Version 0.1.0

.coveragerc

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+# .coveragerc
+
+[run]
+source = qspy
+
+[report]
+omit =
+    */tests/*
+    */site-packages/*

CHANGELOG.md

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+# Change Log
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/)
+and this project adheres to [Semantic Versioning](http://semver.org/).
+
+## [0.1.0] - 2025-07-03
+
+### Added
+- Initial development version of the package, prepared for release.
+
+------
+
+## Entry format
+
+## [Unreleased] - yyyy-mm-dd
+
+N/A
+
+### Added
+
+### Changed
+
+### Fixed

CODE_OF_CONDUCT.md

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+
+# Contributor Covenant Code of Conduct
+
+[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md) 
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+- Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+- The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[INSERT CONTACT METHOD].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the
+[Contributor Covenant](https://www.contributor-covenant.org/), version 2.1,
+available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct/>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/inclusion).
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq/>. Translations are available at
+<https://www.contributor-covenant.org/translations/>.
+

CONTRIBUTING.md

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+# Before getting started
+
+Thank you for contributing! Bug reports, feature requests, bug fixes or other contributions are all welcomed. 
+
+## Coding conventions
+
+GitHub is used to host code, track issues, and accept pull requests. This project uses [semantic versioning](https://semver.org/) and keeps a [CHANGELOG](./CHANGELOG.md). Google style docstrings are used, and [Ruff formatting](https://docs.astral.sh/ruff/formatter/) is applied to code. For new functions, it is requested that type annotations be included in the function definition.    
+
+
+# How to contribute
+
+
+## Issues
+
+One great non-code way to contribute is to open an issue. 
+
+### Types of Issues
+
+Here are the different types of Issues you can contribute:
+
+  * :bug: **Bug Reports**: Problem, errors, or other issues where the code is not working as expected. Please use the `bug` label. 
+  * :bulb: **Feauture Request/Suggestion**: Request or suggest some new functionality or an update/change to existing functionality. Please use the `enhancement` label.
+
+### Creating a new issue
+
+You can open issues here: [https://github.com/Borealis-BioModeling/qspy/issues](https://github.com/Borealis-BioModeling/qspy/issues). 
+
+However, before creating a new issue, please check the existing issues first to see if your issue or a similar one has already been raised. If it has, please add a comment to the existing issue rather than creating a new duplicate issue; e.g., with a bug report commenting with something like "I am also experiencing this problem" along with any additional context about your specific environment and package versions should suffice. 
+
+For all Bug Report issues, please provide context, including the environment and relevant package versions, code snippets for the offending code/use when applicable, a description of the expected outcome, and the actual outcome with associated error messages when applicable. 
+
+ ### Support
+
+If you have support questions you can email them to [blakeaw1102@gmail.com](mailto:blakeaw1102@gmail.com)
+
+## Pull Requests
+
+If you want to contribute code that fixes bugs or adds new features you can fork the repository and open a pull request as described below. 
+
+However, before doing so, please ask first. You can do so by commenting on the relevant Issue. This helps prevent duplicated or wasted efforts. 
+
+Note that for automated testing and coverage analysis requires the following:
+[pytest](https://docs.pytest.org/en/stable/getting-started.html), [Coverage.py](https://coverage.readthedocs.io/en/7.6.10/install.html), and [nose](https://nose.readthedocs.io/en/latest/).
+```
+pip install pytest coverage nose
+```
+
+PR contribution steps:
+
+1. [Fork the repo](https://github.com/Borealis-BioModeling/qspy/fork)
+2. Create a new branch, e.g.:
+   * **Bug Fix:** `fix/issue-number`, e.g. `fix/11`
+   * **New Feature** `feature/new-feature`, e.g. `feature/foo-bar`   
+3. For feature additions, please include additional tests for the new feature.
+4. Run all the tests using pytest: `python -m pytest` - or also with coverage (Coverage.py) analysis: `coverage run -m pytest`
+5. Once your branch passes all the tests, commit your changes, e.g. `git commit -am 'Add the new-feature feature.'`
+7. Push the branch to your fork, e.g. `git push origin feature/new-feature`
+8. Create a new [Pull request](https://github.com/Borealis-BioModeling/qspy/pulls). Reference any relevant Issues in the PR description.
+
+Please note that any code contributions will be licensed according to this project's [LICENSE](./LICENSE).  
+
+## Code of Conduct
+
+All contributions will be considered based solely on their quality and fit with the overall direction of the project.   
+
+All contributors are expected to be kind and respectful to one another. Behavior that is harmful to your fellow contributors is not acceptable. 

CONTRIBUTORS.md

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+# QSPy Contributors
+
+Thank you to everyone who has contributed to the success of this project!
+
+## Core Contributors
+
+*   **Blake A. Wilson** (@blakeaw) - Lead Developer, Project Maintainer
+
+## Valued Contributors
+
+*   **Your name could be here** (@contributor) - Bug fixes, Documentation improvements, etc.
+
+## Special Thanks
+
+*   **PySB Developers and Contributors** - QSPy is built on top of [PySB](https://pysb.org/), so wouldn't be possible without the hard work of PySB developers and contributors!