Merge pull request #32 from erblast/issue_30

Issue 30
erblast · Dec 6, 2023 · 34d419a · 34d419a
2 parents df22644 + d3bde6f
commit 34d419a
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -9,6 +9,7 @@ on:
     branches:
       - main
       - master
+  workflow_dispatch:
 
 name: R-CMD-check
 
@@ -18,16 +19,17 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
-      - uses: r-lib/actions/setup-pandoc@master
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-          Sys.setenv('_R_CHECK_SYSTEM_CLOCK_' = 0)
-        shell: Rscript {0}
-      - name: Check
-        run: |
-          rcmdcheck::rcmdcheck(args = c("--as-cran", "--no-manual"), error_on = "note")
-        shell: Rscript {0}
+      - uses: actions/checkout@v3
+
+      - 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:
+          error-on: '"note"'
diff --git a/.github/workflows/articles.yml b/.github/workflows/articles.yml
@@ -1,26 +1,31 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
+  workflow_dispatch:
 
 name: articles
 
 jobs:
   articles:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: actions/checkout@v3
+
+      - 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
       - name: Install dependencies
         run: |
           install.packages(c("remotes", "devtools", "tidyverse", "pkgdown"))

diff --git a/.github/workflows/coverage.yaml b/.github/workflows/coverage.yaml
@@ -1,46 +1,51 @@
+# 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:
-      - master
+    branches: [main, master]
+  workflow_dispatch:
 
 name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
 
-      - name: Query dependencies
+      - name: Test coverage
         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")
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v1
-        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
+      - name: Show testthat output
+        if: always()
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.github/workflows/parcats.yml b/.github/workflows/parcats.yml
@@ -1,26 +1,31 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
+  workflow_dispatch:
 
 name: parcats
 
 jobs:
   parcats:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: actions/checkout@v3
+
+      - 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
       - name: Install dependencies
         run: |
           install.packages(c("remotes", "devtools"))

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,52 +1,55 @@
+# 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
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    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.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-pandoc@master
-
-      - 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
+      - uses: r-lib/actions/setup-r@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-
+          use-public-rspm: true
 
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
       - name: Install dependencies
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("tidyverse")
-          install.packages("pkgdown", type = "binary")
+          install.packages("devtools")
           system("git clone https://github.com/erblast/parcats.git")
-          remotes::install_deps("parcats/", dependencies = TRUE)
-          devtools::install("parcats/")
+          devtools::install("parcats/", dependencies = TRUE)
         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, run_dont_run = 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
diff --git a/.gitignore b/.gitignore
@@ -8,4 +8,5 @@ docs/
 *.rdx
 *.RData
 *.rdb
-vignettes/model_response_cache/
+vignettes/model_response_cache/
+.DS_Store
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: easyalluvial
 Title: Generate Alluvial Plots with a Single Line of Code
-Version: 0.3.1
+Version: 0.3.1.900
 Authors@R: person( "Bjoern", "Koneswarakantha", role = c("aut","cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-4585-7799") )
 URL: https://github.com/erblast/easyalluvial/
 Description: Alluvial plots are similar to sankey diagrams and visualise categorical data 
@@ -39,7 +39,7 @@ Suggests:
     rpart,
     glmnet,
     xgboost
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Imports:
   purrr
   , tidyr (>= 1.0.0)

diff --git a/NEWS.md b/NEWS.md
@@ -49,7 +49,7 @@ argument which will be converted to bin label.
 # 20181812 0.1.7
 CRAN released
 
-# 20181118
+# 20181118 0.0.1
 CRAN submission
 
 
diff --git a/R/alluvial_model_response.R b/R/alluvial_model_response.R
@@ -1095,7 +1095,8 @@ alluvial_model_response_caret = function(train, data_input, degree = 4, bins = 5
 #'@inheritSection get_pdp_predictions Parallel Processing
 #' @examples
 #' 
-#' if(check_pkg_installed("parsnip", raise_error = FALSE)) {
+#' if(check_pkg_installed("parsnip", raise_error = FALSE) &
+#'    check_pkg_installed("vip", raise_error = FALSE)) {
 #'   df = mtcars2[, ! names(mtcars2) %in% 'ids' ]
 #'
 #'   m = parsnip::rand_forest(mode = "regression") %>%

diff --git a/man/alluvial_model_response_parsnip.Rd b/man/alluvial_model_response_parsnip.Rd