Version 5.0

.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
@@ -50,6 +50,8 @@ jobs:
           sudo apt-get install --assume-yes libxml2-dev
           sudo apt-get install --assume-yes libglpk-dev
           sudo apt-get install --assume-yes libfontconfig1-dev
+          sudo apt-get install --assume-yes libssl-dev
+          sudo apt-get install --assume-yes libcurl4-openssl-dev
           sudo su -c "echo 'deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/' >> /etc/apt/sources.list"
           wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
 
@@ -62,8 +64,42 @@ jobs:
         run: Rscript install.R
 
       - name: Run Tests
+        id: run_tests
         run: Rscript tests.R
 
       - name: Run Showcase
         run: Rscript showcase.R
         if: always()
+
+      - name: Generate Coverage Report
+        id: gen_coverage
+        run: Rscript coverage.R
+        if: matrix.r-version == 'latest' && steps.run_tests.outcome == 'success'
+
+      - name: Store coverage report
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report
+          path: cobertura.xml
+        if: matrix.r-version == 'latest' && steps.gen_coverage.outcome == 'success'
+
+  upload-coverage-report:
+    name: Upload coverage report
+    needs: build
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Load coverage report
+        uses: actions/download-artifact@v4
+        with:
+          name: coverage-report
+
+      - name: Upload Report to CodeCov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: cobertura.xml
+          disable_search: true
+          fail_ci_if_error: true
+          verbose: true
+

CONTRIBUTING.md

@@ -114,8 +114,8 @@ In our development process, we pursue the following idea:
 - The current development will be performed on the branch `dev`, i.e., all incoming pull requests are against this branch.
 
 The current build status is as follows:
-- `master`: ![Build Status](https://github.com/se-sic/coronet/actions/workflows/pull_request.yml/badge.svg?branch=master)
-- `dev`: ![Build Status](https://github.com/se-sic/coronet/actions/workflows/pull_request.yml/badge.svg?branch=dev)
+- `master`: ![Build Status](https://github.com/se-sic/coronet/actions/workflows/pull_request.yml/badge.svg?branch=master) [![Coverage Status](https://codecov.io/gh/se-sic/coronet/branch/master/graph/badge.svg?token=2dhAb3ScLy)](https://codecov.io/gh/se-sic/coronet)
+- `dev`: ![Build Status](https://github.com/se-sic/coronet/actions/workflows/pull_request.yml/badge.svg?branch=dev) [![Coverage Status](https://codecov.io/gh/se-sic/coronet/branch/dev/graph/badge.svg?token=2dhAb3ScLy)](https://codecov.io/gh/se-sic/coronet)
 
 ### Pull Requests
 

NEWS.md

@@ -2,6 +2,48 @@
 
 # coronet – Changelog
 
+## 5.0
+
+### 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.
+- The plotting module of `coronet` is not compatible with `ggplot2` versions below 3.5.0 anymore. This is due to the simultaneous deprecation of the `scale_name` parameter of `discrete_scale` (which is used within the function `plot.network` of `coronet`) in `ggplot2` version 3.5.0.
+
+### 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, f591528a0f1f11b1a4390949ab770f3f74a766f9, 4c4b6545ba03280f08dc6d1ccfc2610d6670df96) 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` or `create.artifact.network` if the `artifact.relation` or `author.relation` is configured to be `commit.interaction` (PR #252, d82857fbebd1111bb16588a4223bb24a8dcd07de, 329d97ec3de36a9e1bcadc0c7a53c1d92e8b481c) as well as tests for these features (PR #252, 07e7ed744209b0251217fa8f7f35d9b9875face2, 7068cfa10d993dcae3f5e3f76f8cafa99fa8b350)
+- Add commit network as a new type of network. It uses commits as vertices and connects them either via cochange or commit interactions. This includes adding new configuration parameters and the function `add.vertex.attribute.commit.network` for adding vertex attributes to a commit network (PR #263, ab73271781e8e9a0715f784936df4b371d64c338, ab73271781e8e9a0715f784936df4b371d64c338, cd9a930fcb54ff465c2a5a7c43cfe82ac15c134d)
+- Add the possibility to split data time-based by multiple data sources (PR #261, 1088395f46b84028c8d7c463ca86b5dc38500c26, e1f79fc9e40cd6f41c946be42db364b2101cfe10, 0bb187fec0fd801d7634bf8d5180525770f6ab0b, 371a97ac6ebf3de4fe9360dea79d62e2ed3ef585)
+- Add `remove.duplicate.edges` function that takes a network as input and conflates identical edges (PR #268, d9a4be417b340812b744f59398ba6460ba527e1c, 0c2f47c4fea6f5f2f582c0259f8cf23af985058a, c6e90dd9cb462232563f753f414da14a24b392a3)
+- Add `cumulative` as an argument to `construct.ranges` which enables the creation of cumulative ranges from given revisions (PR #268, a135f6bb6f83ccb03ae27c735c2700fccc1ee0c8, 8ec207f1e306ef6a641fb0205a9982fa89c7e0d9)
+- Add function `get.last.activity.data` to compute developers' last activities in a project, as well as function `add.vertex.attribute.author.last.activity` to add a developer's date of last activity as vertex attribute to a network, as well as helper functions `get.aggregated.activity.data` and `add.vertex.attribute.author.aggregated.activity` to allow for other activity aggregations than first and last activity (PR #275, 9f231612fcd33a283362c79b35a94295ff3d4ef9, 8660ed763ba4b69e909e7fbb01e27e1999522047)
+- Add four new metrics that can be used for the classification of authors into core and peripheral: betweenness, closeness, pagerank, and eccentricity (PR #276, e27acb5ad7b4c4532e787d793301d06f13e8bbba, 217880809a07f970b055bd3b84c05cb6e61ac6af)
+- 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 tests for uncovered functionality in `util-misc.R` and `util-networks.R` (PR #264, ff30f3238b1bf2539280d0d055a5d925c197c271, af80551d0615a49b86e45ff596bd75941ee88f91)
+
+### 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, PR #274, PR #279, 0df9d5bf6bafbb5d440f4c47db4ec901cf11f037, 7ac840d287a862eff61b1a84e194a4cba399f9e5, e3617b8c6b21fb4242c1d392124813501069ca84, 4b0d5221dd56bb3c9ddf196f67719d4f503d9b61, f29662b2c11768cc01eb0f86d32e039099c618ae)
+- Remove deprecated parameter of `ggplot2::discrete_scale` (PR #279, 027ce79cdc85a81a5b386bf925f3545632426433)
+- 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)
+- Update necessary `ggplot2` version to 3.5.0 in `README.md` (PR #279, 027ce79cdc85a81a5b386bf925f3545632426433)
+- Include core/peripheral classification in`README.md` (PR #276, 6101e11f5c4ac1b5883e85cebd01a3cd7c76e056, c6744c00d3dc0d4e45a96c2d80ae78727e22cce2, 5fc2da5ece6604a6a87d8dd5f79237a82fb2b5ca)
+
+### Fixed
+
+- Fix the creation of edgelists for issue-based artifact-networks by correctly iterating over the issue data (PR #264, 321d85043112971c04998249c14a0677a32c9004)
+- 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)
+- 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)
+- 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
 
 ### Announcement