Merge pull request #255 from alan-turing-institute/param6

Param6

.github/workflows/pkgdown.yml

@@ -30,11 +30,13 @@ jobs:
           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
+        run: brew install harfbuzz fribidi
+
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown")
-          remotes::install_github("mlr-org/mlr3pkgdowntemplate")
+          install.packages(c("pkgdown", "textshaping"))
         shell: Rscript {0}
 
       - name: Install package
@@ -45,4 +47,3 @@ jobs:
           git config --local user.email "[email protected]"
           git config --local user.name "GitHub Actions"
           Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
-          

.github/workflows/rcmdcheck.yml

@@ -4,76 +4,104 @@ on:
   schedule:
     - cron: "0 4 * * *"
 
-name: Check/Codecov/Render
+name: R-CMD-check
 
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
-    name: R CMD Check (${{ matrix.config.os }} (${{ matrix.config.r }}))
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
     strategy:
       fail-fast: false
       matrix:
         config:
-          - { os: macOS-latest, r: "3.6" }
-          - { os: macOS-latest, r: "devel" }
-          - { os: macOS-latest, r: "release" }
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v1
+        id: install-r
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v1
 
-      - name: Query dependencies
+      - name: Install pak and query dependencies
         run: |
-          install.packages(c("remotes", "devtools"))
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v1
+      - name: Restore R package cache
+        uses: actions/cache@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-
+          path: |
+            ${{ env.R_LIBS_USER }}/*
+            !${{ env.R_LIBS_USER }}/pak
+          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
+        shell: Rscript {0}
 
       - name: Install dependencies
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
       - name: Check
         env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+          _R_CHECK_CRAN_INCOMING_: false
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
           path: check
 
-      - name: Install covr
-        if: ${{ github.event_name == 'pull_request' && runner.os == 'macOS' }}
-        run: install.packages('covr')
-        shell: Rscript {0}
+      - name: Don't use tar from old Rtools to store the cache
+        if: ${{ runner.os == 'Windows' && startsWith(steps.install-r.outputs.installed-r-version, '3.6' ) }}
+        shell: bash
+        run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH
 
       - name: Test coverage
-        if: ${{ github.event_name == 'pull_request' && runner.os == 'macOS' }}
-        run: covr::codecov()
+        if: ${{ runner.os == 'Linux' && matrix.config.r == 'release'}}
+        run: |
+          install.packages('covr')
+          covr::codecov()
         shell: Rscript {0}
 
       - name: Render rmd

.gitignore

@@ -14,3 +14,5 @@ CRAN-RELEASE
 *.o
 *.so
 *.dll
+/doc/
+/Meta/

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: distr6
 Title: The Complete R6 Probability Distributions Interface
-Version: 1.5.6
+Version: 1.6.0
 Authors@R:
-      c(person(given = "Raphael",
+    c(person(given = "Raphael",
              family = "Sonabend",
-             role = c("aut","cre"),
+             role = c("aut", "cre"),
              email = "[email protected]",
              comment = c(ORCID = "0000-0001-9225-4654")),
       person(given = "Franz",
@@ -15,12 +15,12 @@ Authors@R:
              family = "Ruckdeschel",
              role = "ctb",
              email = "[email protected]",
-             comment = c("Author of distr")),
+             comment = "Author of distr"),
       person(given = "Matthias",
              family = "Kohl",
              role = "ctb",
              email = "[email protected]",
-             comment = c("Author of distr")),
+             comment = "Author of distr"),
       person(given = "Nurul Ain",
              family = "Toha",
              role = "ctb",
@@ -64,33 +64,48 @@ Authors@R:
       person(given = "Qian",
              family = "Zhou",
              role = "ctb",
-             email = "[email protected]")
-        )
-Description: An R6 object oriented distributions package. Unified interface for 42 probability distributions and 11 kernels including functionality for multiple scientific types. Additionally functionality for composite distributions and numerical imputation. Design patterns including wrappers and decorators are described in Gamma et al. (1994, ISBN:0-201-63361-2). For quick reference of probability distributions including d/p/q/r functions and results we refer to McLaughlin, M. P. (2001). Additionally Devroye (1986, ISBN:0-387-96305-7) for sampling the Dirichlet distribution, Gentle (2009) <doi:10.1007/978-0-387-98144-4> for sampling the Multivariate Normal distribution and Michael et al. (1976) <doi:10.2307/2683801> for sampling the Wald distribution.
+             email = "[email protected]"))
+Description: An R6 object oriented distributions package. Unified
+    interface for 42 probability distributions and 11 kernels including
+    functionality for multiple scientific types. Additionally
+    functionality for composite distributions and numerical imputation.
+    Design patterns including wrappers and decorators are described in
+    Gamma et al. (1994, ISBN:0-201-63361-2). For quick reference of
+    probability distributions including d/p/q/r functions and results we
+    refer to McLaughlin, M. P. (2001). Additionally Devroye (1986,
+    ISBN:0-387-96305-7) for sampling the Dirichlet distribution, Gentle
+    (2009) <doi:10.1007/978-0-387-98144-4> for sampling the Multivariate
+    Normal distribution and Michael et al. (1976) <doi:10.2307/2683801>
+    for sampling the Wald distribution.
+License: MIT + file LICENSE
+URL: https://alan-turing-institute.github.io/distr6/,
+    https://github.com/alan-turing-institute/distr6/
+BugReports: https://github.com/alan-turing-institute/distr6/issues
 Imports:
     checkmate,
     data.table,
+    param6 (>= 0.2.1),
     R6,
+    Rcpp,
+    set6 (>= 0.2.3),
+    stats
+Suggests:
+    actuar,
+    cubature,
+    extraDistr,
+    GoFKernel,
+    knitr,
+    magrittr,
+    plotly,
+    pracma,
     R62S3 (>= 1.4.0),
-    set6 (>= 0.2.0),
-    stats,
+    rmarkdown,
+    testthat
+LinkingTo:
     Rcpp
-Suggests:
-  cubature,
-  GoFKernel,
-  knitr,
-  testthat,
-  rmarkdown,
-  magrittr,
-  extraDistr,
-  actuar,
-  plotly,
-  pracma
-License: MIT + file LICENSE
-URL: https://alan-turing-institute.github.io/distr6/, https://github.com/alan-turing-institute/distr6/
-BugReports: https://github.com/alan-turing-institute/distr6/issues
 VignetteBuilder:
     knitr
+Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE, r6 = TRUE)
 RoxygenNote: 7.1.1
@@ -116,8 +131,6 @@ Collate:
     'Kernel_Tricube.R'
     'Kernel_Triweight.R'
     'Kernel_Uniform.R'
-    'ParameterSet.R'
-    'ParameterSetCollection.R'
     'RcppExports.R'
     'SDistribution_Arcsine.R'
     'SDistribution_Bernoulli.R'
@@ -209,5 +222,3 @@ Collate:
     'skewType.R'
     'sugar.R'
     'zzz.R'
-LinkingTo:
-    Rcpp