https://github.com/climdyn/auto-auto
An AUTO-07p automatic search algorithm codebase
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Published in Journal of Open Source Software
Repository
An AUTO-07p automatic search algorithm codebase
Basic Info
- Host: GitHub
- Owner: Climdyn
- License: mit
- Language: Python
- Default Branch: main
- Size: 4.01 MB
Statistics
- Stars: 4
- Watchers: 1
- Forks: 0
- Open Issues: 6
- Releases: 5
Metadata Files
README.md
auto-AUTO (or AUTO²)
General Information
AUTO² or auto-AUTO is an AUTO 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
- perform these computations in Jupyter notebooks
About
(c) 2025 Jonathan Demaeyer and Oisín Hamilton.
See LICENSE.txt for license information.
Please consult the auto-AUTO code repository for updates.
Installation
Installing AUTO
To use auto-AUTO, you need the bleeding edge version of AUTO 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. 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.
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
Tests are available. Simply run
python -m pytest --nbmake "./notebooks/auto-demos"
to check your installation.
You can also test yourself the Jupyter notebooks present in the notebooks folder. 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.
The documentation is also available online at https://climdyn.github.io/auto-AUTO .
Forthcoming developments
- Regime diagrams object
- Graph theory based construction of the bifurcation trees
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.
Owner
- Name: RMIB - Dynamical Meteorology and Climatology
- Login: Climdyn
- Kind: organization
- Location: Brussels, Belgium
- Website: http://climdyn.meteo.be
- Repositories: 3
- Profile: https://github.com/Climdyn
The Dynamical Meteorology and Climatology Unit is part of the R&D Department of the Royal Meteorological Institute of Belgium.
JOSS Publication
auto-AUTO: A Python Layer for Automatically Running the AUTO-07p Continuation Software
Authors
Meteorological and Climatological Information Service, Royal Meteorological Institute of Belgium, Brussels, Belgium
Meteorological and Climatological Information Service, Royal Meteorological Institute of Belgium, Brussels, Belgium, UCLouvain --- Earth and Life Institute, Belgium
Editor
Daniel S. Katz
Tags
Bifurcation Analysis Continuation Dynamical SystemsGitHub Events
Total
- Create event: 15
- Issues event: 10
- Release event: 5
- Watch event: 4
- Delete event: 11
- Issue comment event: 18
- Public event: 1
- Push event: 66
- Pull request review event: 3
- Pull request event: 20
- Fork event: 1
Last Year
- Create event: 15
- Issues event: 10
- Release event: 5
- Watch event: 4
- Delete event: 11
- Issue comment event: 18
- Public event: 1
- Push event: 66
- Pull request review event: 3
- Pull request event: 20
- Fork event: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 9
- Total pull requests: 10
- Average time to close issues: N/A
- Average time to close pull requests: about 15 hours
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.5
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 9
- Pull requests: 10
- Average time to close issues: N/A
- Average time to close pull requests: about 15 hours
- Issue authors: 3
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.5
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jodemaey (6)
- lockwo (1)
- epspebble (1)
Pull Request Authors
- jodemaey (10)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 50 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
pypi.org: auto-auto
An AUTO-07p automatic search algorithm codebase
- Documentation: https://auto-auto.readthedocs.io/
- 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.
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Latest release: 0.5.4
published 6 months ago
Rankings
Maintainers (1)
Dependencies
- ipython *
- jupyter *
- matplotlib >=3.4
- numba *
- numpy *
- scipy *
- sphinxcontrib-bibtex *