🔀 Merge pull request #28 from cnr-ibba/devel

🔖 release v0.2.0

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

@@ -1,8 +1,8 @@
-# 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, devel]
+    branches: [master]
   pull_request:
     branches: [master, devel]
 
@@ -16,41 +16,32 @@ env:
 
 jobs:
   R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    runs-on: ubuntu-latest
 
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Install dependencies on Linux
         if: runner.os == 'Linux'
         run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev
              libgdal-dev libudunits2-dev libharfbuzz-dev libfribidi-dev
 
-      - name: Install dependencies on MacOS
-        if: runner.os == 'macOS'
-        run: brew install gdal
-
       - 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 }}
+          r-version: 'release'
+          http-user-agent: 'default'
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-renv@v2
         with:
-          cache-version: 2
+          cache-version: 1
+          profile: '"dev"'
 
       - uses: r-lib/actions/check-r-package@v2
         with:
@@ -65,5 +56,5 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@main
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          name: Linux-rrelease-results
           path: check

.github/workflows/install.yaml

@@ -0,0 +1,60 @@
+# 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]
+  pull_request:
+    branches: [master, devel]
+
+name: install
+
+env:
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+  R_KEEP_PKG_SOURCE: yes
+  SMARTER_API_USERNAME: ${{ secrets.SMARTER_API_USERNAME }}
+  SMARTER_API_PASSWORD: ${{ secrets.SMARTER_API_PASSWORD }}
+
+jobs:
+  install:
+    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:
+
+      - name: Install dependencies on Linux
+        if: runner.os == 'Linux'
+        run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev
+             libgdal-dev libudunits2-dev libharfbuzz-dev libfribidi-dev
+
+      - name: Install dependencies on MacOS
+        if: runner.os == 'macOS'
+        run: brew install gdal
+
+      - 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
+
+      - name: Install devtools dependency
+        run: install.packages("devtools")
+        shell: Rscript {0}
+
+      - name: Install package with devtools
+        run: devtools::install_github("cnr-ibba/r-smarter-api")
+        shell: Rscript {0}

.github/workflows/lint.yaml

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [master, devel]
+    branches: [master]
   pull_request:
     branches: [master, devel]
 
@@ -16,7 +16,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Install dependencies on Linux
         run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev
@@ -28,7 +28,8 @@ jobs:
 
       - uses: r-lib/actions/setup-renv@v2
         with:
-          cache-version: 2
+          cache-version: 1
+          profile: '"dev"'
 
       - name: Lint
         run: lintr::lint_package()

.github/workflows/pkgdown.yaml

@@ -20,7 +20,7 @@ jobs:
       SMARTER_API_PASSWORD: ${{ secrets.SMARTER_API_PASSWORD }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Install dependencies on Linux
         run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev
@@ -34,7 +34,8 @@ jobs:
 
       - uses: r-lib/actions/setup-renv@v2
         with:
-          cache-version: 2
+          cache-version: 1
+          profile: '"dev"'
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)

.gitignore

@@ -6,3 +6,4 @@
 docs
 inst/doc
 vignettes/*.txt
+*.zip

DESCRIPTION

@@ -1,28 +1,31 @@
 Package: smarterapi
-Title: Fetch SMARTER data through REST API
-Version: 0.1.2
-Authors@R: 
-    person("Paolo", "Cozzi", , "[email protected]", 
-           role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0003-0388-6874"))
-Description: smarterapi is an interface which interacts with SMARTER REST API
-    by querying data using token authentication and providing results into 
-    dataframes.
+Title: Fetch SMARTER Data Through REST API
+Version: 0.2.0.9000
+Authors@R:
+    person(
+        "Paolo", "Cozzi",
+        email = "[email protected]",
+        role = c("aut", "cre"),
+        comment = c(ORCID = "0000-0003-0388-6874")
+    )
+Description:
+    Provides functions to fetch data from the SMARTER API, a RESTful
+    web service that provides access to data from the SMARTER database.
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
-Suggests: 
+RoxygenNote: 7.3.1
+Suggests:
     lintr,
     styler,
     testthat (>= 3.0.0),
     rcmdcheck,
     roxygen2,
-    utils,
     usethis,
     leaflet,
     knitr,
     rmarkdown,
+    yaml,
     pander,
     ggplot2,
     ggspatial,
@@ -33,15 +36,26 @@ Suggests:
     rnaturalearth,
     rnaturalearthdata
 Config/testthat/edition: 3
-Imports: 
+Config/renv/profiles/dev/dependencies:
+    lintr,
+    rcmdcheck,
+    roxygen2,
+    styler,
+    testthat,
+    usethis,
+    devtools
+Imports:
     jsonlite,
     httr,
     urltools,
-    lubridate,
+    RCurl,
+    fs,
+    utils,
     logger,
     dplyr,
     tidyr,
-    sf
+    sf,
+    geojsonsf
 URL: https://cnr-ibba.github.io/r-smarter-api/
 BugReports: https://github.com/cnr-ibba/r-smarter-api/issues
 VignetteBuilder: knitr

NAMESPACE

@@ -3,9 +3,9 @@
 export(get_smarter_breeds)
 export(get_smarter_countries)
 export(get_smarter_datasets)
+export(get_smarter_genotypes)
 export(get_smarter_geojson)
 export(get_smarter_info)
 export(get_smarter_samples)
 export(get_smarter_supportedchips)
-export(get_smarter_token)
 export(get_smarter_variants)

R/breeds.R

@@ -2,11 +2,8 @@
 #' Get SMARTER Breeds
 #'
 #' Fetch SMARTER REST API breeds endpoint and returns results in a dataframe.
-#' Cached token is used or a new token is generated if not provided when calling
-#' this function (see \code{\link{get_smarter_token}} for more information)
 #'
 #' @param query a \code{list} of query arguments
-#' @param token a string with a valid token
 #'
 #' @return Returns a dataframe with selected breeds
 #' @export
@@ -26,16 +23,10 @@
 #'
 #' selected_breeds <- get_smarter_breeds(query = list(search = "mer"))
 #' \dontrun{
-#'
 #' all_breeds <- get_smarter_breeds()
-#'
 #' sheep_breeds <- get_smarter_breeds(query = list(species = "Sheep"))
 #' }
-get_smarter_breeds <- function(query = list(), token = NULL) {
-  if (is.null(token)) {
-    token <- smarterapi::get_smarter_token()
-  }
-
+get_smarter_breeds <- function(query = list()) {
   logger::log_info("Get data from breeds endpoint")
 
   # setting the URL endpoint
@@ -45,7 +36,7 @@ get_smarter_breeds <- function(query = list(), token = NULL) {
   )
 
   # reading our data
-  data <- get_smarter_data(url, token, query)
+  data <- get_smarter_data(url, query)
 
   logger::log_info("Done!")