Release v0.2.0

.github/workflows/R-CMD-check.yaml

@@ -2,12 +2,15 @@ on:
   push:
   pull_request:
     branches:
-      - master
+      - main
   schedule:
-    - cron: '0 8 * * 5'
+    - cron: '0 8 1 * *'
 
 name: R-CMD-check
 
+permissions:
+  contents: write
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -21,14 +24,14 @@ jobs:
         config:
         - { os: windows-latest, r: 'release'}
         - { os: macOS-latest, r: 'release'}
-         #- { os: ubuntu-16.04, r: 'release', bioc: 'release', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
         - { os: ubuntu-latest, r: 'release'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       CRAN: ${{ matrix.config.cran }}
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
       - name: Check out repo
@@ -63,7 +66,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows' && matrix.config.image == null
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }}
@@ -101,39 +104,63 @@ jobs:
           BiocCheck::BiocCheck(".")
         shell: Rscript {0}
 
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@HEAD
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-results
           path: check
 
+      - name: pkgdown dependencies
+        if: github.event_name == 'push' && matrix.config.os == 'ubuntu-latest'
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::., any::covr, any::xml2
+          needs: website, coverage
+
       - name: Test coverage
-        if: matrix.config.os == 'macOS-latest'
+        if: github.event_name == 'push' && matrix.config.os == 'ubuntu-latest'
         run: |
-          install.packages("covr")
-          covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - name: pkgdown dependencies
-        if: github.event_name == 'push' && matrix.config.os == 'macOS-latest'
-        uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: codecov/codecov-action@v5
+        if: github.event_name == 'push' && matrix.config.os == 'ubuntu-latest'
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
         with:
-          extra-packages: any::pkgdown, local::.
-          needs: website
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
 
       - name: Build site
-        if: github.event_name == 'push' && matrix.config.os == 'macOS-latest'
+        if: github.event_name == 'push' && matrix.config.os == 'ubuntu-latest'
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
-        if: github.event_name == 'push' && matrix.config.os == 'macOS-latest'
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main' && matrix.config.os == 'ubuntu-latest'
         uses: JamesIves/github-pages-deploy-action@v4.4.1
         with:
           clean: false

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: batchtma
 Title: Batch Effect Adjustments
-Version: 0.1.7
+Version: 0.2.0
 Authors@R: 
     c(person(given = "Konrad",
            family = "Stopsack",
@@ -19,11 +19,13 @@ Description: Different adjustment methods for batch effects in biomarker data,
 License: GPL-3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.3
 biocViews:
+Depends:
+    R (>= 4.1.0)
 Imports:
     broom (>= 0.7.0),
-    dplyr (>= 1.0.0),
+    dplyr (>= 1.0.4),
     geepack,
     ggplot2,
     limma,
@@ -33,10 +35,11 @@ Imports:
     rlang (>= 0.4.0),
     stringr,
     tibble,
-    tidyr (>= 1.1.0),
-    magrittr
+    tidyr (>= 1.1.0)
 Suggests: 
     knitr,
-    rmarkdown
+    rmarkdown,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
 URL: https://stopsack.github.io/batchtma, https://github.com/stopsack/batchtma
+Config/testthat/edition: 3

NAMESPACE

@@ -5,6 +5,5 @@ export(adjust_batch)
 export(diagnose_models)
 export(plot_batch)
 importFrom(ggplot2,labs)
-importFrom(magrittr,"%>%")
 importFrom(rlang,":=")
 importFrom(rlang,.data)

NEWS.md

@@ -1,3 +1,15 @@
+# batchtma 0.2.0
+
+* Breaking change: Require R >= 4.1
+* No other user-visible changes.
+* Internal changes:
+  + Replace long-deprecated `filter(across())` with `if_all()` to be {dplyr} 
+    1.2.0-compatible (#3, thanks to @DavisVaughan).
+  + Split code into multiple files.
+  + Use modern tidyselect, pipe, and anonymous functions.
+  + Add some unit tests.
+
+
 # batchtma 0.1.7
 
 * Separately call tidyverse packages
@@ -16,7 +28,7 @@
 
 # batchtma 0.1.4
 
-* Bioconductor limma dependency added for `remotes::install_github()``
+* Bioconductor limma dependency added for `remotes::install_github()`
 * Code review, updates to curly-curly, and tidyverse style changes,
   thanks to @tgerke