.

Author: gregorgorjanc

.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)$'

RcppTskit/R/RcppTskit-package.R

@@ -24,7 +24,7 @@
 #' @importFrom reticulate import is_py_object py_module_available py_require
 #'
 #' @examples
-#' vignette(package="RcppTskit_intro")
+#' 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