From 8ac8b840f3cc729972b55ed0d83a2d0797daec5b Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Mon, 2 Mar 2026 19:45:53 +0100 Subject: [PATCH 1/9] Update test coverage workflow --- .github/workflows/test-coverage.yaml | 46 ++++++++++++++++++++++------ 1 file changed, 37 insertions(+), 9 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 0efc119..ccc2031 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -1,10 +1,8 @@ on: push: - branches: - - master + branches: [main, master] pull_request: - branches: - - master + branches: [main, master] name: test-coverage @@ -14,14 +12,16 @@ permissions: jobs: test-coverage: - runs-on: macOS-latest + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: - r-version: 'release' + use-public-rspm: true - name: Install dependencies run: | @@ -31,7 +31,35 @@ jobs: shell: Rscript {0} - name: Test coverage - run: covr::codecov() + run: | + 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} - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file + + - uses: codecov/codecov-action@v5 + 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: + name: coverage-test-failures + path: ${{ runner.temp }}/package From 1b83a8a61f3e0cb8af7f79b67d89acb683bcbfa8 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Mon, 2 Mar 2026 19:46:04 +0100 Subject: [PATCH 2/9] Update README --- README.Rmd | 10 +++++++++- README.md | 12 +++++++++++- 2 files changed, 20 insertions(+), 2 deletions(-) diff --git a/README.Rmd b/README.Rmd index 4bdd760..32e55ca 100644 --- a/README.Rmd +++ b/README.Rmd @@ -22,13 +22,21 @@ knitr::opts_chunk$set( [![status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![R build status](https://github.com/sbthandras/tailor/workflows/R-CMD-check/badge.svg)](https://github.com/sbthandras/tailor/actions) -[![Coverage](https://codecov.io/github/sbthandras/tailor/coverage.svg?branch=master)](https://app.codecov.io/gh/sbthandras/tailor/branch/master) +[![Coverage](https://codecov.io/github/sbthandras/tailor/graph/badge.svg?branch=master)](https://app.codecov.io/gh/sbthandras/tailor/branch/master) [![DOI](https://img.shields.io/badge/DOI-10.64898%2F2026.02.20.706991-blue)](https://doi.org/10.64898/2026.02.20.706991) `tailor` is a **T**ool for **A**dapter-domain **I**dentification and **L**inking **O**f **R**BPs. +# IMPORANT NOTICE + +The latest version of this repository was publised in https://github.com/sbthandras/tailor on 2 March 2026. + +Following publication this development repository was archived. + +Please refer to https://github.com/sbthandras/tailor for the latest version of the package and documentation. + ## Installation #### Install from Github (development version) diff --git a/README.md b/README.md index 54f1ad8..e838ed1 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ [![status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![R build status](https://github.com/sbthandras/tailor/workflows/R-CMD-check/badge.svg)](https://github.com/sbthandras/tailor/actions) -[![Coverage](https://codecov.io/github/sbthandras/tailor/coverage.svg?branch=master)](https://app.codecov.io/gh/sbthandras/tailor/branch/master) +[![Coverage](https://codecov.io/github/sbthandras/tailor/graph/badge.svg?branch=master)](https://app.codecov.io/gh/sbthandras/tailor/branch/master) [![DOI](https://img.shields.io/badge/DOI-10.64898%2F2026.02.20.706991-blue)](https://doi.org/10.64898/2026.02.20.706991) @@ -16,6 +16,16 @@ status](https://github.com/sbthandras/tailor/workflows/R-CMD-check/badge.svg)](h `tailor` is a **T**ool for **A**dapter-domain **I**dentification and **L**inking **O**f **R**BPs. +# IMPORANT NOTICE + +The latest version of this repository was publised in + on 2 March 2026. + +Following publication this development repository was archived. + +Please refer to for the latest +version of the package and documentation. + ## Installation #### Install from Github (development version) From 481074cf57936038823db270cc9383391a475e72 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Mon, 2 Mar 2026 19:46:13 +0100 Subject: [PATCH 3/9] Bump version number --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5528a23..48545dd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: tailor Type: Package Title: Tool