ci: update workflows (#106)

* ci: update workflows

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* ci: add dependabot for github actions

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: skip tests when suggested dependencies are missing

Skip tests that require `tibble` (needed by `sf::read_sf()`) and
`future.callr` when these packages are not installed, fixing the
no-suggest-cmd-check CI workflow.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: guard predict_spatial example with tibble check

The example uses `tsk("leipzig")` which calls `sf::read_sf()`,
requiring `tibble` at runtime. Wrap in `requireNamespace()` guard
so R CMD check passes without suggested dependencies.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: replace `read_sf()` with `st_read()` to avoid tibble dependency

`sf::read_sf()` requires `tibble` which is only a suggested dependency
of `sf`. Use `sf::st_read()` instead which returns a plain data.frame
and works without `tibble` installed.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: be-marc

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/no-suggest-cmd-check.yml

@@ -0,0 +1,75 @@
+# R CMD check workflow without suggested packages v0.4.0
+# Without `cache: false` packages can leak from the cache of the previous workflow runs
+# You can remove the `services.redis` section if the package does not require `rush` for the tests
+# https://github.com/mlr-org/actions
+on:
+  workflow_dispatch:
+    inputs:
+      debug_enabled:
+        type: boolean
+        description: 'Run the build with tmate debugging enabled'
+        required: false
+        default: false
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+name: no-suggest-cmd-check
+
+jobs:
+  no-suggest-cmd-check:
+    runs-on: ${{ matrix.config.os }}
+    services:
+      redis:
+        image: redis
+        options: >-
+          --health-cmd "redis-cli ping"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 6379:6379
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RUSH_TEST_USE_REDIS: true
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,   r: 'release'}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::knitr
+            any::rmarkdown
+          needs: check
+          dependencies: '"hard"'
+          cache: false
+
+      - uses: mxschmitt/action-tmate@v3
+        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
+        with:
+          limit-access-to-actor: true
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual", "--as-cran")'

.github/workflows/pkgdown.yml

@@ -1,4 +1,5 @@
-# pkgdown workflow of the mlr3 ecosystem v0.1.0
+# pkgdown workflow of the mlr3 ecosystem v0.2.0
+# You can remove the `services.redis` section if the package does not require `rush` for the tests
 # https://github.com/mlr-org/actions
 on:
   push:
@@ -17,13 +18,26 @@ name: pkgdown
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    services:
+      redis:
+        image: redis
+        options: >-
+          --health-cmd "redis-cli ping"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 6379:6379
+
 
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -44,7 +58,7 @@ jobs:
 
       - name: Deploy
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.8.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/r-cmd-check.yml

@@ -1,4 +1,5 @@
-# r cmd check workflow of the mlr3 ecosystem v0.4.0
+# r cmd check workflow of the mlr3 ecosystem v0.6.0
+# You can remove the `services.redis` section if the package does not require `rush` for the tests
 # https://github.com/mlr-org/actions
 on:
   workflow_dispatch:
@@ -20,11 +21,22 @@ name: r-cmd-check
 jobs:
   r-cmd-check:
     runs-on: ${{ matrix.config.os }}
+    services:
+      redis:
+        image: redis
+        options: >-
+          --health-cmd "redis-cli ping"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 6379:6379
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RUSH_TEST_USE_REDIS: true
 
     strategy:
       fail-fast: false
@@ -34,7 +46,7 @@ jobs:
           - {os: ubuntu-latest,   r: 'release'}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -46,7 +58,6 @@ jobs:
         with:
           extra-packages: any::rcmdcheck
           needs: check
-          error-on: '"note"'
 
       - uses: mxschmitt/action-tmate@v3
         if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
@@ -55,4 +66,5 @@ jobs:
 
       - uses: r-lib/actions/check-r-package@v2
         with:
+          error-on: '"note"'
           args: 'c("--no-manual", "--as-cran")'

R/TaskClassif_leipzig.R

@@ -21,7 +21,7 @@
 NULL
 
 load_task_leipzig = function(id = "leipzig") {
-  vector = sf::read_sf(system.file("extdata", "leipzig_points.gpkg", package = "mlr3spatial"), stringsAsFactors = TRUE)
+  vector = sf::st_read(system.file("extdata", "leipzig_points.gpkg", package = "mlr3spatial"), stringsAsFactors = TRUE, quiet = TRUE)
   task = as_task_classif_st(vector, id = id, target = "land_cover", label = "Leipzig Land Cover")
   task$backend$hash = task$man = "mlr3::mlr_tasks_leipzig"
   task

man/predict_spatial.Rd

@@ -1,5 +1,5 @@
 test_that("DataBackendVector works", {
-  vector = sf::read_sf(system.file("extdata", "leipzig_points.gpkg", package = "mlr3spatial"), stringsAsFactors = TRUE)
+  vector = sf::st_read(system.file("extdata", "leipzig_points.gpkg", package = "mlr3spatial"), stringsAsFactors = TRUE, quiet = TRUE)
   primary_key = "..row_id"
   vector[[primary_key]] = seq_row(vector)
   backend = DataBackendVector$new(vector, primary_key = primary_key)
@@ -9,7 +9,7 @@ test_that("DataBackendVector works", {
 })
 
 test_that("as_data_backend.sf works", {
-  vector = sf::read_sf(system.file("extdata", "leipzig_points.gpkg", package = "mlr3spatial"), stringsAsFactors = TRUE)
+  vector = sf::st_read(system.file("extdata", "leipzig_points.gpkg", package = "mlr3spatial"), stringsAsFactors = TRUE, quiet = TRUE)
   backend = as_data_backend(vector)
 
   expect_class(backend, "DataBackendVector")

tests/testthat/test_DataBackendVector.R

@@ -61,7 +61,7 @@ test_that("as_task_unsupervised works on RasterStack objects", {
 })
 
 test_that("as_task_unsupervised works on sf objects", {
-  vector = sf::read_sf(system.file("extdata", "leipzig_points.gpkg", package = "mlr3spatial"), stringsAsFactors = TRUE)
+  vector = sf::st_read(system.file("extdata", "leipzig_points.gpkg", package = "mlr3spatial"), stringsAsFactors = TRUE, quiet = TRUE)
   vector$land_cover = NULL
 
   expect_class(as_task_unsupervised(vector), "TaskUnsupervised")

tests/testthat/test_as_task_unsupervised.R

@@ -140,6 +140,7 @@ test_that("parallel execution works with multisession", {
 })
 
 test_that("parallel execution works with callr", {
+  skip_if_not_installed("future.callr")
   # train
   stack = generate_stack(
     list(
@@ -276,7 +277,7 @@ test_that("prediction are written to sf vector", {
   learner = lrn("classif.rpart")
   learner$train(task)
 
-  vector = sf::read_sf(system.file("extdata", "leipzig_points.gpkg", package = "mlr3spatial"), stringsAsFactors = TRUE)
+  vector = sf::st_read(system.file("extdata", "leipzig_points.gpkg", package = "mlr3spatial"), stringsAsFactors = TRUE, quiet = TRUE)
   vector$land_cover = NULL
   task_predict = as_task_unsupervised(vector)
   pred = predict_spatial(task_predict, learner)