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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