Metadata-Version: 2.1
Name: pyked
Version: 0.4.2a1
Summary: Package for manipulating Chemical Kinetics Experimental Data (ChemKED) files.
Home-page: https://github.com/pr-omethe-us/PyKED
Author: Kyle Niemeyer
Author-email: kyle.niemeyer@gmail.com
License: BSD-3-Clause
Keywords: chemical kinetics
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: ~=3.5
Description-Content-Type: text/markdown
Provides-Extra: dataframes
License-File: LICENSE

# PyKED
<img src="logo/pyked-logo.png" align="right" width="150" />

[![DOI](https://zenodo.org/badge/66023863.svg)](https://zenodo.org/badge/latestdoi/66023863)
[![Travis Build Status](https://travis-ci.org/pr-omethe-us/PyKED.svg?branch=master)](https://travis-ci.org/pr-omethe-us/PyKED)
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[![codecov](https://codecov.io/gh/pr-omethe-us/PyKED/branch/master/graph/badge.svg)](https://codecov.io/gh/pr-omethe-us/PyKED)
[![Dependency Status](https://dependencyci.com/github/pr-omethe-us/PyKED/badge)](https://dependencyci.com/github/pr-omethe-us/PyKED)
[![Code of Conduct](https://img.shields.io/badge/code%20of%20conduct-contributor%20covenant-green.svg)](http://contributor-covenant.org/version/1/4/)
[![License](https://img.shields.io/badge/license-BSD-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
[![Anaconda-Server Badge](https://anaconda.org/pr-omethe-us/pyked/badges/version.svg)](https://anaconda.org/pr-omethe-us/pyked)

PyKED is a Python-based software package for validating and interacting with ChemKED (Chemical Kinetics Experimental Data format) files that describe fundamental experimental measurements of combustion phenomena.

An installation guide, usage examples, and API docs are provided in the online documentation: https://pr-omethe-us.github.io/PyKED/

## Code of Conduct

In order to have a more open and welcoming community, PyKED adheres to a code of conduct adapted from the [Contributor Covenant](http://contributor-covenant.org) code of conduct. The code of conduct for PyKED is available in the GitHub Repository  in the [CODE_OF_CONDUCT.md](https://github.com/pr-omethe-us/PyKED/blob/master/CODE_OF_CONDUCT.md) file.

Please adhere to this code of conduct in any interactions you have in the PyKED community. It is strictly enforced on all official PyKED repositories, websites, and resources. If you encounter someone violating these terms, please let a maintainer ([@kyleniemeyer](https://github.com/kyleniemeyer), [@bryanwweber](https://github.com/bryanwweber), or via email at chemked@googlegroups.com) know and we will address it as soon as possible.

## License

PyKED is released under the BSD-3 clause license, see [LICENSE](https://github.com/pr-omethe-us/PyKED/blob/master/LICENSE) for details.

If you use this package as part of a scholarly work, please refer to [CITATION.md](https://github.com/pr-omethe-us/PyKED/blob/master/CITATION.md) for guidance on citing this resource.


# 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/).

## [Unreleased]
### Added
- Add codemeta file

### Changed
- Directly use the Markdown formatting of the README on pypi, rather than converting to reST
- Remove unnecessary `orcid` package from the test environment
- Specify versions of all package dependencies
- Use pip to install package in conda build
- Composition type is included in the pandas data-frame resulting from `to_dataframe()`

### Fixed

## [0.4.1] - 2018-03-09
### Added
- Documentation for old versions is available on the Releases page of the docs

### Changed

### Fixed
- Doctr deploys on tags now
- Syntax changes for example files in the documentation

## [0.4.0] - 2018-03-07
### Added
- New method to instantiate a `ChemKED` class directly from a ReSpecTh XML file
- The `__version__` attribute can be imported from the top-level module
- New `time-histories` field to replace the `volume-history`. This field allows specification of several other relevant parameters besides volume.
- Added `rcm-data` field and moved `compressed-temperature`, `compressed-pressure`, and `compression-time` to this field
- Added `stroke`, `clearance`, and `compression-ratio` to the `rcm-data` field
- Added conda-forge instructions to the installation documentation
- Allow alpha versions to be specified during testing

