Merge pull request #3 from michael-denyer/master

Modernised to support python 3.10+

Author: satchellhong

.gitignore

@@ -134,4 +134,5 @@ qqman/*.jpg
 qqman/*.jpeg
 qqman/*.gif
 qqman/*.tif
-qqman/*.tiff
+qqman/*.tiff
+.DS_Store

README.md

@@ -1,10 +1,27 @@
 <h1 style="text-align:center">qqman for Python</h1>
 
-![Install with pypi or anaconda](https://img.shields.io/badge/version-v1.0.6-green)
+![Install with pypi or anaconda](https://img.shields.io/badge/version-v1.0.8-green)
+![Python Version](https://img.shields.io/badge/python-3.10%2B-blue)
+![License](https://img.shields.io/badge/license-MIT-green)
 
-If you want to check out the source code or have any issues please leave a comment at my [github](https://github.com/satchellhong/qqman) repository. <br>
-This library is inspired by r-qqman (see [here](https://github.com/stephenturner/qqman)). <br>
-It also contains/will contain other methods for python users.<br>
+## About This Fork
+
+This is a modernized fork of [satchellhong/qqman](https://github.com/satchellhong/qqman) with the following enhancements:
+
+- **Added Parameters**: Additional `point_size` parameter for Manhattan plots to control marker size
+- **Modernized Dependencies**: Updated to support Python 3.9+ and newer python package versions
+- **Modern Packaging**: Added `pyproject.toml` and updated dependency specifications
+
+### Original Project
+
+The original qqman library was created by [satchellhong](https://github.com/satchellhong) and is inspired by the R package [r-qqman](https://github.com/stephenturner/qqman).
+
+### License
+
+This fork maintains the original MIT License. See the [LICENSE](LICENSE) file for details.
+
+**Original Copyright**: Copyright (c) 2020 satchellhong
+**Fork Enhancements**: Additional parameters and modernization updates
 
 ---
 ## Contents
@@ -29,24 +46,24 @@ $ pip install qqman
 ```
 
 ### <a name="h12">1.2. Requirements</a>
-- matplotlib
-- pandas
-- numpy
+- Python 3.10+
+- matplotlib >= 3.7.0
+- pandas >= 1.5.3
+- numpy >= 1.23.5
 
-#### pip
+#### Using uv (recommended - 10-100x faster)
 ```console
-$ pip install numpy
-$ pip install pandas
-$ pip install matplotlib
+$ pip install uv
+$ uv pip install qqman
 ```
 
-#### ananconda
+#### Using pip
 ```console
-$ conda install -c anaconda numpy
-$ conda install -y -c anaconda pandas
-$ conda install -y -c conda-forge matplotlib
+$ pip install qqman
 ```
 
+All dependencies will be installed automatically.
+
 ### <a name="h13">1.3. Features</a>
 1. [Manhattan Plot](#h2)<br>
 2. [QQ Plot](#h3)<br>
@@ -134,7 +151,11 @@ Draws Manhattan plot from PLINK --assoc output or any assoc formatted data that
 </tr>
 <tr>
 <th><code>col_snp</code> : string<br>( optional : default="SNP" )</th>
-<th>A string denoting the column name for the SNP name (rs number). Defaults to PLINK’s "SNP" Said column should be a character</th>
+<th>A string denoting the column name for the SNP name (rs number). Defaults to PLINK's "SNP" Said column should be a character</th>
+</tr>
+<tr>
+<th><code>point_size</code> : int<br>( optional : default=8 )</th>
+<th>The size of the scatter plot markers in the Manhattan plot</th>
 </tr>
 <tr>
 <th><code>suggestiveline</code> : string<br>( optional : default=-log_10(1e-5) )</th>
@@ -202,6 +223,10 @@ types: [string, pandas.DataFrame, numpy.array, list]
 <th>Output path and file name of the plot. (ie. out="./Manhattan.png")</th>
 </tr>
 <tr>
+<th><code>point_size</code> : int<br>( optional )</th>
+<th>The size of the scatter graph points (default s=5).</th>
+</tr>
+<tr>
 <th><code>show</code> : bool<br>( optional )</th>
 <th>If true, the plot will be shown on your screen. (This option doesn't work in CUI environment.)</th>
 </tr>
@@ -264,7 +289,7 @@ import matplotlib.pyplot as plt
 if __name__ == "__main__":
 	df_assoc = pd.read_csv("../../temp.assoc", header=0, delim_whitespace=True)
 	p_vals = list(df_assoc['P'])
-	
+
 	figure, axes = plt.subplots(nrows=2, ncols=2, figsize = (20,20))
 
 	qqman.qqplot("../../temp.assoc", ax=axes[0,0],title="From file")
@@ -278,4 +303,4 @@ if __name__ == "__main__":
 	plt.close()
 ```
 
