Changelog

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