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‎AUTHORS.md

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# Credits
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## Development Leads
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* Kyle Niemeyer <[email protected]>
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* Parker Clayton <[email protected]>
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## Contributors
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None yet. Why not be the first?

‎CHANGELOG.md

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# Change Log
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All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](http://keepachangelog.com/)
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and this project adheres to [Semantic Versioning](http://semver.org/).
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## [Unreleased]
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### Added
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-
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### Changed
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-
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### Fixed
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-
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## [0.0.1] - 2017-04-01
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### Added
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- Added preliminary project files (README, CODE_OF_CONDUCT, etc.) without any
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actual source code
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[Unreleased]: https://github.com/Niemeyer-Research-Group/pyMARS/compare/v0.1.0...HEAD
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[0.1.0]: https://github.com/Niemeyer-Research-Group/pyMARS/compare/v0.0.1...v0.1.0

‎CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to making participation in our project and
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our community a harassment-free experience for everyone, regardless of age, body
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size, disability, ethnicity, gender identity and expression, level of experience,
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nationality, personal appearance, race, religion, or sexual identity and
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orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment
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include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or
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advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic
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address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or
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reject comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct, or to ban temporarily or
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permanently any contributor for other behaviors that they deem inappropriate,
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threatening, offensive, or harmful.
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## Scope
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This Code of Conduct applies both within project spaces and in public spaces
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when an individual is representing the project or its community. Examples of
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representing a project or community include using an official project e-mail
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address, posting via an official social media account, or acting as an appointed
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representative at an online or offline event. Representation of a project may be
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further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting the project lead, @kyleniemeyer, at <[email protected]>. All
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complaints will be reviewed and investigated and will result in a response that
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is deemed necessary and appropriate to the circumstances. The project team is
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obligated to maintain confidentiality with regard to the reporter of an incident.
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Further details of specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
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available at [http://contributor-covenant.org/version/1/4][version]
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[homepage]: http://contributor-covenant.org
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[version]: http://contributor-covenant.org/version/1/4/

‎CONTRIBUTING.md

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# Contributing
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We welcome contributions in the form of bug reports, bug fixes, improvements to the documentation, ideas for enhancements, or the enhancements themselves!
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You can find a [list of current issues](https://github.com/Niemeyer-Research-Group/pyMARS/issues) in the project's GitHub repository. Feel free to tackle any existing bugs or enhancement ideas by submitting a [pull request](https://github.com/Niemeyer-Research-Group/pyMARS/pulls). Some issues are marked as `beginner-friendly`. These issues are a great place to start working with pyMARS, if you're new here.
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## Bug Reports
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* Please include a short (but detailed) Python snippet or explanation for reproducing the problem. Attach or include a link to any input files that will be needed to reproduce the error.
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* Explain the behavior you expected, and how what you got differed.
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* Include the full text of any error messages that are printed on the screen.
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## Pull Requests
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* If you're unfamiliar with Pull Requests, please take a look at the [GitHub documentation for them](https://help.github.com/articles/proposing-changes-to-a-project-with-pull-requests/).
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* **Make sure the test suite passes** on your computer, and that test coverage doesn't go down. To do this, run `pytest -vv --cov=./` from the top-level directory.
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* *Always* add tests and docs for your code.
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* The use of emoji in Pull Requests is encouraged with the format ":emoji: Commit summary". See [this list of suggested emoji.](https://github.com/slashsBin/styleguide-git-commit-message#suggested-emojis)
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* Please reference relevant GitHub issues in your commit messages using `GH123` or `#123`.
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* Changes should be [PEP8](https://www.python.org/dev/peps/pep-0008/) and [PEP257](https://www.python.org/dev/peps/pep-0257/) compatible.
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* Keep style fixes to a separate commit to make your pull request more readable.
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* Add your changes into the [`CHANGELOG`](https://github.com/Niemeyer-Research-Group/pyMARS/blob/master/CHANGELOG.md)
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* Docstrings are required and should follow the [Google style](http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
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* When you start working on a pull request, start by creating a new branch pointing at the latest commit on [GitHub master](https://github.com/Niemeyer-Research-Group/pyMARS/tree/master).
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* The copyright policy is detailed in the [`LICENSE`](https://github.com/Niemeyer-Research-Group/pyMARS/blob/master/LICENSE).
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## Meta
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Thanks to the useful [contributing guide of pyrk](https://github.com/pyrk/pyrk/blob/master/CONTRIBUTING.md), which served as an inspiration and starting point for this guide.

