Changelog

Version 2.2.0 (May 19, 2025)

Test improvements (determinism + increased coverage)
Sanitize calc_tm input (see issue #115)
Modernize build system & release process (see issue #154)

Version 2.1.0 (February 26, 2025)

Support for python 3.13
Silence stderr output during ascii structure generation (issue #146)
Updated default formamide concentration to match latest primer3web value + oligotm default (issue #140)

Version 2.0.3 (February 15, 2024)

Fix _ThermoAnalysis._set_globals_and_seq_args for improper checks on misprime_lib and mishyb_lib leading to incorrect initialization of mp_lib and mh_lib. See issue #133

Version 2.0.2 (February 9, 2024)

Support for python 3.12 (build, test, docs)

Version 2.0.1 (September 18, 2023)

Fixed bug in todict method of ThermoAnalysis

Version 2.0.0 (May 30, 2023)

Migrated primer3 header file Cython extern imports to thermoanalysis.pxi
Optional C structure string argument c_ascii_structure added to _ThermoAnalysis methods to enable 3rd party use for structures
Version bump to 2.0.0 due to breaking change
Fix issue whereby no_structure is not correctly 1 set to 1 when no secondary structure in found
Add list version of PRIMER_{PAIR, LEFT, RIGHT, INTERNAL} to design output dictionary keys. Retaining original keys as well for compatibility.
Fix for missing thal_result.sec_struct and dpal_results.sec_struct initialization to NULL in recalc_primer_sec_struct

Version 1.2.2 (May 16, 2023)

Bug fixes for output formatting related to penalty, “problem”, and mispriming fields

Version 1.2.1 (April 28, 2023)

Bug fixes for pdh_create_seq_lib to correct missing seq_lib datastructure allocation and variable name typos.
Increase test coverage to include misprime_lib and mishyb_lib arguments

Version 1.2.0 (March 22, 2023)

Threadsafe changes made to thal.c resulting in new thalflex.c and thalflex.h and thalflexsignatures.h.
Threadsafe changes made to libprimer3.c resulting in new libprimer3flex.c and ibprimer3flex.c.h.
libprimer3.seq_args datatype is now renamed to libprimer3.seq_args_t
test_threadsafe.py add and nogil instituted for calls to thal() and seqtm() added run_design and calc_heterodimer threadsafe tests
ThermoAnalysis class no longer needs to be a Singleton so this was removed as a parent class
p3helpers.pyx houses new sequence and design helper functions
setup.py package_data and MANIFEST.in to assist with future builds from tar.gz (conda)

Version 1.1.0 (March 1, 2023)

Added specificity to error non-N IUPAC error for issue #59
Wheel build support for python 3.8 to move towards following the CPython EOL model for issue #88. See https://devguide.python.org/versions/

Version 1.0.0 (February 11, 2023)

Migrated primer3 source to 2.6.1 version, which adds new arguments for melting temperature code
Intergrated all Python C-API related code into thermoanalysis.pyx/pxd
Deprecated camelCase related functions and added snake_case functions / methods in bindings.py and thermoanalysis.pyx
Migrated primer3/wrappers.py to tests/wrappers.py to indicate it should not be used.
Expanded test coverage and now using pytest for testing
Added pre-commit hooks
Call signature update and pattern update: designPrimers now design_primers integrates setting of sequence arguments and global arguments as they are coupled in primer3_boulder_main.c. Note primer3.primerdesign was removed, including setGlobals. Replace setGlobals(GLOBALS, MISPRIME, MISHYB) and designPrimers(SEQARGS) with a single call design_primers(SEQARGS, GLOBALS, MISPRIME, MISHYB).
primer3 C code bug fixes to improve compiler warnings
Using primer3 read_boulder_record to setup primer3 data structures instead of reproducing code in primer3-py C or Cython via a code signature update
drawDimer and drawHairpin updates to unify sequence structure output for testing
Integrated GitHub Actions for CI testing
Updated sphinx documentation
Begin process of making primer3-py code thread-safe
Documentation migrated to MyST Markdown
Autobuild GitHub action for PyPI wheels and dist tar.gz on version tag
Autobuild GitHub action sphinx documentation updates on version tag

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

Version 0.6.0 (May 10, 2019)

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

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 0.5.6 (July 12, 2018)

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

Version 0.5.5 (October 30, 2017)

Remove unicode character from README.rst

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 0.5.3 (May 6, 2017)

Fixed improper assignment of "PRIMER_PAIR_MAX_COMPL_END_TH" during design arg parsing

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 0.5.1 (May 25, 2016)

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

Version 0.5.0 (February 25, 2016)

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

Version 0.4.3 (December 1, 2015)

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

Version 0.4.2 (September 18, 2015)

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

Version 0.4.1 (November 28, 2014)

Better documentation regarding max. seq. lengths for thermo. calcs
calcHairpin, calcHomodimer, calcHeterodimer, and calcEndStability now raise RuntimeErrors as appropriate

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 0.3.1 (August 13, 2014)

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

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 0.2.5 (August 7, 2014)

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

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 0.2.3 (June 5, 2014)

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

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 0.2.1 (April 24, 2014)

C API path fix

Version 0.2 (April 23, 2014)

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

Version 0.1 (March 3, 2014)

Initial release