Prymer

Miscellaneous Tasks

- Fix publishing workflow (123) (a0fd228c)

Bug Fixes

- Change int weights to float weights, update doctest examples (61) (f71dc658)
- Check against `HN` tag instead of `is_unmapped` property (69) (364a9dcb)
- Pad target region by `max_amplicon_length` (23) (dd844f54)
- Executable path validation tests should not be dependent on the user environment (25) (8f151a0d)

Documentation

- Expand the documentation for `OffTargetDetector` (46) (c434b1db)
- Add bioconda badge (9) (8d332df2)

Features

- Use OffTargetDetector and ExecutableRunner as ContextManagers (64) (5515d050)
- Remove pysam and bwa warmup hack (65) (a132a52d)
- Use bwa-aln-interactive and upgrade developer's docs (32) (d87e740d)
- Redirect BwaAlnInteractive stderr to debug logging (74) (5d79a520)
- Add thermodynamic-related weights and parameters for `PickHybProbeOnly` task (60) (9f51325a)
- Ensure FileBasedVariantLookup is used as a context manager (71) (7e2e7845)
- Speed improvements for primer pair hit building from single primer hits (99) (baf2e65c)
- Add parameter validation for `OffTargetDetector.__init__` (103) (a193734e)
- Add support for `min_primer_pair_hits` to `OffTargetDetector` (44) (0e640079)
- Make `OffTargetDetector.filter()` generic (19) (02a57b1d)

Miscellaneous Tasks

- Export PickHybProbeOnly task (70) (8638e3b4)
- Unpin fgpyo dependency (97) (3c3ed807)
- Unpin pybedlite dependency (98) (fbd1aa10)
- On publish only upload prymer wheels (33) (9c4858af)

Refactor

- Export Primer3Parameters and Primer3Weights (36) (bc0622df)
- Export OffTargetDetector (37) (14519383)
- Primer -> Oligo, PrimerLike -> OligoLike (51) (93ea6e71)
- Make `PrimerPair.amplicon` a cached property (93) (385e1b1d)

CI

- Migrate ubuntu-latest to ubuntu-24.04 (96) (f62c4b52)

Miscellaneous Tasks

- Bump version to 2.0.1-dev after 2.0.0 release (2) (348de4f8)
- Update the readme badges (4) (2a2e11ae)
- Update lock file (22) (ed5c25c8)
- Fix PyPi trusted publishing in GitHub Actions (26) (45c3b42a)
- Fix README publish prymer badge URL (29) (e942368c)

Features

- Add support for `min_primer_pair_hits` to `OffTargetDetector` (44) (0e640079)

Miscellaneous Tasks

- On publish, only upload prymer wheels (33) (9c4858af)

Bug Fixes

- Pad target region by `max_amplicon_length` (23) (dd844f54)
- Executable path validation tests should not be dependent on the user environment (25) (8f151a0d)

Documentation

- Add bioconda badge (9) (8d332df2)

Features

- Make `OffTargetDetector.filter()` generic (19) (02a57b1d)

Miscellaneous Tasks

- Bump version to 2.0.1-dev after 2.0.0 release (2) (348de4f8)
- Update the readme badges (4) (2a2e11ae)
- Update lock file (22) (ed5c25c8)
- Fix PyPi trusted publishing in GitHub Actions (26) (45c3b42a)
- Fix README publish prymer badge URL (29) (e942368c)

New Contributors
* msto made their first contribution in https://github.com/fulcrumgenomics/prymer/pull/19
* clintval made their first contribution in https://github.com/fulcrumgenomics/prymer/pull/26

**Full Changelog**: https://github.com/fulcrumgenomics/prymer/compare/2.0.0...2.1.0

This point release is a hotfix to `2.0.0` to solve an issue where the underlying bwa process would deadlock after processing many primers or primer pairs.

Features

- Redirect BwaAlnInteractive stderr to debug logging (74) (c8bae071)

Miscellaneous Tasks

- Fix GitHub Actions auto-publish (16032acc)