Version 4.0.0

This is version 4.0.0 of PhiSpy. A new release with a whole raft of changes and improvements, bug fixes, and speed up.

You should update to version 4.0.0. using pip install --upgrade phispy or conda update phispy as appropriate. See the Installation Instructions.

See the README for more details about the improvements and enhancements

pip and conda versions

A version that is acceptable to PyPi and bioconda for easy installation.

PyPi allows easy installation with pip. See the PhiSpy project page.

bioconda allows easy installation with conda. See the PR to integrate PhiSpy with bioconda.

Improvements to repeatfinder

In this release we internalize repeatfinder to become a python external module that we have renamed PhiSpyRepeatFinder as there are many other modules called RepeatFinder out there. The C++ code is now directly called from the Python code, removing the need for some confusing temporary files.

We have also initiated the availability of PhiSpy through PyPi by adding setup.py.

Version 3.4.5

Several important fixes and improvements following our v3.4 release and we are on the way to v3.5, but wanted to get these out sooner.

Version 3.4

We have made many updates and changes between v3.3 and v3.4 and most of that work has been done by @deprekate and @pdec.

We have fixed numerous issues, moved away from R to keep the random forests in Python, redeveloped the k-mers, and many, many other changes.

If you find issues with version 3.4, please post them under issues.

Version 3.4 prerelease

This is version 3.4 prerelease for testing. Please create an issue if you find one.