Default RETICULATE_PYTHON to managed for ir run

docs/run.qmd

@@ -82,6 +82,10 @@ Use `python-packages` or `python-version` to ask `ir run` for a Python environme
 - It sets `RETICULATE_PYTHON` to the resolved Python executable.
 
 Declare `reticulate` under `packages` when the R script loads reticulate.
+When Python metadata is absent, `ir run` sets `RETICULATE_PYTHON=managed` if `RETICULATE_PYTHON` is unset.
+This lets reticulate create its lazy managed environment from `py_require()` declarations made by R packages.
+This portable default intentionally takes precedence over reticulate's other Python selectors.
+To opt out, set `RETICULATE_PYTHON` to a concrete interpreter before launch, or unset it in the script before configuring reticulate.
 
 ```r
 #!/usr/bin/env -S ir run

src/quickstart.txt

@@ -39,6 +39,8 @@ Python:
   `ir preview` also set QUARTO_PYTHON and inject jupyter.
   Add `reticulate` under `packages` when R code loads reticulate; `ir render`
   and `ir preview` add it for knitr-backed Quarto documents with Python chunks.
+  Without Python metadata, `ir run` defaults an unset RETICULATE_PYTHON to
+  managed; set it explicitly to keep another Python selection.
   `exclude-newer` also applies to Python unless `python-exclude-newer` is set.
 
 Bioconductor:

src/runtime.rs

@@ -876,6 +876,13 @@ fn run_script(
     if let Some(python) = python {
         cmd.env("RETICULATE_PYTHON", python);
         activate_python_env(&mut cmd, python)?;
+    } else if env::var_os("RETICULATE_PYTHON").is_none() {
+        // `ir run` owns Python selection by default so package-level
+        // `py_require()` declarations produce portable scripts. This
+        // intentionally outranks reticulate's other selectors and requires a
+        // reticulate release that supports `managed`; do not add runtime probes
+        // for older releases or externally managed environments here.
+        cmd.env("RETICULATE_PYTHON", "managed");
     }
 
     if isolated {

tests/run.rs

@@ -546,6 +546,37 @@ cat("frontmatter.user_library=", Sys.getenv("R_LIBS_USER", unset = "<unset>"), "
     assert_stdout_contains(&out, "frontmatter.user_library=NULL");
 }
 
+#[test]
+fn run_without_python_metadata_defaults_reticulate_python_to_managed() {
+    let script = temp_path("ir-run-reticulate-python-default", "R");
+    fs::write(
+        &script,
+        r#"cat("reticulate_python=", Sys.getenv("RETICULATE_PYTHON", unset = "<unset>"), "\n", sep = "")
+"#,
+    )
+    .unwrap();
+
+    let out = ir()
+        .env_remove("RETICULATE_PYTHON")
+        .args(["run", "--vanilla"])
+        .arg(&script)
+        .output()
+        .unwrap();
+
+    assert_success(&out);
+    assert_stdout_contains(&out, "reticulate_python=managed");
+
+    let out = ir()
+        .env("RETICULATE_PYTHON", "configured-python")
+        .args(["run", "--vanilla"])
+        .arg(&script)
+        .output()
+        .unwrap();
+
+    assert_success(&out);
+    assert_stdout_contains(&out, "reticulate_python=configured-python");
+}
+
 #[cfg(unix)]
 #[test]
 fn run_script_frontmatter_sets_reticulate_python_and_activates_env() {

tests/snapshots/quickstart.stdout

@@ -39,6 +39,8 @@ Python:
   `ir preview` also set QUARTO_PYTHON and inject jupyter.
   Add `reticulate` under `packages` when R code loads reticulate; `ir render`
   and `ir preview` add it for knitr-backed Quarto documents with Python chunks.
+  Without Python metadata, `ir run` defaults an unset RETICULATE_PYTHON to
+  managed; set it explicitly to keep another Python selection.
   `exclude-newer` also applies to Python unless `python-exclude-newer` is set.
 
 Bioconductor: