| Files | Last commit | Last update |
|---|---|---|
add new / updated primer3 design test input files for `test_primerdesign` coverage | 3 years ago | |
cleared __init__.py in tests cuz unused | 11 years ago | |
fix typos (closes #45, #54) | 3 years ago | |
merged primerdesign.pyx into thermoanalysis.pyx. thermoanalysis now has c extension class_ThermoAnalysis and ThermoAnalysis subclass exists to provide Singleton class to ensure multiple instances of the now _ThermoAnalysis class are not instanciated added threading.Lock to all python method primer3-related calls in thermoanalysis.ThermoAnalysis to ensure thread safety. There is a performance hit related to this that we should measure to ensure its worth it. added new primer3 binaries to LIBPRIMER3_BINARIES in setup.py migrated all code to snake case and added deprecated warning versions of old camelCase versions that will remain in the 1.0.0 release. incremented release to 1.0.0a4 | 3 years 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 | |
Make tests deterministic (#158) * make tests deterministic * add regression and behavior tests using fixed sequences | 1 year 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 | |
update test for windows support | 3 years ago | |
Sanitize `calc_tm` input (#156) * sanitize calc_tm inputs * cleanup type hinting * remove performance assertions (dependant on memory load on test rig) * addional type hinting fixes; windows check fix * explicitly null terminate strings during sanitization * fix memory check approach for linter compliance * move null termination back into helper function * add more docs for copy_c_char_buffer; move null termination outside again for safety * re-add return type hint to _set_globals_and_seq_args * randArgs --> rand_args | 1 year 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 | |
Make tests deterministic (#158) * make tests deterministic * add regression and behavior tests using fixed sequences | 1 year ago | |
2.3.0 release (#168) * doc conformity for test module * Opportunistic support for python 3.14 * 2.3.0 release | 8 months ago | |
Make tests deterministic (#158) * make tests deterministic * add regression and behavior tests using fixed sequences | 1 year ago | |
Make tests deterministic (#158) * make tests deterministic * add regression and behavior tests using fixed sequences | 1 year ago | |
2.2.0 release (#159) | 1 year ago | |
update test for windows support | 3 years ago |
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