This file lists *major* changes between releases, for a full list see git log.

2.1.3
----------------------------------
- Bugfix for large envelopes crashing under Python in specific circumstances
- Implement stochastic envelopes in C++ and Python

2.1.2 (R-only release)
----------------------------------
- Workaround for CRAN threatening to remove package because of C++11 function usage, in spite of C++14 being clearly listed in SystemDependencies

2.1.1
----------------------------------
- Speed improvements
- Bugfixes
- Support for calculating basic statistics of FixedEnvelopes
- Support for negative atom counts in formulas in Python. This is useful in conjunction with FASTA argument, to represent protein modification

2.1.0
----------------------------------
- Support for using nominal mass in calculations
- FASTA file parsing
- More speed improvements
- Support for Wasserstein distance
- Basic operations on fixed envelopes (addition, normalization, convolution...)

2.0.1 (R-only release)
----------------------------------
- Fix compilation of IsoSpecR on Windows

2.0.0
----------------------------------
- Major algorithmic improvements in IsoLayered
- Added support for fixed envelopes, restored quicktrim option
- R now returns probabilities instead of logprobabilites by default
- Some API changes
- Performance improvements and bugfixes all over the place

1.9.3 (C++/Python-only release)
----------------------------------
- Improve API and examples for radiolabelling in C++/Python

1.9.2
----------------------------------
- Mostly documentation improvements

1.9.1
----------------------------------
- R bindings brought up to speed
- Improvements for 1.0.X backward compatibility in Python module
- Minor fixes and cleanups

1.9.0
----------------------------------
- We no longer override $CXX to use clang when available - the difference in speed of
produced code is no longer large enough to justify it
- Some more minor code cleanups
- Python wrapper now returns probabilities of configurations instead of logprobabilities 
  by default. This is controllable through (optional) parameter.
- Expose LayeredTabulator in Python

----------------------------------
1.9.0beta2

- API change: rename eprob() functions to prob()
- Added more tests
- Some bugfixes

----------------------------------
1.9.0beta1

- Added more tests
- Code cleanups
- Some bugfixes

----------------------------------
1.9.0alpha3

- Brought C++/Python examples up to the new API
- Small change of Python API 
- Speed improvements in IsoThresholdGenerator
- Code cleanup, ripped out much of experimental stuff which will be postponed until 2.0

----------------------------------
1.9.0alpha2

- Rudimentary module for backward-compatibility with IsoSpecPy 1.0.X API
- Bugfix (and usability improvement) for getting configurations in 
  IsoThreshold

----------------------------------
1.9.0alpha1

- Almost complete rewrite of the entire codebase
- Improvements in the core algorithms, resulting in 10x-1000x speed increase
  as well as lower memory consumption
- Reworked API to be more sensible
- Laying the groundwork for multithreaded operation (not complete yet)
- Expose generators in Python (enabling processing configurations on the fly,
  as they are produced without the need to compute and store all of them first
  (using up memory) and process them later)
- More modular Python part
- C/C++ and Python-only release, R will follow soon after
- Some features from 1.0.5 are not yet (re-)implemented: IsoLayered is only 
  exposed as a generator, not yet as a fixed table; as a consequence quicktrim
  to get the optimal p-set is still missing
- THIS IS AN ALPHA RELEASE: IT'S NOT YET EXHAUSTIVELY TESTED AND MAY CRASH OR 
  PRODUCE WRONG RESULTS
- API is still not yet finalized.

----------------------------------
1.0.7 (Python-only release)

- Bugfix in Python's getConfs()

----------------------------------
1.0.6 (Python-only release)

- Compatibility fixes for Python3.6

----------------------------------
1.0.5 (Python-only release)

- Only affecting IsoSpecPy: Speed improvements in IsoFromFormula

----------------------------------
1.0.4

- ??? FIXME

----------------------------------
1.0.3

- Only affecting IsoSpecR: improve the efficiency of R to C++ interface
- Add an option to skip discarding the superfluous configurations

----------------------------------
1.0.2

- Some further Python+Windows compatibility improvements

----------------------------------
1.0.1

- Only affecting IsoSpecPy: provide prebuilt library
- Only affecting IsoSpecPy: Improve Python/cygwin functionality

----------------------------------
1.0.0

- Initial release

