| Name | auto-AUTO JSON |
| Version |
0.5.2
JSON |
| download |
| home_page | None |
| Summary | An AUTO-07p automatic search algorithm codebase |
| upload_time | 2025-02-20 16:29:00 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | MIT License
Copyright (c) 2025 Jonathan Demaeyer and Oísin Hamilton
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 |
bifurcation
bifurcation analysis
auto
automation
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
auto-AUTO (or AUTO²)
====================
[](https://badge.fury.io/py/auto-auto)
[](https://pypi.org/project/auto-auto/)
[](https://doi.org/10.5281/zenodo.14901321)
[](https://auto-auto.readthedocs.io/en/latest/?badge=latest)
[](https://opensource.org/licenses/MIT)
General Information
-------------------
AUTO² or auto-AUTO is an [AUTO](https://github.com/auto-07p/auto-07p) automatic search algorithm codebase
to enhance the original AUTO-07p Python interface with a top layer which allows users to:
* automate the continuation of as many branches as possible, branching whenever possible to construct full
bifurcation trees, and finishing computations based on a predefined logic
(meeting other branches, looping branches, etc...)
* plot results with [Matplotlib](https://matplotlib.org)
* perform these computations in [Jupyter](https://jupyter.org) notebooks
About
-----
(c) 2025 Jonathan Demaeyer and Oísin Hamilton.
See [LICENSE.txt](https://raw.githubusercontent.com/Climdyn/auto-AUTO/master/LICENSE.txt) for license information.
Please consult the auto-AUTO [code repository](http://www.github.com/Climdyn/auto-AUTO) for updates.
Installation
------------
#### Installing AUTO
> To use auto-AUTO, you need the [bleeding edge version of AUTO](https://github.com/auto-07p/auto-07p) available
> on GitHub for this codebase to work properly !
Here how to install AUTO from GitHub:
First clone the AUTO repository somewhere:
git clone https://github.com/auto-07p/auto-07p.git
Then in a terminal, in the created folder, run:
./configure
make
Your AUTO installation should now be finished, but you still need to add the
following line to your `.bashrc` file:
source [path-to-auto-07p]/cmds/auto.env.sh
In addition, we recommend that you edit the file `auto.env.sh` so that the `AUTO_DIR` environment
variable specified there points to the correct folder where you installed AUTO.
> Be sure to have all the AUTO requirements pre-installed. See AUTO documentation for
> more details. In case of issues, we recommend reading the documentation completely.
After that last step, you should be able to launch AUTO in command line by typing:
auto
If it works, you will end up in the AUTO Python prompt.
It means you have AUTO properly configured and are ready to install auto-AUTO.
> If AUTO version is changing over time, you need to update the version from GitHub and do
> the installation again.
#### Installing auto-AUTO with pip
The easiest way to install and run qgs is to use [pip](https://pypi.org/).
Type in a terminal
pip install auto-AUTO
and you are set!
#### Installing auto-AUTO with Anaconda
The second-easiest way to install and run qgs is to use an appropriate
environment created through [Anaconda](https://www.anaconda.com/).
First install Anaconda and clone the repository:
git clone https://github.com/Climdyn/auto-AUTO.git
Then install and activate the Python3 Anaconda environment:
conda env create -f environment.yml
conda activate auto2
and the code is installed.
#### Testing the installation
You can test the Jupyter notebooks present in the
[notebooks folder](./notebooks).
For instance, running
conda activate auto2
cd notebooks
jupyter-notebook
will lead you to your favorite browser where you can load and run the examples.
Documentation
-------------
To build the documentation, please run (with the conda environment activated):
cd documentation
make html
Once built, the documentation is available [here](./documentation/build/html/index.html).
The documentation is also available online on read the docs: [https://auto-auto.readthedocs.io/](https://auto-auto.readthedocs.io/)
Forthcoming developments
------------------------
* Regime diagrams object
Contributing to auto-AUTO
-------------------------
If you want to contribute actively, please contact the main authors.
In addition, if you have made changes that you think will be useful to others, please feel free to suggest these as a pull request on the [auto-AUTO Github repository](https://github.com/Climdyn/auto-AUTO).
