pyfauxseq 0.1.0__tar.gz

pyfauxseq-0.1.0/.gitignore

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+# From https://github.com/github/gitignore/blob/main/Python.gitignore 2025-07-30
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml
+# pixi environments
+.pixi/*
+!.pixi/config.toml

pyfauxseq-0.1.0/CONTRIBUTING.md

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+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+## Types of Contributions
+
+### Report Bugs
+
+Report bugs at https://github.com/bharathananth/pyfauxseq/issues.
+
+If you are reporting a bug, please include:
+
+- Your operating system name and version.
+- Any details about your local setup that might be helpful in troubleshooting.
+- Detailed steps to reproduce the bug.
+
+### Fix Bugs
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitHub issues for features. Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it.
+
+### Write Documentation
+
+Python Implementation of the R package fauxseq could always use more documentation, whether as part of the official docs, in docstrings, or even on the web in blog posts, articles, and such.
+
+### Submit Feedback
+
+The best way to send feedback is to file an issue at https://github.com/bharathananth/pyfauxseq/issues.
+
+If you are proposing a feature:
+
+- Explain in detail how it would work.
+- Keep the scope as narrow as possible, to make it easier to implement.
+- Remember that this is a volunteer-driven project, and that contributions are welcome :)
+
+## Get Started!
+
+Ready to contribute? Here's how to set up `pyfauxseq` for local development.
+
+1. Fork the `pyfauxseq` repo on GitHub.
+2. Clone your fork locally:
+
+   ```sh
+   git clone git@github.com:your_name_here/pyfauxseq.git
+   ```
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:
+
+   ```sh
+   mkvirtualenv pyfauxseq
+   cd pyfauxseq/
+   python setup.py develop
+   ```
+
+4. Create a branch for local development:
+
+   ```sh
+   git checkout -b name-of-your-bugfix-or-feature
+   ```
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox:
+
+   ```sh
+   make lint
+   make test
+   # Or
+   make test-all
+   ```
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub:
+
+   ```sh
+   git add .
+   git commit -m "Your detailed description of your changes."
+   git push origin name-of-your-bugfix-or-feature
+   ```
+
+7. Submit a pull request through the GitHub website.
+
+## Pull Request Guidelines
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.md.
+3. The pull request should work for Python 3.12 and 3.13. Tests run in GitHub Actions on every pull request to the main branch, make sure that the tests pass for all supported Python versions.
+
+## Deploying
+
+A reminder for the maintainers on how to deploy. Make sure all your changes are committed (including an entry in HISTORY.md). Then run:
+
+```sh
+bump2version patch # possible: major / minor / patch
+git push
+git push --tags
+```
+
+You can set up a [GitHub Actions workflow](https://docs.github.com/en/actions/use-cases-and-examples/building-and-testing/building-and-testing-python#publishing-to-pypi) to automatically deploy your package to PyPI when you push a new tag.
+
+## Code of Conduct
+
+Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms.

pyfauxseq-0.1.0/HISTORY.md

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+# History
+
+## 0.1.0 (2026-03-18)
+
+* First release on PyPI.

pyfauxseq-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025, Bharath Ananthasubramaniam
+
+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.

pyfauxseq-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pyfauxseq
+Version: 0.1.0
+Summary: This package can generate synthetic timeseries RNA-seq data with a fraction of rhythmic genes and empirical relationship between mean expression and variability across replicates of genes.
+Project-URL: bugs, https://github.com/bharathananth/pyfauxseq/issues
+Project-URL: homepage, https://github.com/bharathananth/pyfauxseq
+Project-URL: documentation, https://bharathananth.github.io/pypfauxseq
+Author-email: Bharath Ananthasubramaniam <bharath.ananthasubramaniam@hu-berlin.de>
+Maintainer-email: Bharath Ananthasubramaniam <bharath.ananthasubramaniam@hu-berlin.de>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scipy
+Provides-Extra: docs
+Requires-Dist: mkdocs; extra == 'docs'
+Requires-Dist: mkdocs-material; extra == 'docs'
+Requires-Dist: mkdocstrings-python; extra == 'docs'
+Provides-Extra: test
+Requires-Dist: coverage; extra == 'test'
+Requires-Dist: hypothesis; extra == 'test'
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: ruff; extra == 'test'
+Requires-Dist: ty; extra == 'test'
+Description-Content-Type: text/markdown
+
+# pyfauxseq
+### A python Implementation of the R package fauxseq
+
+![PyPI - Version](https://img.shields.io/pypi/v/pyfauxseq)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/pyfauxseq)
+![GitHub Downloads (all assets, all releases)](https://img.shields.io/github/downloads/bharathananth/pyfauxseq/total)
+
+## What pyfauxseq does
+
+This package can generate synthetic timeseries RNA-seq data with a fraction of rhythmic genes and empirical relationship between mean expression and variability across replicates of genes.
+
+`pyfauxseq` improves upon previous tools as follows:
+- generates negative-binomial count data with empirically-estimated mean-dispersion properties.
+- generates data with either differential expression or differential rhythmicity or both.
+
+## How to install pyfauxseq
+```python -m pip install pyfauxseq```
+
+## Get started with pyfauxseq
+Get started with synthetic RNA-seq data with the ground truth with the default parameters using
+```python
+import pyfauxseq as pf
+sim_data = pf.generate_rhythmic_rnaseq()
+sim_data["counts"] # the count data
+sim_data["params"] # parameters of the rhythmic genes
+sim_data["exp_design"] # time labels of the individual sample (columns) of count data
+```
+## How to cite pyfauxseq
+Please cite this software using CITATION.CFF or the "Cite this repository" link in the right sidebar.
+
+## Credits
+
+This package was created with [Cookiecutter](https://github.com/audreyfeldroy/cookiecutter) and the [audreyfeldroy/cookiecutter-pypackage](https://github.com/audreyfeldroy/cookiecutter-pypackage) project template.

