rpy-bridge 0.3.1__py3-none-any.whl → 0.3.3__py3-none-any.whl

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,
 )
 

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.dist-info → rpy_bridge-0.3.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rpy-bridge
-Version: 0.3.1
+Version: 0.3.3
 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
@@ -31,12 +31,17 @@ License: MIT License
         
 Project-URL: Homepage, https://github.com/vic-cheung/rpy-bridge
 Project-URL: Issue Tracker, https://github.com/vic-cheung/rpy-bridge/issues
+Keywords: python,r,rpy2,python-r,interoperability,data-science,statistics,bioinformatics
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE

rpy_bridge-0.3.3.dist-info/RECORD

@@ -0,0 +1,8 @@
+rpy_bridge/__init__.py,sha256=1cyWVzhVnSqMRY6OkSo8RYjTKWjmaV9WR-otu4Y5dJc,829
+rpy_bridge/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+rpy_bridge/rpy2_utils.py,sha256=n58oSoqkZRv320dtgxEW597G8PrzCO8jCeGPZQH_5t8,29234
+rpy_bridge-0.3.3.dist-info/licenses/LICENSE,sha256=JwbWVcSfeoLfZ2M_ZiyygKVDvhBDW3zbqTWwXOJwmrA,1276
+rpy_bridge-0.3.3.dist-info/METADATA,sha256=Frw8qT49nSrWClRKCMKfU8cvLQVVKvpz3By99rTB_3A,9591
+rpy_bridge-0.3.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rpy_bridge-0.3.3.dist-info/top_level.txt,sha256=z9UZ77ZuUPoLqMDQEpP4btstsaM1IpXb9Cn9yBVaHmU,11
+rpy_bridge-0.3.3.dist-info/RECORD,,

rpy_bridge-0.3.1.dist-info/RECORD

@@ -1,8 +0,0 @@
-rpy_bridge/__init__.py,sha256=fXINFO0OFsSkxNccFPlSPIVsye5WGLVzu6Puf7o1Ao4,829
-rpy_bridge/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-rpy_bridge/rpy2_utils.py,sha256=D8hCv9axFbHGM71NFNO6E4oZIIBA5fBioOvzLDEVAHM,27842
-rpy_bridge-0.3.1.dist-info/licenses/LICENSE,sha256=JwbWVcSfeoLfZ2M_ZiyygKVDvhBDW3zbqTWwXOJwmrA,1276
-rpy_bridge-0.3.1.dist-info/METADATA,sha256=LeJLe_ETz_1bJxnjHUG-LJg3U7fG7Mq6O8YHccNZiVg,9267
-rpy_bridge-0.3.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rpy_bridge-0.3.1.dist-info/top_level.txt,sha256=z9UZ77ZuUPoLqMDQEpP4btstsaM1IpXb9Cn9yBVaHmU,11
-rpy_bridge-0.3.1.dist-info/RECORD,,