Holiday maintanance for re-release on CRAN

.Rbuildignore

@@ -1,8 +1,12 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-.git
-.gitignore
+^\.git
+^\.gitignore
+^\.vscode
 ^\.github$
+^\.builds
+^\.lintr$
+^\.pytest_cache
 LICENSE.md
 README.md
 CONTRIBUTING.md

.github/workflows/lint.yaml

@@ -0,0 +1,33 @@
+# 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]
+  pull_request:
+    branches: [main]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - 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::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: false
+          LINTR_COMMENT_BOT: false

.github/workflows/r.yml

@@ -10,6 +10,8 @@
 # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
 
 on:
+  schedule:
+    - cron: '30 20 1 1-12 *'
   push:
     branches:
       - main
@@ -33,63 +35,30 @@ jobs:
         config:
           - {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: 'release'}
+          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     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: Cache R packages
-        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

.gitignore

@@ -2,8 +2,10 @@
 .Rhistory
 .Rapp.history
 
-# Session Data files
+# Session and environemnt Data files
 .RData
+.Ruserdata
+.Renviron
 
 # Example code in package build process
 *-Ex.R
@@ -27,8 +29,12 @@ vignettes/*.pdf
 # knitr and R markdown default cache directories
 /*_cache/
 /cache/
+*_cache/
 
 # Temporary files created by R markdown
 *.utf8.md
 *.knit.md
 .Rproj.user
+
+# Mac OS X File
+.DS_Store

.lintr

@@ -0,0 +1,20 @@
+linters: linters_with_defaults(
+    line_length_linter(120),
+    # Nice to haves
+    commented_code_linter = NULL,
+    object_name_linter=NULL,
+    single_quotes_linter = NULL,
+    commas_linter = NULL,
+    infix_spaces_linter = NULL,
+    cyclocomp_linter = NULL,
+    # Should haves
+    seq_linter = NULL,
+    object_usage_linter = NULL,
+    vector_logic_linter = NULL
+  )
+exclusions: list(
+  "inst",
+  "man",
+  "tests"
+ )
+encoding: "UTF-8"

DESCRIPTION

@@ -1,22 +1,22 @@
 Package: paramGUI
 Title: A Shiny GUI for some Parameter Estimation Examples
-Version: 2.1.4
-Authors@R: c(person("Joris", "Snellenburg", role = c("cre","aut"),
-		     email = "j.snellenburg@vu.nl"),
-	      person("Katharine", "Mullen", role = "aut"),
-	      person("Ivo", "van Stokkum", role = "aut",
-		     email = "ivo@few.vu.nl"))
-Description: Allows specification and fitting of some parameter
-    estimation examples inspired by time-resolved spectroscopy via
-    a Shiny GUI.
+Version: 2.1.5
+Authors@R: c(
+    person("Joris", "Snellenburg", , "j.snellenburg@vu.nl", role = c("cre", "aut")),
+    person("Katharine", "Mullen", role = "aut"),
+    person("Ivo", "van Stokkum", , "ivo@few.vu.nl", role = "aut")
+  )
+Description: Allows specification and fitting of some parameter estimation
+    examples inspired by time-resolved spectroscopy via a Shiny GUI.
+License: GPL (>= 2)
 Depends:
+    colorspace,
+    fields,
     R (>= 3.0.0),
-    TIMP,
     shiny,
     shinydashboard,
-    colorspace,
-    fields
-License: GPL (>= 2)
+    TIMP
 Encoding: UTF-8
+Language: en-US
 LazyData: true
-RoxygenNote: 7.0.2
+RoxygenNote: 7.2.3

R/example_dataset.R

@@ -1,12 +1,12 @@
-#' This is data to be included in my package
+#' This is an example dataset included in this package
 #'
 #' @name example_dataset
 #' @aliases datamat times waves
 #' @docType data
 #' @author Ivo van Stokkum \email{i.h.m.van.stokkum@vu.nl}
-#' @references \url{https://dx.doi.org/10.1016/j.chemphys.2008.10.005}
+#' @references \doi{10.1016/j.chemphys.2008.10.005}
 #' @keywords data
-#' @description Dispersion corrected time-resolved transient-absoprtion data 
-#' of the peridinin chlorophyll protein (PCP) excited with 490 nm laser light 
+#' @description Dispersion corrected time-resolved transient-absorption data
+#' of the peridinin chlorophyll protein (PCP) excited with 490 nm laser light
 #' from the publication of Stokkum et.al. (2009)
 NULL

R/paramGUI-package.R

@@ -1,8 +1,9 @@
 #' paramGUI
 #'
 #' @name paramGUI
+#' @description Allows specification and fitting of some parameter estimation
+#' examples inspired by time-resolved spectroscopy via a Shiny GUI.
 #' @docType package
 #' @import shiny shinydashboard
 #' @importFrom TIMP initModel fitModel
 NULL
-