Merge pull request #10 from umccr/gha-test

Dependency update to R v4.3

.Rbuildignore

@@ -1,4 +1,4 @@
-^\.bumpversion\.cfg$
+^\.bumpversion\.toml$
 ^data-raw$
 ^docs$
 ^LICENSE\.md$

.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.1.2.1"
+current_version = "0.1.2.5"
 search = "{current_version}"
 replace = "{new_version}"
 message = "Bump version: {current_version} → {new_version}"

.github/workflows/deploy.yaml

@@ -4,12 +4,13 @@ on:
   push:
     branches:
       - main
+      - gha-test
 env:
   atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}
   recipe_path: conda/recipe
   env_yaml_path: conda/env/yaml
   env_lock_path: conda/env/lock
-  VERSION: '0.1.2.1' # versioned by bump2version
+  VERSION: '0.1.2.5' # versioned by bump2version
   GDRIVE_CREDENTIALS_DATA: ${{ secrets.GDRIVE_CREDENTIALS_DATA }}
 
 jobs:
@@ -25,47 +26,36 @@ jobs:
     steps:
       - name: Code checkout
         uses: actions/checkout@v4
-      - name: Miniconda setup
-        uses: conda-incubator/setup-miniconda@v2
+      - name: MicroMamba setup
+        uses: mamba-org/setup-micromamba@v2
         with:
-          auto-update-conda: true
-          add-pip-as-python-dependency: false # conda-lock goes crazy if pip pre-installed
-          activate-environment: env1
-          mamba-version: "*"
-          channels: "umccr,conda-forge,bioconda"
+          environment-file: ${{ env.env_yaml_path }}/condabuild.yaml
       - name: 🐍 Conda pkg build and upload
         run: |
-          conda activate
-          mamba create --name cbuildenv conda-build conda-verify anaconda-client boa
-          conda activate cbuildenv
-          conda mambabuild --R 4.2 ${recipe_path} --token ${atoken}
+          conda mambabuild ${recipe_path} -c umccr -c conda-forge -c bioconda --token ${atoken}
       - name: 🔒 Conda lock
         run: |
-          conda activate
-          mamba create --name lockenv conda-lock pip
-          conda activate lockenv
-          conda-lock --file ${env_yaml_path}/sigrap.yaml --platform linux-64
-          mv conda-lock.yml ${env_lock_path}/conda-lock.yml
+          # 1. generate a combined lock file
+          # 2. render platform-specific locks
+          conda-lock lock --file ${env_yaml_path}/sigrap.yaml -p osx-64 -p linux-64
+          conda-lock render --kind explicit -p osx-64 -p linux-64 conda-lock.yml --filename-template 'sigrap-{platform}.lock' && rm conda-lock.yml
+          mv sigrap-*.lock ${env_lock_path}/
       - name: 💾 Commit lockfile
         run: |
-          # TODO: the version bumping guarantees there will be changes,
-          # but during testing this can be problematic - need to
-          # commit only if changes exist.
           git status
           git config --local user.email "actions@github.com"
           git config --local user.name "GitHub Actions"
-          MSG="[bot] Updating conda-lock file (v${VERSION})"
+          MSG="[bot] Updating conda-lock files (v${VERSION})"
           git add .
           git commit -m "${MSG}"
           git push
 
-      - name: 🌐 Website publish
-        run: |
-          conda activate
-          mamba env create -n pkgdownenv -f ${env_yaml_path}/pkgdown.yaml
-          conda activate pkgdownenv
-          sigrap.R --version
-          Rscript -e "pkgdown::deploy_to_branch(pkg = '.', commit_message = paste(pkgdown:::construct_commit_message('.'), '- see https://umccr.github.io/sigrap/'), branch = 'gh-pages', new_process = FALSE)"
+#     - name: 🌐 Website publish
+#       run: |
+#         micromamba env create -n pkgdownenv -f ${env_yaml_path}/pkgdown.yaml
+#         micromamba activate pkgdownenv
+#         sigrap.R --version
+#         Rscript -e "pkgdown::deploy_to_branch(pkg = '.', commit_message = paste(pkgdown:::construct_commit_message('.'), '- see https://umccr.github.io/sigrap/'), branch = 'gh-pages', new_process = FALSE)"
 
