rpy-bridge 0.4.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

rpy_bridge-0.4.0.dist-info/METADATA

@@ -1,258 +0,0 @@
-Metadata-Version: 2.4
-Name: rpy-bridge
-Version: 0.4.0
-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
-        
-        Copyright (c) 2025 Victoria Cheung
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-        SOFTWARE.
-        
-        Acknowledgement: This project builds on work originally developed at
-        Revolution Medicines and interfaces with the rpy2 project, which is licensed
-        under the GNU General Public License version 2 or later.
-        
-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
-Requires-Dist: numpy>=1.24
-Requires-Dist: pandas>=2.0
-Requires-Dist: loguru>=0.7
-Provides-Extra: r
-Requires-Dist: rpy2>=3.5; extra == "r"
-Provides-Extra: dev
-Requires-Dist: ipykernel>=7.1.0; extra == "dev"
-Provides-Extra: docs
-Requires-Dist: sphinx; extra == "docs"
-Requires-Dist: myst-parser; extra == "docs"
-Dynamic: license-file
-
-# rpy-bridge
-
-rpy-bridge is a Python-to-R a robust interoperability engine that combines environment management, type-safe conversions, data normalization, and safe function execution to make Python-R collaboration seamless.
-
-It enables Python developers to call R functions, scripts, and packages safely while preserving type fidelity and project-specific R environments. This is ideal for bilingual teams where R authors maintain core logic, and Python-centric users need reliable access without rewriting code.
-
-**Latest release:** [`rpy-bridge` on PyPI](https://pypi.org/project/rpy-bridge/)
-
----
-
-## Key layers and capabilities
-
-### 1. Lazy and robust R integration
-
-- Automatically detects or sets R_HOME and ensures rpy2 is installed.
-- Configures platform-specific dynamic library paths for macOS/Linux.
-
-### 2. Environment management
-
-- Activates renv projects and loads project-specific libraries if it exists, otherwise use current environemnt.
-- Sources .Renviron and .Rprofile files to replicate the R project environment in Python.
-
-### 3. Python ↔ R type conversion
-
-- Converts Python scalars, lists, dicts, and pandas DataFrames into appropriate R objects.
-- Converts R atomic vectors, ListVector/NamedList, and data.frames back into Python-native objects.
-- Handles nested structures, mixed types, and missing values robustly (NA_* → None/pd.NA).
-
-### 4. Data hygiene and normalization
-
-- Post-processes R DataFrames: fixes dtypes, numeric/date conversions, and timezone issues.
-- Normalizes and aligns column types for accurate Python comparisons.
-- Supports comparing Python and R DataFrames with mismatch diagnostics.
-
-### 5. Function calling
-
-- Calls functions from R scripts, base R, or installed packages safely.
-- Automatically converts arguments and return values, including keyword arguments.
-- Supports mixed data types, nested structures, and DataFrames seamlessly.
-
-### 6. Python-first workflow for R code
-
-- Enables Python developers to reuse R functions without needing deep R knowledge.
-- Keeps network, token, and SSL concerns outside the package when sourcing scripts locally.
-- Designed for reproducibility and safe execution in CI or cross-platform environments.
-
----
-
-## Installation
-
-**Prerequisites**
-
-- System R installed and available on `PATH` (rpy2 requires a working R installation).
-- Python 3.12+
-
-**From PyPI:**
-
-Install rpy-bridge with rpy2 for full R support
-
-```bash
-python3 -m pip install rpy-bridge rpy2
-```
-
-or using `uv`:
-
-```bash
-uv add rpy-bridge rpy2
-```
-
-**During development (editable install):**
-
-```bash
-python3 -m pip install -e .
-```
-
-or using `uv`:
-
-```bash
-uv sync
-```
-
-**Required Python packages** (the installer will pull these in):
-
-- `rpy2` (GPLv2 or later)
-- `pandas`
-- `numpy`
-
----
-
-## Usage
-
-```python
-from pathlib import Path
-from rpy_bridge import RFunctionCaller
-
-rfc = RFunctionCaller(
