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Installation on Windows
Combinato works well on Windows, but it is primarily developed for Linux. Combinato is organized as a set of command line tools, which is optimal for remote servers and shell scripting, but might be cumbersome on Windows computers.
So please consider using Combinato on Linux or MacOS. If you decide to use Windows, here are the instructions.
Any distribution of Python3 should work. We use Combinato with Anaconda for Windows.
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/refs/heads/main.zip
Save the repository to a convenient place, for example C:\Users\YourUsername\PythonCode.
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.
Go to the Combinato folder that you downloaded. Inside this folder is another folder called combinato. This inner Combinato folder has to be in the Python search path. The simplest way to achieve that is to move it to the site-packages, for example C:\Users\YourUsername\Anaconda\Lib\site-packages.
- Open a new shell
- Navigate to the Combinato repository (in our example
C:\Users\YourUsername\PythonCode). - 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.
In Windows, you cannot simply run the scripts named css-*, but you have to prepend python to each command. For example, to run css-simple-clustering, enter
python css-simple-clustering,
or, if the current directory of your command prompt is different from the Combinato repository (this will almost always be the case!),
python C:\Path\To\Combinato\css-simple-clustering.
This is cumbersome, and this problem does not exist with Linux and MacOS. See the FAQ to learn why Combinato is made this way.
In case of any errors, feel free to contact me (Johannes) at [email protected].