       - name: 📥 Pull lock commit
         id: pull_lock_commit
@@ -75,7 +65,7 @@ jobs:
           LATEST_COMMIT_HASH="$(git --no-pager log -1 --format='%H')"
           echo "latest_commit_hash=${LATEST_COMMIT_HASH}" >> $GITHUB_OUTPUT
       - name: 🔖 Create tag
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         env:
           LATEST_COMMIT_HASH: ${{ steps.pull_lock_commit.outputs.latest_commit_hash }}
         with:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: sigrap
 Title: Wrappers for somatic mutation signature analysis tools
-Version: 0.1.2.1
+Version: 0.1.2.5
 Description: Wraps functionality from somatic signature analysis tools.
 Authors@R:
     person(given = "Peter",
@@ -14,7 +14,6 @@ License: MIT + file LICENSE
 Depends:
     R (>= 4.1)
 Remotes:
-    umccr/gpgr,
     umccr/signature.tools.lib,
     UMCUGenetics/CHORD
 Imports:
@@ -23,8 +22,9 @@ Imports:
     cli,
     CHORD,
     dplyr,
+    fs,
     ggplot2,
-    gpgr (>= 1.0.0),
+    jsonlite,
     MutationalPatterns,
     readr,
     rlang,
@@ -55,5 +55,4 @@ ByteCompile: true
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
-VignetteBuilder: knitr
+RoxygenNote: 7.3.1

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(chord_mantavcf2df)
 export(chord_run)
+export(date_log)
 export(get_genome_obj)
 export(hrdetect_prep_cnv)
 export(hrdetect_prep_snvindel)
@@ -10,6 +11,7 @@ export(hrdetect_read_purple_cnv)
 export(hrdetect_read_snvindel_vcf)
 export(hrdetect_read_sv_vcf)
 export(hrdetect_run)
+export(pkg_exists)
 export(sig_contribution)
 export(sig_contribution_table)
 export(sig_count_dbs)
@@ -19,5 +21,6 @@ export(sig_plot_dbs)
 export(sig_plot_indel)
 export(sig_plot_snv)
 export(sig_workflow_run)
+export(write_jsongz)
 importFrom(rlang,":=")
 importFrom(rlang,.data)

R/chord.R

@@ -16,7 +16,7 @@
 #'            <https://github.com/UMCUGenetics/CHORD/blob/d7c963/R/extractSigsChord.R>.
 #'
 #' @examples
-#'
+#' \dontrun{
 #' snv <- system.file("extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz", package = "gpgr")
 #' sv <- system.file("extdata/umccrise/sv/manta.vcf.gz", package = "gpgr")
 #' chord_res <- chord_run(
@@ -25,13 +25,7 @@
 #' )
 #' # chord_res2 <- chord_run(vcf.snv = snv, vcf.sv = sv, sample.name = "foo",
 #' #                         outpath = "nogit/chord_results.json.gz")
-#' @testexamples
-#'
-#' expect_equal(length(chord_res), 2)
-#' expect_equal(names(chord_res), c("contexts", "prediction"))
-#' expect_equal(chord_res[["prediction"]][, 1, drop = TRUE], "foo")
-#'
-#'
+#' }
 #' @return List with extracted signatures and HRD prediction.
 #'
 #' @export
@@ -75,7 +69,7 @@ chord_run <- function(vcf.snv = NULL, vcf.sv = NULL, df.sv = NULL,
 
   # write json.gz to file
   if (!is.null(outpath)) {
-    gpgr::write_jsongz(x = prediction, path = outpath)
+    write_jsongz(x = prediction, path = outpath)
   }
 
   list(
@@ -93,12 +87,10 @@ chord_run <- function(vcf.snv = NULL, vcf.sv = NULL, df.sv = NULL,
 #' @return Tibble with two columns: sv_type and sv_len (INFO/SVTYPE and INFO/SVLEN from VCF).
 #'
 #' @examples
+#' \dontrun{
 #' in_vcf <- system.file("extdata/umccrise/sv/manta.vcf.gz", package = "gpgr")
 #' d <- chord_mantavcf2df(in_vcf)
-#' @testexamples
-#' expect_equal(d$sv_len[1], "-108")
-#' expect_equal(d$sv_type[1], "DEL")
-#'
+#' }
 #' @export
 chord_mantavcf2df <- function(in_vcf) {
   assertthat::assert_that(file.exists(in_vcf))
@@ -140,7 +132,7 @@ get_genome_obj <- function(genome = "hg38") {
       "{paste(names(bsgenome), collapse = ', ')}"
     )
   )
-  if (!gpgr::pkg_exists(pkg)) {
+  if (!pkg_exists(pkg)) {
     stop(glue::glue(
       "{pkg} is not installed on your system.\n",
       "Please install with:\n'BiocManager::install(\"{pkg}\")'"

