Merge pull request #45 from poissonconsulting/upkeep

.github/workflows/R-CMD-check.yaml

@@ -1,19 +1,16 @@
 # 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]
   pull_request:
     branches: [main, master]
-  schedule:
-    - cron:  '0 8 * * 0'
-
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
-    if: "!contains(github.event.head_commit.message, 'skip ci')"
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -25,24 +22,19 @@ jobs:
           - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
-          # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
+          # use 4.0 or 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: 'oldrel-4'}
 
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
-          - {os: ubuntu-latest,   r: 'oldrel-4'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -60,14 +52,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-
-      - name: action-slack
-        if: failure()
-        env:
-          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
-        uses: 8398a7/[email protected]
-        with:
-          status: ${{ job.status }}
-          author_name: "github action: ${{github.workflow}}"
-          fields: repo, ref, commit, author, message
-
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -22,7 +24,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +43,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -8,43 +8,54 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -34,7 +34,7 @@ License: MIT + file LICENSE
 URL: https://github.com/poissonconsulting/nlist
 BugReports: https://github.com/poissonconsulting/nlist/issues
 Depends: 
-    R (>= 3.5)
+    R (>= 4.0)
 Imports:
     abind,
     chk,
@@ -60,5 +60,5 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr

NAMESPACE

@@ -66,6 +66,7 @@ S3method(nterms,mcmc)
 S3method(nterms,mcmc.list)
 S3method(nterms,nlist)
 S3method(nterms,nlists)
+S3method(numericise,list)
 S3method(pars,mcmc)
 S3method(pars,mcmc.list)
 S3method(pars,nlist)
@@ -152,9 +153,30 @@ importFrom(abind,abind)
 importFrom(coda,as.mcmc)
 importFrom(coda,as.mcmc.list)
 importFrom(coda,thin)
+importFrom(extras,fill_all)
+importFrom(extras,fill_na)
+importFrom(extras,lower)
+importFrom(extras,pvalue)
+importFrom(extras,svalue)
+importFrom(extras,upper)
+importFrom(extras,zscore)
+importFrom(generics,tidy)
 importFrom(purrr,transpose)
 importFrom(stats,aggregate)
 importFrom(stats,median)
 importFrom(term,as.term)
 importFrom(term,as_term)
 importFrom(term,complete_terms)
+importFrom(universals,"pars<-")
+importFrom(universals,bind_iterations)
+importFrom(universals,collapse_chains)
+importFrom(universals,estimates)
+importFrom(universals,nchains)
+importFrom(universals,niters)
+importFrom(universals,npdims)
+importFrom(universals,nsims)
+importFrom(universals,nterms)
+importFrom(universals,pars)
+importFrom(universals,pdims)
+importFrom(universals,set_pars)
+importFrom(universals,split_chains)

R/as-nlist.R

@@ -17,8 +17,8 @@ as_nlist <- function(x, ...) {
 #' @export
 as.nlist <- function(x, ...) {
   deprecate_warn("0.1.1",
-                 what = "nlist::as.nlist()",
-                 with = "nlist::as_nlist()"
+    what = "nlist::as.nlist()",
+    with = "nlist::as_nlist()"
   )
   UseMethod("as_nlist")
 }
@@ -31,7 +31,7 @@ as_nlist.numeric <- function(x, ...) {
   chk_not_any_na(names(x))
   chk_unique(names(x))
   chk_unused(...)
-  
+
   if (!length(x)) {
     return(nlist())
   }
@@ -70,7 +70,7 @@ as_nlist.data.frame <- function(x, ...) as_nlist(as.list(x))
 #' @export
 as_nlist.mcmc <- function(x, ...) {
   chk_unused(...)
-  if(!identical(nrow(x), 1L)) abort_chk("`x` must have one iteration.")
+  if (!identical(nrow(x), 1L)) abort_chk("`x` must have one iteration.")
 
   x <- complete_terms(x)
 
@@ -89,4 +89,3 @@ as_nlist.mcmc.list <- function(x, ...) {
 
 #' @export
 as_nlist.nlist <- function(x, ...) x
-

R/as-nlists.R

@@ -45,8 +45,9 @@ as_nlists.mcmc.list <- function(x, ...) {
   nchains <- nchains(x)
   x <- as_mcmc(x)
   x <- as_nlists(x)
-  if(nchains != 1L)
+  if (nchains != 1L) {
     attr(x, "nchains") <- nchains
+  }
   x
 }
 

R/as-term-frame.R

@@ -15,7 +15,7 @@ as_term_frame <- function(x, ...) {
 
 #' Coerce nlist Object to Data Frame
 #'
-#' Coerces an nlist object to a data.frame with an term column 
+#' Coerces an nlist object to a data.frame with an term column
 #' and a value column.
 #'
 #' @export
@@ -62,7 +62,7 @@ as_term_frame_nlist_impl <- function(x, sample = NULL) {
 
