ggplot2-python 4.0.2.9000__tar.gz

ggplot2_python-4.0.2.9000/.gitattributes

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+# GitHub language statistics: only count Python
+*.py linguist-detectable
+*.ipynb linguist-documentation
+*.html linguist-documentation
+*.css linguist-documentation
+*.js linguist-documentation
+*.json linguist-documentation
+*.yml linguist-documentation
+*.yaml linguist-documentation
+*.md linguist-documentation
+*.R linguist-documentation
+*.csv linguist-documentation
+site/** linguist-documentation
+docs/** linguist-documentation
+tutorials/** linguist-documentation

ggplot2_python-4.0.2.9000/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+dist/
+build/
+.eggs/
+
+# Virtual environments
+.venv/
+.tox/
+
+# Compiled extensions
+*.so
+*.pyd
+*.dylib
+
+# IDE
+.idea/
+.vscode/
+*.swp
+
+# OS
+.DS_Store
+Thumbs.db
+.coverage
+
+# Docs build
+site/
+.cache/
+.ipynb_checkpoints/

ggplot2_python-4.0.2.9000/LICENSE

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+# MIT
+
+See DESCRIPTION from R package.

ggplot2_python-4.0.2.9000/PKG-INFO

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+Metadata-Version: 2.4
+Name: ggplot2-python
+Version: 4.0.2.9000
+Summary: Python port of the R ggplot2 package (tracks R ggplot2 4.0.2.9000)
+Project-URL: Homepage, https://github.com/Bio-Babel/ggplot2-python
+Project-URL: Repository, https://github.com/Bio-Babel/ggplot2-python
+Project-URL: Issues, https://github.com/Bio-Babel/ggplot2-python/issues
+Project-URL: Documentation, https://github.com/Bio-Babel/ggplot2-python#readme
+Author-email: Jeffery Liu <jeffliu.lucky@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: R-port,data-visualization,ggplot2,grammar-of-graphics,plotting,statistical-graphics,visualization
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Requires-Dist: contourpy>=1.0
+Requires-Dist: geopandas>=0.12
+Requires-Dist: gtable-python>=0.3.6
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=1.5
+Requires-Dist: pillow>=9.0
+Requires-Dist: rgrid-python>=4.5.3
+Requires-Dist: scales-python>=1.4.0
+Requires-Dist: scipy>=1.10
+Requires-Dist: statsmodels>=0.13
+Provides-Extra: dev
+Requires-Dist: build; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: twine; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs; extra == 'docs'
+Requires-Dist: mkdocs-jupyter; extra == 'docs'
+Requires-Dist: mkdocs-material; extra == 'docs'
+Requires-Dist: mkdocstrings[python]; extra == 'docs'
+Description-Content-Type: text/markdown
+
+# ggplot2_py <a href="https://github.com/R2pyBioinformatics/ggplot2_py"><img src="assets/ggplot2_py_logo.png" align="right" height="138" alt="ggplot2_py logo" /></a>
+
+AI-assisted Python port of the R **ggplot2** package — Create Elegant Data Visualisations Using the Grammar of Graphics.
+
+## Overview
+
+ggplot2_py implements the grammar of graphics in Python, faithfully porting R's ggplot2 using pandas DataFrames as the data container and a Cairo-based rendering backend. It supports 47 geoms, 32 stats, faceting, coordinate systems, themes, guides, and 130+ scales.
+
+Beyond a direct port, ggplot2_py adds **Python-exclusive features** that extend the Grammar of Graphics with Python-native idioms while preserving full orthogonality of GOG components.
+
+## Python-Exclusive Features
+
+These capabilities have no R equivalent and leverage Python-specific language features:
+
+| Feature | Python mechanism | What it enables |
+|---------|-----------------|-----------------|
+| **Callable `aes()` expressions** | First-class functions / lambdas | `aes(y=lambda d: np.log(d["mpg"]))` — inline data transforms without pre-computing columns |
+| **`after_stat()` / `after_scale()` callables** | Same | `after_stat(lambda d: d["count"] / d["count"].sum())` — arbitrary expressions at each pipeline stage |
+| **`singledispatch` extensibility** | `functools.singledispatch` | `@update_ggplot.register(MyClass)` — any Python class can be added to a plot with `+` |
+| **Build hooks** | Dict-keyed callback lists | `plot.add_build_hook("after", BuildStage.COMPUTE_STAT, fn)` — intercept data at any of 16 named pipeline stages |
+| **Auto-registration** | `__init_subclass__` | `class GeomStar(Geom): ...` auto-registers; no manual wiring needed |
+| **Protocol contracts** | `typing.Protocol` | `isinstance(my_geom, GeomProtocol)` — structural type checking for extensions |