R/hrdetect.R

@@ -8,14 +8,10 @@
 #'         for SNVs and INDELs in separate tibbles.
 #'
 #' @examples
+#' \dontrun{
 #' x <- system.file("extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz", package = "gpgr")
 #' (l <- hrdetect_read_snvindel_vcf(x))
-#' @testexamples
-#' expect_equal(length(l), 2)
-#' expect_equal(names(l), c("snv", "indel"))
-#' expect_equal(colnames(l$snv), c("chr", "position", "REF", "ALT"))
-#' expect_equal(colnames(l$indel), c("chr", "position", "REF", "ALT"))
-#'
+#' }
 #' @export
 hrdetect_read_snvindel_vcf <- function(x) {
   assertthat::assert_that(file.exists(x))
@@ -61,13 +57,11 @@ hrdetect_read_snvindel_vcf <- function(x) {
 #'
 #'
 #' @examples
+#' \dontrun{
 #' x <- system.file("extdata/umccrise/sv/manta.vcf.gz", package = "gpgr")
 #' sv_bedpe <- hrdetect_read_sv_vcf(x, nm = "SAMPLE")
 #' head(sv_bedpe)
-#' @testexamples
-#' expect_equal(nrow(sv_bedpe), 190)
-#' expect_equal(colnames(sv_bedpe), c("chrom1", "start1", "end1", "chrom2",
-#'              "start2", "end2", "sample", "strand1", "strand2"))
+#' }
 #' @export
 hrdetect_read_sv_vcf <- function(x, nm = NULL, genome = "hg38") {
   assertthat::assert_that(file.exists(x))
@@ -103,13 +97,10 @@ hrdetect_read_sv_vcf <- function(x, nm = NULL, genome = "hg38") {
 #' - minorAllelePloidy
 #'
 #' @examples
+#' \dontrun{
 #' x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
 #' (cnv <- hrdetect_read_purple_cnv(x))
-#' @testexamples
-#' expect_equal(colnames(cnv), c("Chromosome", "chromStart", "chromEnd",
-#'                               "total.copy.number.inTumour",
-#'                               "minor.copy.number.inTumour"))
-#'
+#' }
 #' @export
 hrdetect_read_purple_cnv <- function(x) {
   assertthat::assert_that(file.exists(x))
@@ -143,12 +134,10 @@ hrdetect_read_purple_cnv <- function(x) {
 #' - indel_results: tibble with a summary of the count of indels and their proportion.
 #'
 #' @examples
+#' \dontrun{
 #' x <- system.file("extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz", package = "gpgr")
 #' (l <- hrdetect_prep_snvindel(x, nm = "sampleA"))
-#' @testexamples
-#' expect_equal(c("snv_results", "indel_results"), names(l))
-#' expect_equal(c("sig", "exposure"), colnames(l[["snv_results"]]))
-#' expect_equal(colnames(l[["indel_results"]])[c(1, 7)], c("sample", "del.mh.prop"))
+#' }
 #'
 #' @export
 hrdetect_prep_snvindel <- function(x, nm = NULL, genome = "hg38",
@@ -219,13 +208,11 @@ hrdetect_prep_snvindel <- function(x, nm = NULL, genome = "hg38",
 #' @return Single-column data.frame (with rownames) with counts for each SV category.
 #'
 #' @examples
+#' \dontrun{
 #' x <- system.file("extdata/umccrise/sv/manta.vcf.gz", package = "gpgr")
 #' nm <- "SampleA"
 #' (d <- hrdetect_prep_sv(x, nm))
-#' @testexamples
-#' expect_equal(colnames(d), nm)
-#' expect_true(inherits(d, "data.frame"))
-#'
+#' }
 #' @export
 hrdetect_prep_sv <- function(x, nm = NULL, genome = "hg38") {
   assertthat::assert_that(file.exists(x))
@@ -248,12 +235,10 @@ hrdetect_prep_sv <- function(x, nm = NULL, genome = "hg38") {
 #' @return Tibble with sample name and HRD-LOH index.
 #'
 #' @examples
+#' \dontrun{
 #' x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
 #' (l <- hrdetect_prep_cnv(x, nm = "SampleA"))
-#' @testexamples
-#' expect_equal(colnames(l), c("name", "hrdloh_index"))
-#' expect_equal(nrow(l), 1)
-#'
+#' }
 #' @export
 hrdetect_prep_cnv <- function(x, nm = NULL) {
   assertthat::assert_that(file.exists(x))
@@ -283,6 +268,7 @@ hrdetect_prep_cnv <- function(x, nm = NULL) {
 #' @return Tibble with sample name and HRD probability in first two columns.
 #'
 #' @examples
+#' \dontrun{
 #' snvindel_vcf <- system.file(
 #'   "extdata/umccrise/snv/somatic-ensemble-PASS.vcf.gz",
 #'   package = "gpgr"
@@ -294,11 +280,7 @@ hrdetect_prep_cnv <- function(x, nm = NULL) {
 #' (res <- hrdetect_run(nm, snvindel_vcf, sv_vcf, cnv_tsv, genome))
 #' # hrdetect_run(nm, snvindel_vcf, sv_vcf, cnv_tsv, genome,
 #' #              outpath = "nogit/hrdetect_results.json.gz")
-#' @testexamples
-#' expect_equal(colnames(res), c("sample", "Probability", "intercept", "del.mh.prop", "SNV3",
-#'                               "SV3", "SV5", "hrdloh_index", "SNV8"))
-#' expect_true(inherits(res, "data.frame"))
-#'
+#' }
 #' @export
 hrdetect_run <- function(nm, snvindel_vcf, sv_vcf, cnv_tsv, genome = "hg38",
                          sigsToUse = c(1, 2, 3, 5, 6, 8, 13, 17, 18, 20, 26, 30),
@@ -358,7 +340,7 @@ hrdetect_run <- function(nm, snvindel_vcf, sv_vcf, cnv_tsv, genome = "hg38",
 
