Installer for Linux

[mfitzp]

Currently it's not possible to install Pathomx on Linux. This is largely due to the fact that most Linux distributions ship PyQt5 for Python3 only. Switching to Python3 is planned however there are a number of dependent libraries that don't currently support it (e.g. nmrglue).

It would be easier to support this if we were using a plugin system (e.g. distutils) that didn't require us to ship the dependencies of our plugins with our core code.

[mfitzp]

As described in #12 support for Python 3 is now in master. Building using cx_Freeze for binary debs to be attempted.

[pbandyop]

I think Linux support is very essential for this tool to get popular. What possibilities are currently available for linux users?

[mfitzp]

@pbandyop At the moment it works on Linux using apt-get to install all the dependent packages + pip install to install Pathomx from PyPi. But that's a bit more complicated than I would like.

There was an issue in that it depended on PyQt5 which on Ubuntu is only on Python 3 - which limits access to some packages. But as of last week it now runs on PyQt4 too.

There are tools available to bundle Python apps into a source .deb file so that would be the route to go - but I'm currently focused on getting v3 (based on IPython) releasable.

If you can help with this in any way that would be great!

[mfitzp]

The current install documentation is here: http://docs.pathomx.org/en/latest/dev_install.html#linux

If you're using Python 2.7 you should be able to just replace all the python3- names with python- and pip3 with pip. If you have any problems let me know and I'll update the documentation.

[PhE]

So if I get it right, the preferred install method for Linux dev is using Python 2.7 ant NOT Python3 ?

[mfitzp]

Quite the opposite! Python3 is recommended for Linux assuming all the necessary packages are available for that. I currently develop on 2.7 but am in the process of migrating my system to python3. The next full release will be python3 only.

@PhE Just to confirm I've tested the latest code with Python (+Qt5+PyQt5) and it works fine.

[joshlk]

Any update regarding an installer for Linux (Ubuntu)?

[mfitzp]

Hey @joshlk thanks for your interest. I stopped developing Pathomx after taking a postdoctoral research position in a different field (proteomics rather that metabolomics). However I think Pathomx (or something derived from it) has potential as a general data analysis platform -- moving away from copy-paste Excel hacking.

My current contract ends in October after which point I'll be picking this up again full time. I expect to be doing some maintenance/restructuring in the meantime. If you would be interested in helping to develop custom tools for your own use-cases that would be fantastic.

[joshlk]

Hi @mfitzp thanks for the reply. The project looks really interesting and I would definitely would find it useful. Unfortunately I don't have any time at the moment to help in the development. I will keep a watchful eye on the project 😃