Hallongrotta v5.5.11

What's Changed

• Simplified how the Dseqrecord add handles features. by @BjornFJohansson in #598
• Bump pytest from 9.0.2 to 9.0.3 by @dependabot[bot] in #599
• Modify only_adjacent_edges to rely on overlapping locations only by @manulera in #602
• Add inversion assemblies #603

Full Changelog: v5.5.10...v5.5.11

Runebergstårta v5.5.10

What's Changed

• removed unused and commented by @BjornFJohansson in #588
• Fix notebook output by @manulera in #592
• removed more cruft in assembly by @BjornFJohansson in #594
• Remove gpl.txt by @manulera in #596
• proposed fix by @BjornFJohansson in #595
• Allow restriction fragments as inputs to restriction_ligation_overlap algorithm by @manulera in #593
• Bump pillow from 12.1.1 to 12.2.0 by @dependabot[bot] in #591
• Bump regex from 2026.3.32 to 2026.4.4 by @dependabot[bot] in #590

Full Changelog: v5.5.9...v5.5.10

Napoleonbakelse v5.5.9

What's Changed

• Parser update by @BjornFJohansson in #573
• Parser upd 2 by @BjornFJohansson in #574
• Bump coverage from 7.13.4 to 7.13.5 by @dependabot[bot] in #577
• Bump pytest-cov from 7.0.0 to 7.1.0 by @dependabot[bot] in #576
• Validate history by @manulera in #575
• Improve validation and normalization of history by @manulera in #579
• Parse snapgene history from .dna files by @manulera in #580
• Bug in crispr by @BjornFJohansson in #582
• Update to biopython 1.87 by @manulera in #587

Full Changelog: v5.5.8...v5.5.9

Jordgubbstårta v5.5.8

What's Changed

• Generalised recombinase functionality by @manulera in #564
• Fix test to support biopython 1.86 by @manulera in #566
• Fix melting functions and add shift_melt_cutsite_pairs by @manulera in #565
• Dseq join that respects sticky ends by @BjornFJohansson in #572
• Refactor parsers by @manulera in #567

Dependencies

• Bump black from 25.12.0 to 26.3.1 by @dependabot[bot] in #571
• Bump tornado from 6.5.4 to 6.5.5 by @dependabot[bot] in #570
• Bump pillow from 12.1.0 to 12.1.1 by @dependabot[bot] in #562
• Bump coverage from 7.13.2 to 7.13.4 by @dependabot[bot] in #561
• Bump pytest-doctestplus from 1.7.0 to 1.7.1 by @dependabot[bot] in #555

Full Changelog: v5.5.7...v5.5.8

Prinsesstårta-patch v5.5.7

What's Changed

• Bump pydivsufsort from 0.0.18 to 0.0.20 by @dependabot[bot] in #549
• Bump regex from 2024.11.6 to 2026.1.15 by @dependabot[bot] in #548
• Bump coverage from 7.13.1 to 7.13.2 by @dependabot[bot] in #547
• Bump wheel from 0.45.1 to 0.46.2 by @dependabot[bot] in #539
• renamed import of BioPython SeqRecord in order to make it more obvious… by @BjornFJohansson in #552
• changed the Dseq.repr for Dseqs that are single stranded for clarity. by @BjornFJohansson in #553
• try fix flaky tests/test_module_contig2.py::test_mpl2 by @BjornFJohansson in #551
• Temporary solution to a problem caused by #557 by @manulera in #558

Full Changelog: v5.5.6...v5.5.7

Prinsesstårta v5.5.6

What's Changed

• Remove download by @BjornFJohansson in #531
• Fix usage of circular_only in in-fusion and fusion pcr assemblies by @manulera in #534
• removed id and name settings for Dseqrecord slices by @BjornFJohansson in #536
• fixed seguid for seqs with U (uracil) by @BjornFJohansson in #540
• skipped test as not to irritate server by @BjornFJohansson in #541
• Correctly trim 5' or 3' in Gibson / in-fusion assembly algorithms by @manulera in #538
• allowing dscode in format Dseqrecord method optionally by @BjornFJohansson in #544
• added a test and a line that removes repeated enzymes in the Dseq.getcutsites by @BjornFJohansson in #542

Full Changelog: v5.5.5...v5.5.6

Wienerbröd v5.5.5

New

• A graphic representation for the Contig class by @BjornFJohansson in #514
• Adding the primer_screen module by @BjornFJohansson in #513