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"description": "\nauto-AUTO (or AUTO\u00b2)\n====================\n\n[](https://badge.fury.io/py/auto-auto)\n[](https://pypi.org/project/auto-auto/)\n[](https://doi.org/10.5281/zenodo.14901321)\n[](https://auto-auto.readthedocs.io/en/latest/?badge=latest)\n[](https://opensource.org/licenses/MIT)\n\nGeneral Information\n-------------------\n\nAUTO\u00b2 or auto-AUTO is an [AUTO](https://github.com/auto-07p/auto-07p) automatic search algorithm codebase\nto enhance the original AUTO-07p Python interface with a top layer which allows users to:\n\n* automate the continuation of as many branches as possible, branching whenever possible to construct full\n bifurcation trees, and finishing computations based on a predefined logic\n (meeting other branches, looping branches, etc...)\n* plot results with [Matplotlib](https://matplotlib.org)\n* perform these computations in [Jupyter](https://jupyter.org) notebooks\n\nAbout\n-----\n\n(c) 2025 Jonathan Demaeyer and O\u00edsin Hamilton. \n\nSee [LICENSE.txt](https://raw.githubusercontent.com/Climdyn/auto-AUTO/master/LICENSE.txt) for license information.\n\nPlease consult the auto-AUTO [code repository](http://www.github.com/Climdyn/auto-AUTO) for updates.\n\nInstallation\n------------\n\n#### Installing AUTO\n\n> To use auto-AUTO, you need the [bleeding edge version of AUTO](https://github.com/auto-07p/auto-07p) available \n> on GitHub for this codebase to work properly !\n\nHere how to install AUTO from GitHub:\n\nFirst clone the AUTO repository somewhere:\n\n git clone https://github.com/auto-07p/auto-07p.git\n\nThen in a terminal, in the created folder, run:\n\n ./configure\n make\n\nYour AUTO installation should now be finished, but you still need to add the \nfollowing line to your `.bashrc` file:\n\n source [path-to-auto-07p]/cmds/auto.env.sh\n\nIn addition, we recommend that you edit the file `auto.env.sh` so that the `AUTO_DIR` environment \nvariable specified there points to the correct folder where you installed AUTO.\n\n > Be sure to have all the AUTO requirements pre-installed. See AUTO documentation for \n> more details. In case of issues, we recommend reading the documentation completely.\n\nAfter that last step, you should be able to launch AUTO in command line by typing:\n\n auto\n\nIf it works, you will end up in the AUTO Python prompt.\nIt means you have AUTO properly configured and are ready to install auto-AUTO.\n\n> If AUTO version is changing over time, you need to update the version from GitHub and do\n> the installation again.\n\n#### Installing auto-AUTO with pip\n\nThe easiest way to install and run qgs is to use [pip](https://pypi.org/).\nType in a terminal\n\n pip install auto-AUTO\n\nand you are set!\n\n#### Installing auto-AUTO with Anaconda\n\nThe second-easiest way to install and run qgs is to use an appropriate \nenvironment created through [Anaconda](https://www.anaconda.com/).\n\nFirst install Anaconda and clone the repository:\n\n git clone https://github.com/Climdyn/auto-AUTO.git\n\nThen install and activate the Python3 Anaconda environment:\n\n conda env create -f environment.yml\n conda activate auto2\n\nand the code is installed. \n\n\n#### Testing the installation\n\nYou can test the Jupyter notebooks present in the \n[notebooks folder](./notebooks).\nFor instance, running\n\n conda activate auto2\n cd notebooks\n jupyter-notebook\n\nwill lead you to your favorite browser where you can load and run the examples.\n\nDocumentation\n-------------\n\nTo build the documentation, please run (with the conda environment activated):\n\n cd documentation\n make html\n\nOnce built, the documentation is available [here](./documentation/build/html/index.html).\n\nThe documentation is also available online on read the docs: [https://auto-auto.readthedocs.io/](https://auto-auto.readthedocs.io/)\n\nForthcoming developments\n------------------------\n\n* Regime diagrams object\n\nContributing to auto-AUTO\n-------------------------\n\nIf you want to contribute actively, please contact the main authors.\n\nIn addition, if you have made changes that you think will be useful to others, please feel free to suggest these as a pull request on the [auto-AUTO Github repository](https://github.com/Climdyn/auto-AUTO).\n",
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