ggsci 0.1.0__tar.gz

ggsci-0.1.0/.gitignore

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+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# Virtual environments
+.venv

ggsci-0.1.0/.python-version

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+3.13.7

ggsci-0.1.0/CHANGELOG.md

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+# Changelog
+
+## py-ggsci 0.1.0
+
+### New features
+
+- Port four experimental color scales for plotnine from the R package ggsci.
+  - Add palette functions for direct color access.
+  - Support alpha transparency for all scales.
+  - Reverse parameter for continuous scales.
+  - British spelling aliases.

ggsci-0.1.0/CLAUDE.md

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+# py-ggsci package design notes
+
+## Overview
+
+Python port of the R package ggsci providing color palettes for plotnine.
+
+## Package structure
+
+```
+src/ggsci/
+├── __init__.py     # Main exports
+├── data.py         # Color palette data (hex strings)
+├── palettes.py     # Palette generation functions
+├── scales.py       # Plotnine scale implementations
+└── utils.py        # Color utilities (alpha, interpolation)
+```
+
+## Key design decisions
+
+### 1. Pure Python data storage
+
+- Color data stored directly in Python dict (not TOML)
+- No runtime parsing overhead
+- Better IDE support and type hints
+- Follows mizani pattern
+
+### 2. Two scale patterns
+
+**Discrete scales**: Use `@dataclass` with `InitVar` and `__post_init__`
+
+```python
+@dataclass
+class scale_color_npg(scale_discrete):
+    palette: InitVar[str] = "nrc"
+    alpha: InitVar[float] = 1.0
+
+    def __post_init__(self, palette, alpha):
+        super().__post_init__()
+        self.palette = npg_pal(palette, alpha)
+```
+
+**Continuous scales**: Use functions that return `scale_*_gradientn`
+
+```python
+def scale_color_gsea(palette="default", alpha=1.0, reverse=False, **kwargs):
+    colors = gsea_pal(palette, n=512, alpha=alpha, reverse=reverse)
+    return scale_color_gradientn(colors=colors, **kwargs)
+```
+
+### 3. Palette function types
+
+- **Discrete**: Return callable `(n: int) -> List[str]`
+- **Continuous**: Return `List[str]` directly
+
+## Implemented scales
+
+| Scale | Type | Variants | Notes |
+|-------|------|----------|-------|
+| NPG | Discrete | nrc | Nature Publishing Group |
+| FlatUI | Discrete | default, flattastic, aussie | 3 variations |
+| GSEA | Continuous | default | Diverging heatmap colors |
+| BS5 | Continuous | 11 colors | Sequential Bootstrap 5 |
+
+## Critical implementation details
+
+### Plotnine imports
+
+```python
+from plotnine.scales.scale_discrete import scale_discrete
+from plotnine.scales import scale_color_gradientn, scale_fill_gradientn
+```
+
+### Alpha handling
+
+- Discrete: Applied in palette function, returns RGBA hex
+- Continuous: Applied during interpolation
+
+### Aliases
+
+```python
+scale_colour_npg = scale_color_npg  # etc.
+```
+
+## Testing & demo
+
+- `tests/`: Unit tests using pytest
+- `examples/demo.py`: Visual demos with plot generation
+
+## Commands for development
+
+```bash
+# Run tests
+uv run python test.py
+
+# Generate demo plots
+uv run python examples/demo.py
+
+# Check structure
+find src/ -name "*.py"
+```
+
+## Import usage
+
+```python
+from ggsci import (
+    scale_color_npg, scale_fill_npg,        # Discrete NPG
+    scale_color_flatui,                     # Discrete FlatUI
+    scale_color_gsea, scale_fill_gsea,      # Continuous diverging
+    scale_color_bs5, scale_fill_bs5,        # Continuous sequential
+    npg_pal, flatui_pal, gsea_pal, bs5_pal  # Palette functions
+)
+```
+
+## Architecture benefits
+
+- **Clean**: Flattened structure, no nested subdirs
+- **Pythonic**: Follows plotnine/dataclass patterns
+- **Performant**: No file parsing, direct data access
+- **Extensible**: Clear patterns for adding new scales
+- **Compatible**: Seamless plotnine integration

ggsci-0.1.0/LICENSE

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+Copyright (c) 2025, py-ggsci authors
+
+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.