+| **Scoped defaults** | `contextvars.ContextVar` | `with ggplot_defaults(theme=theme_minimal()): ...` — thread-safe scoped defaults |
+
+## Installation
+
+```bash
+# From PyPI
+pip install ggplot2-python
+```
+
+For a local development:
+
+```bash
+git clone https://github.com/Bio-Babel/ggplot2-python.git
+cd ggplot2_py
+pip install -e ".[dev]"
+```
+
+## Quick Start
+
+```python
+from ggplot2_py import *
+from ggplot2_py.datasets import mpg
+
+(ggplot(mpg, aes(x="displ", y="hwy", colour="class"))
+ + geom_point()
+ + geom_smooth(method="lm")
+ + facet_wrap("drv")
+ + theme_minimal()
+ + labs(title="Engine Displacement vs Highway MPG"))
+```
+
+### Callable expressions in aes (Python-exclusive)
+
+```python
+import numpy as np
+from ggplot2_py import ggplot, aes, geom_point, geom_histogram, after_stat
+
+# Inline data transform — no need to pre-compute a column
+ggplot(mpg, aes(x=lambda d: np.log(d["displ"]), y="hwy")) + geom_point()
+
+# Normalised histogram — callable in after_stat
+(ggplot(mpg, aes(x="hwy"))
+ + geom_histogram(aes(y=after_stat(lambda d: d["count"] / d["count"].sum())), bins=15))
+```
+
+### Extending with custom types (Python-exclusive)
+
+```python
+from ggplot2_py import update_ggplot
+
+class Watermark:
+    def __init__(self, text): self.text = text
+
+@update_ggplot.register(Watermark)
+def _add_watermark(obj, plot, object_name=""):
+    plot.labels["caption"] = f"[{obj.text}]"
+    return plot
+
+# Now use with +
+ggplot(mpg, aes("displ", "hwy")) + geom_point() + Watermark("DRAFT")
+```
+
+### Scoped defaults (Python-exclusive)
+
+```python
+from ggplot2_py import ggplot_defaults
+
+with ggplot_defaults(theme=theme_minimal()):
+    p1 = ggplot(df, aes("x", "y")) + geom_point()   # theme_minimal applied
+    p2 = ggplot(df, aes("x", "y")) + geom_bar()     # theme_minimal applied
+# Outside: no defaults
+```
+
+## Tutorials
+
+### User Tutorials
+- [Getting Started](tutorials/ggplot2.ipynb) — core concepts: data, aes, geoms, stats, scales, facets, coords, themes
+- [Geom Gallery](tutorials/geoms_gallery.ipynb) — boxplot, violin, density, tile, hex and combinations
+- [Labels & Facets](tutorials/labels_and_facets.ipynb) — axis titles, plot title/subtitle/caption, facet strip labels
+- [Aesthetic Specs](tutorials/aesthetic_specs.ipynb) — colour, fill, alpha, linetype, shape, size, colour scales
+- [Extending ggplot2](tutorials/extending_ggplot2.ipynb) — custom stats, geoms, themes via ggproto
+
+### Python-Exclusive Feature Tutorials
+- [Callable aes Expressions](tutorials/aes_expressions.ipynb) — lambdas in `aes()`, `after_stat()`, `after_scale()`, `stage()`
+- [Extensible Pipeline](tutorials/pipeline_dispatch.ipynb) — `singledispatch` registration, custom types with `+`
+- [Build Hooks](tutorials/build_hooks.ipynb) — intercepting the 16-stage build pipeline
+
+### Developer Guide
+- [Developer Guide: Extending ggplot2_py](tutorials/developer_guide.ipynb) — comprehensive guide covering ggproto system, custom Stat/Geom creation, Protocol contracts, singledispatch, hooks, auto-registration, context manager, and packaging
+
+## Extension Architecture
+
+ggplot2_py is designed as an **extensible platform**. The following table summarises all extension points:
+
+| Extension point | Mechanism | How to use |
+|----------------|-----------|-----------|
+| Custom Stat | Subclass `Stat` | Override `compute_group()` — auto-registered via `__init_subclass__` |
+| Custom Geom | Subclass `Geom` | Override `draw_panel()` — auto-registered |
+| Custom Scale | Subclass `ScaleContinuous` / `ScaleDiscrete` | Implement `train()`, `map()`, `get_breaks()` |
+| Custom Coord | Subclass `Coord` | Override `transform()`, `setup_panel_params()` |
+| Custom Facet | Subclass `Facet` | Override `compute_layout()`, `map_data()` |
+| Custom Position | Subclass `Position` | Override `compute_layer()` — auto-registered |
+| Custom `+` types | `@update_ggplot.register(MyClass)` | Register any Python class for the `+` operator |
+| Custom plot types | `@ggplot_build.register(MyPlot)` | Override the entire build pipeline |
+| Build hooks | `plot.add_build_hook(timing, stage, fn)` | Intercept data at any pipeline stage |
+| Protocol validation | `isinstance(obj, GeomProtocol)` | Verify structural conformance |
+| Scoped defaults | `with ggplot_defaults(theme=...):` | Thread-safe scoped defaults |

