TST: fix test errors due to deprecations in numpy 1.9.0

Due to deprecation of boolean array subtraction and indexing
with multiple ellipsis.
TST: fix a test failure in stats.mstats reported in gh-3554.

The ``mstats.trim`` test is still failing; looks like a regression in numpy
master.
TST: reduce test tolerance for LSMR test by 1 decimal.  See gh-3554.

Reported failing with numpy master by several people.
TST: avoid using nans in stats.mstats tests.

Nans may trigger RuntimeWarnings from numpy (not consistent on
all platforms), which lead to test failures with dev versions of numpy.
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.
Merge pull request #3564 from rgommers/numpy-deps

Fix test failures with numpy master. Closes gh-3554