se-sic · bockthom · Oct 2, 2025 · Jan 21, 2025 · Jan 21, 2025 · Jan 24, 2025
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -11,8 +11,9 @@
 ## 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@stud.uni-saarland.de>
+## Copyright 2023-2025 by Maximilian Löffler <s8maloef@stud.uni-saarland.de>
 ## Copyright 2024 by Thomas Bock <bockthom@cs.uni-saarland.de>
+## Copyright 2025 by Leo Sendelbach <s8lesend@stud.uni-saarland.de>
 ## All Rights Reserved.
 
 name: Build Status
@@ -37,7 +38,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        r-version: ['4.0', '4.1', '4.2', '4.3', '4.4', 'latest']
+        r-version: ['4.1', '4.2', '4.3', '4.4', '4.5', 'latest']
 
     steps:
       - name: Checkout Repo
@@ -89,17 +90,20 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
+      - name: Checkout Repo
+        uses: actions/checkout@v4
+
       - name: Load coverage report
         uses: actions/download-artifact@v4
         with:
           name: coverage-report
 
       - name: Upload Report to CodeCov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          file: cobertura.xml
+          files: cobertura.xml
           disable_search: true
+          disable_telem: true
           fail_ci_if_error: true
           verbose: true
-
diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,38 @@
 
