| 2.3.0 release (#168) * doc conformity for test module * Opportunistic support for python 3.14 * 2.3.0 release | 8 months ago |
| Modernize build system, release process and pin Cython version (#155) * Modernize build system - Update and pin Cython version - Add Python 3.13 support - Improve build configuration and testing - Add custom build extensions * Update release process and documentation - Enable manual branch selection for docs workflow - Update release process documentation - Document setuptools package warnings - Rename workflow files for consistency - Replace build-wheels-pypi.yml with release.yml * additional documentation cleanup * migrate bash markdown to console w/ prompt symbol tokenization * consolidate deps in pyproject.toml + update MANIFEST.in | 1 year ago |
| Example search using `ThermoAnalysis` added with `examples/orthogonalprimers.py` Example design added in `examples/basicprimerdesign.py` Updated `thal.c` to suppress printing to `stderr` No secondary structure could be calculated in the `thal()` function | 3 years ago |
| Fix misprime_lib/mishyb_lib rejecting bytes sequence values (#174) pdh_create_seq_lib validated the sequence value by testing the type of the dict key (seq_name_str) instead of the value (seq_str), so a str key with a bytes value fell through to the else branch and raised TypeError (surfaced as an empty OSError). Test seq_str instead. Add a regression test asserting bytes and str library values produce identical design output. Fixes #173 | 2 months ago |
| Fix misprime_lib/mishyb_lib rejecting bytes sequence values (#174) pdh_create_seq_lib validated the sequence value by testing the type of the dict key (seq_name_str) instead of the value (seq_str), so a str key with a bytes value fell through to the else branch and raised TypeError (surfaced as an empty OSError). Test seq_str instead. Add a regression test asserting bytes and str library values produce identical design output. Fixes #173 | 2 months ago |
| p3helpers.pyx houses new sequence and design helper functions Sequence sanitization of IUPAC non-{A,C,G,T,a,c,g,t} bases become {N, n} and also reverse complement added. Separate methods exist for byte strings and unicode strings with error handling documentation update for p3helpers.pyx | 3 years ago |
| Modernize build system, release process and pin Cython version (#155) * Modernize build system - Update and pin Cython version - Add Python 3.13 support - Improve build configuration and testing - Add custom build extensions * Update release process and documentation - Enable manual branch selection for docs workflow - Update release process documentation - Document setuptools package warnings - Rename workflow files for consistency - Replace build-wheels-pypi.yml with release.yml * additional documentation cleanup * migrate bash markdown to console w/ prompt symbol tokenization * consolidate deps in pyproject.toml + update MANIFEST.in | 1 year ago |
| Updated `AUTHORS`, `MANIFEST.IN`. Validated all files in tar.gz and wheel. renamed docs/requirements.txt to docs/doc-requirements.txt. Renamed top-level requirements.txt to dev-requirements.txt and added content, `Cython`, `pre-commit`, and `pytest` Fixed `sphinx` documenting of inherited members of `ThermoAnalysis`. updated `README.md` header to markdown format | 3 years ago |
| 2.3.0 release (#168) * doc conformity for test module * Opportunistic support for python 3.14 * 2.3.0 release | 8 months ago |
| Initial commit | 12 years ago |
| Modernize build system, release process and pin Cython version (#155) * Modernize build system - Update and pin Cython version - Add Python 3.13 support - Improve build configuration and testing - Add custom build extensions * Update release process and documentation - Enable manual branch selection for docs workflow - Update release process documentation - Document setuptools package warnings - Rename workflow files for consistency - Replace build-wheels-pypi.yml with release.yml * additional documentation cleanup * migrate bash markdown to console w/ prompt symbol tokenization * consolidate deps in pyproject.toml + update MANIFEST.in | 1 year ago |
| Update README.md (#172) Fixes #171 | 4 months ago |
| 2.3.0 release (#168) * doc conformity for test module * Opportunistic support for python 3.14 * 2.3.0 release | 8 months ago |
| thal.c and thal.h updated for 2.6.1 drawDimer and drawHairpin code is legacy with an updated due to variable output from 2.6.1 code for CLI and non CLI. test_thermoanalysis tests pass Bugs fixed in upstream oligotm_main.c as the argc > 14 was not enough needed to bump it to argc > 20. Also the new -dm and -df arguments colided with the parser for -d and broke that when both where specified. This was fixed by strncmp("-d", argv[i], 2) -> strncmp("-d", argv[i], 3) libprimer3.c update for 2.6.1. primerdesign.pyx created to replace primerdesign_py.c and primerdesign_helpers.c. global args and sequence arges are passed to the choose_primers function using read_boulder.read_boulder_record. added support for masking and PRIMER_MASK_KMERLIST_PATH global argument Utility boulder generation and parsing now in argdefaults.py instead of wrappers.py as is it is used by primerdesign module now in addition to wrappers see argdefaults.format_boulder_io for details of output generation this function should be updated to support new 2.6.1 keys in a future PR moved wrap and unwrap code from tessts._simulatedbindings to argdefaults module Enable repeat use of keys in boulder files using TAGS_APPEND. Added test_argdefaults.py to allow round trip testing from boulder to python dict unwrap/wrap works. Fixed unwrap lambda parsing to check for decimal points in floating point values to increase accuracy for sim to binding testing additional camelCase to snake_case conversion. snakecase for parse_multirecord_boulder_io and parse_boulder_io Added not to indicate we need to make wrap/unwrap work round trip tests updated for new code. IOErrors are now OSErrors per Python 3 convention isort update to 5.12.0 for pre-commit to fix linux subprocess failure with a poetry environment | 3 years ago |
| Modernize build system, release process and pin Cython version (#155) * Modernize build system - Update and pin Cython version - Add Python 3.13 support - Improve build configuration and testing - Add custom build extensions * Update release process and documentation - Enable manual branch selection for docs workflow - Update release process documentation - Document setuptools package warnings - Rename workflow files for consistency - Replace build-wheels-pypi.yml with release.yml * additional documentation cleanup * migrate bash markdown to console w/ prompt symbol tokenization * consolidate deps in pyproject.toml + update MANIFEST.in | 1 year ago |
| added pre-commit hooks initial. - Following work will add in `mypy` and `isort` - added in pre-commit documentation in `quickstart.rst` Github python action initial commit added GitHub Action workflow badge fix MacOS memory delta allowance in test_primerdesign.test_memoryLeaks. Delta remains the same on Linux thal.c type comparison issues update: if ('\0' == oligo_f) --> if (oligo_f == NULL) if ('\0' == oligo_r) --> if (oligo_r == NULL) oligotm.c type comparison issue update: seq != '\0' removed removed Travis as a CI Updated testing documentation to `pytest` | 3 years ago |
