Primer3-py

Latest version: v2.0.3

Safety actively analyzes 629532 Python packages for vulnerabilities to keep your Python projects secure.

Scan your dependencies

Page 2 of 6

1.2.0

- 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`)

1.1.0

- 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/

1.0.0

- 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`.
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

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

0.6.0

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

0.5.7

- 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`

Page 2 of 6

© 2024 Safety CLI Cybersecurity Inc. All Rights Reserved.