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