prepare for jamovi 2.4

sbalci · Jun 1, 2023 · f37d32c · f37d32c
1 parent acb9ced
commit f37d32c
Show file tree

Hide file tree

Showing 28 changed files with 400 additions and 483 deletions.
diff --git a/.github/workflows/check-release.yaml b/.github/workflows/check-release.yaml
@@ -1,33 +1,29 @@
-# 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:
-  workflow_dispatch:
-  # push:
-  #   branches:
-  #     - main
-  #     - master
-  # pull_request:
-  #   branches:
-  #     - main
-  #     - master
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
 
 name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    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
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-        shell: Rscript {0}
-      - name: Check
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
-        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
diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
@@ -1,15 +1,10 @@
-# 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:
-  workflow_dispatch:
-  # push:
-  #   branches:
-  #     - main
-  #     - master
-  # pull_request:
-  #   branches:
-  #     - main
-  #     - master
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -23,65 +18,32 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     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-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-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: Restore R package cache
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@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 system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,48 +1,48 @@
+# 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@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}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@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-
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         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)'
+      - 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/.github/workflows/r.yml b/.github/workflows/r.yml
diff --git a/ClinicoPathDescriptives.Rproj b/ClinicoPathDescriptives.Rproj
@@ -17,5 +17,4 @@ StripTrailingWhitespace: Yes
 
 BuildType: Package
 PackageUseDevtools: Yes
-PackageCleanBeforeInstall: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: ClinicoPathDescriptives
 Title: Descriptives Functions for Clinicopathological Research
-Version: 0.0.2.05
-Date: 2022-09-20
+Version: 0.0.2.06
+Date: 2023-06-01
 Authors@R: 
     person(given = "Serdar",
            family = "Balci",
@@ -54,4 +54,4 @@ Remotes:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/R/agepyramid.b.R b/R/agepyramid.b.R
@@ -1,8 +1,4 @@
 #' @title Age Pyramid
-#'
-#'
-#'
-#'
 #' @importFrom R6 R6Class
 #' @import jmvcore
 #'

diff --git a/R/agepyramid.h.R b/R/agepyramid.h.R
@@ -117,7 +117,8 @@ agepyramidBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 revision = revision,
                 pause = NULL,
                 completeWhenFilled = FALSE,
-                requiresMissings = FALSE)
+                requiresMissings = FALSE,
+                weightsSupport = 'auto')
         }))
 
 #' Age Pyramid

diff --git a/R/alluvial.h.R b/R/alluvial.h.R
@@ -174,7 +174,8 @@ alluvialBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 revision = revision,
                 pause = NULL,
                 completeWhenFilled = FALSE,
-                requiresMissings = FALSE)
+                requiresMissings = FALSE,
+                weightsSupport = 'auto')
         }))
 
 #' Alluvial Diagrams

diff --git a/R/benford.h.R b/R/benford.h.R
@@ -86,7 +86,8 @@ benfordBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 revision = revision,
                 pause = NULL,
                 completeWhenFilled = FALSE,
-                requiresMissings = FALSE)
+                requiresMissings = FALSE,
+                weightsSupport = 'auto')
         }))
 
 #' Benford Analysis

diff --git a/R/crosstable.b.R b/R/crosstable.b.R
@@ -1,6 +1,4 @@
 #' @title Cross Table
-#'
-#'
 #' @importFrom R6 R6Class
 #' @import jmvcore
 #'

diff --git a/R/crosstable.h.R b/R/crosstable.h.R
@@ -166,7 +166,8 @@ crosstableBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 revision = revision,
                 pause = NULL,
                 completeWhenFilled = FALSE,
-                requiresMissings = FALSE)
+                requiresMissings = FALSE,
+                weightsSupport = 'auto')
         }))
 
 #' Cross Tables

diff --git a/R/reportcat.h.R b/R/reportcat.h.R
@@ -75,7 +75,8 @@ reportcatBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 revision = revision,
                 pause = NULL,
                 completeWhenFilled = FALSE,
-                requiresMissings = FALSE)
+                requiresMissings = FALSE,
+                weightsSupport = 'auto')
         }))
 
 #' Summary of Categorical Variables

diff --git a/R/summarydata.b.R b/R/summarydata.b.R
@@ -1,6 +1,4 @@
 #' @title Summary of Continuous Variables
-#'
-#'
 #' @return Text
 #'
 #' @importFrom R6 R6Class

diff --git a/R/summarydata.h.R b/R/summarydata.h.R
@@ -71,7 +71,8 @@ summarydataBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 revision = revision,
                 pause = NULL,
                 completeWhenFilled = FALSE,
-                requiresMissings = FALSE)
+                requiresMissings = FALSE,
+                weightsSupport = 'auto')
         }))
 
 #' Summary of Continuous Variables

diff --git a/R/tableone.h.R b/R/tableone.h.R
@@ -123,7 +123,8 @@ tableoneBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 revision = revision,
                 pause = NULL,
                 completeWhenFilled = FALSE,
-                requiresMissings = FALSE)
+                requiresMissings = FALSE,
+                weightsSupport = 'auto')
         }))
 
 #' Table One