Release 0.16.2
27 Jun 2017Just a few weeks after our last release, we are releasing MDAnalysis version 0.16.2. The release notes list the full details of the changes in this version. This version fixes some bugs, but it mostly introduces deprecation warnings for changes that will occur in subsequent versions.
The first feature to be deprecated is the Timeseries module
that will be removed in version 0.17.0. The
MDAnalysis.analysis.base.analysis_class function can be
used to replace the deprecated Timeseries. analysis_class was introduced in version 0.16.0 and you can read more about it in a previous blog post.
Instant selectors are also deprecated and will be removed in release 1.0. These
shortcuts allow you to access segments, residues, or atoms using there names as
attribute. For instance, such selectors allow you to access a segment called
“SYSTEM” from a universe u by calling u.SYSTEM, or to select all the lysine
of a residue group rg by calling rg.LYS. Although these shortcuts used to be
reasonably useful for interactive work, they also introduce
unexpected behaviours for a Python object, and are fragile mechanisms that are
difficult to maintain. You can read the discussion in issue 1377
to learn how to replace the different selectors.
Finally, the global flags will disappear in release 1.0 to be replaced with more granular keyword arguments in the appropriate methods. The flags introduce a global state that could make MDAnalysis scripts run differently for different users and could thus lead to difficult to reproduce results. The discussion about removing the flags is happening in issue 782.
Removing outdated code allows us to keep MDAnalysis robust and consistent as we prepare for 1.0 when the user interface will become frozen. We are confident that these features were not much used or have better replacement. Come to the mailing lists or our github repository to join the conversation.
Thank you to all the contributors who reported issues or contributed code to this version. Thank you also to Dominik ‘Rathann’ Mierzejewski for his first contribution to the code base.
Upgrade
You can upgrade with pip install --upgrade MDAnalysis . If you use the conda
package manager run conda update -c conda-forge mdanalysis
