CHANGES

Changelog
=========

Version 0.1:                                                      March 3, 2014
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- Initial release

Version 0.2:                                                     April 23, 2014
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- Corrected installation issue (replace inplace with build_lib in setup.cfg)
- Documentation updates

Version 0.2.1                                                    April 24, 2014
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- C API path fix

Version 0.2.2:                                                     June 3, 2014
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- Corrected issue with parsing "SEQUENCE_PRIMER_PAIR_OK_REGION_LIST" as a
  python sequence object. "SEQUENCE_PRIMER_PAIR_OK_REGION_LIST" should now
  be provided as a list of lists or tuple of tuples (or a combination of the
  two). -1 should be used in the case where an index is ommitted. For example::

      Primer3 boulder IO input:   100,50,300,50 ; 900,60,,
      Primer3 python input:       [[100,50,300,50], [900,60,-1,-1]]

Version 0.2.3:                                                     June 5, 2014
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- Corrected several potential sources of memory leaks in the C API design
  bindings.

Version 0.2.4:                                                    June 17, 2014
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- Addressed bug in mispriming/mishybridization library parsing in which
  memory for the global parameters struct was not being properly allocated

Version 0.2.5:                                                   August 7, 2014
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- Fixed incorrect tm/salt correction method lookups in calcTm function in
  both bindings and wrappers

Version 0.3.0:                                                  August 12, 2014
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- Fixed memory leak in global param struct allocation for design bindings
- Integrated C API patch code into libprimer3
- Refactored libprimer3 to pure C (khash lib is now used in lieu of hashmap)
- Corrected many minor compiler warnings in libprimer3
- (POTENTIAL BREAKING CHANGE) Refactored thermodynamic alignment bindings to
  always return a thermoresult namedtuple (in the previous embodiment, if no
  structure was found, the return value was `None`) 

Version 0.3.1:                                                  August 13, 2014
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- Improved support for sequences stored in Bytes objects
- Renamed getThermoParams to loadThermoParams for clarity

Version 0.4.0:                                                November 25, 2014
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- Several major bug fixes in the design bindings pipeline
- Better testing framework for the design bindings
- New documentation system
- Better under-the-hood thermodynamic analysis abstraction 

Version 0.4.1:                                                November 28, 2014
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- Better documentation regarding max. seq. lengths for thermo. calcs
- calcHairpin, calcHomodimer, calcHeterodimer, and calcEndStability now raise
  ``RuntimeError``s as appropriate

Version 0.4.2:                                               September 18, 2015
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- Added misprimingCheck function to `primer3/thermoanalysis.pyx`
- Corrected unclear syntax in C API code