| Name | wakeflow JSON |
| Version |
1.4.0
JSON |
| download |
| home_page | https://github.com/TomHilder/wakeflow |
| Summary | Generate and manipulate semi-analytic models of planet wakes |
| upload_time | 2023-06-02 07:37:25 |
| maintainer | |
| docs_url | None |
| author | Thomas Hilder |
| requires_python | >=3.6 |
| license | MIT License Copyright (c) 2022 Thomas Hilder 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. |
| keywords |
astronomy
astrophysics
research
protoplanets
analytic
modelling
planet wake
protoplanetary
discs
disks
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
<div id="top"></div>
<!-- PROJECT SHIELDS -->
[![PyPI Package][pypi-shield]][pypi-url]
[![Python][python-shield]][python-url]
[![License][license-shield]][license-url]
[![JOSS][JOSS-shield]][JOSS-url]
[![Docs][docs-status-shield]][docs-status-url]
<!-- PROJECT LOGO -->
<br />
<div align="center">
<a href="https://github.com/TomHilder/wakeflow">
<img src="https://github.com/TomHilder/wakeflow/blob/master/logo.png?raw=true" alt="Logo" width="500" height="500">
</a>
<!-- <h3 align="center">Wakeflow</h3> -->
<p align="center">
Generate and manipulate semi-analytic models of planet wakes
<br />
<br />
<a href="https://wakeflow.readthedocs.io/en/latest/tutorials/quickstart.html"><strong>Quickstart tutorial »</strong></a>
<br />
<a href="https://wakeflow.readthedocs.io/en/latest/index.html"><strong>Documentation »</strong></a>
<br />
</p>
</div>
<!-- ABOUT THE PROJECT -->
# Overview
`wakeflow` is a Python package primarily for calculating tidally-induced perturbations resulting from a planet embedded in a gas disk. It is an implementation of both the linear theory for planet wake generation ([Goldreich and Tremaine 1979](https://ui.adsabs.harvard.edu/abs/1979ApJ...233..857G)) and the non-linear theory of wake propagation ([Rafikov 2002](https://ui.adsabs.harvard.edu/abs/2002ApJ...569..997R/abstract)) in 2D. `wakeflow` lets you generate these models by specifying disk and system properties as typically parameterised in the planet formation literature. It also contains additional tools allowing you to:
* Visualise your results
* Create 3D models under some assumptions
* Interface directly with the radiative transfer code [`MCFOST`](https://github.com/cpinte/mcfost) to generate synthetic images of these models
* (Planned) Rotate and project your models to create line-of-sight maps of velocity perturbations at some emitting layer
* (Planned) Create analytic predictions for peak velocity maps as found in [Calcino et al. 2022](https://ui.adsabs.harvard.edu/abs/2022ApJ...929L..25C/abstract)
`wakeflow` is intended to allow both theorists and observers to easily generate models of the interaction between disks and embedded planets, instead of having to run expensive fluid simulations. In particular, `wakeflow` allows researchers to easily test whether a planet can explain kinematic perturbations observed in some set of disk observations, so-called _velocity kinks_ (see for example [Pinte et al. 2018](https://ui.adsabs.harvard.edu/abs/2018ApJ...860L..13P/abstract)). `wakeflow` therefore also allows for a fast exploration of disk and planet parameters in order to determine those most likely to recreate observations, before resources are spent on 3D simulations. In addition, `wakeflow` models may be used with [`MCFOST`](https://github.com/cpinte/mcfost) to create synthetic images that may be compared directly with observations.
<p align="right">(<a href="#top">back to top</a>)</p>
<!-- GETTING STARTED -->
## Installation
`wakeflow` may be most easily installed from the Python Package Index ([PyPI](https://pypi.org/project/wakeflow/)), or can also be installed from the [GitHub repository](https://github.com/TomHilder/wakeflow) if you wish to make contributions. Dependencies for `wakeflow` consist mostly of standard python libraries. We recommend using a package manager such as [Anaconda](https://www.anaconda.com/products/distribution) to make your life easier, but this is not required.