for Adapter-domain Identification and Linking Of RBPs -Version: 0.1.0 +Version: 0.1.1 Authors@R: c( person("András", "Asbóth", role = c("aut", "cre"), email = "sbthandras+bioinfo@gmail.com", From e42fdbdc4deaf755cb9d50f2c913c77acad59972 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Mon, 2 Mar 2026 19:48:40 +0100 Subject: [PATCH 4/9] Remove redundant LICENSE.md --- LICENSE.md | 595 ----------------------------------------------------- 1 file changed, 595 deletions(-) delete mode 100644 LICENSE.md diff --git a/LICENSE.md b/LICENSE.md deleted file mode 100644 index 175443c..0000000 --- a/LICENSE.md +++ /dev/null @@ -1,595 +0,0 @@ -GNU General Public License -========================== - -_Version 3, 29 June 2007_ -_Copyright © 2007 Free Software Foundation, Inc. <>_ - -Everyone is permitted to copy and distribute verbatim copies of this license -document, but changing it is not allowed. - -## Preamble - -The GNU General Public License is a free, copyleft license for software and other -kinds of works. - -The licenses for most software and other practical works are designed to take away -your freedom to share and change the works. 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From d7aa6cb3aadba60155e3a1ba1e2f73e9c0b84cd7 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Mon, 2 Mar 2026 20:39:46 +0100 Subject: [PATCH 5/9] Only use parallelisation when using multiple cores --- R/adapter_matrix.R | 40 ++++++++++++++++++++++++++++-------- R/cluster_adapters.R | 20 +++++++++++++----- R/find_all_adapters.R | 47 ++++++++++++++++++++++++++++++++++--------- 3 files changed, 85 insertions(+), 22 deletions(-) diff --git a/R/adapter_matrix.R b/R/adapter_matrix.R index 43b47e9..ad491ec 100644 --- a/R/adapter_matrix.R +++ b/R/adapter_matrix.R @@ -57,16 +57,15 @@ adapter_matrix <- function( } } value <- match.arg(value, c("pident", "mean_score", "end")) - cl <- parallel::makeCluster(cores, type = "PSOCK") - doParallel::registerDoParallel(cl) - on.exit(parallel::stopCluster(cl), add = TRUE) + dmat <- matrix(NA, nrow = length(ids), ncol = length(ids)) rownames(dmat) = ids colnames(dmat) = ids - dmat <- foreach::foreach( - i = seq_len(nrow(dmat)), .combine = 'rbind',.inorder=TRUE) %dopar% { - i <- i - for (j in seq_len(ncol(dmat))){ + + if (cores == 1) { + # Use regular for loop when cores = 1 + for (i in seq_len(nrow(dmat))) { + for (j in seq_len(ncol(dmat))) { if (i == j) next() adapter <- adapters |> filter_comparisons(ids[i]) |> @@ -79,8 +78,33 @@ adapter_matrix <- function( stop("Multiple comparisons found for ids: ", ids[i], ", ", ids[j], ".") } } - return(dmat[i,]) } + } else { + # Use parallelization when cores > 1 + cl <- parallel::makeCluster(cores, type = "PSOCK") + doParallel::registerDoParallel(cl) + on.exit(parallel::stopCluster(cl), add = TRUE) + + dmat <- foreach::foreach( + i = seq_len(nrow(dmat)), .combine = 'rbind', .inorder = TRUE) %dopar% { + i <- i + for (j in seq_len(ncol(dmat))) { + if (i == j) next() + adapter <- adapters |> + filter_comparisons(ids[i]) |> + filter_comparisons(ids[j]) + if (nrow(adapter) == 0) { + stop("No comparisons found for ids: ", ids[i], ", ", ids[j], ".") + } else if (nrow(adapter) == 1) { + dmat[i, j] <- ifelse(is.na(adapter[[value]]), 0, adapter[[value]]) + } else { + stop("Multiple comparisons found for ids: ", ids[i], ", ", ids[j], ".") + } + } + return(dmat[i, ]) + } + } + if (value == "pident") diag(dmat) <- 1 rownames(dmat) <- ids colnames(dmat) <- ids diff --git a/R/cluster_adapters.R b/R/cluster_adapters.R index d044d0f..3a4c687 100644 --- a/R/cluster_adapters.R +++ b/R/cluster_adapters.R @@ -40,12 +40,22 @@ cluster_adapters <- function( if (is.null(k_max)) k_max <- nrow(mat) - cl <- parallel::makeCluster(cores, type = "PSOCK") - doParallel::registerDoParallel(cl) - on.exit(parallel::stopCluster(cl), add = TRUE) + if (cores == 1) { + # Use regular for loop when cores = 1 + schocos_list <- list() + for (k in k_min:k_max) { + schocos_list[[length(schocos_list) + 1]] <- schoco(mat, k, homogeneity_thr, completeness_thr) + } + schocos <- do.call(rbind, schocos_list) + } else { + # Use parallelization when cores > 1 + cl <- parallel::makeCluster(cores, type = "PSOCK") + doParallel::registerDoParallel(cl) + on.exit(parallel::stopCluster(cl), add = TRUE) - schocos <- foreach::foreach(k = k_min:k_max, .combine = 'rbind') %dopar% { - schoco(mat, k, homogeneity_thr, completeness_thr) + schocos <- foreach::foreach(k = k_min:k_max, .combine = 'rbind') %dopar% { + schoco(mat, k, homogeneity_thr, completeness_thr) + } } schocos <- split(schocos, schocos$nclust) |> unname() diff --git a/R/find_all_adapters.R b/R/find_all_adapters.R index 1815b15..00118e3 100644 --- a/R/find_all_adapters.R +++ b/R/find_all_adapters.R @@ -50,14 +50,10 @@ find_all_adapters <- function( names(pairs) <- c("pattern", "subject") adapters <- data.frame() - cl <- parallel::makeCluster(cores, type = "PSOCK") - doParallel::registerDoParallel(cl) - on.exit(parallel::stopCluster(cl), add = TRUE) - - adapters <- foreach::foreach( - i = seq_len(nrow(pairs)), .combine = 'rbind' - ) %dopar% { - i <- i + if (cores == 1) { + # Use regular for loop when cores = 1 + adapters_list <- list() + for (i in seq_len(nrow(pairs))) { pattern <- pairs$pattern[i] subject <- pairs$subject[i] ps <- position_scores( @@ -76,8 +72,41 @@ find_all_adapters <- function( start_threshold = start_threshold, merge = merge ) - return(adapter) + adapters_list[[i]] <- adapter + } + adapters <- do.call(rbind, adapters_list) + } else { + # Use parallelization when cores > 1 + cl <- parallel::makeCluster(cores, type = "PSOCK") + doParallel::registerDoParallel(cl) + on.exit(parallel::stopCluster(cl), add = TRUE) + + adapters <- foreach::foreach( + i = seq_len(nrow(pairs)), .combine = 'rbind' + ) %dopar% { + i <- i + pattern <- pairs$pattern[i] + subject <- pairs$subject[i] + ps <- position_scores( + pattern_id = pattern, + subject_id = subject, + id_var = id_var, + seq_var = seq_var, + submat = submat, + data = data, + verbose = verbose + ) + adapter <- ps |> + find_breakpoints(method = method, ...) |> + find_adapter( + pident_threshold = pident_threshold, + start_threshold = start_threshold, + merge = merge + ) + return(adapter) + } } + class(adapters) <- c("adapter", class(adapters)) return(adapters) } From 3d37310cfb18b33890db9099676f51280805bd34 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Mon, 2 Mar 2026 20:41:23 +0100 Subject: [PATCH 6/9] Remove LICENSE file we are using a standard license so extra file is confusing --- LICENSE | 674 -------------------------------------------------------- 1 file changed, 674 deletions(-) delete mode 100644 LICENSE diff --git a/LICENSE b/LICENSE deleted file mode 100644 index f288702..0000000 --- a/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - 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From d920afcee8e47186cf88d5850f029106ed8c0d87 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Mon, 2 Mar 2026 21:25:30 +0100 Subject: [PATCH 7/9] Add testthat.R which fixes covr locally --- tests/testthat.R | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 tests/testthat.R diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..28f24b9 --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,4 @@ +library(testthat) +library(tailor) + +test_check("tailor") From 5acd6e41938d6ed58561a496dbc60592d5290827 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Mon, 2 Mar 2026 21:25:45 +0100 Subject: [PATCH 8/9] Add testthat to Suggests --- DESCRIPTION | 2 ++ 1 file changed, 2 insertions(+) diff --git a/DESCRIPTION b/DESCRIPTION index 48545dd..f2e8c42 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -29,6 +29,8 @@ Imports: reshape2, tibble, tidyr +Suggests: + testthat Remotes: stitam/breakpoint License: GPL (>= 3) From b5d2760423585db993087a93e9e978b5d1a4bd40 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Mon, 2 Mar 2026 21:31:30 +0100 Subject: [PATCH 9/9] Update test-coverage workflow --- .github/workflows/test-coverage.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index ccc2031..7d520f5 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -23,11 +23,15 @@ jobs: with: use-public-rspm: true - - name: Install dependencies + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage + + - name: Install package dependencies run: | install.packages("pak") pak::pkg_install(".", dependencies = TRUE) - pak::pkg_install("covr") shell: Rscript {0} - name: Test coverage