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Installation on MacOS
Any distribution of Python 3should work. We use Combinato with Anaconda for MacOS.
You can download Anaconda from https://www.anaconda.com/products/individual.
Anaconda contains all packages that Combinato depends on (scipy, matplotlib, pytables, pywt, pyqt).
If you use git, clone the repository:
git clone https://github.com/jniediek/combinato.git
If you do not use git, download Combinato from https://github.com/jniediek/combinato/archive/master.zip.
Save the repository to a convenient place, for example
/Applications/anaconda/lib/python3.8/site-packages.
Combinato uses an executable file as backend for clustering. To automatically select the correct file for your operating system, navigate your shell to the Combinato repository and run
python setup_options.py.
Combinato is organized as a collection of executable scripts. These are the files named css-* in the repository's main folder. To be able to execute these scripts, add the repository's folder to your $PATH: The path is set in the file .bash_profile in your user directory. For example, this file should contain a line like
export PATH=$PATH:/Applications/anaconda/lib/python3.8/site-packages/combinato.
For some of the tools in the subdirectories signalviewer and tools, it is necessary to add the repository's folder to $PYTHONPATH as well.
- Open a new shell
- Navigate to the Combinato repository
- Enter
python tools/test_installation.py
In case everything worked, you will see the following output:
Found Combinato
Found SPC binary
Your version of pytables is 3.6.1
Combinato clustering setup: no problems detected.
Found display
Found 'montage', plotting continuous data possible.
If you see Plotting continuous data will not work, don't worry. This feature requires ImageMagick, but it is not crucial.
You are now ready to do the Combinato tutorial.
In case of any errors, feel free to contact me (Johannes) at [email protected].