### PyPI (pip)
The easiest way to install `wakeflow` is via [PyPI](https://pypi.org/project/wakeflow/), using `pip`:
```sh
pip install wakeflow
```
that's it!
### From source (GitHub)
If you want to contribute to, or modify `wakeflow`, you should install it from the [GitHub repository](https://github.com/TomHilder/wakeflow). After installing the dependencies (see below), simply fork the repo using the button in the top right, and then clone it:
```sh
git clone https://github.com/<replace-by-your-username>/wakeflow.git
```
Alternatively, you may install from source even if you do not wish to edit `wakeflow`, in which case I would recommend skipping the fork and simply cloning the repo directly:
```sh
git clone https://github.com/TomHilder/wakeflow.git
```
Navigate to the directory it is installed in:
```sh
cd wakeflow
```
You can verify that you are in the correct directory by checking that you see `README.md` when you run:
```sh
ls
```
Now we use `pip` to create a local and _editable_ install of `wakeflow`:
```sh
python -m pip install -e .
```
Do not forget the dot (.) in the above command, as it tells `pip` to look in the current working directory (where `wakeflow` is). The advantage of installing this way is that it places a _link_ to `wakeflow` in your `site-packages` folder instead of _moving_ it there. Now when you edit the code in `wakeflow/src/wakeflow/` it will edit your installation!
<p align="right">(<a href="#top">back to top</a>)</p>
### Dependencies
Python packages:
* `numpy`
* `matplotlib`
* `astropy`
* `scipy`
* `setuptools`
* `pyyaml`
* `tqdm`
* `pytest` (optional)
* `pytest-cov` (optional)
* [`pymcfost`](https://github.com/cpinte/pymcfost) (optional, only if interfacing with [MCFOST](https://github.com/cpinte/mcfost))
If you install `wakeflow` using `pip` then the required dependencies will be automatically installed.
<!-- USAGE EXAMPLES -->
## Usage
Please refer to the [Quickstart tutorial](https://wakeflow.readthedocs.io/en/latest/tutorials/quickstart.html) for the most typical usage of `wakeflow` including generating models and reading the results. Additional examples of more advanced usage can be found in the [Documentation](https://wakeflow.readthedocs.io/en/latest/index.html).
<p align="right">(<a href="#top">back to top</a>)</p>
<!-- USAGE EXAMPLES -->
## Testing
`wakeflow` is automatically unit-tested on Github using Actions and [`tox`](https://github.com/tox-dev/tox). If you have installed `wakeflow` from source, you may run a local test on your machine provided that you have `pytest` and `pytest-cov` installed. Simply navigate to your installation directory and run:
```sh
pytest
```
<!-- CONTRIBUTING -->
## Contributing
Contributions to `wakeflow` are welcome. If you would like to implement a new feature, please:
1. Install using the above installation from source instructions
2. Create your Feature Branch (`git checkout -b feature/NewFeature`)
3. Commit your Changes (`git commit -m 'Added some NewFeature'`)
4. Push to the Branch (`git push origin feature/NewFeature`)
5. Open a Pull Request
If you have a suggestion that would improve `wakeflow` but do not have the time or means to implement it yourself, please simply open an issue with the tag "enhancement". If you would like to report a bug, please open an issue with the tag "bug".
Don't forget to give the project a star!
<p align="right">(<a href="#top">back to top</a>)</p>
<!-- LICENSE -->
## License
Distributed under the MIT License. See `LICENSE.txt` for more information.
<p align="right">(<a href="#top">back to top</a>)</p>
<!-- CITATION -->
## Citing
Please cite [Hilder et al. (2023)](https://joss.theoj.org/papers/10.21105/joss.04863) and [Bollati et al. (2021)](https://ui.adsabs.harvard.edu/abs/2021MNRAS.504.5444B/abstract) in any work where `wakeflow` has been used. Please contact us if `wakeflow` is useful to you, we welcome any collaboration opportunities.