‎README.md

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pyMARS
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===============
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# pyMARS
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Python-based (chemical kinetic) Model Automatic Reduction Software (MARS), which consists of multiple techniques for reducing the size and complexity of detailed chemical kinetic models.
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See the following publications for more detail:
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* KE Niemeyer, CJ Sung, and MP Raju. Skeletal mechanism generation for surrogate fuels using directed relation graph with error propagation and sensitivity analysis. *Combust. Flame*, 157(9):1760--1770, 2010. doi:[10.1016/j.combustflflame.2009.12.022](http://dx.doi.org/10.1016/j.combustflflame.2009.12.022)
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* KE Niemeyer, CJ Sung, and MP Raju. Skeletal mechanism generation for surrogate fuels using directed relation graph with error propagation and sensitivity analysis. *Combust. Flame*, 157(9):1760--1770, 2010. doi:[10.1016/j.combustflflame.2009.12.022](http://dx.doi.org/10.1016/j.combustflflame.2009.12.022)
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* KE Niemeyer and CJ Sung. On the importance of graph search algorithms for DRGEP-based mechanism reduction methods. *Combust. Flame*, 158(8):1439--1443, 2011. doi:[10.1016/j.combustflflame.2010.12.010](http://dx.doi.org/10.1016/j.combustflflame.2010.12.010).
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* KE Niemeyer and CJ Sung. Mechanism reduction for multicomponent surrogates: A case study using toluene reference fuels. *Combust. Flame*, in press, 2014. doi:[10.1016/j.combustflame.2014.05.001](http://dx.doi.org/10.1016/j.combustflame.2014.05.001)
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* TF Lu and CK Law. *Combustion and Flame*, 154:153--163, 2008. doi:[10.1016/j.combustflame.2007.11.013](http://dx.doi.org/10.1016/j.combustflame.2007.11.013)
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Usage
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-----
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## Usage
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Options
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-------
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## Options
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License
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-------
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## License
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pyMARS is released under the MIT license, see LICENSE for details.
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If you use this package as part of a scholarly publication, please cite the following papers in addition to this resource:
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* KE Niemeyer, CJ Sung, and MP Raju. Skeletal mechanism generation for surrogate fuels using directed relation graph with error propagation and sensitivity analysis. *Combust. Flame*, 157(9):1760--1770, 2010. doi:[10.1016/j.combustflflame.2009.12.022](http://dx.doi.org/10.1016/j.combustflflame.2009.12.022)
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* KE Niemeyer, CJ Sung, and MP Raju. Skeletal mechanism generation for surrogate fuels using directed relation graph with error propagation and sensitivity analysis. *Combust. Flame*, 157(9):1760--1770, 2010. doi:[10.1016/j.combustflflame.2009.12.022](http://dx.doi.org/10.1016/j.combustflflame.2009.12.022)
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* KE Niemeyer and CJ Sung. On the importance of graph search algorithms for DRGEP-based mechanism reduction methods. *Combust. Flame*, 158(8):1439--1443, 2011. doi:[10.1016/j.combustflflame.2010.12.010](http://dx.doi.org/10.1016/j.combustflflame.2010.12.010).
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* KE Niemeyer and CJ Sung. Mechanism reduction for multicomponent surrogates: A case study using toluene reference fuels. *Combust. Flame*, in press, 2014. doi:[10.1016/j.combustflame.2014.05.001](http://dx.doi.org/10.1016/j.combustflame.2014.05.001)
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* KE Niemeyer and CJ Sung. Mechanism reduction for multicomponent surrogates: A case study using toluene reference fuels. *Combust. Flame*, in press, 2014. doi:[10.1016/j.combustflame.2014.05.001](http://dx.doi.org/10.1016/j.combustflame.2014.05.001)
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## Code of Conduct
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In order to have a more open and welcoming community, pyMARS adheres to a code of conduct adapted from the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
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Authors
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Kyle E. Niemeyer, Oregon State University
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[[email protected]](mailto:[email protected])
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Please adhere to this code of conduct in any interactions you have in the pyMARS community. It is strictly enforced on all official PyKED repositories, websites, and resources. If you encounter someone violating these terms, please let the project lead (@kyleniemeyer) know via email at <[email protected]>) know and we will address it as soon as possible.

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