rpy-bridge 0.3.1__tar.gz → 0.3.2__tar.gz

{rpy_bridge-0.3.1/src/rpy_bridge.egg-info → rpy_bridge-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rpy-bridge
-Version: 0.3.1
+Version: 0.3.2
 Summary: Python-to-R interoperability engine with environment management, type-safe conversions, data normalization, and safe R function execution.
 Author-email: Victoria Cheung <victoriakcheung@gmail.com>
 License: MIT License

{rpy_bridge-0.3.1 → rpy_bridge-0.3.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rpy-bridge"
-version = "0.3.1"
+version = "0.3.2"
 description = "Python-to-R interoperability engine with environment management, type-safe conversions, data normalization, and safe R function execution."
 readme = "README.md"
 license = { file = "LICENSE" }
@@ -9,7 +9,6 @@ authors = [
 ]
 requires-python = ">=3.11"
 
-# Core dependencies: safe to install without system R
 dependencies = [
     "numpy>=1.24",
     "pandas>=2.0",
@@ -26,21 +25,9 @@ classifiers = [
 ]
 
 [project.optional-dependencies]
-# R-backed functionality
-r = [
-    "rpy2>=3.5",
-]
-
-# Interactive / notebook usage
-dev = [
-    "ipykernel>=7.1.0",
-]
-
-# Documentation build dependencies (optional but recommended)
-docs = [
-    "sphinx",
-    "myst-parser",
-]
+r = ["rpy2>=3.5"]
+dev = ["ipykernel>=7.1.0"]
+docs = ["sphinx", "myst-parser"]
 
 [project.urls]
 Homepage = "https://github.com/vic-cheung/rpy-bridge"
@@ -50,6 +37,9 @@ Homepage = "https://github.com/vic-cheung/rpy-bridge"
 requires = ["setuptools>=61"]
 build-backend = "setuptools.build_meta"
 
+# -------------------------------
+# uv dev dependencies
+# -------------------------------
 [tool.uv]
 dev-dependencies = [
     "ruff>=0.6",
@@ -57,4 +47,27 @@ dev-dependencies = [
     "build>=1.0",
     "twine>=4.0",
     "certifi>=2025.0",
+    "ty>=0.0.1a34",
 ]
+
+# -------------------------------
+# Ruff configuration
+# -------------------------------
+[tool.ruff]
+line-length = 100
+select = ["E", "F", "W", "I"]
+ignore = ["E501"]  # optional, ignore long lines
+
+# -------------------------------
+# Ty configuration
+# -------------------------------
+[tool.ty.environment]
+root = ["src/rpy_bridge"]
+
+[tool.ty.rules]
+possibly-missing-attribute = "ignore" # suppress warnings from rpy2 dynamic attributes
+non-subscriptable = "ignore" # suppress errors when typing unknown dict-like objects e.g. NULLType = r["NULLType"]
+call-non-callable = "ignore" # suppress errors for dynamic callable objects
+# invalid-assignment = "ignore" # suppress errors for dynamic dict assignment
+# invalid-return-type = "ignore" # suppress return type mismatch warnings
+unresolved-import = "ignore" # suppress errors for unable to resolve imported module

{rpy_bridge-0.3.1 → rpy_bridge-0.3.2}/src/rpy_bridge/rpy2_utils.py

@@ -10,24 +10,36 @@ Ensure compatibility with your R project's renv setup (or other virtual env/base
 # ruff: noqa: E402
 # %%
 # Import libraries
+import importlib.util
 import os
+import subprocess
+import sys
 import warnings
-
-warnings.filterwarnings("ignore", message="Environment variable .* redefined by R")
-
 from pathlib import Path
-import sys
-import subprocess
+from typing import TYPE_CHECKING, Any, Union
 
-import math
 import numpy as np
 import pandas as pd
 
+warnings.filterwarnings("ignore", message="Environment variable .* redefined by R")
+
+
+if TYPE_CHECKING:
+    import logging as logging_module
+
+    from loguru import Logger as LoguruLogger
+
+    LoggerType = LoggerType = Union[LoguruLogger, logging_module.Logger]
+else:
+    LoggerType = None  # runtime doesn’t need the type object
+
+import logging
+
 try:
-    from loguru import logger  # type: ignore
-except Exception:
-    import logging
+    from loguru import logger as loguru_logger  # type: ignore
 
