# Changelog

## 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`
- `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 in `t`hermoanalysis.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
  `RuntimeError`s 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
