Install request: MDAnalysis

[ikirker]

From: IN:02748765

MDAnalysis and its tests package MDAnalysisTests install easily off pip. It depends on numpy and some other things, and fails a few of its unit tests on Python 3 (ones around universal density), and once you manage to find the note saying that Python 3 support is experimental, that's not surprising. It succeeds with Python 2.7.12, so it'll just go in the Python 2 list of packages.

Unfortunately installing this is currently stuck behind biocore/emperor#631 because of the way we build Python environments: we rebuild the whole Python environment (i.e. reinstall all packages in the bundle) whenever the list of packages changes, and because emperor won't install, we can't update the Python 2 bundle, as emperor is installed as a dependency of QIIME and QIIME is only installed with Python 2.

The current version of emperor was installed from a wheel, I think, but that wheel doesn't seem to exist anymore?

From a user usage perspective, we can't just remove emperor because that would remove/break QIIME, so if any of our users are using that, their jobs would suddenly break, and we could pin the version down to a previous one in the list, but that would expose them to old bugs.

I guess this is our fault for not having made a plan for if this sort of thing happens. 😞

[ikirker]

The fix for emperor is now in, but we'll still need to wait for a new release version to appear in PyPi, or else use pip install --pre (not recommended).

[ikirker]

Reviewed this and the associated ticket; user is running this on their own local machine instead, and said they'll contact us again if they need it on the cluster. 🤷‍♀️

So, closing.