minor_update

.github/workflows/r.yml

@@ -52,3 +52,5 @@ jobs:
         with:
           upload-snapshots: true
           error-on: '"error"'
+
+

.github/workflows/test-coverage.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

DESCRIPTION

@@ -10,7 +10,7 @@ Encoding: UTF-8
 LazyData: true
 biocViews: Software
 Depends: R (>= 4.0.0),
-Imports:          
+Imports: 
          ape,
          Biostrings,
          chromoMap,
@@ -39,13 +39,15 @@ Imports:
          utils,
          VariantAnnotation
 Suggests:
-         phytools,
-         ggtree,
-         ggnewscale,
-         spam,
-         spam64
+    phytools,
+    ggtree,
+    ggnewscale,
+    spam,
+    spam64,
+    testthat (>= 3.0.0)
 LinkingTo: Rcpp, RcppArmadillo
 RoxygenNote: 7.3.2
 URL: https://github.com/Sudaraka88/LDWeaver
 BugReports: https://github.com/Sudaraka88/LDWeaver/issues
 Biarch: TRUE
+Config/testthat/edition: 3

R/computePairwiseMI.R

@@ -80,7 +80,7 @@ perform_MI_computation = function(snp.dat, hdw, cds_var, ncores, lr_save_path =
       message("This feature requires spam and spam64 packages.")
       return(invisible())
     } else {
-      hsq = spam::as.spam(hsq)
+      # hsq = spam::as.spam(hsq)
     }
   }
 

R/io_functions.R

@@ -305,7 +305,6 @@ cleanup = function(dset, delete_after_moving = F){
     mv_success = c(mv_success, idx)
   }
 
-
   #### Relocate or delete moved files ####
   moved_idx = sort(unique(mv_success))
   if(length(moved_idx) > 0){
@@ -316,6 +315,15 @@ cleanup = function(dset, delete_after_moving = F){
     }
     unlink(file.path(dset, files[moved_idx]), recursive = T)
   }
+
+  ### Sometimes there are a couple of snpEff files being generated in the working directory, move them to Temp
+  files = dir(getwd())
+  idx = c(grep("snpEff_genes.txt", files), grep("snpEff_summary.html", files))
+  if(length(idx) > 0){
+    fldr = file.path(dset, "Temp")
+    cleanup_support(files = file.path(getwd(), files[idx]), fldr)
+    unlink(file.path(getwd(), files[idx]))
+  }
 }
 
 #' cleanup_support

inst/CITATION

@@ -1,8 +1,7 @@
-citHeader("If you find LDWeaver useful, please cite:")
-
-citEntry(entry = "Article",
-title        = "Detecting co-selection through excess linkage disequilibrium in bacterial genomes",
-author       = personList(as.person("Sudaraka Mallawaarachchi"),
+bibentry(
+  bibtype  = "Article",
+  title    = "Detecting co-selection through excess linkage disequilibrium in bacterial genomes",
+  author   = personList(as.person("Sudaraka Mallawaarachchi"),
                  as.person("Gerry Tonkin-Hill"),
                  as.person("Anna K. Pöntinen"),
                  as.person("Jessica K. Calland"),
@@ -14,10 +13,10 @@ author       = personList(as.person("Sudaraka Mallawaarachchi"),
                  as.person("David Balding"),
                  as.person("Nicholas J. Croucher"),
                  as.person("Jukka Corander")),
-journal      = "bioRxiv",
-year         = "2023",
-pages        = "2023.08.04.551407",
-url          = "https://doi.org/10.1101/2023.08.04.551407",
-
-textVersion  = "Sudaraka Mallawaarachchi et al. (2023) Detecting co-selection through excess linkage disequilibrium in bacterial genomes. bioRxiv https://doi.org/10.1101/2023.08.04.551407."
+  journal  = "NAR Genomics and Bioinformatics",
+  year     = "2024",
+  volume   = "6",
+  number   = "2",
+  pages    = "lqae061",
+  doi      = "10.1093/nargab/lqae061"
 )