rpy-bridge 0.5.1__py3-none-any.whl → 0.5.2__py3-none-any.whl

rpy_bridge/core.py

@@ -188,6 +188,16 @@ class RFunctionCaller:
         except Exception:
             pass
 
+        # Pass the current Python interpreter path to R so reticulate can use the same Python
+        # This is critical for nested Python→R→Python calls via reticulate
+        import sys
+
+        python_executable = sys.executable
+        venv_path = os.environ.get("VIRTUAL_ENV", "")
+        r(f'Sys.setenv(RPY_BRIDGE_PYTHON_EXECUTABLE = "{python_executable}")')
+        if venv_path:
+            r(f'Sys.setenv(VIRTUAL_ENV = "{venv_path}")')
+
         self.ensure_r_package("withr")
 
         if not hasattr(self, "_namespaces"):
@@ -357,9 +367,33 @@ class RFunctionCaller:
         with localconverter(robjects.default_converter + pandas2ri.converter):
             if is_na(obj):
                 return robjects.NULL
+            if isinstance(obj, pd.Timestamp):
+                # Convert single Timestamp to R Date (days since 1970-01-01)
+                days_since_epoch = (obj - pd.Timestamp("1970-01-01")).days
+                r = self.robjects.r
+                return r(f"as.Date({days_since_epoch}, origin='1970-01-01')")
             if isinstance(obj, pd.DataFrame):
-                return pandas2ri.py2rpy(obj)
+                # Convert datetime columns to numeric (days since epoch) before R conversion
+                df_copy = obj.copy()
+                for col in df_copy.columns:
+                    if pd.api.types.is_datetime64_any_dtype(df_copy[col]):
+                        df_copy[col] = (df_copy[col] - pd.Timestamp("1970-01-01")).dt.days
+                r_df = pandas2ri.py2rpy(df_copy)
+                # Convert numeric date columns back to R Date class
+                r = self.robjects.r
+                for col in obj.columns:
+                    if pd.api.types.is_datetime64_any_dtype(obj[col]):
+                        r(f'class({r_df.rx2(col).r_repr()}) <- "Date"')
+                return r_df
             if isinstance(obj, pd.Series):
+                if pd.api.types.is_datetime64_any_dtype(obj):
+                    # Convert datetime Series to R Date vector
+                    days = (obj - pd.Timestamp("1970-01-01")).dt.days.tolist()
+                    r = self.robjects.r
+                    days_vec = FloatVector(
+                        [robjects.NA_Real if pd.isna(d) else float(d) for d in days]
+                    )
+                    return r("function(x) { class(x) <- 'Date'; x }")(days_vec)
                 return self._py2r(obj.tolist())
             if isinstance(obj, (int, float, bool, str)):
                 return obj

rpy_bridge/dataframe.py

@@ -4,6 +4,8 @@ DataFrame cleaning and post-processing utilities for R ↔ Python workflows.
 
 from __future__ import annotations
 
+import re
+
 import numpy as np
 import pandas as pd
 
@@ -34,6 +36,21 @@ def normalize_single_df_dtypes(df: pd.DataFrame) -> pd.DataFrame:
     return df
 
 
+# Token-based patterns to detect date/time columns; avoids substring matches like "endotoxin" or "runtime".
+_DATE_TOKEN_RE = re.compile(
+    r"(?<![a-z0-9])"
+    r"(?:date|dt|time|dob|visit|start|end|created|updated|modified|timestamp|datetime|ts|dos)"
+    r"(?![a-z0-9])",
+    re.IGNORECASE,
+)
+
+
+def _looks_like_date_column(col_name: str) -> bool:
+    """Check if column name suggests it contains date values."""
+    col_lower = str(col_name).lower()
+    return bool(_DATE_TOKEN_RE.search(col_lower))
+
+
 def fix_r_dataframe_types(df: pd.DataFrame) -> pd.DataFrame:
     for col in df.columns:
         series = df[col]
@@ -41,13 +58,18 @@ def fix_r_dataframe_types(df: pd.DataFrame) -> pd.DataFrame:
             df[col] = series.mask(series == -2147483648, pd.NA)
         if pd.api.types.is_numeric_dtype(series):
             values = series.dropna()
-            if not values.empty and values.between(10000, 40000).all():
+            # Only convert to date if values are in R's date range AND column name suggests a date
+            if (
+                not values.empty
+                and values.between(10000, 40000).all()
+                and _looks_like_date_column(col)
+            ):
                 try:
                     df[col] = pd.to_datetime("1970-01-01") + pd.to_timedelta(series, unit="D")
                 except Exception:
                     pass
         if pd.api.types.is_datetime64tz_dtype(series):
-            df[col] = series.dt.tz_localize(None)
+            df[col] = series.dt.tz_convert(None)
     return df
 
