Release 0.4.0

[dwhswenson]

The two main enhancements in contact_map 0.4.0 are:

1. "Atom slicing": By only processing the atoms that are used, the contact map calculation is now much faster in most common cases (e.g., allowing you to ignore all waters for a protein contact map).

2. Contact concurrences: This is a new way of visualizing contacts during a trajectory, which assists in identifying specific sets of contacts that occur simultaneously. That can be useful for identifying stable states in molecular systems.

New features

• Easy access to haystack/query residue indices and range (Easy access to haystack/query residue indices and range #43)
• Use atom slice (Use atom slice #35) @sroet #performance
• Contact concurrences (Concurrence #28)

Bugs fixed

• Fix dask+atom_slice (Fix dask+atom_slice #54) @sroet

Miscellaneous improvements

• Improvements to documentation and examples (Add example for concurrences #47, Fix docs #52)
• Warn when there is less than 1 pixel per contact (Warn when there is less than 1 pixel per contact #50) @sroet
• Improvements on dask testing procedures (fix dask travis error #40 [@sroet], Handle dask TimeoutError exception in tests #44)
• fixed pandas future warn about as_matrix (fixed pandas future warn about as_matrix #37) @sroet

[dwhswenson]

We've been way overdue for a release; features like the contact concurrences that are shown in the docs aren't available through pip/conda-installed versions!

I'm holding off on merging this until @sroet has a chance to tell me whether #50 actually was an API break or not (if so, we need to include that in the release notes). Merging should auto-update pypi, and then I can use that to update conda-forge.

[sroet]

LGTM, feel free to merge after altering/removing the API break ;)