The 0.14.0 release blog-post

_posts/2016-02-28-release-0.14.0.md

@@ -0,0 +1,97 @@
+---
+layout: post
+title: Release 0.14.0
+---
+
+We have just released MDAnalysis version 0.14.0. This release contains a large
+number of new features and bug fixes. The highlights are listed below but for
+more details see the
+[release notes](https://github.com/MDAnalysis/mdanalysis/wiki/ReleaseNotes0140).
+
+# Upgrade
+
+You can upgrade with `pip install --upgrade MDAnalysis`
+
+# Noticable Changes
+
+## Implicit *OR* in selections
+
+Many long selection strings used in select_atoms have been simplified through
+allowing implicit *OR* in the arguments.  For example to select all atoms
+with one of a few names previous required lots of ORs
+
+```python
+# OLD
+u.select_atoms('name Ca or name N or name Ch')
+
+# NEW
+u.select_atoms('name Ca N Ch')
+```
+
+The new syntax allows multiple arguments after the keyword `name`.
+The selection will keep eating arguments till it hits a keyword.
+The use of wildcards is still possible too, making the selection
+of all atoms with a type beginning with 'C' or 'N' as simple as:
+
+```python
+u.select_atoms('type C* N*')
+```
+
+Similarly, for selecting ranges of resids
+
+```python
+# OLD
+u.select_atoms('resid 1:10 or resid 40:50 or resid 56 or resid 67')
+
+# NEW
+u.select_atoms('resid 1:10 40:50 56 67')
+```
+
+This new behaviour works for *name, type, resname, segid, altLoc, resid,
+resnum and bynum* selections!  The old behaviour will still work,
+but we feel this should save a lot of typing!
+
+## Boolean indexing of trajectories
+You can now treat trajectories like numpy arrays in a fully pythonic fashion:
+You could already do fancy indexing and now you can also do boolean indexing. One application
+is building simple re-usable trajectory filters with ease, e.g., in order to slice
+data.
+
+```python
+# build a filter array for re-use: only frames where the centroids
+# of groups A and B are closer than 3 A
+idx = [np.linalg.norm(A.centroid() - B.centroid()) < 3.0 for ts in u.trajectory]
+
+for ts in u.trajectory[idx]:
+   # analyze the frames where |A - B| distance < 3
+
+for ts in u.trajectory[np.logical_not(idx)]:
+   # do analysis on the other frames, |A - B| >= 3
+```
+
+## New analysis module to calculate linear densities
+The
+[MDAnalysis.analysis.lineardensity](http://pythonhosted.org/MDAnalysis/documentation_pages/analysis/lineardensity.html)
+module contains the class `LinearDensity` that simplifies calculation of mass
+and charge densities profiles along the primary axes of a simulation cell.
+
+## Rewrite of TRR and XTC file handling
+
+Our wrapper of the Gromacs library
+[xdrlib](http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library)
+has been completely rewritten in cython. This changes brings us one
+step closer towards supporting Python 3. The only user facing API change is that
+we don't save persistent frame offsets with the pickle module anymore but
+with numpy's 'npz' format. This improves reopening of xtc/trr files.
+
+## Experimental Python 3 Support
+
+With this release it is possible to run MDAnalysis under Python 3. We have
+ported most of our coordinate readers, DCD is still missing, and topology
+readers to be python2/3 compatible. Most features should already work but expect
+there to be some minor glitches.
+
+## Others
+
+This release contains other performance enhancements and fixes. For a detailed
+list see the [release notes](https://github.com/MDAnalysis/mdanalysis/wiki/ReleaseNotes0140).