 

{rpy_bridge-0.5.1.dist-info → rpy_bridge-0.5.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rpy-bridge
-Version: 0.5.1
+Version: 0.5.2
 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
@@ -52,12 +52,6 @@ Provides-Extra: r
 Requires-Dist: rpy2>=3.5; extra == "r"
 Provides-Extra: dev
 Requires-Dist: ipykernel>=7.1.0; extra == "dev"
-Requires-Dist: pytest>=8.0; extra == "dev"
-Requires-Dist: ruff>=0.6; extra == "dev"
-Requires-Dist: build>=1.0; extra == "dev"
-Requires-Dist: twine>=4.0; extra == "dev"
-Requires-Dist: certifi>=2025.0; extra == "dev"
-Requires-Dist: ty>=0.0.1a34; extra == "dev"
 Provides-Extra: docs
 Requires-Dist: sphinx; extra == "docs"
 Requires-Dist: myst-parser; extra == "docs"

{rpy_bridge-0.5.1.dist-info → rpy_bridge-0.5.2.dist-info}/RECORD

@@ -1,15 +1,15 @@
 rpy_bridge/__init__.py,sha256=3UP1OOLuBaX7I9XsTaRsxr3EPYsGJere-Jh3xgc24QI,313
 rpy_bridge/compare.py,sha256=pwNOYLMrm7zJlsxzTooPl7OSmhPw-dc7owngJvV-7-0,4129
 rpy_bridge/convert.py,sha256=7DzdIGWl0eUYKzsfA5npL1DWKyhfk3gZ0CT2zAg2xfs,1952
-rpy_bridge/core.py,sha256=pkdsYsy0mXM7CDOkGA8Hev2KdfPn5NCsl_pP6zBalp0,18493
-rpy_bridge/dataframe.py,sha256=nocmc3yTyk1omCRKb1otNuwO73FzfxFeoVunH8oZC-Y,2310
+rpy_bridge/core.py,sha256=QqCSxrClz0uQ_I-U-pcVXfnYaNW8Xe4_6XfTskFWn08,20389
+rpy_bridge/dataframe.py,sha256=L5ck9VTmkaWDRzhmsQSERM9avwfSwMhgdPoKUTvS6-4,3020
 rpy_bridge/env.py,sha256=YN3tvl1eUp9IhbTmPgjSVKpRLTuf0OARgkMobQJd0Ks,3581
 rpy_bridge/logging.py,sha256=9U2RJHmxLqrXEwS38TkrSqeETXxn1AAfL8BGTjnzSGY,1360
 rpy_bridge/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rpy_bridge/renv.py,sha256=BYBFXP8SslKzD-GZ0yi7T-nMwqcIx2hYPY3BC_xSSZU,4511
 rpy_bridge/rpy2_loader.py,sha256=rQEnAiJbzkTzb4UlcOsG8D4MXZ0LWtYLMP8DequBNzg,1874
-rpy_bridge-0.5.1.dist-info/licenses/LICENSE,sha256=JwbWVcSfeoLfZ2M_ZiyygKVDvhBDW3zbqTWwXOJwmrA,1276
-rpy_bridge-0.5.1.dist-info/METADATA,sha256=6AbvKbd8fOgmfoRn2s5D2tqFo_vkZjK4S-eKhRJbNEw,10256
-rpy_bridge-0.5.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rpy_bridge-0.5.1.dist-info/top_level.txt,sha256=z9UZ77ZuUPoLqMDQEpP4btstsaM1IpXb9Cn9yBVaHmU,11
-rpy_bridge-0.5.1.dist-info/RECORD,,
+rpy_bridge-0.5.2.dist-info/licenses/LICENSE,sha256=JwbWVcSfeoLfZ2M_ZiyygKVDvhBDW3zbqTWwXOJwmrA,1276
+rpy_bridge-0.5.2.dist-info/METADATA,sha256=uMlRJtLBBK3uVXjNBpQ2d2bqaWgHXcqy4mZnoJi3Avk,9997
+rpy_bridge-0.5.2.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+rpy_bridge-0.5.2.dist-info/top_level.txt,sha256=z9UZ77ZuUPoLqMDQEpP4btstsaM1IpXb9Cn9yBVaHmU,11
+rpy_bridge-0.5.2.dist-info/RECORD,,

{rpy_bridge-0.5.1.dist-info → rpy_bridge-0.5.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any