(commit.data) = 1:nrow(commit.data)

tests/test-data.R

@@ -0,0 +1,125 @@
+## This file is part of codeface-extraction-r, which is free software: you
+## can redistribute it and/or modify it under the terms of the GNU General
+## Public License as published by  the Free Software Foundation, version 2.
+##
+## This program is distributed in the hope that it will be useful,
+## but WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+## GNU General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License along
+## with this program; if not, write to the Free Software Foundation, Inc.,
+## 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+##
+## Copyright 2018 by Christian Hechtl <[email protected]>
+## Copyright 2018 by Claus Hunsen <[email protected]>
+## All Rights Reserved.
+
+
+context("Tests for ProjectData functionalities.")
+
+##
+## Context
+##
+
+CF.DATA = file.path(".", "codeface-data")
+CF.SELECTION.PROCESS = "testing"
+CASESTUDY = "test"
+ARTIFACT = "feature"
+
+## use only when debugging this file independently
+if (!dir.exists(CF.DATA)) CF.DATA = file.path(".", "tests", "codeface-data")
+
+test_that("Compare two ProjectData objects", {
+
+    ##initialize a ProjectData object with the ProjectConf and clone it into another one
+    proj.conf = ProjectConf$new(CF.DATA, CF.SELECTION.PROCESS, CASESTUDY, ARTIFACT)
+    proj.data.one = ProjectData$new(project.conf = proj.conf)
+    proj.data.two = proj.data.one$clone()
+
+    expect_true(proj.data.one$equals(proj.data.two), info = "Two identical ProjectData objects.")
+
+    ## Always change one data source in the one object, test for inequality, change it in the
+    ## second object, as well, and test for equality.
+
+    ##change the second data object
+    proj.data.one$get.commits()
+
+    expect_false(proj.data.one$equals(proj.data.two), "Two not identical ProjectData objects.")
+
+    proj.data.two$get.commits()
+
+    expect_true(proj.data.one$equals(proj.data.two), "Two identical ProjectData objects.")
+
+    proj.data.two$get.pasta()
+
+    expect_false(proj.data.one$equals(proj.data.two), "Two not identical ProjectData objects.")
+
+    proj.data.one$get.pasta()
+
+    expect_true(proj.data.one$equals(proj.data.two), "Two identical ProjectData objects.")
+
+    proj.data.two$get.mails()
+
+    expect_false(proj.data.one$equals(proj.data.two), "Two not identical ProjectData objects.")
+
+    proj.data.one$get.mails()
+
+    expect_true(proj.data.one$equals(proj.data.two), "Two identical ProjectData objects.")
+
+    proj.data.one$get.issues()
+
+    expect_false(proj.data.one$equals(proj.data.two), "Two not identical ProjectData objects.")
+
+    proj.data.two$get.issues()
+
+    expect_true(proj.data.one$equals(proj.data.two), "Two identical ProjectData objects.")
+
+    proj.data.two$get.authors()
+
+    expect_false(proj.data.one$equals(proj.data.two), "Two not identical ProjectData objects.")
+
+    proj.data.one$get.authors()
+
+    expect_true(proj.data.one$equals(proj.data.two), "Two identical ProjectData objects.")
+
+    proj.data.one$get.synchronicity()
+
+    expect_false(proj.data.one$equals(proj.data.two), "Two not identical ProjectData objects.")
+
+    proj.data.two$get.synchronicity()
+
+    expect_true(proj.data.one$equals(proj.data.two), "Two identical ProjectData objects.")
+})
+
+test_that("Compare two RangeData objects", {
+
+    ## initialize a ProjectData object with the ProjectConf
+    ## cut it on the base of commits and clone the resulting RangeData object
+    proj.conf = ProjectConf$new(CF.DATA, CF.SELECTION.PROCESS, CASESTUDY, ARTIFACT)
+    proj.data.base = ProjectData$new(project.conf = proj.conf)
+    range.data.one = proj.data.base$get.data.cut.to.same.date("commits")
+    range.data.two = range.data.one$clone()
+
+    ## compare the two equal RangeData objects
+    expect_true(range.data.one$equals(range.data.two))
+
+    ## cut the ProjectData object on base of issues in order to get another
+    ## RangeData object to check for inequality
+    range.data.three = proj.data.base$get.data.cut.to.same.date("issues")
+
+    expect_false(range.data.one$equals(range.data.three))
+
+    ## check whether a ProjectData object can be compared to a RangeData object
+    expect_false(range.data.one$equals(proj.data.base))
+    expect_false(proj.data.base$equals(range.data.one))
+
+    ## create a RangeData object with the same data sources as proj.data.base
+    ## and check for inequality
+    timestamps = proj.data.base$get.data.timestamps(outermost = TRUE)
+    range.data.four = split.data.time.based(proj.data.base, bins =
+                                                c(timestamps[["start"]][[1]], timestamps[["end"]][[1]]))[[1]]
+
+    expect_false(proj.data.base$equals(range.data.four))
+
+})