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Future of MDAnalysis support in ESPResSo

From: Jean-Noël Grad
Subject: Future of MDAnalysis support in ESPResSo
Date: Tue, 31 May 2022 16:55:18 +0200
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Dear ESPResSo users,

The ESPResSo python interface currently provides bindings to the python package MDAnalysis. The 2.0 release of MDAnalysis came with significant API changes that broke the bindings.

ESPResSo still works with the 1.0 line of MDAnalysis, however that line is no longer officially maintained. The 1.0.0 release is no longer pip installable in Ubuntu 22.04 for some compiler toolchains, in which case one has to manually compile the package and work around 14 compiler warnings and 10 compiler errors. The procedure to manually install MDAnalysis 1.0.0 and setup a compatible Python environment will increase in complexity over the next few months due to the NEP 29 release schedule [1], as official support for the Python and Numpy versions compatible with the 1.0 line is progressively being dropped. In particular, the 1.0 line depends on Python <= 3.8, but as of now Python 3.8 is no longer packaged in new Linux distributions, and is absent from official repositories in Ubuntu 22.04, Debian Bullseye and Fedora 36.

To support the 2.0 line of MDAnalysis, one would have to rewrite several parts of the bindings in ESPResSo. There is an outline in ticket #4395 [2]. If you are using the MDAnalysis bindings in ESPResSo and are willing to contribute to its rewrite, please manifest yourself here or on the ticket, and start a draft rewrite until June 30 2022. You can attend one of the ESPResSo coding days on Zoom if you need assistance from our developers to rewrite the bindings. After that date, if no draft has been brought to our attention, we will have to consider dropping MDAnalysis support in the development branch of ESPResSo. The MDAnalysis bindings will still be available in the 4.2.0 release.

Best regards,
Jean-Noël Grad

Institute for Computational Physics
University of Stuttgart
Allmandring 3
70569 Stuttgart
Phone: +49(0)711/685-67715


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