+    logger = loguru_logger
+except ImportError:
     logging.basicConfig()
     logger = logging.getLogger("rpy-bridge")
 
@@ -35,41 +47,45 @@ except Exception:
 # ---------------------------------------------------------------------
 # R detection and rpy2 installation
 # ---------------------------------------------------------------------
-def ensure_rpy2_installed(r_home: str):
-    os.environ["R_HOME"] = r_home
-    try:
-        import rpy2  # noqa: F401
-    except ImportError:
-        logger.info(
-            f"[Info] rpy2 not installed or incompatible with R_HOME={r_home}. Installing..."
-        )
-        subprocess.check_call(
-            [sys.executable, "-m", "pip", "install", "--force-reinstall", "rpy2"]
+def ensure_rpy2_available() -> None:
+    """
+    Ensure rpy2 is importable.
+    Do NOT attempt to install dynamically; fail with clear instructions instead.
+    """
+    if importlib.util.find_spec("rpy2") is None:
+        raise RuntimeError(
+            "\n[Error] rpy2 is not installed. Please install it in your Python environment:\n"
+            "  pip install rpy2\n\n"
+            "Make sure your Python environment can access your system R installation.\n"
+            "On macOS with Homebrew: brew install r\n"
+            "On Linux: apt install r-base  (Debian/Ubuntu) or yum install R (CentOS/RHEL)\n"
+            "On Windows: install R from https://cran.r-project.org\n"
         )
-        import rpy2  # noqa: F401
 
 
-def find_r_home():
+def find_r_home() -> str | None:
+    """Detect system R installation."""
     try:
         r_home = subprocess.check_output(
             ["R", "--vanilla", "--slave", "-e", "cat(R.home())"],
             stderr=subprocess.PIPE,
             text=True,
         ).strip()
-        if r_home.endswith(">"):
+        if r_home.endswith(">"):  # sometimes R console prints >
             r_home = r_home[:-1].strip()
         return r_home
     except FileNotFoundError:
+        # fallback paths (Linux, macOS Homebrew, Windows)
         possible_paths = [
             "/usr/lib/R",
             "/usr/local/lib/R",
-            "/opt/homebrew/Cellar/r/4.5.2/lib/R",  # Homebrew macOS
+            "/opt/homebrew/Cellar/r/4.5.2/lib/R",  # macOS Homebrew
             "C:\\Program Files\\R\\R-4.5.2",  # Windows
         ]
         for p in possible_paths:
             if os.path.exists(p):
                 return p
-        return None
+    return None
 
 
 R_HOME = find_r_home()
@@ -78,7 +94,7 @@ if not R_HOME:
 
 logger.info(f"R_HOME = {R_HOME}")
 os.environ["R_HOME"] = R_HOME
-ensure_rpy2_installed(R_HOME)
+ensure_rpy2_available()
 
 # macOS dynamic library path
 if sys.platform == "darwin":
@@ -107,6 +123,8 @@ def _require_rpy2(raise_on_missing: bool = True) -> dict | None:
     try:
         import rpy2.robjects as ro
         from rpy2 import robjects
+        from rpy2.rinterface_lib.sexp import NULLType
+        from rpy2.rlike.container import NamedList
         from rpy2.robjects import pandas2ri
         from rpy2.robjects.conversion import localconverter
         from rpy2.robjects.vectors import (
@@ -116,8 +134,6 @@ def _require_rpy2(raise_on_missing: bool = True) -> dict | None:
             ListVector,
             StrVector,
         )
-        from rpy2.rinterface_lib.sexp import NULLType
-        from rpy2.rlike.container import NamedList
 
         _RPY2 = {
             "ro": ro,
@@ -146,6 +162,7 @@ def _ensure_rpy2() -> dict:
     global _RPY2
     if _RPY2 is None:
         _RPY2 = _require_rpy2()
+    assert _RPY2 is not None, "_require_rpy2() returned None"
     return _RPY2
 
