Releases | Open Source Science

primer3-py - v2.2.0

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

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Published by benpruitt about 1 year ago

primer3-py - v2.1.0

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)

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Published by benpruitt over 1 year ago

primer3-py - v2.0.3

Clarify how to replace setGlobals as of v1.0.0 (#134)
Fix ThermoAnalysis.setglobalsandseqargs for improper checks on misprimelib and mishyblib (#135)

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Published by benpruitt over 2 years ago

primer3-py - v2.0.2

Support for python 3.12 (build, test, docs) (#129)
Update cibuildwheel to latest release for python 3.12 build support (#131)

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Published by benpruitt over 2 years ago

primer3-py - v2.0.1

Fixed bug in todict method of ThermoAnalysis (#123)

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Published by benpruitt almost 3 years ago

primer3-py - v2.0.0

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 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

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Published by grinner about 3 years ago

primer3-py - v1.2.2

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

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Published by benpruitt about 3 years ago

primer3-py - v1.2.1

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

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Published by grinner about 3 years ago

primer3-py - v1.2.0

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)

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Published by grinner over 3 years ago

primer3-py - v1.1.0

Added specificity to error non-N IUPAC error for issue https://github.com/libnano/primer3-py/issues/59
Wheel build support for python 3.8 to move towards following the CPython EOL model for issue https://github.com/libnano/primer3-py/issues/88. See https://devguide.python.org/versions/

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Published by grinner over 3 years ago

primer3-py - v1.0.0

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
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

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Published by benpruitt over 3 years ago

primer3-py - 0.6.1

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

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Published by benpruitt about 6 years ago

primer3-py - 0.6.0

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

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Published by benpruitt about 7 years ago

primer3-py - lower case fix for calcTm

calcTm returns a non-zero answer for lower case sequence strings.

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Published by grinner almost 8 years ago

primer3-py - 0.5.6

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

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Published by grinner about 8 years ago

primer3-py - Remove unicode character from README.rst

Remove unicode character from README.rst

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Published by benpruitt over 8 years ago

primer3-py - Migration from build_ext to build_clib

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

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Published by benpruitt about 9 years ago

primer3-py - Fixed improper assignment during design arg parsing

Fixed improper assignment of "PRIMERPAIRMAXCOMPLEND_TH" during design arg parsing

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Published by benpruitt about 9 years ago

primer3-py - Fixes to binding internals

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

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Published by benpruitt about 9 years ago

primer3-py - Incorporate traceback fix in thal.c

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

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Published by benpruitt about 10 years ago

primer3-py - Update libprimer3 to version 2.3.7

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

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Published by benpruitt over 10 years ago

primer3-py - Fixed setup issues, mispriming library memory management problem

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

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Published by benpruitt over 10 years ago

primer3-py - Add misprimeCheck, C API bug fix, Python 3.5 support

Added misprimingCheck function to primer3/thermoanalysis.pyx
Corrected unclear syntax in C API code
Verify Python 3.5 support

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Published by benpruitt almost 11 years ago

primer3-py - More clarity regarding seq. length ceiling for thermo calcs, respective error handling implementation

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

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Published by benpruitt over 11 years ago

primer3-py - Bug fixes, major documentation build-out

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

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Published by benpruitt over 11 years ago

primer3-py - libprimer3 refactor, compilation fixes, API formalization

-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 -[POTENTIALL 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)

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Published by benpruitt almost 12 years ago

primer3-py - Tm/salt correction method lookup corrections

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

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Published by benpruitt almost 12 years ago

primer3-py - Addressed mispriming/mishybridization bug

Addressed bug in mispriming/mishybridization library parsing in which memory for the global parameters struct was not being properly allocated.