contact_map 0.7.0

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

contact_map 0.6.0

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)

contact_map 0.5.1

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

contact_map 0.5.0

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

contact_map 0.4.0

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

contact_map 0.3.3

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

contact_map 0.3.1

Very minor updates; mainly dropping official testing of Python 3.4 since code we depend on no longer supports it (making our testing impossible).

Miscellaneous improvements

• Pylint/Codacy clean-up (#34)
• Drop Python 3.4 support (because pandas no longer supports it) (#36)

contact_map 0.3.0

The marquee feature in contact_map 0.3.0 is support for parallelization using dask.distributed, as well as other improvements to facilitate parallelization using other tools.

New features

• Colorbars in default plotter (#31)
• Parallelization of ContactFrequency with dask.distributed (#30)
• Contact Object Serialization (#29)
• Add/subtract contact frequencies (#3)

contact_map 0.2.0

First public-ready release of contact_map. This marks the version that will be used for the E-CAM module.

Future release notes will details new features and other improvements. API breaks will also be included in the release notes. Following semver, during the 0.x.y cycle, API breaks are allowed (although we will try to only make them between 0.x.y and 0.(x+1).0). After 1.0, API breaks will require a change of the major version number.

Some of the details in the progress to date can be seen in the release notes from the experimental releases of the 0.1.x sequence. More complete documentation is available at https://contact-map.readthedocs.io/

contact_map 0.1.5

The 0.1.x release cycle is primarily for testing automated release process we're putting in place. The first release for public use will be 0.2.0. This is a test release for 0.2.0.

This release fixes a bug in the deployment process from the previous release. See the release notes for 0.1.3 for more information about new features and other improvements.