-    path_to_renv=Path("/path/to/project"),
-    script=Path("/path/to/script.R"),
-)
-
-summary_df = rfc.call("summarize_cohort", cohort_df)
-```
-
----
-
-## Round-trip Python ↔ R behavior
-
-`rpy-bridge` attempts to convert Python objects to R and back. Most objects used in scientific/ML pipelines round-trip cleanly, but some heterogeneous Python structures may be wrapped or slightly altered. This is normal due to R's type system.
-
-| Python type                                    | Round-trip fidelity | Notes                                                                 |
-| ---------------------------------------------- | ------------------- | --------------------------------------------------------------------- |
-| `int`, `float`, `bool`, `str`                  | ✅ High              | Scalars convert directly                                              |
-| Homogeneous `list` of numbers/strings/booleans | ✅ High              | Converted to atomic R vectors                                         |
-| Nested lists of homogeneous types              | ✅ High              | Converted to nested R `ListVector`                                    |
-| `pandas.DataFrame` / `pd.Series`               | ✅ High              | Converted to `data.frame` / R vector, post-processed back             |
-| Mixed-type `list` or heterogeneous `dict`      | ⚠️ Partial          | Elements wrapped in single-element vectors; round-trip may alter type |
-| Python `None` / `pd.NA`                        | ✅ High              | Converted to R `NULL`                                                 |
-
-# Guidance
-
-- Typical workflows (DataFrames, numeric arrays, series, homogeneous lists) are fully supported.
-- Rare or highly heterogeneous Python objects may not round-trip perfectly.
-- Round-trip fidelity is mainly a “nice-to-have” for debugging. For production pipelines, it’s safe to focus on supported types.
-
----
-
-## Examples
-
-### Basic — run a local R script
-
-```python
-from pathlib import Path
-from rpy_bridge import RFunctionCaller
-
-project_dir = Path("/path/to/your-r-project")
-script = project_dir / "scripts" / "example.R"
-
-caller = RFunctionCaller(path_to_renv=project_dir, script_path=script)
-result = caller.call("some_function", 42, named_arg="value")
-print(type(result))
-```
-
-### Call installed R packages (no local script)
-
-```python
-from rpy_bridge import RFunctionCaller
-
-caller = RFunctionCaller(path_to_renv=None, packages=["stats"])
-samples = caller.call("rnorm", 5, mean=10)
-print(type(samples))  # typically a numpy.ndarray
-
-median_val = caller.call("stats::median", samples)
-print(median_val)
-```
-
----
-
-## R Setup
-
-If you plan to execute R code with `rpy-bridge`, use the helper scripts in
-`examples/r-deps/` to prepare an R environment.
-
-- On macOS (Homebrew) install system deps:
-
-```bash
-bash examples/r-deps/install_r_dev_deps_homebrew.sh
-```
-
-- Initialize a project `renv` (run in an R session):
-
-```r
-source("examples/r-deps/setup_env.R")
-```
-
-- Restore the environment on a new machine:
-
-```r
-renv::restore()
-```
-
----
-
-## Collaboration note
-
-This repository provides example R setup scripts for teams working across Python and R. Each project may require different R packages — check the package list in `examples/r-deps/setup_env.R` and commit a `renv.lock` for project-specific reproducibility.
-
-Clone repositories containing R scripts locally or use your preferred tooling to obtain scripts before execution.
-
----
-
-## Licensing
-
-- `rpy-bridge` is released under the MIT License © 2025 Victoria Cheung.
-- The project depends on [`rpy2`](https://rpy2.github.io) which is licensed under the GNU General Public License v2 (or later).
-
-### Thanks
-
-This package was spun out of internal tooling at Revolution Medicines.
-Many thanks to the team there for allowing the code to be open sourced.

rpy_bridge-0.4.0.dist-info/RECORD

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