 # coronet – Changelog
 
+## 5.1
+
+### Added
+
+- Add the possibility to split networks that contain simplified edges (PR #278, 9798d33512dcdf50d3b88a1223fc4913a2a88eeb, 0ed437c14423c1917f1ba470e7e55db4626d380b, 67a6651b94d50cb7c2ab4a74888b0556d607b102, 98ef83158204be2a67b115cb25df5ba375cccf60, 7ec4d83fdeb308a24a350acd808941807b9511f1, 637d62ab70f098f26f241e588a99cdc49d10f56a, 2c70666f128f96a3a573f29a0cbbef14d803d193, 1cbc6fa36859d6db3a7ff4493ef19763e87d2de3, 41788ff029d038969bfc6b5773e919201c5ac595, b042c0dd08e2229514ccd25dee7a119f25b1ab45, 36d23d657f412aa1953c4773076e593273f19d8e, 402c256d9a05e4ffb297d4ea1fc25d0230787bc0, 54af2b19a112070f10d191b98b055482748426a7, 894414a4a970822b9ecd59c0b6c480860707f636, 0fe32a259ef703c2de79135bfa6932a595fdc1c5)
+- Add functionality for commit-message content analysis, such as NLP tools including stemming, tokenization, and lemmatization, as well as a function to search for keywords in commit messages and a function to measure the length of the messages (PR #281, 5aa4e4193f0c00095fedf961c6060a5c035ef9c6, 99f0638566c0062b987617bc3fe3ace1db7729ee, e469d3a0cf2881c378469b6ccfea9c204d13f19b, 7d8fd39f164c776921e3fb36daf79256e7be7426, ef689f71f248059cc69be4792ca14ce3b95dcac8, 6e642242a3063663bcc3c7f5cca0650dfebb6bb4, f54439486115cada08dac23864b2f7605edca9ea, dd9246b2f4506d3d58f1c1f37fc198aaaafebb0d)
+- Add `unlist.timestamps.if.possible` parameter to `get.edgelist.with.timestamps` which allows callers to request a conversion of the timestamps from list to vector if possible, i.e., when there are no simplified edges in the network (PR #289, 39bf1ddc570057fcae093252d7631e13bc0b5a55)
+
+### Changed/Improved
+
+- For consistency reasons: Ensure that the values of edge attributes are always lists even when they represent singular values (PR #278, 6fae1843740ed8e48c89c2ee4e61f995b5d0b8f5, 416c817998540fc0b82d9959574838b571b4d6fb)
+- Reduce the amount of redundantly built networks by caching network data internally. This should improve the performance of building multi-networks, especially, when parts of the multi-networks have been built before (#119, PR #282, 06a814c945f0b20af842d20247126083523cde55, 4793eab02e8792b0640fad88a90018292b1b2ab9, 8ba907fff0534c6fef39bd289ab163c90b053530, 28d22902e32e93c0d4990576da2ef3de88fdffbd, 3608214b9bcf1ac5edc0c47182993c4fcc95d8b0, b30c7f2b5b0a6d12e8024fafada5490170530ebe, 1fa340d6347090a327b4c32ece705c1f700234e5, 40cd55423be7b6521e2fc35f5aa200ff0594e77c, 8fcc74439c28b1592e964dd753bfc1cd57c062be, ca348f1de8e3b4e5786a6d2726ca14e530446896, 1d233af734f79e677d3388f7c3589ce186cc3a8d, 5dd5fc18940ce9ac9598902f175193167b471966)
+- Internally cache commit-network data and bipartite-network data similarly to how we cache network data for author-, and artifact-networks (PR #282, PR #285, 3608214b9bcf1ac5edc0c47182993c4fcc95d8b0, aa7e3fae9f45df73054f7d9c6a96177575106c7d)
+- Ensure that configured or implicitly-enforced undirectedness in partial networks is always dominant over configured or implicitly-enforced directedness. Furthermore, ensure consistency in the directedness used for edge generation and as a network attribute, especially in networks that consist of multiple partial networks such as multi-networks (PR #282, 65ead39b7b971e5a0acbaee4e787efcf194aafc4, a776caf72256200e1bfa5578106a9b53547b00e7, 257a1c8a6a9b1c3e2a72960cc4051a87950753ee, 41cff01cf141a377c96048f0645e05fb200138e9)
+- Remove redundant entries from the list of allowed edge attributes and instead add `event.info.1` and `event.info.2` (PR #282, 1b156c17f261d8b70d8d48c6cb94d3ee591559f3)
+- Allow the issue data attributes `event.info.1` and `event.info.2` on network edges (PR #282, 1b156c17f261d8b70d8d48c6cb94d3ee591559f3)
+- Add a `network.type` parameter to `get.networks` in which the caller can specify the types of networks to be constructed. This improves performance in cases where not all network types are needed, such as when building multi-networks (PR #285, bc2efd643d92da547d4677f9026540c25e730a03, e9a0c1681a0b63bd831fe7657ce25a9d50dc6e83)
+- Rename the `list.attributes` parameter in `add.vertex.attribute` and `split.and.add.vertex.attribute` to `flatten.values` with inverted semantics and introduce documentation for it to improve comprehensibility (PR #285, 7dab04a5251d89c9cb286452528ef8b6775a7347)
+- Sort author data by `author.name` instead of `author.id` when reading it from a file (PR #286, 61b538b7cf81c4b6638951bfaf051e376d0986b3)
+- Enhance codeface testing data by ensuring that commit ids are unique between proximity and feature data and by adding commit data that includes (1) different commits that touch the same file / function, (2) commits that are authored at the same time by different authors (PR #286, 7481099af109e1897b9e5754beb1c7da9f39ffb9, 3e53285426010cf7bf48fa23daa484f29f80ac78)
+- Deprecate support for R version 4.0 because of breaking dependencies (PR #281, 3dc91b155b3e0e2a55378592db448606381f902e)
+
+### Fixed
+
+- Fix a bug in `construct.edge.list.from.key.value.list` that could cause a crash when constructing a network where different vertices have identical associated timestamps (PR #285, d694a6847c36d32dfee60f7d5b082e1d3ba57e01)
+- Fix a bug in network construction that could lead to edges having an unwanted `author.name.1` attribute (PR #285, 105fec1acc436378a9282c40fcae0eb0257f00be)
+- Ensure that POSIXct values are correctly handled in `add.vertex.attribute`, i.e., that they are not converted to numeric values (PR #285, 7dab04a5251d89c9cb286452528ef8b6775a7347, 4924ac23737dec6f915edaeb350a5cbaebbeec79)
+- Handle empty edges when constructing commit networks using commit-interaction data (PR #285, d5e1e4801230224e6272cd66873bd43bb7f04a00)
+- Correctly retain order of commit and mail data when merging it with PAStA, synchronicity, and commit message data (PR #286, 50b9b68effd49f853b8bcb335676357a854d1f97)
+- Fix `get.edgelist.with.timestamps` to work correctly on networks with dates in default (list) format (PR #289, 35b34bf1d5049904d75122ace847debe0d1595f7)
+
+
 ## 5.0
 
 ### Announcement

diff --git a/README.md b/README.md
@@ -37,6 +37,7 @@ If you wonder: The name `coronet` derives as an acronym from the words "configur
       - [Core/Peripheral classification](#coreperipheral-classification)
            - [Count-based metrics](#count-based-metrics)
            - [Network-based metrics](#network-based-metrics)
+      - [Commit-message content analysis](#commit-message-content-analysis)
     - [How-to](#how-to)
     - [File/Module overview](#filemodule-overview)
   - [Configuration classes](#configuration-classes)
@@ -62,9 +63,9 @@ While using the package, we require the following infrastructure.
 