ggplot2_python-4.0.2.9000/README.md

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+# ggplot2_py <a href="https://github.com/R2pyBioinformatics/ggplot2_py"><img src="assets/ggplot2_py_logo.png" align="right" height="138" alt="ggplot2_py logo" /></a>
+
+AI-assisted Python port of the R **ggplot2** package — Create Elegant Data Visualisations Using the Grammar of Graphics.
+
+## Overview
+
+ggplot2_py implements the grammar of graphics in Python, faithfully porting R's ggplot2 using pandas DataFrames as the data container and a Cairo-based rendering backend. It supports 47 geoms, 32 stats, faceting, coordinate systems, themes, guides, and 130+ scales.
+
+Beyond a direct port, ggplot2_py adds **Python-exclusive features** that extend the Grammar of Graphics with Python-native idioms while preserving full orthogonality of GOG components.
+
+## Python-Exclusive Features
+
+These capabilities have no R equivalent and leverage Python-specific language features:
+
+| Feature | Python mechanism | What it enables |
+|---------|-----------------|-----------------|
+| **Callable `aes()` expressions** | First-class functions / lambdas | `aes(y=lambda d: np.log(d["mpg"]))` — inline data transforms without pre-computing columns |
+| **`after_stat()` / `after_scale()` callables** | Same | `after_stat(lambda d: d["count"] / d["count"].sum())` — arbitrary expressions at each pipeline stage |
+| **`singledispatch` extensibility** | `functools.singledispatch` | `@update_ggplot.register(MyClass)` — any Python class can be added to a plot with `+` |
+| **Build hooks** | Dict-keyed callback lists | `plot.add_build_hook("after", BuildStage.COMPUTE_STAT, fn)` — intercept data at any of 16 named pipeline stages |
+| **Auto-registration** | `__init_subclass__` | `class GeomStar(Geom): ...` auto-registers; no manual wiring needed |
+| **Protocol contracts** | `typing.Protocol` | `isinstance(my_geom, GeomProtocol)` — structural type checking for extensions |
+| **Scoped defaults** | `contextvars.ContextVar` | `with ggplot_defaults(theme=theme_minimal()): ...` — thread-safe scoped defaults |
+
+## Installation
+
+```bash
+# From PyPI
+pip install ggplot2-python
+```
+
+For a local development:
+
+```bash
+git clone https://github.com/Bio-Babel/ggplot2-python.git
+cd ggplot2_py
+pip install -e ".[dev]"
+```
+
+## Quick Start
+
+```python
+from ggplot2_py import *
+from ggplot2_py.datasets import mpg
+
+(ggplot(mpg, aes(x="displ", y="hwy", colour="class"))
+ + geom_point()
+ + geom_smooth(method="lm")
+ + facet_wrap("drv")
+ + theme_minimal()
+ + labs(title="Engine Displacement vs Highway MPG"))
+```
+
+### Callable expressions in aes (Python-exclusive)
+
+```python
+import numpy as np
+from ggplot2_py import ggplot, aes, geom_point, geom_histogram, after_stat
+
+# Inline data transform — no need to pre-compute a column
+ggplot(mpg, aes(x=lambda d: np.log(d["displ"]), y="hwy")) + geom_point()
+
+# Normalised histogram — callable in after_stat
+(ggplot(mpg, aes(x="hwy"))
+ + geom_histogram(aes(y=after_stat(lambda d: d["count"] / d["count"].sum())), bins=15))
+```
+
+### Extending with custom types (Python-exclusive)
+
+```python
