Merge Alignment branch to master

Wait a bit to see if more issues raised, then merge to master as 4.0.4. 

Might be good to rename the 2 tags vx.y.z to rel_x.y.z to clearly distinguish branches from releases. Or rename the v3.4 branch to py2.7 and rename the rel_3.4.2 tag to v3.4.2, maybe that's better. 