From 83650942198dd631f8b54a3d7a36b7788a4733f8 Mon Sep 17 00:00:00 2001 From: emsonder Date: Wed, 9 Jul 2025 17:12:43 +0200 Subject: [PATCH 1/4] Initial attempt to add test-coverage badge to repository --- .../workflows/{r_cmd_check.yaml => r_cmd_check_coverage.yaml} | 0 DESCRIPTION | 1 + README.md | 1 + 3 files changed, 2 insertions(+) rename .github/workflows/{r_cmd_check.yaml => r_cmd_check_coverage.yaml} (100%) diff --git a/.github/workflows/r_cmd_check.yaml b/.github/workflows/r_cmd_check_coverage.yaml similarity index 100% rename from .github/workflows/r_cmd_check.yaml rename to .github/workflows/r_cmd_check_coverage.yaml diff --git a/DESCRIPTION b/DESCRIPTION index 42a42e5..d951e0d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -54,6 +54,7 @@ Imports: universalmotif Suggests: testthat (>= 3.0.0), + covr, BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38 Config/testthat/edition: 3 diff --git a/README.md b/README.md index e4a2e88..3a27d1a 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # TFBlearner [![R-CMD-check](https://github.com/ETHZ-INS/TFBlearner/actions/workflows/r_cmd_check.yaml/badge.svg)](https://github.com/ETHZ-INS/TFBlearner/actions/workflows/r_cmd_check.yaml) + [![codecov](https://codecov.io/gh/ETHZ-INS/TFBlearner/graph/badge.svg)](https://codecov.io/gh/ETHZ-INS/TFBlearner) Package for computing features and training of TF-specific models for TF-binding predictions based on ATAC-seq data.
From 34dd3b9fd7d31f82d24d210bfd0b08dfeaa64404 Mon Sep 17 00:00:00 2001 From: emsonder Date: Thu, 10 Jul 2025 09:30:37 +0200 Subject: [PATCH 2/4] Testing coverage on pushes to this branch --- .github/workflows/r_cmd_check_coverage.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/r_cmd_check_coverage.yaml b/.github/workflows/r_cmd_check_coverage.yaml index 12df0d2..f520be6 100644 --- a/.github/workflows/r_cmd_check_coverage.yaml +++ b/.github/workflows/r_cmd_check_coverage.yaml @@ -3,7 +3,7 @@ on: push: branches: - - main + - test_coverage_badge pull_request: branches: - main From 6ce459acc3a4d89970027a6e1fc3cd78a104692d Mon Sep 17 00:00:00 2001 From: emsonder Date: Thu, 10 Jul 2025 09:43:46 +0200 Subject: [PATCH 3/4] Added code coverage step in workflow --- .github/workflows/r_cmd_check_coverage.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/r_cmd_check_coverage.yaml b/.github/workflows/r_cmd_check_coverage.yaml index f520be6..03480f5 100644 --- a/.github/workflows/r_cmd_check_coverage.yaml +++ b/.github/workflows/r_cmd_check_coverage.yaml @@ -47,3 +47,9 @@ jobs: upload-snapshots: true build_args: 'c("--no-manual")' error-on: '"warning"' + + - name: Test coverage + env: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} + run: covr::codecov(token = Sys.getenv("CODECOV_TOKEN")) + shell: Rscript {0} From 3779ef3f4b90bb3e9cccdd6c15d0685c77fd942c Mon Sep 17 00:00:00 2001 From: emsonder Date: Thu, 10 Jul 2025 11:34:02 +0200 Subject: [PATCH 4/4] Trigger CI/CD workflow only for main --- .github/workflows/r_cmd_check_coverage.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/r_cmd_check_coverage.yaml b/.github/workflows/r_cmd_check_coverage.yaml index 03480f5..b586dc9 100644 --- a/.github/workflows/r_cmd_check_coverage.yaml +++ b/.github/workflows/r_cmd_check_coverage.yaml @@ -3,7 +3,7 @@ on: push: branches: - - test_coverage_badge + - main pull_request: branches: - main