Contact-map

Contact Map Explorer 0.7 adds the ability to do differences between maps that don't include exactly the same atoms/residues. It also includes significant cleanup of the API.

**API Breaks:**

* `ContactMap` has been removed; in 0.8 `ContactFrequency` will be renamed `ContactMap`. See 82 for more.
* `ContactObject.contact_map` is now private (`._contact_map`)
* `ContactFrequency.frames` removed, as well as the `frames` option in its initialization.
* Several functions related to atom slicing have been moved. See 87 for details. (It is unlikely that anyone was using these.)

New features
* Allow mismatched ContactDifference (77, 95)

Miscellaneous improvements
* Enable binder in readme and docs (92, 93)
* API cleanup: private `ContactObject._contact_map`; remove `frames` from `ContactFrequency` (91) api_break
* Remove `ContactMap` (allowing rename `ContactFrequency` => `ContactMap`) (88) api_break deprecation
* IndexManagers for atom slicing (87) api_break

The main new feature in Contact Map Explorer 0.6.0 is the `ContactTrajectory`, which facilitates analysis of the time evolution of contacts. This release also adds more flexibility in plotting, by allowing users to provide the matplotlib `Axes` object to be plotted on.

**DEPRECATION**: Because `ContactMap` is redundant with `ContactFrequency`, the `ContactMap` class has been deprecated and will be removed in Contact Map Explorer 0.7.0. Use `ContactFrequency` instead. See 82 for more.

New features
* Contact trajectories (81)
* rework plotting to allow for plot_axes (79)

Miscellaneous improvements
* Deprecate `ContactMap` (allowing rename `ContactFrequency` => `ContactMap`) (84)
* Improvements to continuous integration (83)

Minor update, mainly to add compatibility with recent releases of other software. Pandas 1.0 brought major changes to the its treatment of sparse matrices, which broke the way we convert contact matrices to Pandas DataFrames. MDTraj no longer supports Python 2, so we no longer test against Python 2. Python 2 support will be officially dropped in the next release of Contact Map Explorer.

Miscellaneous improvements

* Drop Py27 and Win32; add Py38 (75) upstream_changed
* Fix RTD docs build (72) docs
* Fixes for sparse matrix in Pandas 1.0 (69) upstream_changed

The most obvious change in Contact Map Explorer 0.5.0 is the new name: the project is officially called Contact Map Explorer!

It also includes several small updates, and an important bugfix when dealing with nonperiodic trajectories (without unitcell vectors).

Also, sroet is now a core contributor, so we don't list his name next to every PR he contributes in the changelog.

Bug fixes

* Fix when no unitcells are reported (nonperiodic systems) (64 nffaruk, 65)

Miscellaneous improvements
* Better colorbar scaling (64 nffaruk)
* Rename to Contact Map Explorer (61)
* Miscellaneous improvements to CI (41, 63, 66)
* Pin `pandas<1.0` (70) upstream_changed

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 (43)
* Use atom slice (35) sroet performance
* Contact concurrences (28)

Bugs fixed
* Fix dask+atom_slice (54) sroet

Miscellaneous improvements
* Improvements to documentation and examples (47, 52)
* Warn when there is less than 1 pixel per contact (50) sroet
* Improvements on dask testing procedures (40 [sroet], 44)
* fixed pandas future warn about as_matrix (37) sroet

Quick fix for problems in our testing procedure. See 45 for details. This should have no effect on users.