ci: Change branches in ci config (#2)

* ci: Change branches in ci config

* ci: Update r-cmd-check version

* ci: Remove old CI

* docs: Remove useless examples and redocument

* refactor: Update utils-pipe

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

@@ -0,0 +1,49 @@
+# 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: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {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'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -1,47 +1,47 @@
 on:
-  push:
-    branches:
-      - dev
+    push:
+        branches:
+            - master
 
 name: pkgdown
 
 jobs:
-  pkgdown:
-    runs-on: macOS-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
-        shell: Rscript {0}
-
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Deploy package
-        run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+    pkgdown:
+        runs-on: macOS-latest
+        env:
+            GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        steps:
+            - uses: actions/checkout@v2
+
+            - uses: r-lib/actions/setup-r@v1
+
+            - uses: r-lib/actions/setup-pandoc@v1
+
+            - name: Query dependencies
+              run: |
+                  install.packages('remotes')
+                  saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+                  writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+              shell: Rscript {0}
+
+            - name: Cache R packages
+              uses: actions/cache@v2
+              with:
+                  path: ${{ env.R_LIBS_USER }}
+                  key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+                  restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+            - name: Install dependencies
+              run: |
+                  remotes::install_deps(dependencies = TRUE)
+                  install.packages("pkgdown", type = "binary")
+              shell: Rscript {0}
+
+            - name: Install package
+              run: R CMD INSTALL .
+
+            - name: Deploy package
+              run: |
+                  git config --local user.email "[email protected]"
+                  git config --local user.name "GitHub Actions"
+                  Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

DESCRIPTION

@@ -23,7 +23,7 @@ Suggests:
     testthat,
     knitr,
     rmarkdown
-RoxygenNote: 7.1.0
+RoxygenNote: 7.2.3
 Imports: 
     magrittr,
     dplyr,

R/utils-pipe.R

@@ -8,5 +8,7 @@
 #' @export
 #' @importFrom magrittr %>%
 #' @usage lhs \%>\% rhs
-#' @noRd
+#' @param lhs A value or the magrittr placeholder.
+#' @param rhs A function call using the magrittr semantics.
+#' @return The result of calling `rhs(lhs)`.
 NULL

R/utils.R

@@ -4,8 +4,6 @@
 #' @param quotes A logical to indicate whether or not to encase in quotes
 #'
 #' @return A SPARQL-compatible string of the values
-#' @examples
-#' .collapse_as_values(c("GO:0006936", "GO:0008152"))
 .collapse_as_values <- function(item_vector, quotes = FALSE) {
   unique_items <- stringr::str_trim(unique(item_vector))
 
@@ -21,8 +19,6 @@
 #' @param column The column of the dataframe to substitute
 #'
 #' @return A character vector
-#' @examples
-#' .remove_wdt_url("http://www.wikidata.org/entity/Q18031649")
 .remove_wdt_url <- function(column) {
   stringr::str_replace_all(
     column, "http://www.wikidata.org/entity/",
@@ -35,9 +31,6 @@
 #' @param species_name The scientific name of the species
 #'
 #' @return The Wikidata item for said species
-#'
-#' @examples
-#' .get_species_item("Homo sapiens")
 .get_species_item <- function(species_name) {
   values <- c("Q15978631", "Q83310")
   names(values) <- c("Homo sapiens", "Mus musculus")

README.Rmd

@@ -18,8 +18,8 @@ devtools::load_all()
 
 
 <!-- badges: start -->
-[![R build status](https://github.com/jvfe/go2cell/workflows/R-CMD-check/badge.svg)](https://github.com/jvfe/go2cell/actions)
 [![docs](https://github.com/jvfe/go2cell/workflows/pkgdown/badge.svg)](https://jvfe.github.io/go2cell/index.html)
+[![R-CMD-check](https://github.com/jvfe/go2cell/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jvfe/go2cell/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 By using [Wikidata](https://www.wikidata.org/wiki/Wikidata:Main_Page), go2cell links Gene Ontology terms to cell types, therefore enriching Omics results with open semantic knowledge.

README.md

@@ -5,9 +5,8 @@
 
 <!-- badges: start -->
 
-[![R build
-status](https://github.com/jvfe/go2cell/workflows/R-CMD-check/badge.svg)](https://github.com/jvfe/go2cell/actions)
 [![docs](https://github.com/jvfe/go2cell/workflows/pkgdown/badge.svg)](https://jvfe.github.io/go2cell/index.html)
+[![R-CMD-check](https://github.com/jvfe/go2cell/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jvfe/go2cell/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 By using [Wikidata](https://www.wikidata.org/wiki/Wikidata:Main_Page),
@@ -36,11 +35,11 @@ go_ids <- c("GO:0006936", "GO:0009100")
 results <- go2cell(go_ids)
 ```
 
-| cell\_type    | cell\_typeLabel     | go\_ids      | go\_termLabel      | geneLabel |
-| :------------ | :------------------ | :----------- | :----------------- | :-------- |
-| wd:Q101404903 | human myocyte       | <GO:0006936> | muscle contraction | ANKRD2    |
-| wd:Q101404861 | human fibroblast    | <GO:0006936> | muscle contraction | TBX20     |
-| wd:Q101405077 | human cardiomyocyte | <GO:0006936> | muscle contraction | TBX20     |
-| wd:Q101405077 | human cardiomyocyte | <GO:0006936> | muscle contraction | CKMT2     |
-| wd:Q101405077 | human cardiomyocyte | <GO:0006936> | muscle contraction | MYBPC3    |
-| wd:Q101404903 | human myocyte       | <GO:0006936> | muscle contraction | MYH1      |
+| cell_type     | cell_typeLabel              | go_ids       | go_termLabel       | geneLabel |
+|:--------------|:----------------------------|:-------------|:-------------------|:----------|
+| wd:Q101404903 | human myocyte               | <GO:0006936> | muscle contraction | ACTN2     |
+| wd:Q101405077 | human cardiomyocyte         | <GO:0006936> | muscle contraction | ACTN2     |
+| wd:Q101404861 | human fibroblast            | <GO:0006936> | muscle contraction | TBX20     |
+| wd:Q101405077 | human cardiomyocyte         | <GO:0006936> | muscle contraction | TBX20     |
+| wd:Q68620817  | human hepatic stellate cell | <GO:0006936> | muscle contraction | DES       |
+| wd:Q101404901 | human smooth muscle cell    | <GO:0006936> | muscle contraction | DES       |