-<img src="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/satchellhong/qqman/blob/master/static/images/SubQQplot.png?raw=true" alt="Simple Manhattan Plot" width="600" height="600">
+<img src="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/satchellhong/qqman/blob/master/static/images/SubQQplot.png?raw=true" alt="Simple Manhattan Plot" width="600" height="600">

build.sh

@@ -1,6 +1,15 @@
+#!/bin/bash
+# Modern Python package build script using uv and pyproject.toml
+
+set -e  # Exit on error
+
+echo "🧹 Cleaning previous builds..."
 rm -rf build dist *.egg-info
-conda install setuptools wheel twine -y
-conda update setuptools wheel twine -y
 
-python setup.py sdist bdist_wheel
-twine upload dist/* --verbose
+echo "📦 Building package with uv..."
+uv build
+
+echo "🚀 Uploading to PyPI..."
+uv publish
+
+echo "✅ Build and publish complete!"

pyproject.toml

@@ -0,0 +1,68 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "qqman"
+version = "1.0.8"
+description = "Draws Manhattan plot and QQ plot using plink assoc output"
+readme = "README.md"
+license = {text = "MIT"}
+authors = [
+    {name = "chol hong", email = "shulkhorn@gmail.com"}
+]
+maintainers = [
+    {name = "chol hong", email = "shulkhorn@gmail.com"}
+]
+requires-python = ">=3.10"
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Visualization",
+]
+keywords = ["bioinformatics", "gwas", "manhattan plot", "qq plot", "visualization", "genomics"]
+
+dependencies = [
+    "numpy>=1.23.5,<3.0.0",
+    "pandas>=1.5.3,<3.0.0",
+    "matplotlib>=3.7.0,<4.0.0",
+]
+
+[project.urls]
+Homepage = "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/satchellhong/qqman"
+"Bug Tracker" = "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/satchellhong/qqman/issues"
+"Source Code" = "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/satchellhong/qqman"
+
+# Optional development dependencies
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0.0",
+    "pytest-cov>=4.0.0",
+    "ruff>=0.4.8",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["qqman"]
+
+# uv-specific configuration
+[tool.uv]
+dev-dependencies = [
+    "pytest>=7.0.0",
+    "pytest-cov>=4.0.0",
+    "ruff>=0.4.8",
+]
+
+# Ruff configuration for numpy 2.0 compatibility checking
+[tool.ruff]
+line-length = 88
+target-version = "py310"
+
+[tool.ruff.lint]
+select = ["E", "F", "W", "I", "NPY201"]  # NPY201 checks numpy 2.0 compatibility

qqman/__init__.py

@@ -1,2 +1,2 @@
 name = "qqman"
-from . import qqman
+from . import qqman

qqman/biostats.py

@@ -1,17 +1,16 @@
-import numpy as np
 import numbers
 
+import numpy as np
+
+
 def ppoints(n, a=None):
-	""" numpy analogue or `R`'s `ppoints` function
-		see details at https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/ppoints
-		https://docs.tibco.com/pub/enterprise-runtime-for-R/5.0.0/doc/html/Language_Reference/stats/ppoints.html
-		:param n: array type or number"""
-	
-	if isinstance(n, numbers.Number):
-		n = float(n)
-	else:
-		n = float(len(n))
-	if a == None:
-		a = .375 if n<=10 else .5
-		
-	return (np.arange(n) + 1 - a)/(n + 1 - 2*a)
+    """numpy analogue or `R`'s `ppoints` function
+    see details at https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/ppoints
+    https://docs.tibco.com/pub/enterprise-runtime-for-R/5.0.0/doc/html/Language_Reference/stats/ppoints.html
+    :param n: array type or number"""
+
+    n = np.float64(n) if isinstance(n, numbers.Number) else np.float64(len(n))
+    if a is None:
+        a = 0.375 if n <= 10 else 0.5
+
+    return (np.arange(n) + 1 - a) / (n + 1 - 2 * a)