ggsci-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: ggsci
+Version: 0.1.0
+Summary: Plotnine color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows
+Project-URL: Homepage, https://nanx.me/py-ggsci/
+Project-URL: Documentation, https://nanx.me/py-ggsci/
+Project-URL: Repository, https://github.com/nanxstats/py-ggsci
+Project-URL: Issues, https://github.com/nanxstats/py-ggsci/issues
+Project-URL: Changelog, https://github.com/nanxstats/py-ggsci/blob/main/CHANGELOG.md
+Author-email: Nan Xiao <me@nanx.me>
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: matplotlib>=3.10.6
+Requires-Dist: numpy>=2.2.6
+Requires-Dist: plotnine>=0.15.0
+Description-Content-Type: text/markdown
+
+# ggsci for Python
+
+[![PyPI version](https://img.shields.io/pypi/v/ggsci)](https://pypi.org/project/ggsci/)
+![Python versions](https://img.shields.io/pypi/pyversions/ggsci)
+[![Checked with mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](https://mypy-lang.org/)
+[![CI Tests](https://github.com/nanxstats/py-ggsci/actions/workflows/ci-tests.yml/badge.svg)](https://github.com/nanxstats/py-ggsci/actions/workflows/ci-tests.yml)
+[![mkdocs](https://github.com/nanxstats/py-ggsci/actions/workflows/mkdocs.yml/badge.svg)](https://nanx.me/py-ggsci/)
+![License](https://img.shields.io/pypi/l/ggsci)
+
+ggsci for Python provides color palettes for plotnine.
+
+## Installation
+
+You can install py-ggsci from PyPI:
+
+```bash
+pip install ggsci
+```
+
+Or install the development version from GitHub:
+
+```bash
+git clone https://github.com/nanxstats/py-ggsci.git
+cd py-ggsci
+python3 -m pip install -e .
+```

ggsci-0.1.0/README.md

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+# ggsci for Python
+
+[![PyPI version](https://img.shields.io/pypi/v/ggsci)](https://pypi.org/project/ggsci/)
+![Python versions](https://img.shields.io/pypi/pyversions/ggsci)
+[![Checked with mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](https://mypy-lang.org/)
+[![CI Tests](https://github.com/nanxstats/py-ggsci/actions/workflows/ci-tests.yml/badge.svg)](https://github.com/nanxstats/py-ggsci/actions/workflows/ci-tests.yml)
+[![mkdocs](https://github.com/nanxstats/py-ggsci/actions/workflows/mkdocs.yml/badge.svg)](https://nanx.me/py-ggsci/)
+![License](https://img.shields.io/pypi/l/ggsci)
+
+ggsci for Python provides color palettes for plotnine.
+
+## Installation
+
+You can install py-ggsci from PyPI:
+
+```bash
+pip install ggsci
+```
+
+Or install the development version from GitHub:
+
+```bash
+git clone https://github.com/nanxstats/py-ggsci.git
+cd py-ggsci
+python3 -m pip install -e .
+```