 #### [`R`](https://www.r-project.org/)
 
-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.)
+Minimum requirement is `R` version `4.1.1`. 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 `4.3.0` 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 `4.3.0` or `4.5.1` 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)
 
@@ -147,6 +148,9 @@ Alternatively, you can run `Rscript install.R` to install the packages.
 - `Matrix`: For sparse matrix representation of large adjacency matrices (package version `1.3.0` or higher is required)
 - `fastmap`: For fast implementation of a map
 - `purrr`: For fast implementation of a mapping function
+- `tm`: For NLP tasks used on commit messages
+- `textstem`: For lemmatization of commit messages
+- `SnowballC`: For text stemming, used by NLP package `tm`
 
 ### Submodule
 
@@ -429,6 +433,10 @@ In this section, we provide descriptions of the different algorithms we provide
     * calculates scores based on the eccentricity of vertices in a network
     * eccentricity measures the length of the shortest path to each vertex's furthest reachable vertex
 
+#### Commit-message content analysis
+
+In this section, we give an overview of the functionalities we offer regarding the textual analysis of commit messages. These consist of basic NLP tasks, such as stemming (`get.stemmed.commit.messages`), tokenization (`get.tokenized.commit.messages`), and lemmatization (`get.lemmatized.commit.messages`), as well as preprocessing steps (`get.preprocessed.commit.messages`) such as lowercase transformation and removal of punctuation, stopwords, and extra whitespaces. Apart from these, there is the option of searching for a set of strings in commit messages for matching commits (`get.commit.messages.by.strings`) as well as getting token counts for commit messages (`get.commit.message.counts`).
+
 ### How-to
 
 In this section, we give a short example on how to initialize all needed objects and build a bipartite network.

diff --git a/install.R b/install.R
@@ -19,7 +19,7 @@
 ## Copyright 2020-2024 by Thomas Bock <bockthom@cs.uni-saarland.de>
 ## Copyright 2019 by Anselm Fehnker <fehnker@fim.uni-passau.de>
 ## Copyright 2021 by Christian Hechtl <hechtl@cs.uni-saarland.de>
-## Copyright 2024 by Leo Sendelbach <s8lesend@stud.uni-saarland.de>
+## Copyright 2024-2025 by Leo Sendelbach <s8lesend@stud.uni-saarland.de>
 ## Copyright 2024 by Maximilian Löffler <s8@maloef@stud.uni-saarland.de>
 ## All Rights Reserved.
 ##
@@ -48,6 +48,9 @@ packages = c(
     "Matrix",
     "fastmap",
     "purrr",
+    "tm",
+    "textstem",
+    "SnowballC",
     "testthat",
     "patrick",
     "covr"
@@ -76,11 +79,14 @@ 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)
+    if (compareVersion(Matrix.version, "1.5.0") == -1) {
+        print("WARNING: Matrix version 1.5.0 or higher is necessary for using coronet. Re-install package Matrix...")
+        matrix.1.5.0.url = "https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.5-0.tar.gz"
+        install.packages(matrix.1.5.0.url, repos = NULL, dependencies = NA, verbose = TRUE, quiet = TRUE)
+        ## redo installation of textstem, which fails if matrix is outdated or not present
+        install.packages("textstem", dependencies = NA, verbose = TRUE, quiet = TRUE)
         Matrix.version = installed.packages()[rownames(installed.packages()) == "Matrix", "Version"]
-        if (compareVersion(Matrix.version, "1.3.0") == -1) {
+        if (compareVersion(Matrix.version, "1.5.0") == -1) {
             print("WARNING: Re-installation of package Matrix did not end up in the necessary package version.")
         }
     }

diff --git a/showcase.R b/showcase.R
@@ -24,7 +24,7 @@
 ## Copyright 2021 by Niklas Schneider <s8nlschn@stud.uni-saarland.de>
 ## Copyright 2022 by Jonathan Baumann <joba00002@stud.uni-saarland.de>
 ## Copyright 2024 by Maximilian Löffler <s8maloef@stud.uni-saarland.de>
-## Copyright 2024 by Leo Sendelbach <s8lesend@stud.uni-saarland.de>
+## Copyright 2024-2025 by Leo Sendelbach <s8lesend@stud.uni-saarland.de>
 ## All Rights Reserved.
 