<p align="right">(<a href="#top">back to top</a>)</p>
<!-- CONTACT -->
## Getting Help
If you are experiencing issues with `wakeflow`, please try the following:
1. Check the [documentation](https://wakeflow.readthedocs.io/en/latest/index.html) to see if it may be easily resolved
2. Open an [issue](https://github.com/TomHilder/wakeflow/issues) on the [repository](https://github.com/TomHilder/wakeflow)
3. Feel free to contact us directly using the details below
<!-- CONTACT -->
## Contact
If you are having difficulties installing or using `wakeflow`, please let us know! We are happy to answer any questions or provide assistance.
Thomas Hilder - thil0004@student.monash.edu
Project Link: [https://github.com/TomHilder/wakeflow](https://github.com/TomHilder/wakeflow)
<p align="right">(<a href="#top">back to top</a>)</p>
<!-- ACKNOWLEDGMENTS -->
## Acknowledgments
`wakeflow` is based on the semi-analytic theory of planets wakes described in [Rafikov (2002)](https://iopscience.iop.org/article/10.1086/339399) and [Bollati et al. (2021)](https://academic.oup.com/mnras/article-abstract/504/4/5444/6255419). The code is partially adapted from `analytical kinks` which was written by Francesco Bollati, Daniele Fasano and Thomas Hilder, and can be found [here](https://github.com/DanieleFasano/Analytical_Kinks).
Additional acknowledgements:
* [Img Shields](https://shields.io)
* [Best-README-Template](https://github.com/othneildrew/Best-README-Template)
* [Tox](https://github.com/tox-dev/tox)
* [Tox GH Actions](https://github.com/ymyzk/tox-gh-actions)
<p align="right">(<a href="#top">back to top</a>)</p>
<!-- MARKDOWN LINKS & IMAGES -->
<!-- https://www.markdownguide.org/basic-syntax/#reference-style-links -->
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"description": "<div id=\"top\"></div>\n\n<!-- PROJECT SHIELDS -->\n[![PyPI Package][pypi-shield]][pypi-url]\n[![Python][python-shield]][python-url]\n[![License][license-shield]][license-url]\n[![JOSS][JOSS-shield]][JOSS-url]\n\n\n\n[![Docs][docs-status-shield]][docs-status-url]\n\n\n<!-- PROJECT LOGO -->\n<br />\n<div align=\"center\">\n <a href=\"https://github.com/TomHilder/wakeflow\">\n <img src=\"https://github.com/TomHilder/wakeflow/blob/master/logo.png?raw=true\" alt=\"Logo\" width=\"500\" height=\"500\">\n </a>\n\n\n\n<!-- <h3 align=\"center\">Wakeflow</h3> -->\n\n <p align=\"center\">\n Generate and manipulate semi-analytic models of planet wakes\n <br />\n <br />\n <a href=\"https://wakeflow.readthedocs.io/en/latest/tutorials/quickstart.html\"><strong>Quickstart tutorial \u00bb</strong></a>\n <br />\n <a href=\"https://wakeflow.readthedocs.io/en/latest/index.html\"><strong>Documentation \u00bb</strong></a>\n <br />\n </p>\n</div>\n\n\n<!-- ABOUT THE PROJECT -->\n# Overview\n\n`wakeflow` is a Python package primarily for calculating tidally-induced perturbations resulting from a planet embedded in a gas disk. It is an implementation of both the linear theory for planet wake generation ([Goldreich and Tremaine 1979](https://ui.adsabs.harvard.edu/abs/1979ApJ...233..857G)) and the non-linear theory of wake propagation ([Rafikov 2002](https://ui.adsabs.harvard.edu/abs/2002ApJ...569..997R/abstract)) in 2D. `wakeflow` lets you generate these models by specifying disk and system properties as typically parameterised in the planet formation literature. It also contains additional tools allowing you to:\n* Visualise your results\n* Create 3D models under some assumptions\n* Interface directly with the radiative transfer code [`MCFOST`](https://github.com/cpinte/mcfost) to generate synthetic images of these models\n* (Planned) Rotate and project your models to create line-of-sight maps of velocity perturbations at some emitting layer\n* (Planned) Create analytic predictions for peak velocity maps as found in [Calcino et al. 2022](https://ui.adsabs.harvard.edu/abs/2022ApJ...929L..25C/abstract)\n\n\n`wakeflow` is intended to allow both theorists and observers to easily generate models of the interaction between disks and embedded planets, instead of having to