ggsci-0.1.0/examples/demo.py

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+"""
+Demo of py-ggsci scales with plotnine
+
+This script demonstrates how to use the py-ggsci color scales
+with plotnine for creating publication-ready plots.
+"""
+
+import numpy as np
+import pandas as pd
+from plotnine import (
+    aes,
+    facet_wrap,
+    geom_bar,
+    geom_point,
+    geom_tile,
+    ggplot,
+    labs,
+    theme_minimal,
+)
+
+from ggsci import scale_color_npg, scale_fill_bs5, scale_fill_flatui, scale_fill_gsea
+
+
+def demo_npg_discrete():
+    """Demo NPG discrete scale with scatter plot."""
+    # Create sample data
+    np.random.seed(42)
+    data = pd.DataFrame(
+        {
+            "x": np.random.randn(100),
+            "y": np.random.randn(100),
+            "category": np.random.choice(["A", "B", "C", "D", "E"], 100),
+        }
+    )
+
+    # Create plot
+    plot = (
+        ggplot(data, aes(x="x", y="y", color="category"))
+        + geom_point(size=3, alpha=0.7)
+        + scale_color_npg()
+        + theme_minimal()
+        + labs(
+            title="NPG Color Scale Demo",
+            subtitle="Nature Publishing Group inspired colors",
+            x="X Value",
+            y="Y Value",
+        )
+    )
+
+    return plot
+
+
+def demo_flatui_variations():
+    """Demo FlatUI scale with its three variations."""
+    # Create sample data
+    np.random.seed(42)
+    categories = ["A", "B", "C", "D", "E", "F"]
+    values = np.random.randint(10, 100, len(categories))
+    data = pd.DataFrame({"category": categories, "value": values})
+
+    # Create and save three separate plots
+    palettes = ["default", "flattastic", "aussie"]
+    for palette in palettes:
+        plot = (
+            ggplot(data, aes(x="category", y="value", fill="category"))
+            + geom_bar(stat="identity")
+            + scale_fill_flatui(palette=palette)
+            + theme_minimal()
+            + labs(
+                title=f"Flat UI Color Scale - {palette.title()}",
+                x="Category",
+                y="Value",
+            )
+        )
+        plot.save(f"flatui_{palette}.png", dpi=150, width=8, height=6)
+        print(f"Saved flatui_{palette}.png")
+
+    # Return None since we've already saved the individual files
+    return None
+
+
+def demo_gsea_continuous():
+    """Demo GSEA continuous diverging scale with heatmap."""
+    # Create correlation matrix data
+    np.random.seed(42)
+    n_vars = 10
+    corr_matrix = np.random.randn(n_vars, n_vars)
+    corr_matrix = (corr_matrix + corr_matrix.T) / 2  # Make symmetric
+    np.fill_diagonal(corr_matrix, 1)
+
+    # Convert to long format for plotnine
+    data = []
+    for i in range(n_vars):
+        for j in range(n_vars):
+            data.append(
+                {
+                    "var1": f"V{i + 1}",
+                    "var2": f"V{j + 1}",
+                    "correlation": corr_matrix[i, j],
+                }
+            )
+
+    data = pd.DataFrame(data)
+
+    # Create heatmap
+    plot = (
+        ggplot(data, aes(x="var1", y="var2", fill="correlation"))
+        + geom_tile()
+        + scale_fill_gsea()
+        + theme_minimal()
+        + labs(
+            title="GSEA Diverging Color Scale",
+            subtitle="GSEA GenePattern inspired heatmap colors",
+            x="Variable 1",
+            y="Variable 2",
+        )
+    )
+
+    return plot
+
+
+def demo_bs5_sequential():
+    """Demo BS5 continuous sequential scale."""
+    # Create gradient data
+    x = np.linspace(0, 10, 100)
+    y = np.linspace(0, 10, 100)
+    X, Y = np.meshgrid(x, y)
+    Z = np.sin(np.sqrt(X**2 + Y**2))
+
+    # Convert to dataframe
+    data = pd.DataFrame({"x": X.flatten(), "y": Y.flatten(), "z": Z.flatten()})
+
+    # Create plot with different BS5 palettes
+    plot = (
+        ggplot(data.sample(5000), aes(x="x", y="y", fill="z"))
+        + geom_tile()
+        + scale_fill_bs5(palette="teal")
+        + theme_minimal()
+        + labs(
+            title="Bootstrap 5 Sequential Color Scale",
+            subtitle='Using the "teal" palette',
+            x="X",
+            y="Y",
+            fill="Value",
+        )
+    )
+
+    return plot
+
+
+if __name__ == "__main__":
+    print("Generating demo plots...")
+
+    # Demo each scale type
+    plots = {
+        "npg_discrete": demo_npg_discrete(),
+        "flatui_variations": demo_flatui_variations(),
+        "gsea_continuous": demo_gsea_continuous(),
+        "bs5_sequential": demo_bs5_sequential(),
+    }
+
+    # Save plots (requires plotnine to be properly configured)
+    for name, plot in plots.items():
+        if plot is not None:  # Skip None plots (like flatui_variations)
+            try:
+                plot.save(f"{name}.png", dpi=150, width=10, height=8)
+                print(f"Saved {name}.png")
+            except Exception as e:
+                print(f"Could not save {name}.png: {e}")
+
+    print("\nDemo complete!")
+    print("\nYou can use these scales in your plotnine plots:")
+    print("- scale_color_npg() / scale_fill_npg()")
+    print("- scale_color_flatui() / scale_fill_flatui()")
+    print("- scale_color_gsea() / scale_fill_gsea()")
+    print("- scale_color_bs5() / scale_fill_bs5()")