### Changed
- Crossref lookups via Habanero now comply with the "be-nice" policy
- Removed `UnboundLocalError` from error processing for reference validation
- Switch to flake8 for style checking in CI services
- `file-author` field is now a list called `file-authors`
- ReSpecTh->ChemKED converter function now returns a dictionary, while the command-line entry points write out files
- Require Habanero>=0.6.0 to support the `mailto` argument
- Require pytest>=3.2.0 to support the `pytest.mark.filterwarnings` decorator
- Deprecate the `volume-history` field in the ChemKED YAML file and replace with `time-histories`
- ORCID lookups are now done by a function in the local `orcid.py` module, removing an external dependency
- Composition in a `DataPoint` is now stored in a dictionary of `namedtuple`s (called `Composition`) rather than a list of dictionaries

### Fixed
- Crossref lookups in the converters use the common API instance from validation
- `d/dt max extrapolated` ignition type can be converted to/from ReSpecTh
- Tests now check for appropriate warnings and ignore unrelated warnings

## [0.3.0] - 2017-10-09
### Added
- New extrapolated ignition type, where the maximum slope is extrapolated to the baseline
- Tests that the composition type is stored properly in the `DataPoint`
- `species_conversion` dictionary can be passed to the `get_cantera_mole_fraction` and `get_cantera_mass_fraction` functions to change the name of a species in the output string
- Jupyter Notebook examples of usage

### Removed
- Removes `elemental-composition` as a synonym for `atomic-composition`

### Fixed
- Fixes `test_incorrect_doi_period_at_end` docstring

### Changed
- Conda builds are now noarch - one package for all Pythons!
- pip installs now require Python compatible with 3.5
- Appveyor runs a single job and no longer builds conda packages
- Remove journal from required fields in the reference

## [0.2.1] - 2017-08-31
### Fixed
- Fixes Cantera convenience output functions

## [0.2.0] - 2017-08-10
### Added
- Adds ChemKED method to write new file, with tests
- Adds converters to and from ReSpecTh files, with tests
- Adds command-line entry points for converter scripts
- Add docs for converters

### Fixed
- `ignition_type` dictionary in `DataPoint` is now `deepcopy`d

## [0.1.6] - 2017-07-17
### Added
- Added logo files to repo
- Added `first_stage_ignition_delay`, `compressed_pressure`, and `compressed_temperature` as properties

### Changed
- Added Zenodo collection DOI to CITATION.md

## [0.1.5] - 2017-05-22
### Added
- Schema can now be split into multiple files via `!include` directive

### Fixed
- Remove Python 2.7 classifier from `setup.py`
- DataFrame output for datapoints lists with multiple compositions (i.e., a species not in all compositions)

### Changed
- Improved tests with no internet
- Improved tests with no warning

## [0.1.4] - 2017-04-21
### Added
- Add `skip_validation` keyword argument to the `ChemKED` initializer

### Removed
- Python 2.7 support is removed again

## [0.1.3] - 2017-04-13
### Added
- Add back Python 2.7 support
- Add Appveyor builds for Windows conda packages

## [0.1.2] - 2017-04-13
### Added
- Tests of the composition uncertainty in the DataPoint
- Tests of the values in the references
- Packaging for conda and PyPI
- Add Anaconda-Server badge to README

### Changed
- All fixed DOIs in CITATION.md are now specified with placeholders

## [0.1.1] - 2017-04-02
### Added
- Added Zenodo DOI badge to README
- Added CITATION file, and mention of license to README

### Fixed
- Fixed chemked-version bug in schema introduced in 0.1.0

## [0.1.0] - 2017-04-02
### Added
- First minor release of PyKED, supporting autoignition experiments.
- Basic API documentation is available via https://pr-omethe-us.github.io/PyKED/

