Fixing vignette not found

.pre-commit-config.yaml

@@ -28,14 +28,14 @@ repos:
     hooks:
       - id: air-format
         name: air format
-        entry: air format .
+        entry: RcppTskit/tools/run-local-tool.sh air format .
         language: system
         pass_filenames: false
         files: '\.(R|Rmd|rmd|qmd|Qmd)$'
 
       - id: jarl-lint
         name: jarl lint
-        entry: jarl check .
+        entry: RcppTskit/tools/run-local-tool.sh jarl check .
         language: system
         pass_filenames: false
         files: '\.(R|Rmd|rmd|qmd|Qmd)$'

README.md

@@ -73,6 +73,7 @@ To install the published release from [CRAN](https://cran.r-project.org) use:
 #       https://github.com/HighlanderLab/RcppTskit/issues/14
 #       https://github.com/HighlanderLab/RcppTskit/issues/45
 # install.packages("RcppTskit")
+# vignette("RcppTskit_intro")
 ```
 
 To install the latest development version (possibly unstable!) from
@@ -99,10 +100,14 @@ https://mac.r-project.org/tools for macOS tools.
 # remotes::install_github("HighlanderLab/RcppTskit/RcppTskit")
 
 # Main branch
-remotes::install_github("HighlanderLab/RcppTskit/RcppTskit@main")
+remotes::install_github("HighlanderLab/RcppTskit/RcppTskit@main",
+  build_vignettes=TRUE)
 
 # Development branch
-remotes::install_github("HighlanderLab/RcppTskit/RcppTskit@devel")
+remotes::install_github("HighlanderLab/RcppTskit/RcppTskit@devel",
+  build_vignettes=TRUE)
+
+vignette("RcppTskit_intro")
 ```
 
 ## Development

RcppTskit/R/RcppTskit-package.R

@@ -24,7 +24,7 @@
 #' @importFrom reticulate import is_py_object py_module_available py_require
 #'
 #' @examples
-#' vignette(package="RcppTskit")
+#' vignette("RcppTskit_intro")
 "_PACKAGE"
 
 #' Provide an inline plugin so we can call the tskit C API with functions like

RcppTskit/tools/run-local-tool.sh

@@ -0,0 +1,35 @@
+#!/usr/bin/env sh
+set -eu
+
+if [ "$#" -lt 1 ]; then
+  echo "Usage: $0 <tool> [args...]" >&2
+  exit 2
+fi
+
+tool="$1"
+shift
+
+if command -v "$tool" >/dev/null 2>&1; then
+  exec "$tool" "$@"
+fi
+
+# Follow project guidance by checking user-local bin directories.
+if [ -n "${HOME:-}" ]; then
+  PATH="${HOME}/.local/bin:${HOME}/bin:${PATH}"
+  export PATH
+  if command -v "$tool" >/dev/null 2>&1; then
+    exec "$tool" "$@"
+  fi
+fi
+
+# As a last resort, query the user's login shell PATH.
+if [ -n "${SHELL:-}" ] && [ -x "${SHELL:-}" ]; then
+  resolved="$("${SHELL}" -lc "command -v \"$tool\"" 2>/dev/null || true)"
+  if [ -n "$resolved" ] && [ -x "$resolved" ]; then
+    exec "$resolved" "$@"
+  fi
+fi
+
+echo "Executable '$tool' not found on PATH." >&2
+echo "Install '$tool' and ensure your shell PATH exports it." >&2
+exit 3

RcppTskit/vignettes/RcppTskit_intro.qmd

@@ -141,21 +141,20 @@ to record a tree sequence in a multi-generation simulation with many individuals
 
 Given the current tree sequence ecosystem,
 the aims of the `RcppTskit` package are to provide an easy-to-install R package
-that supports users in four typical cases.
+that supports users in four typical cases of working with tree sequences
+and table collection.
 The authors are open to expanding this scope of `RcppTskit`
 depending on user demand and engagement.
 The four typical cases are:
 
-1. Load a tree sequence[^ts_and_tc_note] into R and summarise it,
+1. Load a tree sequence into R and summarise it,
 
-2. Pass a tree sequence[^ts_and_tc_note] between R and reticulate or standard Python,
+2. Pass a tree sequence between R and reticulate or standard Python,
 
 3. Call the `tskit` C API from C++ in an R session or script, and
 
 4. Call the `tskit` C API from C++ in another R package.
 
-[^ts_and_tc_note]: Both tree sequence and table collection types are supported.
-
 Examples for all of these cases are provided below
 after we describe the implemented data and class model.
 
@@ -213,7 +212,7 @@ if (!test) {
 }
 ```
 
-### 1) Load a tree sequence[^ts_and_tc_note] into R and summarise it
+### 1) Load a tree sequence into R and summarise it
 
 ```{r}
 #| label: use_case_1
@@ -239,7 +238,7 @@ ts2 <- tc$tree_sequence()
 help(package = "RcppTskit")
 ```
 
-### 2) Pass a tree sequence[^ts_and_tc_note] between R and reticulate or standard Python
+### 2) Pass a tree sequence between R and reticulate or standard Python
 
 ```{r}
 #| label: use_case_2