   # write json.gz to file
   if (!is.null(outpath)) {
-    gpgr::write_jsongz(x = res, path = outpath)
+    write_jsongz(x = res, path = outpath)
   }
 
   res

R/mutationalpatterns.R

@@ -82,7 +82,7 @@ sig_contribution_table <- function(contr, type, outdir = NULL) {
   # if an outdir is specified, copy out the COSMIC plots to be linked to
   if (!is.null(outdir)) {
     img_cp_dir <- file.path(outdir, "sig_plots", type)
-    gpgr::mkdir(img_cp_dir)
+    fs::dir_create(img_cp_dir)
     sig_table <-
       readr::read_tsv(file = file.path(sig_dir, "description.tsv"), col_types = "cc") |>
       dplyr::mutate(
@@ -276,14 +276,14 @@ sig_plot_dbs <- function(dbs_counts) {
 #'
 #' @export
 sig_workflow_run <- function(vcf, sample_nm, ref_genome = "hg38", outdir) {
-  gpgr::mkdir(outdir)
+  fs::dir_create(outdir)
   outdir <- normalizePath(outdir)
   ref_genome <- get_genome_obj(ref_genome)
 
   save_plot_list <- function(pl, outdir) {
     assertthat::assert_that(is.list(pl), length(pl) > 0)
     assertthat::assert_that(all(sapply(pl, inherits, "ggplot")))
-    gpgr::mkdir(outdir)
+    fs::dir_create(outdir)
     for (i in seq_len(length(pl))) {
       nm <- names(pl)[i]
       fn <- file.path(outdir, paste0(nm, ".png"))
@@ -292,7 +292,7 @@ sig_workflow_run <- function(vcf, sample_nm, ref_genome = "hg38", outdir) {
     }
   }
 
-  cli::cli_h2(glue::glue("{gpgr::date_log()} Start of MutationalPatterns workflow"))
+  cli::cli_h2(glue::glue("{date_log()} Start of MutationalPatterns workflow"))
   # import VCF
   gr <- MutationalPatterns::read_vcfs_as_granges(
     vcf_files = vcf,
@@ -355,14 +355,13 @@ sig_workflow_run <- function(vcf, sample_nm, ref_genome = "hg38", outdir) {
     }() |>
     sigrap::sig_contribution_table(type = "ID")
 
-  cli::cli_h2(glue::glue("{gpgr::date_log()} Saving MutationalPatterns results to\n'{outdir}'"))
+  cli::cli_h2(glue::glue("{date_log()} Saving MutationalPatterns results to\n'{outdir}'"))
   save_plot_list(p_snv, file.path(outdir, "plot/snv"))
   save_plot_list(p_dbs, file.path(outdir, "plot/dbs"))
   save_plot_list(p_indel, file.path(outdir, "plot/indel"))
-  gpgr::write_jsongz(x = sigs_snv_2015, path = file.path(outdir, "sigs/snv2015.json.gz"))
-  gpgr::write_jsongz(x = sigs_snv_2020, path = file.path(outdir, "sigs/snv2020.json.gz"))
-  gpgr::write_jsongz(x = sigs_dbs, path = file.path(outdir, "sigs/dbs.json.gz"))
-  gpgr::write_jsongz(x = sigs_indel, path = file.path(outdir, "sigs/indel.json.gz"))
-
-  cli::cli_h2(glue::glue("{gpgr::date_log()} End of MutationalPatterns workflow"))
+  write_jsongz(x = sigs_snv_2015, path = file.path(outdir, "sigs/snv2015.json.gz"))
+  write_jsongz(x = sigs_snv_2020, path = file.path(outdir, "sigs/snv2020.json.gz"))
+  write_jsongz(x = sigs_dbs, path = file.path(outdir, "sigs/dbs.json.gz"))
+  write_jsongz(x = sigs_indel, path = file.path(outdir, "sigs/indel.json.gz"))
+  cli::cli_h2(glue::glue("{date_log()} End of MutationalPatterns workflow"))
 }