 
@@ -318,7 +335,6 @@ class RFunctionCaller:
         self._ensure_r_loaded()
         robjects = self.robjects
         pandas2ri = self.pandas2ri
-        IntVector = self.IntVector
         FloatVector = self.FloatVector
         BoolVector = self.BoolVector
         StrVector = self.StrVector
@@ -470,13 +486,25 @@ class RFunctionCaller:
         self._ensure_r_loaded()
 
         # --- Find the function ---
+        func = None
         try:
             func = self.robjects.globalenv[func_name]  # script-defined
         except KeyError:
             try:
                 func = self.robjects.r[func_name]  # base or package function
             except KeyError:
-                raise ValueError(f"R function '{func_name}' not found.")
+                # --- Added: handle namespaced functions like stats::median ---
+                if "::" in func_name:
+                    pkg, fname = func_name.split("::", 1)
+                    try:
+                        func = self.robjects.r(f"{pkg}::{fname}")
+                    except Exception as e:
+                        raise RuntimeError(
+                            f"Failed to load R function '{func_name}' via namespace: {e}"
+                        ) from e
+
+                if func is None:
+                    raise ValueError(f"R function '{func_name}' not found.")
 
         # --- Convert Python args to R ---
         r_args = [self._py2r(a) for a in args]
@@ -749,12 +777,12 @@ def compare_r_py_dataframes(
         dict with mismatch diagnostics, preserving original indices in diffs.
     """
 
-    results = {
+    results: dict[str, Any] = {
         "shape_mismatch": False,
         "columns_mismatch": False,
         "index_mismatch": False,
-        "numeric_diffs": {},
-        "non_numeric_diffs": {},
+        "numeric_diffs": {},  # type: dict[str, pd.DataFrame]
+        "non_numeric_diffs": {},  # type: dict[str, pd.DataFrame]
     }
 
     # --- Preprocessing: fix R-specific issues ---

{rpy_bridge-0.3.1 → rpy_bridge-0.3.2/src/rpy_bridge.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rpy-bridge
-Version: 0.3.1
+Version: 0.3.2
 Summary: Python-to-R interoperability engine with environment management, type-safe conversions, data normalization, and safe R function execution.
 Author-email: Victoria Cheung <victoriakcheung@gmail.com>
 License: MIT License

rpy_bridge-0.3.2/tests/test_package_call.py

@@ -0,0 +1,16 @@
+
+
+# caller fixture is injected from conftest.py
+def test_call_stats_functions(caller):
+    """Smoke test: load `stats` and call `rnorm` and `median`."""
+
+    samples = caller.call("rnorm", 10, mean=5)
+    assert hasattr(samples, "__len__")
+    assert len(samples) == 10
+
+    med = caller.call("stats::median", samples)
+    # median may come back as a scalar or a single-element array
+    if hasattr(med, "__len__") and not isinstance(med, (int, float)):
+        assert len(med) == 1
+    else:
+        assert isinstance(med, (int, float))

{rpy_bridge-0.3.1 → rpy_bridge-0.3.2}/tests/test_py2r.py

@@ -1,11 +1,9 @@
 # %%
-from pathlib import Path
 import pandas as pd
-from rpy_bridge import RFunctionCaller
 
 
-# %%
-def test_py2r_edge_cases(caller: RFunctionCaller):
+# The caller fixture is now injected by pytest
+def test_py2r_edge_cases(caller):
     test_cases = {
         "simple_int_list": [1, 2, 3],
         "simple_float_list": [1.0, 2.5, 3.7],
@@ -26,7 +24,7 @@ def test_py2r_edge_cases(caller: RFunctionCaller):
         "scalar_str": "hello",
     }
 
