Changelog¶

Version 0.1: March 3, 2014¶

Initial release

Version 0.2: April 23, 2014¶

Corrected installation issue (replace inplace with build_lib in setup.cfg)
Documentation updates

Version 0.2.1 April 24, 2014¶

C API path fix

Version 0.2.2: June 3, 2014¶

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¶

Corrected several potential sources of memory leaks in the C API design bindings.

Version 0.2.4: June 17, 2014¶

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¶

Fixed incorrect tm/salt correction method lookups in calcTm function in both bindings and wrappers

Version 0.3.0: August 12, 2014¶

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¶

Improved support for sequences stored in Bytes objects
Renamed getThermoParams to loadThermoParams for clarity

Version 0.4.0: November 25, 2014¶

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¶

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¶

Added misprimingCheck function to primer3/thermoanalysis.pyx
Corrected unclear syntax in C API code

Version 0.4.3 December 1, 2015¶

Fixed compilation errors, unicode-related build problems
Fixed memory allocation / deallocation issues with mispriming libraries

Version 0.5.0 February 25, 2016¶

Update libprimer3 to version 2.3.7
Better test coverage for low level bindings

Version 0.5.1 May 25, 2016¶

Update thal.c to incorporate traceback fix from Primer3 dev team (thanks Triinu)

Version 0.5.2 May 1, 2017¶

Fixed issue where pa->num_intervals was not properly set via the bindings
Fixed typo that caused incorrect output for PRIMER_PAIR_EXPLAIN

Version 0.5.3 May 6, 2017¶

Fixed improper assignment of “PRIMER_PAIR_MAX_COMPL_END_TH” during design arg parsing

Version 0.5.4 June 20, 2017¶

Migration of Cython extension build process to build_clib to remove Cython as a runtime requirement for setup.py (thanks to @tdsmith)

Version 0.5.5 October 30, 2017¶

Remove unicode character from README.rst

Version 0.5.6 July 12, 2018¶

Fixes to primerdesign_helpers.c C macro errors.
Added the todict() methods in thermoanalysis.pyx for serialization help for tests there

Version 0.5.7 August 10, 2018¶

Changes to upper case sequences in seqtm() in oligotm.c because calls to

ThermoAnalysis.calcTm returned 0.0 for strings with lower case letters - disabled existing tests on Windows due to incompatibility with process and memory calls. TODO: create more tests for ThermoAnalysis

Version 0.6.0 May 10, 2019¶

Added functionality for bindings to expose the ASCII representation of computed dimer and hairpin structures

Version 0.6.1 May 9, 2020¶

Fixed issue related to absolute paths populated in SOURCES.txt of sdist
Clean up in setup.py and better Windows build support