first commit

.coveragerc

@@ -1,28 +1,21 @@
-# .coveragerc to control coverage.py
 [run]
 branch = True
 source = ratio_corr_gammas
-# omit = bad_file.py
 
 [paths]
 source =
     src/
     */site-packages/
 
 [report]
-# Regexes for lines to exclude from consideration
 exclude_lines =
-    # Have to re-enable the standard pragma
     pragma: no cover
 
-    # Don't complain about missing debug-only code:
     def __repr__
     if self\.debug
 
-    # Don't complain if tests don't hit defensive assertion code:
     raise AssertionError
     raise NotImplementedError
 
-    # Don't complain if non-runnable code isn't run:
     if 0:
     if __name__ == .__main__.:

.gitignore

@@ -23,6 +23,10 @@ __pycache__/*
 .vscode
 tags
 
+# temp
+CONTRIBUTING.rst
+tests/conftest.py
+
 # Package files
 *.egg
 *.eggs/

.readthedocs.yml

@@ -1,18 +1,8 @@
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
 version: 2
 
-# Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
-# Optionally build your docs in additional formats such as PDF
 formats:
   - pdf
 

AUTHORS.rst

@@ -2,4 +2,4 @@
 Contributors
 ============
 
-* t-silvers <[email protected]>
+* Thomas R. Silvers <[email protected]>

CHANGELOG.rst

@@ -5,6 +5,4 @@ Changelog
 Version 0.1
 ===========
 
-- Feature A added
-- FIX: nasty bug #1729 fixed
-- add your changes here!
+- published to GH

LICENSE.txt

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2024 t-silvers
+Copyright (c) 2024 Thomas R. Silvers
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.rst

@@ -1,28 +1,3 @@
-.. These are examples of badges you might want to add to your README:
-   please update the URLs accordingly
-
-    .. image:: https://api.cirrus-ci.com/github/<USER>/ratio_corr_gammas.svg?branch=main
-        :alt: Built Status
-        :target: https://cirrus-ci.com/github/<USER>/ratio_corr_gammas
-    .. image:: https://readthedocs.org/projects/ratio_corr_gammas/badge/?version=latest
-        :alt: ReadTheDocs
-        :target: https://ratio_corr_gammas.readthedocs.io/en/stable/
-    .. image:: https://img.shields.io/coveralls/github/<USER>/ratio_corr_gammas/main.svg
-        :alt: Coveralls
-        :target: https://coveralls.io/r/<USER>/ratio_corr_gammas
-    .. image:: https://img.shields.io/pypi/v/ratio_corr_gammas.svg
-        :alt: PyPI-Server
-        :target: https://pypi.org/project/ratio_corr_gammas/
-    .. image:: https://img.shields.io/conda/vn/conda-forge/ratio_corr_gammas.svg
-        :alt: Conda-Forge
-        :target: https://anaconda.org/conda-forge/ratio_corr_gammas
-    .. image:: https://pepy.tech/badge/ratio_corr_gammas/month
-        :alt: Monthly Downloads
-        :target: https://pepy.tech/project/ratio_corr_gammas
-    .. image:: https://img.shields.io/twitter/url/http/shields.io.svg?style=social&label=Twitter
-        :alt: Twitter
-        :target: https://twitter.com/ratio_corr_gammas
-
 .. image:: https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold
     :alt: Project generated with PyScaffold
     :target: https://pyscaffold.org/
@@ -34,10 +9,22 @@ ratio_corr_gammas
 =================
 
 
-    Add a short description here!
+    Provides a scipy implementation of the ratio of correlated gammas distribution.
+
+
+This package includes:
+
+* A custom scipy distribution for the ratio of correlated gammas (RCG).
+* A rejection sampler for RCG sampling.
+* A convenience function for efficient sampling based on parameter values.
+
+
+References
+==========
 
+1. Weinhold, L., Wahl, S., Pechlivanis, S., Hoffmann, P., & Schmid, M. (2016). A statistical model for the analysis of beta values in DNA methylation studies. *BMC Bioinformatics*, 17(1). `DOI:10.1186/s12859-016-1347-4 <http://dx.doi.org/10.1186/s12859-016-1347-4>`_
 
-A longer description of your project goes here...
+2. Berger, M., Wagner, M., & Schmid, M. (2019). Modeling biomarker ratios with gamma distributed components. *The Annals of Applied Statistics*, 13(1). `DOI:10.1214/18-AOAS1207 <http://dx.doi.org/10.1214/18-aoas1207>`_
 
 
 .. _pyscaffold-notes:

pyproject.toml

@@ -1,9 +1,6 @@
 [build-system]
-# AVOID CHANGING REQUIRES: IT WILL BE UPDATED BY PYSCAFFOLD!
 requires = ["setuptools>=46.1.0", "setuptools_scm[toml]>=5"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-# For smarter version schemes and other configuration options,
-# check out https://github.com/pypa/setuptools_scm
 version_scheme = "no-guess-dev"

setup.cfg

@@ -1,8 +1,3 @@
-# This file is used to configure your project.
-# Read more about the various options under:
-# https://setuptools.pypa.io/en/latest/userguide/declarative_config.html
-# https://setuptools.pypa.io/en/latest/references/keywords.html
-
 [metadata]
 name = ratio_corr_gammas
 description = Add a short description here!
@@ -13,77 +8,40 @@ license_files = LICENSE.txt
 long_description = file: README.rst
 long_description_content_type = text/x-rst; charset=UTF-8
 url = https://github.com/pyscaffold/pyscaffold/
-# Add here related links, for example:
 project_urls =
     Documentation = https://pyscaffold.org/
-#    Source = https://github.com/pyscaffold/pyscaffold/
-#    Changelog = https://pyscaffold.org/en/latest/changelog.html
-#    Tracker = https://github.com/pyscaffold/pyscaffold/issues
-#    Conda-Forge = https://anaconda.org/conda-forge/pyscaffold
-#    Download = https://pypi.org/project/PyScaffold/#files
-#    Twitter = https://twitter.com/PyScaffold
 
-# Change if running only on Windows, Mac or Linux (comma-separated)
 platforms = any
 
-# Add here all kinds of additional classifiers as defined under
-# https://pypi.org/classifiers/
 classifiers =
     Development Status :: 4 - Beta
     Programming Language :: Python
 
-
 [options]
 zip_safe = False
 packages = find_namespace:
 include_package_data = True
 package_dir =
     =src
 
-# Require a min/specific Python version (comma-separated conditions)
-# python_requires = >=3.8
-
-# Add here dependencies of your project (line-separated), e.g. requests>=2.2,<3.0.
-# Version specifiers like >=2.2,<3.0 avoid problems due to API changes in
-# new major versions. This works if the required packages follow Semantic Versioning.
-# For more information, check out https://semver.org/.
+python_requires = >=3.8
 install_requires =
-    importlib-metadata; python_version<"3.8"
-
+    numdifftools>=0.9
+    numpy>=1.23
+    scipy>=1.11
 
 [options.packages.find]
 where = src
 exclude =
     tests
 
 [options.extras_require]
-# Add here additional requirements for extra features, to install with:
-# `pip install ratio_corr_gammas[PDF]` like:
-# PDF = ReportLab; RXP
-
-# Add here test requirements (semicolon/line-separated)
 testing =
     setuptools
     pytest
     pytest-cov
 
-[options.entry_points]
-# Add here console scripts like:
-# console_scripts =
-#     script_name = ratio_corr_gammas.module:function
-# For example:
-# console_scripts =
-#     fibonacci = ratio_corr_gammas.skeleton:run
-# And any other entry points, for example:
-# pyscaffold.cli =
-#     awesome = pyscaffoldext.awesome.extension:AwesomeExtension
-
 [tool:pytest]
-# Specify command line options as you would do when invoking pytest directly.
-# e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml
-# in order to write a coverage file that can be read by Jenkins.
-# CAUTION: --cov flags may prohibit setting breakpoints while debugging.
-#          Comment those flags to avoid this pytest issue.
 addopts =
     --cov ratio_corr_gammas --cov-report term-missing
     --verbose
@@ -92,23 +50,14 @@ norecursedirs =
     build
     .tox
 testpaths = tests
-# Use pytest markers to select/deselect specific tests
-# markers =
-#     slow: mark tests as slow (deselect with '-m "not slow"')
-#     system: mark end-to-end system tests
 
 [devpi:upload]
-# Options for the devpi: PyPI server and packaging tool
-# VCS export must be deactivated since we are using setuptools-scm
 no_vcs = 1
 formats = bdist_wheel
 
 [flake8]
-# Some sane defaults for the code style checker flake8
 max_line_length = 88
 extend_ignore = E203, W503
-# ^  Black-compatible
-#    E203 and W503 have edge cases handled by black
 exclude =
     .tox
     build
@@ -117,7 +66,5 @@ exclude =
     docs/conf.py
 
 [pyscaffold]
-# PyScaffold's parameters when the project was created.
-# This will be used when updating. Do not change!
 version = 4.5
 package = ratio_corr_gammas

setup.py

@@ -1,10 +1,5 @@
 """
     Setup file for ratio_corr_gammas.
-    Use setup.cfg to configure your project.
-
-    This file was generated with PyScaffold 4.5.
-    PyScaffold helps you to put up the scaffold of your new Python project.
-    Learn more under: https://pyscaffold.org/
 """
 from setuptools import setup