Merge pull request #17 from abichat/dev

v1.0.0

Author: abichat

.Rbuildignore

@@ -7,7 +7,8 @@
 ^appveyor\.yml$
 ^_pkgdown\.yml$
 ^cran-comments\.md$
-^dev_history\.R$
 ^\.github$
 docs/
 pkgdown/
+^dev$
+^data-raw$

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

@@ -0,0 +1,34 @@
+# 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:
+  pull_request:
+    branches:
+      - dev
+
+name: R-CMD-check-prdev
+
+jobs:
+  R-CMD-check:
+    if: "!contains(github.event.head_commit.message, 'skip ci')"
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GH_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

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

@@ -1,15 +1,14 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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, dev]
-  pull_request:
-    branches: [main, master, dev]
 
 name: R-CMD-check
 
 jobs:
   R-CMD-check:
+    if: "!contains(github.event.head_commit.message, 'skip ci')"
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -18,8 +17,8 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
+          - {os: macos-latest,    r: 'release'}
+          - {os: windows-latest,  r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
@@ -29,18 +28,22 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -1,8 +1,10 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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: master
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
@@ -12,24 +14,35 @@ name: pkgdown
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GH_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: pkgdown
+          extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Deploy package
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: yatah
 Title: Yet Another TAxonomy Handler
-Version: 0.2.1
+Version: 1.0.0
 Authors@R: 
     person("Antoine", "Bichat", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-6599-7081"))
@@ -14,6 +14,7 @@ Depends:
     R (>= 2.10)
 Imports: 
     ape,
+    lifecycle,
     purrr,
     stats,
     stringr
@@ -29,4 +30,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.1

NAMESPACE

@@ -1,6 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
 export(all_clades)
+export(get_all_clades)
+export(get_clade)
+export(get_last_clade)
+export(get_last_rank)
+export(is_at_least_rank)
 export(is_clade)
 export(is_lineage)
 export(is_rank)
@@ -14,6 +19,7 @@ export(trim_void)
 importFrom(ape,collapse.singles)
 importFrom(ape,read.tree)
 importFrom(ape,write.tree)
+importFrom(lifecycle,deprecate_warn)
 importFrom(purrr,map)
 importFrom(purrr,transpose)
 importFrom(stats,na.omit)

NEWS.md

@@ -1,3 +1,12 @@
+# yatah 1.0.0
+
+* `last_clade()`, `last_rank()` and `all_clades()` are now deprecated in favor 
+of `get_last_clade()`, `get_last_rank()` and `get_all_clades()` (#11).  
+
+* New functions `get_clade()` (#12) and `is_at_least_rank()`.
+
+* New dataset `all_ranks`. 
+
 # yatah 0.2.1
 
 * Use of Roxygen 7.2.1.

R/abundances.R R/data.R

@@ -14,3 +14,11 @@
 #' dim(abundances)
 #' abundances[1:5, 1:7]
 "abundances"
+
+#' Ranks handled by `yatah`
+#'
+#' @keywords datasets
+#' @examples
+#' all_ranks
+"all_ranks"
+

R/deprecated.R

@@ -0,0 +1,43 @@
+#' Deprecated functions
+#'
+#' @importFrom lifecycle deprecate_warn
+#'
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' Use [get_last_clade()] instead of `last_clade()`.
+#'
+#' @export
+#' @keywords internal
+#' @name deprecated
+last_clade <- function(...) {
+  deprecate_warn("1.0.0", "last_clade()", "get_last_clade()")
+
+  get_last_clade(...)
+}
+
+#' @rdname deprecated
+#'
+#' @description
+#'
+#' Use [get_last_rank()] instead of `last_rank()`.
+#'
+#' @export
+last_rank <- function(...) {
+  deprecate_warn("1.0.0", "last_rank()", "get_last_rank()")
+
+  get_last_rank(...)
+}
+
+#' @rdname deprecated
+#'
+#' @description
+#'
+#' Use [get_all_clades()] instead of `all_clades()`.
+#'
+#' @export
+all_clades <- function(...) {
+  deprecate_warn("1.0.0", "all_clades()", "get_all_clades()")
+
+  get_all_clades(...)
+}