[Unreleased]: https://github.com/pr-omethe-us/PyKED/compare/v0.4.0...HEAD
[0.4.1]: https://github.com/pr-omethe-us/PyKED/compare/v0.4.0...v0.4.1
[0.4.0]: https://github.com/pr-omethe-us/PyKED/compare/v0.3.0...v0.4.0
[0.3.0]: https://github.com/pr-omethe-us/PyKED/compare/v0.2.1...v0.3.0
[0.2.1]: https://github.com/pr-omethe-us/PyKED/compare/v0.2.0...v0.2.1
[0.2.0]: https://github.com/pr-omethe-us/PyKED/compare/v0.1.6...v0.2.0
[0.1.6]: https://github.com/pr-omethe-us/PyKED/compare/v0.1.5...v0.1.6
[0.1.5]: https://github.com/pr-omethe-us/PyKED/compare/v0.1.4...v0.1.5
[0.1.4]: https://github.com/pr-omethe-us/PyKED/compare/v0.1.3...v0.1.4
[0.1.3]: https://github.com/pr-omethe-us/PyKED/compare/v0.1.2...v0.1.3
[0.1.2]: https://github.com/pr-omethe-us/PyKED/compare/v0.1.1...v0.1.2
[0.1.1]: https://github.com/pr-omethe-us/PyKED/compare/v0.1.0...v0.1.1
[0.1.0]: https://github.com/pr-omethe-us/PyKED/compare/75ecf67766a0be2a80e2377391fd9eca420f152c...v0.1.0


# Citation of PyKED

[![DOI](https://zenodo.org/badge/66023863.svg)](https://zenodo.org/badge/latestdoi/66023863)

To cite PyKED in a scholarly article, please use

> K. E. Niemeyer and B. W. Weber. (2018) PyKED v0.4.1 [software]. Zenodo. https://doi.org/10.5281/zenodo.597935

A BibTeX entry for LaTeX users is

```TeX
@misc{PyKED,
    author = {Kyle E Niemeyer and Bryan W Weber},
    year = 2018,
    title = {PyKED v0.4.1},
    doi = {10.5281/zenodo.597935},
    url = {https://github.com/pr-omethe-us/PyKED},
}
```

In both cases, please update the entry with the version used. The DOI for the latest version is
given in the badge at the top, or alternately <https://doi.org/10.5281/zenodo.597935> will
take you to the latest version (and generally represents all versions).
If you would like to cite a specific, older version, the DOIs for each release are:

 * v0.4.1: [10.5281/zenodo.1194920](https://doi.org/10.5281/zenodo.1194920)
 * v0.4.0: [10.5281/zenodo.1193936](https://doi.org/10.5281/zenodo.1193936)
 * v0.3.0: [10.5281/zenodo.1006722](https://doi.org/10.5281/zenodo.1006722)
 * v0.2.1: [10.5281/zenodo.858441](https://doi.org/10.5281/zenodo.858441)
 * v0.2.0: [10.5281/zenodo.841303](https://doi.org/10.5281/zenodo.841303)
 * v0.1.6: [10.5281/zenodo.831332](https://doi.org/10.5281/zenodo.831332)
 * v0.1.5: [10.5281/zenodo.582345](https://doi.org/10.5281/zenodo.582345)
 * v0.1.4: [10.5281/zenodo.582338](https://doi.org/10.5281/zenodo.582338)
 * v0.1.3: [10.5281/zenodo.439720](https://doi.org/10.5281/zenodo.546143)
 * v0.1.2: [10.5281/zenodo.439720](https://doi.org/10.5281/zenodo.546141)
 * v0.1.1: [10.5281/zenodo.439720](https://doi.org/10.5281/zenodo.439720)
 * v0.1.0: [10.5281/zenodo.439716](https://doi.org/10.5281/zenodo.439716)
