ReleaseNotes062

Oliver Beckstein edited this page Sep 26, 2015 · 4 revisions

Availability

Either download the tar file MDAnalysis-0.6.2-rc1.tar.gz from http://code.google.com/p/mdanalysis or checkout the release-0-6-2 branch

svn checkout http://mdanalysis.googlecode.com/svn/branches/release-0-6-2 mdanalysis-0.6.2

or use setuptools' easy_install directly (new!)

easy_install -f http://code.google.com/p/mdanalysis MDAnalysis

Any feedback through the Issue Tracker or the Mailing List is very much appreciated.

Major changes

Automatic installations with setuptools should be working now (if the LAPACK library is in a canonical place such as /usr/lib), i.e. you can simply install the latest version of MDAnalysis with

easy_install -f http://code.google.com/p/mdanalysis/downloads/list MDAnalysis

or upgrade with

easy_install -f http://code.google.com/p/mdanalysis/downloads/list --upgrade MDAnalysis

If this does not work, unpack the source as usual and customize setup.cfg as described in Install. Then run easy_install on the sources

easy_install ./MDAnalysis-0.6.2 MDAnalysis[tests]

If you want to install additional required packages for the UnitTests then list the tests requirement:

easy_install -f http://code.google.com/p/mdanalysis/downloads/list MDAnalysis[tests]

Changes

  • 0.6.2 release
  • removed a number of imports from the top level (such as rms_fitting); this might break some scripts that still rely on the layout that was used for 0.5.x (which is now officially declared deprecated)
  • defined trajectory API
  • deprecated DCD.dcd_header was renamed to DCD._dcd_header
  • XTC and TRR compute numframes by iterating through trajectory (slow!)
  • introduced units: base units are ps (time) and Angstrom (length); see core.flags
  • XTC and TRR automatically convert between native Gromacs units (ps, nm) and base units (uses core.flags['convert_gromacs_lengths'] = True)
  • more test cases (see UnitTests)
  • really FIXED Issue 16 (can easy_install from tar file)
  • FIXED a bug in AtomGroup.principalAxes() (in r297)
  • added dependency information to setup.py (numpy by default; nose for tests)

Project Information

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GNU GPL v2 code license
Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
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