R/extract.R R/get.R

@@ -1,7 +1,7 @@
 #' Extract the last clade of a lineage
 #'
 #' @inheritParams is_rank
-#' @param same logical. Does the lineage have the same depth? Default to TRUE.
+#' @param same logical. Does the lineage have the same depth? Default to `TRUE`.
 #'
 #' @return A string. The last clades of the given lineages.
 #' @importFrom stringr str_remove
@@ -10,8 +10,8 @@
 #' @examples
 #' lineage1 <- "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
 #' lineage2 <- "k__Bacteria|p__Firmicutes|c__Clostridia"
-#' last_clade(c(lineage1, lineage2))
-last_clade <- function(lineage, same = TRUE) {
+#' get_last_clade(c(lineage1, lineage2))
+get_last_clade <- function(lineage, same = TRUE) {
 
   error_lineage(lineage)
 
@@ -20,10 +20,41 @@ last_clade <- function(lineage, same = TRUE) {
   str_remove(lineage, ".*__")
 }
 
+#' Extract the clade of a desired rank in a lineage
+#'
+#' @inheritParams get_last_clade
+#' @param rank The desired rank of the clade.
+#'
+#' @return A string.
+#'
+#' @importFrom stringr str_extract str_remove_all
+#' @export
+#'
+#' @examples
+#' lineage1 <- "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
+#' lineage2 <- "k__Bacteria|p__Firmicutes|c__Clostridia"
+#' get_clade(c(lineage1, lineage2), "phylum")
+get_clade <- function(lineage, rank = yatah::all_ranks, same = TRUE) {
+
+  error_lineage(lineage)
+
+  if (same) depth(lineage)
+
+  rank <- match.arg(rank)
+  letter <- names(which(.ranks == rank))
+
+  sep <- getOption("yatah_sep", default = "\\|")
+
+  str_remove_all(
+    str_extract(lineage, paste0("(?<=", letter, "__).*")),
+    paste0(sep, ".*")
+    )
+}
+
 
 #' Extract the last rank of a lineage
 #'
-#' @inheritParams last_clade
+#' @inheritParams get_last_clade
 #'
 #' @return A string. The last rank of the given lineages.
 #' @importFrom stringr str_remove
@@ -32,8 +63,8 @@ last_clade <- function(lineage, same = TRUE) {
 #' @examples
 #' lineage1 <- "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
 #' lineage2 <- "k__Bacteria|p__Firmicutes|c__Clostridia"
-#' last_rank(c(lineage1, lineage2))
-last_rank <- function(lineage, same = TRUE) {
+#' get_last_rank(c(lineage1, lineage2))
+get_last_rank <- function(lineage, same = TRUE) {
 
   error_lineage(lineage)
 
@@ -54,7 +85,7 @@ last_rank <- function(lineage, same = TRUE) {
 #' clades with same name and same rank when \code{simplify} is set to
 #' \code{FALSE}.
 #'
-#' @inheritParams last_clade
+#' @inheritParams get_last_clade
 #' @param simplify logical. Should the output be a vector or a dataframe?
 #'
 #' @return The clades present in the lineage. Vector of ordered strings
@@ -66,9 +97,9 @@ last_rank <- function(lineage, same = TRUE) {
 #' lineage1 <- "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
 #' lineage2 <- "k__Bacteria|p__Firmicutes|c__Clostridia"
 #' lineage3 <- "k__Bacteria|p__Actinobacteria|c__Actinobacteria"
-#' all_clades(c(lineage1, lineage2, lineage3))
-#' all_clades(c(lineage1, lineage2, lineage3), simplify = FALSE)
-all_clades <- function(lineage, simplify = TRUE) {
+#' get_all_clades(c(lineage1, lineage2, lineage3))
+#' get_all_clades(c(lineage1, lineage2, lineage3), simplify = FALSE)
+get_all_clades <- function(lineage, simplify = TRUE) {
 
   error_lineage(lineage)