Integrate code coverage metric into CI

.github/workflows/pull_request.yml

@@ -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

@@ -9,11 +9,14 @@
 - 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)
+- Add line-based code coverage reports into CI pipeline. Coverage reports are generated by `coverage.R` (PR #262, 10cac49d005e87c3964cc61711e7f5acef749626, b3b9f4ac7a9911bd00293c68fac88e0f9033bdfb, c815d18dc6266d620a7a145493417b87ac08679e, e8093525fdaf46e54f2f7fcc6358ca7892e795e5, 32d04823e2007c63d2a43ce59bea3057327c19a7)
 
 ### Changed/Improved
 
 ### Fixed
 
+- Ensure the correct installation of a compatible `Matrix` version for R 3.6 (PR #262, cb1cf42b2136f35b7e85239d36d5f91ff05d8cd7)
+
 ## 4.4
 
 ### Announcement

coverage.R

@@ -0,0 +1,67 @@
+## This file is part of coronet, 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 2024 by Maximilian Löffler <s8maloef@stud.uni-saarland.de>
+## All Rights Reserved.
+
+## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
+## Initialization ----------------------------------------------------------
+
+source("util-init.R")
+source("tests/testing-utils.R")
+
+
+## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
+## Logging -----------------------------------------------------------------
+
+library("methods") # to prevent weird error during logger initialization (see #153)
+library("logging")
+logging::basicConfig(level = "WARN")
+options(mc.cores = 1L)
+
+
+## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
+## Debug information -------------------------------------------------------
+
+logging::loginfo("Session information:")
+sessionInfo()
+
+
+## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
+## Run tests in subfolder 'tests' ------------------------------------------
+
+logging::loginfo("Generating coverage report.")
+
+## load packages 'testthat' and 'patrick'
+library("testthat")
+requireNamespace("patrick")
+requireNamespace("covr")
+
+## define paths
+test.dir = c("./tests")
+code.dir = c(".")
+excluded.code.files = c("./tests.R", "./coverage.R", "./showcase.R", "./install.R", "./util-init.R")
+excluded.test.files = c()
+
+## obtain files
+test.files = unlist(sapply(test.dir, list.files, pattern = "\\.R$", full.names = TRUE))
+test.files = test.files[!test.files %in% excluded.test.files]
+code.files = unlist(sapply(code.dir, list.files, pattern = "\\.R$", full.names = TRUE))
+code.files = code.files[!code.files %in% excluded.code.files]
+
+## adjust data path prefix when generating coverage reports
+DATA.PATH.PREFIX = "./tests"
+
+## generate and save coverage report
+report = covr::file_coverage(source_files = code.files, test_files = test.files)
+covr::to_cobertura(report)

install.R

@@ -16,10 +16,11 @@
 ## Copyright 2015 by Wolfgang Mauerer <wolfgang.mauerer@oth-regensburg.de>
 ## Copyright 2015-2017 by Claus Hunsen <hunsen@fim.uni-passau.de>
 ## Copyright 2017 by Thomas Bock <bockthom@fim.uni-passau.de>
-## Copyright 2020-2023 by Thomas Bock <bockthom@cs.uni-saarland.de>
+## 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 by Maximilian Löffler <s8@maloef@stud.uni-saarland.de>
 ## All Rights Reserved.
 ##
 ## Adapted from https://github.com/siemens/codeface/blob/be382e9171fb91b4aa99b99b09b2ef64a6dba0d5/packages.r
@@ -36,18 +37,20 @@ packages = c(
     "sqldf",
     "data.table",
     "reshape2",
-    "testthat",
-    "patrick",
     "ggplot2",
     "ggraph",
     "markovchain",
     "lubridate",
     "viridis",
     "jsonlite",
+    "xml2",
     "rTensor",
     "Matrix",
     "fastmap",
-    "purrr"
+    "purrr",
+    "testthat",
+    "patrick",
+    "covr"
 )
 
 
@@ -75,10 +78,12 @@ 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)
+        #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)
         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 packge version.")
+            print("WARNING: Re-installation of package Matrix did not end up in the necessary package version.")
         }
     }
 }

tests/test-data.R

@@ -19,7 +19,7 @@
 ## Copyright 2021 by Johannes Hostert <s8johost@stud.uni-saarland.de>
 ## Copyright 2021 by Mirabdulla Yusifli <s8miyusi@stud.uni-saarland.de>
 ## Copyright 2022 by Jonathan Baumann <joba00002@stud.uni-saarland.de>
-## Copyright 2023 by Maximilian Löffler <s8maloef@stud.uni-saarland.de>
+## Copyright 2023-2024 by Maximilian Löffler <s8maloef@stud.uni-saarland.de>
 ## Copyright 2024 by Leo Sendelbach <s8lesend@stud.uni-saarland.de>
 ## All Rights Reserved.
 
@@ -489,7 +489,7 @@ test_that("Cut data and check for right data path", {
     project.data = ProjectData$new(project.configuration)
     project.data = project.data$get.data.cut.to.same.date(data.sources = c("mails", "commits"))
 
-    expected = "./codeface-data/results/testing/test_feature/feature"
+    expected = paste0(DATA.PATH.PREFIX, "/codeface-data/results/testing/test_feature/feature")
     result = project.data$get.data.path()
     expect_identical(result, expected, info = "RangeData data path.")
 
@@ -514,8 +514,8 @@ test_that("Create RangeData objects from Codeface ranges and check data path", {
     range.paths = run.lapply(data, "get.data.path")
     range.paths = unlist(range.paths, use.names = FALSE)
 
-    expected.paths = c("./codeface-data/results/testing/test_feature/feature/001--v1-v2",
-                       "./codeface-data/results/testing/test_feature/feature/002--v2-v3")
+    expected.paths = c(paste0(DATA.PATH.PREFIX, "/codeface-data/results/testing/test_feature/feature/001--v1-v2"),
+                       paste0(DATA.PATH.PREFIX, "/codeface-data/results/testing/test_feature/feature/002--v2-v3"))
 
     expect_identical(range.paths, expected.paths, "RangeData data paths")
 })

tests/testing-utils.R

@@ -13,6 +13,7 @@
 ##
 ## Copyright 2022 by Jonathan Baumann <joba00002@stud.uni-saarland.de>
 ## Copyright 2024 by Leo Sendelbach <s8lesend@stud.uni-saarland.de>
+## Copyright 2024 by Maximilian Löffler <s8maloef@stud.uni-saarland.de>
 ## All Rights Reserved.
 
 ## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
@@ -21,6 +22,12 @@
 requireNamespace("patrick")
 requireNamespace("igraph")
 
+## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
+## Constants ---------------------------------------------------------------
+
+## The path prefix for data files
+DATA.PATH.PREFIX = "."
+
 #' Construct the 'cross product' of two patrick::cases objects.
 #' Each case of the first object is combined with each case of the second,
 #' test names are joined with a comma.
@@ -150,4 +157,4 @@ assert.sparse.matrices.equal = function(matrix.expected, matrix.actual) {
     for (i in seq_len(expected.size)) {
         expect_equal(matrix.expected[i], matrix.actual[i])
     }
-}
+}