 #' Coerce nlists Object to Data Frame
 #'
-#' Coerces an nlists object to a data.frame with a term, sample 
+#' Coerces an nlists object to a data.frame with a term, sample
 #' and value column.
 #'
 #' @export
@@ -85,7 +85,7 @@ as_term_frame.nlists <- function(x, ...) {
     )))
   }
   x <- mapply(as_term_frame_nlist_impl, x,
-    sample = 1:length(x),
+    sample = seq_along(x),
     SIMPLIFY = FALSE
   )
   do.call("rbind", x)

R/bind-iterations.R

@@ -7,22 +7,22 @@ universals::bind_iterations
 #' bind_iterations(as_mcmc(nlist(x = 1)), as_mcmc(nlist(x = 3)))
 bind_iterations.mcmc <- function(x, x2, ...) {
   chk_s3_class(x2, "mcmc")
-  
+
   x <- sort(x)
   x2 <- sort(x2)
-  
+
   if (!identical(pars(x), pars(x2))) {
     abort_chk("`x` and `x2` must have the same parameters")
   }
-  
+
   if (!identical(pdims(x), pdims(x2))) {
     abort_chk("`x` and `x2` must have the same parameter dimensions")
   }
-  
+
   if (!identical(nchains(x), nchains(x2))) {
     abort_chk("`x` and `x2` must have the same number of chains")
   }
-  
+
   x <- abind(x, x2, along = 1)
   as.mcmc(x)
 }
@@ -32,27 +32,27 @@ bind_iterations.mcmc <- function(x, x2, ...) {
 #' @examples
 #' bind_iterations(as_mcmc_list(nlist(x = 1)), as_mcmc_list(nlist(x = 3)))
 bind_iterations.mcmc.list <- function(x, x2, ...) {
-  if(!(vld_s3_class(x2, "mcmc.list") || vld_s3_class(x2, "mcmc"))) {
+  if (!(vld_s3_class(x2, "mcmc.list") || vld_s3_class(x2, "mcmc"))) {
     if (!vld_all_identical(lapply(x, lapply, dims))) {
       abort_chk("`x2` must inherit from S3 class 'mcmc.list' or 'mcmc'.")
-    }    
+    }
   }
-  
+
   x <- sort(x)
   x2 <- sort(x2)
-  
+
   if (!identical(pars(x), pars(x2))) {
     abort_chk("`x` and `x2` must have the same parameters")
   }
-  
+
   if (!identical(pdims(x), pdims(x2))) {
     abort_chk("`x` and `x2` must have the same parameter dimensions")
   }
-  
+
   if (!identical(nchains(x), nchains(x2))) {
     abort_chk("`x` and `x2` must have the same number of chains")
   }
-  
+
   x <- mapply(x, x2, FUN = bind_iterations, SIMPLIFY = FALSE)
   set_class(x, "mcmc.list")
 }

R/chk.R

@@ -22,8 +22,8 @@ chk_nlist <- function(x, x_name = NULL) {
   chk_named(x, x_name = x_name)
   x_name_names <- backtick_chk(p0("names(", unbacktick_chk(x_name), ")"))
   chk_pars(names(x), x_name = x_name_names)
-  chk_not_any_na(names(x), x_name = x_name_names) 
-  chk_unique(names(x), x_name = x_name_names) 
+  chk_not_any_na(names(x), x_name = x_name_names)
+  chk_unique(names(x), x_name = x_name_names)
   chk_all(x, chk_numeric, x_name = x_name)
 }
 

R/complete-terms.R

@@ -1,5 +1,5 @@
 #' @importFrom term complete_terms
-#' @export 
+#' @export
 term::complete_terms
 
 #' Complete Terms
@@ -21,13 +21,13 @@ term::complete_terms
 complete_terms.mcmc <- function(x, silent = FALSE, ...) {
   chk_flag(silent)
   chk_unused(...)
-  
+
   if (!silent && anyNA(colnames(x))) {
     wrn("terms with missing values have been dropped")
   }
 
   x <- as.matrix(x)
-  x <- x[,!is.na(colnames(x)), drop = FALSE]
+  x <- x[, !is.na(colnames(x)), drop = FALSE]
   colnames(x) <- as.character(as_term(colnames(x), repair = TRUE))
   if (!silent && anyNA(colnames(x))) wrn("invalid terms have been dropped")
   x <- x[, !is.na(colnames(x)), drop = FALSE]
@@ -39,7 +39,7 @@ complete_terms.mcmc <- function(x, silent = FALSE, ...) {
     wrn("inconsistent terms have been dropped")
   }
   x <- x[, consistent, drop = FALSE]
-  
+
   if (!ncol(x)) {
     return(coda::as.mcmc(x))
   }

R/extras.R

@@ -3,7 +3,8 @@ as_list_unnamed_default <- function(x, ...) {
   x <- as.list(x)
   names <- names(x)
   attributes(x) <- NULL
-  if(!is.null(names))
+  if (!is.null(names)) {
     names(x) <- names
+  }
   x
 }