 
@@ -501,3 +501,19 @@ calculate.cohens.kappa(author.classification.list = author.class.overview,
 get.class.turnover.overview(author.class.overview = author.class.overview)
 get.unstable.authors.overview(author.class.overview = author.class.overview, saturation = 2)
 
+## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
+## Commit-message content analysis -----------------------------------------
+
+## analyze all commit messages using tokenization, which does not employ any preprocessing steps
+get.tokenized.commit.messages(y.data)
+
+## analyze the commit message of a specific commit with only one preprocessing step
+get.lemmatized.commit.messages(y.data,
+                               commit.hashes = c("3a0ed78458b3976243db6829f63eba3eead26774"),
+                               preprocessing = "stopwords")
+
+## analyze all commits using default preprocessing
+get.preprocessed.commit.messages(y.data)
+
+## analyze all commit messages with two preprocessing steps
+get.stemmed.commit.messages(y.data, preprocessing = c("whitespaces", "lowercase"))
diff --git a/tests/codeface-data/results/testing/test_feature/feature/002--v2-v3/commits.list b/tests/codeface-data/results/testing/test_feature/feature/002--v2-v3/commits.list
@@ -1,7 +1,9 @@
 32710;"2016-07-12 16:05:41";"Olaf";"olaf@example.org";"2016-07-12 17:05:55";"Thomas";"thomas@example.org";"3a0ed78458b3976243db6829f63eba3eead26774";1;1;0;1;"test2.c";"Base_Feature";"Feature";1
 32710;"2016-07-12 16:05:41";"Olaf";"olaf@example.org";"2016-07-12 17:05:55";"Thomas";"thomas@example.org";"3a0ed78458b3976243db6829f63eba3eead26774";1;1;0;1;"test2.c";"Base_Feature";"FeatureExpression";1
 32714;"2016-07-12 16:06:10";"Karl";"karl@example.org";"2016-07-12 16:06:10";"Karl";"karl@example.org";"1143db502761379c2bfcecc2007fc34282e7ee61";1;1;0;1;"test3.c";"Base_Feature";"Feature";1
-32715;"2016-07-12 16:06:20";"Karl";"karl@example.org";"2016-07-12 16:06:20";"Karl";"karl@example.org";"418d1dc4929ad1df251d2aeb833dd45757b04a6f";1;1;0;1;"";"";"";0
-32716;"2016-07-12 16:06:30";"Thomas";"thomas@example.org";"2016-07-12 16:06:30";"Thomas";"thomas@example.org";"d01921773fae4bed8186b0aa411d6a2f7a6626e6";1;1;0;1;"";"";"";0
+32707;"2016-07-12 16:06:20";"Karl";"karl@example.org";"2016-07-12 16:06:20";"Karl";"karl@example.org";"418d1dc4929ad1df251d2aeb833dd45757b04a6f";1;1;0;1;"";"";"";0
+32708;"2016-07-12 16:06:20";"Thomas";"thomas@example.org";"2016-07-12 16:06:20";"Thomas";"thomas@example.org";"7d5219c4ba15b8962203f0ae37f9854167914915";2;3;1;2;"test2.c";"foo";"Feature";1
+32708;"2016-07-12 16:06:20";"Thomas";"thomas@example.org";"2016-07-12 16:06:20";"Thomas";"thomas@example.org";"7d5219c4ba15b8962203f0ae37f9854167914915";2;3;1;2;"test3.c";"foo";"Feature";2
+32709;"2016-07-12 16:06:30";"Thomas";"thomas@example.org";"2016-07-12 16:06:30";"Thomas";"thomas@example.org";"d01921773fae4bed8186b0aa411d6a2f7a6626e6";1;1;0;1;"";"";"";0
 32711;"2016-07-12 16:06:32";"Thomas";"thomas@example.org";"2016-07-12 16:06:32";"Thomas";"thomas@example.org";"0a1a5c523d835459c42f33e863623138555e2526";1;1;0;1;"test2.c";"Base_Feature";"Feature";1
 32711;"2016-07-12 16:06:32";"Thomas";"thomas@example.org";"2016-07-12 16:06:32";"Thomas";"thomas@example.org";"0a1a5c523d835459c42f33e863623138555e2526";1;1;0;1;"test2.c";"foo";"Feature";1
diff --git a/tests/codeface-data/results/testing/test_feature/feature/commits.list b/tests/codeface-data/results/testing/test_feature/feature/commits.list
@@ -5,8 +5,10 @@
 32710;"2016-07-12 16:05:41";"Olaf";"olaf@example.org";"2016-07-12 17:05:55";"Thomas";"thomas@example.org";"3a0ed78458b3976243db6829f63eba3eead26774";1;1;0;1;"test2.c";"Base_Feature";"Feature";1
 32710;"2016-07-12 16:05:41";"Olaf";"olaf@example.org";"2016-07-12 17:05:55";"Thomas";"thomas@example.org";"3a0ed78458b3976243db6829f63eba3eead26774";1;1;0;1;"test2.c";"Base_Feature";"FeatureExpression";1
 32714;"2016-07-12 16:06:10";"Karl";"karl@example.org";"2016-07-12 16:06:10";"Karl";"karl@example.org";"1143db502761379c2bfcecc2007fc34282e7ee61";1;1;0;1;"test3.c";"Base_Feature";"Feature";1
-32715;"2016-07-12 16:06:20";"Karl";"karl@example.org";"2016-07-12 16:06:20";"Karl";"karl@example.org";"418d1dc4929ad1df251d2aeb833dd45757b04a6f";1;1;0;1;"";"";"";0
-32716;"2016-07-12 16:06:30";"Thomas";"thomas@example.org";"2016-07-12 16:06:30";"Thomas";"thomas@example.org";"d01921773fae4bed8186b0aa411d6a2f7a6626e6";1;1;0;1;"";"";"";0
+32707;"2016-07-12 16:06:20";"Karl";"karl@example.org";"2016-07-12 16:06:20";"Karl";"karl@example.org";"418d1dc4929ad1df251d2aeb833dd45757b04a6f";1;1;0;1;"";"";"";0
+32708;"2016-07-12 16:06:20";"Thomas";"thomas@example.org";"2016-07-12 16:06:20";"Thomas";"thomas@example.org";"7d5219c4ba15b8962203f0ae37f9854167914915";2;3;1;2;"test2.c";"foo";"Feature";1
+32708;"2016-07-12 16:06:20";"Thomas";"thomas@example.org";"2016-07-12 16:06:20";"Thomas";"thomas@example.org";"7d5219c4ba15b8962203f0ae37f9854167914915";2;3;1;2;"test3.c";"foo";"Feature";2
+32709;"2016-07-12 16:06:30";"Thomas";"thomas@example.org";"2016-07-12 16:06:30";"Thomas";"thomas@example.org";"d01921773fae4bed8186b0aa411d6a2f7a6626e6";1;1;0;1;"";"";"";0
 32711;"2016-07-12 16:06:32";"Thomas";"thomas@example.org";"2016-07-12 16:06:32";"Thomas";"thomas@example.org";"0a1a5c523d835459c42f33e863623138555e2526";1;1;0;1;"test2.c";"Base_Feature";"Feature";1
 32711;"2016-07-12 16:06:32";"Thomas";"thomas@example.org";"2016-07-12 16:06:32";"Thomas";"thomas@example.org";"0a1a5c523d835459c42f33e863623138555e2526";1;1;0;1;"test2.c";"foo";"Feature";1
 31711;"2016-07-12 16:06:33";"Thomas";"thomas@example.org";"2016-07-12 16:06:33";"";"thomas@example.org";"2ef7bde608ce5404e97d5f042f95f89f1c232871";1;1;0;1;"test2.c";"foo";"Feature";1