+from ggplot2_py import update_ggplot
+
+class Watermark:
+    def __init__(self, text): self.text = text
+
+@update_ggplot.register(Watermark)
+def _add_watermark(obj, plot, object_name=""):
+    plot.labels["caption"] = f"[{obj.text}]"
+    return plot
+
+# Now use with +
+ggplot(mpg, aes("displ", "hwy")) + geom_point() + Watermark("DRAFT")
+```
+
+### Scoped defaults (Python-exclusive)
+
+```python
+from ggplot2_py import ggplot_defaults
+
+with ggplot_defaults(theme=theme_minimal()):
+    p1 = ggplot(df, aes("x", "y")) + geom_point()   # theme_minimal applied
+    p2 = ggplot(df, aes("x", "y")) + geom_bar()     # theme_minimal applied
+# Outside: no defaults
+```
+
+## Tutorials
+
+### User Tutorials
+- [Getting Started](tutorials/ggplot2.ipynb) — core concepts: data, aes, geoms, stats, scales, facets, coords, themes
+- [Geom Gallery](tutorials/geoms_gallery.ipynb) — boxplot, violin, density, tile, hex and combinations
+- [Labels & Facets](tutorials/labels_and_facets.ipynb) — axis titles, plot title/subtitle/caption, facet strip labels
+- [Aesthetic Specs](tutorials/aesthetic_specs.ipynb) — colour, fill, alpha, linetype, shape, size, colour scales
+- [Extending ggplot2](tutorials/extending_ggplot2.ipynb) — custom stats, geoms, themes via ggproto
+
+### Python-Exclusive Feature Tutorials
+- [Callable aes Expressions](tutorials/aes_expressions.ipynb) — lambdas in `aes()`, `after_stat()`, `after_scale()`, `stage()`
+- [Extensible Pipeline](tutorials/pipeline_dispatch.ipynb) — `singledispatch` registration, custom types with `+`
+- [Build Hooks](tutorials/build_hooks.ipynb) — intercepting the 16-stage build pipeline
+
+### Developer Guide
+- [Developer Guide: Extending ggplot2_py](tutorials/developer_guide.ipynb) — comprehensive guide covering ggproto system, custom Stat/Geom creation, Protocol contracts, singledispatch, hooks, auto-registration, context manager, and packaging
+
+## Extension Architecture
+
+ggplot2_py is designed as an **extensible platform**. The following table summarises all extension points:
+
+| Extension point | Mechanism | How to use |
+|----------------|-----------|-----------|
+| Custom Stat | Subclass `Stat` | Override `compute_group()` — auto-registered via `__init_subclass__` |
+| Custom Geom | Subclass `Geom` | Override `draw_panel()` — auto-registered |
+| Custom Scale | Subclass `ScaleContinuous` / `ScaleDiscrete` | Implement `train()`, `map()`, `get_breaks()` |
+| Custom Coord | Subclass `Coord` | Override `transform()`, `setup_panel_params()` |
+| Custom Facet | Subclass `Facet` | Override `compute_layout()`, `map_data()` |
+| Custom Position | Subclass `Position` | Override `compute_layer()` — auto-registered |
+| Custom `+` types | `@update_ggplot.register(MyClass)` | Register any Python class for the `+` operator |
+| Custom plot types | `@ggplot_build.register(MyPlot)` | Override the entire build pipeline |
+| Build hooks | `plot.add_build_hook(timing, stage, fn)` | Intercept data at any pipeline stage |
+| Protocol validation | `isinstance(obj, GeomProtocol)` | Verify structural conformance |
+| Scoped defaults | `with ggplot_defaults(theme=...):` | Thread-safe scoped defaults |