run expensive fluid simulations. In particular, `wakeflow` allows researchers to easily test whether a planet can explain kinematic perturbations observed in some set of disk observations, so-called _velocity kinks_ (see for example [Pinte et al. 2018](https://ui.adsabs.harvard.edu/abs/2018ApJ...860L..13P/abstract)). `wakeflow` therefore also allows for a fast exploration of disk and planet parameters in order to determine those most likely to recreate observations, before resources are spent on 3D simulations. In addition, `wakeflow` models may be used with [`MCFOST`](https://github.com/cpinte/mcfost) to create synthetic images that may be compared directly with observations. \n\n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n\n\n\n<!-- GETTING STARTED -->\n## Installation\n\n`wakeflow` may be most easily installed from the Python Package Index ([PyPI](https://pypi.org/project/wakeflow/)), or can also be installed from the [GitHub repository](https://github.com/TomHilder/wakeflow) if you wish to make contributions. Dependencies for `wakeflow` consist mostly of standard python libraries. We recommend using a package manager such as [Anaconda](https://www.anaconda.com/products/distribution) to make your life easier, but this is not required.\n\n\n\n\n### PyPI (pip)\n\nThe easiest way to install `wakeflow` is via [PyPI](https://pypi.org/project/wakeflow/), using `pip`:\n```sh\npip install wakeflow\n```\nthat's it!\n\n\n\n### From source (GitHub)\n\nIf you want to contribute to, or modify `wakeflow`, you should install it from the [GitHub repository](https://github.com/TomHilder/wakeflow). After installing the dependencies (see below), simply fork the repo using the button in the top right, and then clone it:\n```sh\ngit clone https://github.com/<replace-by-your-username>/wakeflow.git\n```\nAlternatively, you may install from source even if you do not wish to edit `wakeflow`, in which case I would recommend skipping the fork and simply cloning the repo directly:\n```sh\ngit clone https://github.com/TomHilder/wakeflow.git\n```\nNavigate to the directory it is installed in:\n```sh\ncd wakeflow\n```\nYou can verify that you are in the correct directory by checking that you see `README.md` when you run:\n```sh\nls\n```\nNow we use `pip` to create a local and _editable_ install of `wakeflow`:\n```sh\npython -m pip install -e .\n```\nDo not forget the dot (.) in the above command, as it tells `pip` to look in the current working directory (where `wakeflow` is). The advantage of installing this way is that it places a _link_ to `wakeflow` in your `site-packages` folder instead of _moving_ it there. Now when you edit the code in `wakeflow/src/wakeflow/` it will edit your installation!\n\n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n\n\n\n### Dependencies\n\nPython packages:\n\n* `numpy`\n* `matplotlib`\n* `astropy`\n* `scipy`\n* `setuptools`\n* `pyyaml`\n* `tqdm`\n* `pytest` (optional)\n* `pytest-cov` (optional)\n* [`pymcfost`](https://github.com/cpinte/pymcfost) (optional, only if interfacing with [MCFOST](https://github.com/cpinte/mcfost))\n\nIf you install `wakeflow` using `pip` then the required dependencies will be automatically installed.\n\n\n\n<!-- USAGE EXAMPLES -->\n## Usage\n\nPlease refer to the [Quickstart tutorial](https://wakeflow.readthedocs.io/en/latest/tutorials/quickstart.html) for the most typical usage of `wakeflow` including generating models and reading the results. Additional examples of more advanced usage can be found in the [Documentation](https://wakeflow.readthedocs.io/en/latest/index.html).\n\n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n\n\n<!-- USAGE EXAMPLES -->\n## Testing\n\n`wakeflow` is automatically unit-tested on Github using Actions and [`tox`](https://github.com/tox-dev/tox). If you have installed `wakeflow` from source, you may run a local test on your machine provided that you have `pytest` and `pytest-cov` installed. Simply navigate to your installation directory and run:\n```sh\npytest\n```\n\n\n<!