Biskit

setup.py was still broken with the previous 3.0.0 release. 3.0.1 fixes up things so that installation from source or wheel should work.

This is a bugfix release to bring biskit 3.0 in line with python 3.13 and the latest numpy and Biopython.

Some build- and testing-related bug fixes on the old (classic) 2.x line of development. This will be the last release before the master branch is switched to the backwards-incompatible biskit3.

This is the last major release before switching to the biskit 3.0 line of development. Some more bug-fixing releases may still come but main development will now switch to the biskit3 branch. biskit 3.x will represent a major backwards-incompatible change. The 2.x code base will therefore be maintained on its own branch [biskit-2.x](https://github.com/graik/biskit/tree/biskit-2.x) for those who need to stay on Python 2.x or who need to reproduce old workflows.

Changes

There are only minor changes here as most efforts went into the new biskit3 code branch.

* DSSP wrapper partially re-written to work with latest version of the program (closes issues 12, 14, 13)
* travis-ci continuous integration (run core test suite whenever there is a push to github)
* more platform-independent handling of path names
* The following modules were deprecated:
* Fold-X
* WhatIf

minor changes related to packaging or testing:
- update version number in setup.py
- introduce `__version__` field in `__init__.py`
- fix test failure because of missing cpptraj even though the test didn't need it
- make ColorSpectrum test case independent of biggles installation
- silence "biggles missing" warning in main `__init__.py` (errors will be raised when biggles is needed)
- update debian packaging control files
- update dependencies in setup.py

Changes

This is mostly a long overdue maintainence release to make Biskit again compatible with recent versions of dependencies and third-party software. The dependency to Scientific Python has been removed, which should ease installation. SciPy, by contrast, is now a hard dependency. This is the first release after migration to github.