TST: fix test errors due to deprecations in numpy 1.9.0

Due to deprecation of boolean array subtraction and indexing
with multiple ellipsis.

(backport of 4b4d541c8)
TST: reduce test tolerance for LSMR test by 1 decimal.  See gh-3554.

Reported failing with numpy master by several people.

(backport of 7cd8e3e3c)
TST: split sparse indexing test between multiple and single ellipsis use.

The multiple ellipsis test needs to be skipped for numpy >= 1.9, the
single ellipsis one needs to always run.

(backport of ff3756f82)