ggsci-0.1.0/pyproject.toml

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+[project]
+name = "ggsci"
+version = "0.1.0"
+description = "Plotnine color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows"
+authors = [
+    { name = "Nan Xiao", email = "me@nanx.me" }
+]
+dependencies = [
+    "matplotlib>=3.10.6",
+    "numpy>=2.2.6",
+    "plotnine>=0.15.0",
+]
+readme = "README.md"
+
+requires-python = ">= 3.10"
+
+[project.urls]
+Homepage = "https://nanx.me/py-ggsci/"
+Documentation = "https://nanx.me/py-ggsci/"
+Repository = "https://github.com/nanxstats/py-ggsci"
+Issues = "https://github.com/nanxstats/py-ggsci/issues"
+Changelog = "https://github.com/nanxstats/py-ggsci/blob/main/CHANGELOG.md"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[dependency-groups]
+dev = [
+    "isort>=6.0.1",
+    "mkdocs>=1.6.1",
+    "mkdocs-material>=9.6.19",
+    "mkdocstrings-python>=1.18.2",
+    "mypy>=1.17.1",
+    "pytest>=8.4.2",
+    "pytest-cov>=7.0.0",
+    "ruff>=0.12.12",
+]

ggsci-0.1.0/src/ggsci/__init__.py

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+"""
+py-ggsci: Scientific journal color palettes for Python
+
+A Python implementation of the R ggsci package, providing color palettes
+inspired by scientific journals and sci-fi themes.
+"""
+
+from .palettes import bs5_pal, flatui_pal, gsea_pal, npg_pal
+from .scales import (
+    scale_color_bs5,
+    scale_color_flatui,
+    scale_color_gsea,
+    scale_color_npg,
+    scale_colour_bs5,
+    scale_colour_flatui,
+    scale_colour_gsea,
+    scale_colour_npg,
+    scale_fill_bs5,
+    scale_fill_flatui,
+    scale_fill_gsea,
+    scale_fill_npg,
+)
+
+__version__ = "0.1.0"
+
+__all__ = [
+    "scale_color_npg",
+    "scale_fill_npg",
+    "scale_colour_npg",
+    "scale_color_flatui",
+    "scale_fill_flatui",
+    "scale_colour_flatui",
+    "scale_color_gsea",
+    "scale_fill_gsea",
+    "scale_colour_gsea",
+    "scale_color_bs5",
+    "scale_fill_bs5",
+    "scale_colour_bs5",
+    "npg_pal",
+    "flatui_pal",
+    "gsea_pal",
+    "bs5_pal",
+]