What's Changed

• Fix notebook link by @manulera in #485
• Fix notebook links in docs by @manulera in #493
• New dseq manu bjorn rebased by @manulera in #484
• Dseq mw by @BjornFJohansson in #500
• Add examples for Bioengineering/SynBio projects by @hiyama341 in #486
• Bump urllib3 from 2.5.0 to 2.6.3 by @dependabot[bot] in #501
• Bump filelock from 3.20.0 to 3.20.1 by @dependabot[bot] in #497
• Bump fonttools from 4.60.1 to 4.61.0 by @dependabot[bot] in #491
• Bump pytest from 8.4.2 to 9.0.0 by @dependabot[bot] in #482
• Bump pre-commit from 4.3.0 to 4.4.0 by @dependabot[bot] in #481
• Bump coverage from 7.11.0 to 7.11.3 by @dependabot[bot] in #479
• Bump black from 25.9.0 to 25.11.0 by @dependabot[bot] in #478
• Bump regex from 2024.11.6 to 2025.11.3 by @dependabot[bot] in #480
• Prevent circular sequences to be first or last on linear assemblies by @manulera in #503
• Bump prettytable from 3.16.0 to 3.17.0 by @dependabot[bot] in #508
• Bump pyparsing from 3.2.5 to 3.3.1 by @dependabot[bot] in #507
• Bump pillow from 12.0.0 to 12.1.0 by @dependabot[bot] in #506
• Bump pytest-doctestplus from 1.5.0 to 1.7.0 by @dependabot[bot] in #505
• Bump matplotlib from 3.10.7 to 3.10.8 by @dependabot[bot] in #504
• Cloning history for parsed files and sequences request from genbank + extending opencloning_models by @manulera in #502
• Use only_adjacent_edges=True in restriction_ligation_assembly by @manulera in #509
• [skip ci] update docs readme by @manulera in #516
• Fix printing from the pydna.readers.read when it fails because of too many sequences by @BjornFJohansson in #512
• A graphic representation for the Contig class by @BjornFJohansson in #514
• Adding the primer_screen module by @BjornFJohansson in #513
• Drop underscore imports by @manulera in #524
• Run linters on all python files by @manulera in #525
• Bump coverage from 7.11.3 to 7.13.1 by @dependabot[bot] in #521
• Bump numpydoc from 1.9.0 to 1.10.0 by @dependabot[bot] in #519
• Bump filelock from 3.20.1 to 3.20.3 by @dependabot[bot] in #511
• Bump virtualenv from 20.35.4 to 20.36.1 by @dependabot[bot] in #510
• Bump pre-commit from 4.4.0 to 4.5.1 by @dependabot[bot] in #517
• Bump pytest from 9.0.0 to 9.0.2 by @dependabot[bot] in #518
• Remove unused files by @manulera in #526
• Remove fill_in from assembly2 and use Dseq methods by @manulera in #528
• Update nbstripout by @manulera in #527
• store release names in Gdoc with link from readme by @BjornFJohansson in #529
• removed test code that was never executed. by @BjornFJohansson in #530

Full Changelog: v5.5.4...v5.5.5

Mazarin v5.5.4

What's Changed

• New docs by @manulera in #449
• Bump charset-normalizer from 3.4.2 to 3.4.4 by @dependabot[bot] in #457
• Bump idna from 3.10 to 3.11 by @dependabot[bot] in #454
• Bump rpds-py from 0.26.0 to 0.27.1 by @dependabot[bot] in #447
• Bump tornado from 6.5.1 to 6.5.2 by @dependabot[bot] in #446
• Bump requests from 2.32.4 to 2.32.5 by @dependabot[bot] in #444
• Bump soupsieve from 2.7 to 2.8 by @dependabot[bot] in #464
• Bump fastjsonschema from 2.21.1 to 2.21.2 by @dependabot[bot] in #463
• Bump regex from 2024.11.6 to 2025.10.23 by @dependabot[bot] in #462
• Bump matplotlib-inline from 0.1.7 to 0.2.1 by @dependabot[bot] in #461
• Bump ipykernel from 6.30.0 to 6.31.0 by @dependabot[bot] in #460
• Fix requirements file and update deps by @manulera in #465
• Cloning history by @manulera in #450
• Drop the usage of requirements by @manulera in #467
• Update docs action and documentation by @manulera in #468
• Update history notebook by @manulera in #469
• Update codecov action by @manulera in #473

Full Changelog: v5.5.3...v5.5.4

Hackathon DTU v5.5.3

What's Changed

• Improved test_pYPK7_TDH3_GAL2_PGI1 by @BjornFJohansson in #390
• fix for #389 by @BjornFJohansson in #391
• Remove hook preventing commit to master by @manulera in #394
• Update Contributing section in README by @manulera in #397
• Add Code of Conduct by @manulera in #396
• Add example notebooks and data for HT CAZyme and Kozak library primer design by @manulera in #405
• Sync requirements by @manulera in #408
• Add hackathon notebook by @manulera in #421
• Trim output of cells in hackathon notebook by @manulera in #422
• Update paths of notebooks by @manulera in #423
• Update notebooks with paths2 by @manulera in #424
• re-format test for assemblies with black by @manulera in #430
• Specific assemblies by @manulera in #429

Full Changelog: v5.5.2...v5.5.3

Mockaruta v5.5.2

What's Changed

• New init by @manulera in #366
• New assembly model by @manulera in #369
• Update readme links by @manulera in #376
• Update README.md by @manulera in #378
• Update README.md 2 by @manulera in #379
• Fix action to run coverage on master branch by @manulera in #380
• Separate hooks from codecov in actions by @manulera in #381
• No pre-commit on master branch gh actions by @manulera in #382
• removed conda link by @BjornFJohansson in #386
• Remove Björn's local machine paths from repository files by @Copilot in #385
• Remove conda files by @manulera in #383

New Contributors

• @Copilot made their first contribution in #385

Full Changelog: v5.5.1...v5.5.2