diff --git a/tests/codeface-data/results/testing/test_proximity/proximity/002--v2-v3/commits.list b/tests/codeface-data/results/testing/test_proximity/proximity/002--v2-v3/commits.list
@@ -2,4 +2,6 @@
 32719;"2016-07-12 16:06:10";"Karl";"karl@example.org";"2016-07-12 16:06:10";"Karl";"karl@example.org";"1143db502761379c2bfcecc2007fc34282e7ee61";1;1;0;1;"test3.c";"test_function";"Function";1
 32715;"2016-07-12 16:06:32";"Thomas";"thomas@example.org";"2016-07-12 16:06:32";"Thomas";"thomas@example.org";"0a1a5c523d835459c42f33e863623138555e2526";1;1;0;1;"test2.c";"File_Level";"Function";1
 32720;"2016-07-12 16:06:20";"Karl";"karl@example.org";"2016-07-12 16:06:20";"Karl";"karl@example.org";"418d1dc4929ad1df251d2aeb833dd45757b04a6f";1;1;0;1;"";"";"";0
+32722;"2016-07-12 16:06:20";"Thomas";"thomas@example.org";"2016-07-12 16:06:20";"Thomas";"thomas@example.org";"7d5219c4ba15b8962203f0ae37f9854167914915";2;3;1;2;"test2.c";"test_function";"Function";1
+32722;"2016-07-12 16:06:20";"Thomas";"thomas@example.org";"2016-07-12 16:06:20";"Thomas";"thomas@example.org";"7d5219c4ba15b8962203f0ae37f9854167914915";2;3;1;2;"test3.c";"test_function";"Function";2
 32721;"2016-07-12 16:06:30";"Thomas";"thomas@example.org";"2016-07-12 16:06:30";"Thomas";"thomas@example.org";"d01921773fae4bed8186b0aa411d6a2f7a6626e6";1;1;0;1;"";"";"";0