From fb8758f36b61129d212b85778cbdb44502041629 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <31037261+msberends@users.noreply.github.com>
Date: Sun, 5 Apr 2026 17:26:21 +0200
Subject: [PATCH] fix: convert Python lists to R vectors in wrapper generator
 (#270)

* fix: convert Python lists to R vectors in wrapper to prevent R list coercion errors

Fixes #267. Python lists passed to R functions via rpy2 are received as
R lists, not R character/numeric vectors. This causes is.mic(), is.sir(),
is.disk() etc. to return length > 1 logicals, which break R's && operator.

Added convert_to_r() helper that maps Python list/tuple to the appropriate
typed R vector (StrVector, IntVector, FloatVector) based on element types.
The r_to_python decorator now applies this to all args and kwargs before
calling the R function.

* docs: instruct Claude to install git and gh before computing version
---
 CLAUDE.md                            | 11 ++++++++-
 data-raw/_generate_python_wrapper.sh | 34 +++++++++++++++++++++++++---
 2 files changed, 41 insertions(+), 4 deletions(-)

diff --git a/CLAUDE.md b/CLAUDE.md
index 4892f3c00..cce4f7a73 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -152,7 +152,16 @@ All PRs are **squash-merged**, so each PR lands as exactly **one commit** on the
 
 #### Computing the correct version number
 
-Run the following from the repo root to determine the version string to use:
+**First, ensure `git` and `gh` are installed** — both are required for the version computation and for pushing changes. Install them if missing before doing anything else:
+
+```bash
+which git || apt-get install -y git
+which gh   || apt-get install -y gh
+# Also ensure all tags are fetched so git describe works
+git fetch --tags
+```
+
+Then run the following from the repo root to determine the version string to use:
 
 ```bash
 currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')
diff --git a/data-raw/_generate_python_wrapper.sh b/data-raw/_generate_python_wrapper.sh
index a8b2ee01a..f56b139fd 100644
--- a/data-raw/_generate_python_wrapper.sh
+++ b/data-raw/_generate_python_wrapper.sh
@@ -141,6 +141,32 @@ import numpy as np
 # Import the AMR R package
 amr_r = importr('AMR')
 
+def convert_to_r(value):
+    """Convert Python lists/tuples to typed R vectors.
+
+    rpy2's default_converter passes Python lists to R as R lists, not as
+    character/numeric vectors. This causes element-wise type-check functions
+    such as is.mic(), is.sir(), and is.disk() to return a logical vector
+    rather than a single logical, breaking R's scalar && operator.
+
+    This helper converts Python lists and tuples to the appropriate R vector
+    type based on the element types, so R always receives a proper vector."""
+    if isinstance(value, (list, tuple)):
+        if len(value) == 0:
+            return StrVector([])
+        # bool must be checked before int because bool is a subclass of int
+        if all(isinstance(v, bool) for v in value):
+            return robjects.vectors.BoolVector(value)
+        if all(isinstance(v, int) for v in value):
+            return IntVector(value)
+        if all(isinstance(v, float) for v in value):
+            return FloatVector(value)
+        if all(isinstance(v, str) for v in value):
+            return StrVector(value)
+        # Mixed types: coerce all to string
+        return StrVector([str(v) for v in value])
+    return value
+
 def convert_to_python(r_output):
     # Check if it's a StrVector (R character vector)
     if isinstance(r_output, StrVector):
@@ -166,10 +192,13 @@ def convert_to_python(r_output):
     return r_output
 
 def r_to_python(r_func):
-    """Decorator that runs an rpy2 function under a localconverter
-    and then applies convert_to_python to its output."""
+    """Decorator that converts Python list/tuple inputs to typed R vectors,
+    runs the rpy2 function under a localconverter, and converts the output
+    to a Python type."""
     @functools.wraps(r_func)
     def wrapper(*args, **kwargs):
+        args = tuple(convert_to_r(a) for a in args)
+        kwargs = {k: convert_to_r(v) for k, v in kwargs.items()}
         with localconverter(default_converter + numpy2ri.converter + pandas2ri.converter):
             return convert_to_python(r_func(*args, **kwargs))
     return wrapper
@@ -312,4 +341,3 @@ cd ../PythonPackage/AMR
 pip3 install build
 python3 -m build
 # python3 setup.py sdist bdist_wheel
-