pyfauxseq-0.1.0/README.md

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+# pyfauxseq
+### A python Implementation of the R package fauxseq
+
+![PyPI - Version](https://img.shields.io/pypi/v/pyfauxseq)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/pyfauxseq)
+![GitHub Downloads (all assets, all releases)](https://img.shields.io/github/downloads/bharathananth/pyfauxseq/total)
+
+## What pyfauxseq does
+
+This package can generate synthetic timeseries RNA-seq data with a fraction of rhythmic genes and empirical relationship between mean expression and variability across replicates of genes.
+
+`pyfauxseq` improves upon previous tools as follows:
+- generates negative-binomial count data with empirically-estimated mean-dispersion properties.
+- generates data with either differential expression or differential rhythmicity or both.
+
+## How to install pyfauxseq
+```python -m pip install pyfauxseq```
+
+## Get started with pyfauxseq
+Get started with synthetic RNA-seq data with the ground truth with the default parameters using
+```python
+import pyfauxseq as pf
+sim_data = pf.generate_rhythmic_rnaseq()
+sim_data["counts"] # the count data
+sim_data["params"] # parameters of the rhythmic genes
+sim_data["exp_design"] # time labels of the individual sample (columns) of count data
+```
+## How to cite pyfauxseq
+Please cite this software using CITATION.CFF or the "Cite this repository" link in the right sidebar.
+
+## Credits
+
+This package was created with [Cookiecutter](https://github.com/audreyfeldroy/cookiecutter) and the [audreyfeldroy/cookiecutter-pypackage](https://github.com/audreyfeldroy/cookiecutter-pypackage) project template.

pyfauxseq-0.1.0/docs/api_documentation.md

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+---
+hide:
+  - navigation
+---
+
+# API Documentation
+::: pyfauxseq.generate_rnaseq.generate_rhythmic_rnaseq
+
+::: pyfauxseq.generate_rnaseq.generate_diffrhythmic_rnaseq

pyfauxseq-0.1.0/docs/getting_started.md

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+---
+hide:
+  - navigation
+---
+
+# Getting Started
+
+## Installation
+
+### Stable release
+
+To install Python Implementation of the R package fauxseq, run this command in your terminal:
+
+```sh
+uv add pyfauxseq
+```
+
+Or if you prefer to use `pip`:
+
+```sh
+pip install pyfauxseq
+```
+
+### From source
+
+The source files for Python Implementation of the R package fauxseq can be downloaded from the [Github repo](https://github.com/bharathananth/pyfauxseq).
+
+You can either clone the public repository:
+
+```sh
+git clone git://github.com/bharathananth/pyfauxseq
+```
+
+## Generate synthetic rhythmic RNA-seq data
+```python
+import pyfauxseq as pf
+```
+For timeseries data under one condition:
+```python
+sim_data = pf.generate_rhythmic_rnaseq()
+```
+For timeseries data under two condition:
+```python
+sim_data = pf.generate_diffrhythmic_rnaseq()
+```
+The parameters to customize the data are listed in [API Documentation](api_documentation.md)

pyfauxseq-0.1.0/docs/index.md

@@ -0,0 +1,19 @@
+---
+hide:
+  - navigation
+  - toc
+  - title
+---
+# pyfauxseq
+## A synthetic timeseries RNA-seq data generator
+![Data](https://img.shields.io/badge/RNA--seq-Synthetic_timeseries-blue)
+![Purpose](https://img.shields.io/badge/Purpose-Benchmarking-green)
+[![PyPI version](https://img.shields.io/pypi/v/pyfauxseq.svg)](https://pypi.org/project/pyfauxseq/)
+[![Supported Python versions](https://img.shields.io/pypi/pyversions/pyfauxseq.svg)](https://pypi.org/project/pyfauxseq/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Build Status](https://github.com/bharathananth/pyfauxseq/actions/workflows/test.yml/badge.svg)](https://github.com/bharathananth/pyfauxseq/actions)
+[![codecov](https://codecov.io/gh/bharathananth/pyfauxseq/branch/main/graph/badge.svg)](https://codecov.io/gh/bharathananth/pyfauxseq)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+## Why **pyfauxseq**?
+`pyfauxseq` and its R sister `fauxseq` arose out of a desire to systematically compare methods comparing temporal changes in gene expression in one or two conditions. This package delivers real-world like RNAseq data with ground truth to help with benchmarking and method development.

