3.0.2

Miscellaneous Tasks

• Fix publishing workflow (#123) (a0fd228)

3.0.0

Bug Fixes

• Change int weights to float weights, update doctest examples (#61) (f71dc65)
• Check against HN tag instead of is_unmapped property (#69) (364a9dc)
• Pad target region by max_amplicon_length (#23) (dd844f5)
• Executable path validation tests should not be dependent on the user environment (#25) (8f151a0)

Documentation

• Expand the documentation for OffTargetDetector (#46) (c434b1d)
• Add bioconda badge (#9) (8d332df)

Features

• Use OffTargetDetector and ExecutableRunner as ContextManagers (#64) (5515d05)
• Remove pysam and bwa warmup hack (#65) (a132a52)
• Use bwa-aln-interactive and upgrade developer's docs (#32) (d87e740)
• Redirect BwaAlnInteractive stderr to debug logging (#74) (5d79a52)
• Add thermodynamic-related weights and parameters for PickHybProbeOnly task (#60) (9f51325)
• Ensure FileBasedVariantLookup is used as a context manager (#71) (7e2e784)
• Speed improvements for primer pair hit building from single primer hits (#99) (baf2e65)
• Add parameter validation for OffTargetDetector.__init__ (#103) (a193734)
• Add support for min_primer_pair_hits to OffTargetDetector (#44) (0e64007)
• Make OffTargetDetector.filter() generic (#19) (02a57b1)

Miscellaneous Tasks

• Export PickHybProbeOnly task (#70) (8638e3b)
• Unpin fgpyo dependency (#97) (3c3ed80)
• Unpin pybedlite dependency (#98) (fbd1aa1)
• On publish only upload prymer wheels (#33) (9c4858a)

Refactor

• Export Primer3Parameters and Primer3Weights (#36) (bc0622d)
• Export OffTargetDetector (#37) (1451938)
• Primer -> Oligo, PrimerLike -> OligoLike (#51) (93ea6e7)
• Make PrimerPair.amplicon a cached property (#93) (385e1b1)

CI

• Migrate ubuntu-latest to ubuntu-24.04 (#96) (f62c4b5)

Miscellaneous Tasks

• Bump version to 2.0.1-dev after 2.0.0 release (#2) (348de4f)
• Update the readme badges (#4) (2a2e11a)
• Update lock file (#22) (ed5c25c)
• Fix PyPi trusted publishing in GitHub Actions (#26) (45c3b42)
• Fix README publish prymer badge URL (#29) (e942368)

2.0.1

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) (c8bae07)

Miscellaneous Tasks

• Fix GitHub Actions auto-publish (16032ac)

2.2.0

Features

• Add support for min_primer_pair_hits to OffTargetDetector (#44) (0e64007)

2.1.1

Miscellaneous Tasks

• On publish, only upload prymer wheels (#33) (9c4858a)

2.1.0

Bug Fixes

• Pad target region by max_amplicon_length (#23) (dd844f5)
• Executable path validation tests should not be dependent on the user environment (#25) (8f151a0)

Documentation

• Add bioconda badge (#9) (8d332df)

Features

• Make OffTargetDetector.filter() generic (#19) (02a57b1)

Miscellaneous Tasks

• Bump version to 2.0.1-dev after 2.0.0 release (#2) (348de4f)
• Update the readme badges (#4) (2a2e11a)
• Update lock file (#22) (ed5c25c)
• Fix PyPi trusted publishing in GitHub Actions (#26) (45c3b42)
• Fix README publish prymer badge URL (#29) (e942368)

New Contributors

• @msto made their first contribution in #19
• @clintval made their first contribution in #26

Full Changelog: 2.0.0...2.1.0

2.0.0

This is the first release of prymer, a Python primer design library by Fulcrum Genomics

What's Changed

• chore(release): bump to 2.0.0 by @nh13 in #1

New Contributors

• @nh13
• @msto
• @emmcauley
• @tfenne
• @yfarjoun

Full Changelog: https://github.com/fulcrumgenomics/prymer/commits/2.0.0