-- CONTRIBUTING -->\n## Contributing\n\nContributions to `wakeflow` are welcome. If you would like to implement a new feature, please:\n\n1. Install using the above installation from source instructions\n2. Create your Feature Branch (`git checkout -b feature/NewFeature`)\n3. Commit your Changes (`git commit -m 'Added some NewFeature'`)\n4. Push to the Branch (`git push origin feature/NewFeature`)\n5. Open a Pull Request\n\nIf you have a suggestion that would improve `wakeflow` but do not have the time or means to implement it yourself, please simply open an issue with the tag \"enhancement\". If you would like to report a bug, please open an issue with the tag \"bug\".\n\nDon't forget to give the project a star!\n\n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n\n\n\n<!-- LICENSE -->\n## License\n\nDistributed under the MIT License. See `LICENSE.txt` for more information.\n\n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n\n\n\n<!-- CITATION -->\n## Citing\n\nPlease cite [Hilder et al. (2023)](https://joss.theoj.org/papers/10.21105/joss.04863) and [Bollati et al. (2021)](https://ui.adsabs.harvard.edu/abs/2021MNRAS.504.5444B/abstract) in any work where `wakeflow` has been used. Please contact us if `wakeflow` is useful to you, we welcome any collaboration opportunities.\n\n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n\n\n\n<!-- CONTACT -->\n## Getting Help\n\nIf you are experiencing issues with `wakeflow`, please try the following:\n\n1. Check the [documentation](https://wakeflow.readthedocs.io/en/latest/index.html) to see if it may be easily resolved\n2. Open an [issue](https://github.com/TomHilder/wakeflow/issues) on the [repository](https://github.com/TomHilder/wakeflow)\n3. Feel free to contact us directly using the details below\n\n\n<!-- CONTACT -->\n## Contact\n\nIf you are having difficulties installing or using `wakeflow`, please let us know! We are happy to answer any questions or provide assistance. \n\nThomas Hilder - thil0004@student.monash.edu\n\nProject Link: [https://github.com/TomHilder/wakeflow](https://github.com/TomHilder/wakeflow)\n\n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n\n\n\n<!-- ACKNOWLEDGMENTS -->\n## Acknowledgments\n\n`wakeflow` is based on the semi-analytic theory of planets wakes described in [Rafikov (2002)](https://iopscience.iop.org/article/10.1086/339399) and [Bollati et al. (2021)](https://academic.oup.com/mnras/article-abstract/504/4/5444/6255419). The code is partially adapted from `analytical kinks` which was written by Francesco Bollati, Daniele Fasano and Thomas Hilder, and can be found [here](https://github.com/DanieleFasano/Analytical_Kinks).\n\nAdditional acknowledgements:\n* [Img Shields](https://shields.io)\n* [Best-README-Template](https://github.com/othneildrew/Best-README-Template)\n* [Tox](https://github.com/tox-dev/tox)\n* [Tox GH Actions](https://github.com/ymyzk/tox-gh-actions)\n\n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n\n\n\n<!-- MARKDOWN LINKS & IMAGES -->\n<!-- https://www.markdownguide.org/basic-syntax/#reference-style-links -->\n[pypi-shield]: https://img.shields.io/badge/pypi-1.4.0-green?style=flat-square\n[pypi-url]: https://pypi.org/project/wakeflow/\n[python-shield]: https://img.shields.io/badge/python-3.6%2B-orange?style=flat-square\n[python-url]: https://www.python.org\n[license-shield]: https://img.shields.io/badge/license-MIT-blue?style=flat-square\n[license-url]: https://opensource.org/licenses/MIT\n[JOSS-shield]: https://img.shields.io/badge/JOSS-10.21105/joss.04863-brightgreen?style=flat-square\n[JOSS-url]: https://joss.theoj.org/papers/22d35f9b0bb35a8df4dab85b0b6f4eb7\n[test-status-shield]: https://img.shields.io/github/actions/workflow/status/TomHilder/wakeflow/Tests.yml?label=tests&style=flat-square\n[test-status-url]: https://github.com/TomHilder/wakeflow/actions/workflows/Tests.yml\n[docs-status-shield]: https://readthedocs.org/projects/wakeflow/badge/?version=latest&style=flat-square\n[docs-status-url]: https://wakeflow.readthedocs.io/en/latest/?badge=latest\n",
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