pyfauxseq-0.1.0/pyproject.toml

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+[project]
+name = "pyfauxseq"
+version = "0.1.0"
+description = "This package can generate synthetic timeseries RNA-seq data with a fraction of rhythmic genes and empirical relationship between mean expression and variability across replicates of genes."
+readme = {"file" = "README.md", "content-type" = "text/markdown"}
+requires-python = ">= 3.10"
+license = "MIT"
+authors = [
+  {name = "Bharath Ananthasubramaniam", email = "bharath.ananthasubramaniam@hu-berlin.de"}
+]
+maintainers = [
+  {name = "Bharath Ananthasubramaniam", email = "bharath.ananthasubramaniam@hu-berlin.de"}
+]
+keywords = []
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Operating System :: OS Independent",
+  "Intended Audience :: Science/Research",
+  "Intended Audience :: Healthcare Industry",
+  "Development Status :: 5 - Production/Stable",
+  "License :: OSI Approved :: MIT License"
+]
+dependencies = [
+  "numpy",
+  "scipy",
+  "pandas"]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project.optional-dependencies]
+test = [
+    "coverage",  # testing
+    "pytest",  # testing
+    "ruff",  # linting
+    "ty", # checking types
+    "hypothesis", # for CBT
+]
+docs = [
+  "mkdocs",
+  "mkdocs-material",
+  "mkdocstrings-python"
+]
+
+[project.urls]
+bugs = "https://github.com/bharathananth/pyfauxseq/issues"
+homepage = "https://github.com/bharathananth/pyfauxseq"
+documentation = "https://bharathananth.github.io/pypfauxseq"
+
+[tool.hatch.build.targets.sdist]
+# Hatchling includes README, LICENSE, and pyproject.toml by default.
+include = [
+  "/CONTRIBUTING.md",
+  "/HISTORY.md",
+  "/docs",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/pyfauxseq"]
+
+[tool.hatch.envs.default]
+installer = "uv"
+
+[tool.ty]
+# All rules are enabled as "error" by default; no need to specify unless overriding.
+# Example override: relax a rule for the entire project (uncomment if needed).
+# rules.TY015 = "warn"  # For invalid-argument-type, warn instead of error.
+
+[tool.ty.src]
+exclude = ["tests"]
+
+[tool.ruff]
+line-length = 88
+extend-exclude = ["tests"]
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+docstring-code-format = true
+
+[tool.ruff.lint]
+select = [
+    "E",   # pycodestyle errors
+    "W",   # pycodestyle warnings
+    "F",   # Pyflakes
+    "I",   # isort
+    "B",   # flake8-bugbear
+    "UP",  # pyupgrade
+    "D",   # pydocstyle (enforces docstring conventions like PEP 257)
+    "SIM", # flake8-simplify
+    "RUF", # Ruff-specific rules
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy" # Options: "google", "numpy", or "pep257"
+
+[tool.uv]
+package = true
+
+[tool.pixi.workspace]
+channels = ["conda-forge"]
+platforms = ["linux-64", "osx-64", "win-64", "osx-arm64"]
+
+[tool.pixi.pypi-dependencies]
+pyfauxseq = { path = ".", editable = true }
+
+[tool.pixi.environments]
+default = { solve-group = "default" }
+test = { features = ["test"], solve-group = "default" }
+dev = ["docs", "lint", "test", "usage"]
+
+[tool.pixi.tasks]
+test = { cmd = "pytest", default-environment = "test" }
+
+[tool.pixi.feature.test.dependencies]
+pytest = ">=9.0.2,<10"
+hypothesis = ">=6.151.9,<7"
+ipython = ">=9.11.0,<10"
+
+[tool.pixi.feature.docs.dependencies]
+mkdocs = "<2.0.0"
+mkdocs-material = "*"
+mkdocstrings-python = "*"
+
+[tool.pixi.feature.lint.dependencies]
+ruff = "*"
+ty = "*"
+pandas-stubs = "*"
+validate-pyproject = ">=0.25,<0.26"
+
+[tool.pixi.feature.usage.dependencies]
+matplotlib = "*"
+numpy = "*"
+scipy = "*"
+ipython = ">=9.16.1,<10"
+jupyter = ">=1.1.1,<2"
+notebook = ">=7.6.2,<8"
+ipykernel = ">=7.3.0,<8"
+anndata = ">=0.13.2,<0.14"
+nbstripout = ">=0.9.1,<0.10"
+
+[dependency-groups]
+usage = ["pydeseq2"]