-    caller._ensure_r_loaded()  # Make sure R is loaded
+    caller._ensure_r_loaded()  # Ensure R is loaded
 
     print("\n--- Testing _py2r edge cases ---")
     for name, value in test_cases.items():
@@ -34,7 +32,6 @@ def test_py2r_edge_cases(caller: RFunctionCaller):
             r_obj = caller._py2r(value)
             print(f"\n--- Test case: {name} ---")
             print("R object type:", type(r_obj))
-            # Handle R vectors or ListVector
             if hasattr(r_obj, "__len__") and not isinstance(
                 r_obj, (int, float, bool, str)
             ):
@@ -46,11 +43,3 @@ def test_py2r_edge_cases(caller: RFunctionCaller):
                 print("R object:", r_obj)
         except Exception as e:
             print(f"Error in {name}: {e}")
-
-
-# Example usage
-if __name__ == "__main__":
-    caller = RFunctionCaller()
-    test_py2r_edge_cases(caller)
-
-# %%

{rpy_bridge-0.3.1 → rpy_bridge-0.3.2}/tests/test_roundtrip.py

@@ -1,11 +1,10 @@
 # %%
-import pandas as pd
 import numpy as np
-from rpy_bridge import RFunctionCaller
+import pandas as pd
 
 
-# %%
-def test_py2r_r2py_roundtrip(caller: RFunctionCaller):
+# The caller fixture is now injected by pytest
+def test_py2r_r2py_roundtrip(caller):
     """
     Test round-trip conversion: Python -> R -> Python
     Handles edge cases including scalars, lists, nested structures, dicts, and NA values.
@@ -34,13 +33,9 @@ def test_py2r_r2py_roundtrip(caller: RFunctionCaller):
     for name, py_obj in test_cases.items():
         print(f"\n--- Test case: {name} ---")
         try:
-            # Python -> R
             r_obj = caller._py2r(py_obj)
-
-            # R -> Python
             py_roundtrip = caller._r2py(r_obj)
 
-            # Normalize NA values for comparison
             def normalize(obj):
                 if isinstance(obj, pd.Series):
                     return obj.replace({pd.NA: None}).tolist()
@@ -63,14 +58,3 @@ def test_py2r_r2py_roundtrip(caller: RFunctionCaller):
 
         except Exception as e:
             print("Error during round-trip:", e)
-
-
-# Example usage:
-if __name__ == "__main__":
-    from rpy_bridge import RFunctionCaller
-
-    caller = RFunctionCaller()
-    caller._ensure_r_loaded()  # Ensure R is loaded
-    test_py2r_r2py_roundtrip(caller)
-
-# %%

{rpy_bridge-0.3.1 → rpy_bridge-0.3.2}/tests/test_wrapper.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+
 import pytest
 
 from rpy_bridge import RFunctionCaller

rpy_bridge-0.3.1/tests/test_package_call.py

@@ -1,26 +0,0 @@
-import pytest
-
-from rpy_bridge import RFunctionCaller
-
-
-def test_call_stats_functions():
-    """Smoke test: load `stats` and call `rnorm` and `median`.
-
-    This test will be skipped if R or rpy2 are not available in the test
-    environment.
-    """
-    try:
-        caller = RFunctionCaller(path_to_renv=None, packages=["stats"])
-    except Exception as e:
-        pytest.skip(f"Skipping because R/rpy2 not available: {e}")
-
-    samples = caller.call("rnorm", 10, mean=5)
-    assert hasattr(samples, "__len__")
-    assert len(samples) == 10
-
-    med = caller.call("stats::median", samples)
-    # median may come back as a scalar or a single-element array
-    if hasattr(med, "__len__") and not isinstance(med, (int, float)):
-        assert len(med) == 1
-    else:
-        assert isinstance(med, (int, float))

{rpy_bridge-0.3.1 → rpy_bridge-0.3.2}/src/rpy_bridge/__init__.py

@@ -10,13 +10,13 @@ from .rpy2_utils import (
     activate_renv,
     align_numeric_dtypes,
     clean_r_dataframe,
+    clean_r_missing,
     compare_r_py_dataframes,
     fix_r_dataframe_types,
     fix_string_nans,
     normalize_dtypes,
     normalize_single_df_dtypes,
     postprocess_r_dataframe,
-    clean_r_missing,
     r_namedlist_to_dict,
 )