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Merge `v2` into `main` - #968

Merged

padix-key merged 45 commits into

mainfrom

Oct 16, 2026

Merged

Merge `v2` into `main`#968
padix-key merged 45 commits into
mainfrom
v2

Commits on Jul 16, 2026
- Add FASTQ offset enum
  ehsanestaji
  committed
  ad89e6d
- Use FastqFile.Offset across FASTQ APIs
  ehsanestaji
  committed
  3835331
- Remove obsolete FASTQ legacy offset test
  ehsanestaji
  committed
  eb4753b
Commits on Jul 18, 2026
- Merge pull request #928 from ehsanestaji/feat/923-fastq-offset-enum
  padix-key
  authored
  1b203c7
Commits on Sep 12, 2026
- Merge branch 'main' into v2
  padix-key
  committed
  63613ea
Commits on Sep 14, 2026
- Merge branch 'main' into v2
  padix-key
  committed
  2914c9b
Commits on Sep 22, 2026
- Use NumPy 2.0 API
  padix-key
  committed
  ab923ec
- Fix `hbond()` being able to assigned donor-hydrogen pairs over chain
  padix-key
  committed
  6a6ec44
- Introduce `map_unique()` as generalized way to map a function to unique array elements only
  padix-key
  committed
  b353ae7
- Fix CI failures
  padix-key
  committed
  9059962
Commits on Sep 23, 2026
- Merge pull request #942 from padix-key/issue-919
  padix-key
  authored
  f7a1895
- Merge branch 'main' into v2
  padix-key
  committed
  ab2c363
- Migrate `biotite.sequence.phylo` to `networkx` graphs and Rust
  padix-key
  committed
  5139a12
- Merge pull request #944 from padix-key/phylo-networkx
  padix-key
  authored
  876ce47
- Remove license banner
  padix-key
  committed
  98e4094
Commits on Sep 24, 2026
- Merge pull request #948 from padix-key/issue-947
  padix-key
  authored
  b314fa7
Commits on Oct 14, 2026
- Merge branch 'main' into v2
  padix-key
  committed
  d2581c6
- Make `EValueEstimator.from_samples()` accept a `Generator`
  padix-key
  committed
  a3d25f9
- Do not introduce line breaks in `FastaFile` by default
  padix-key
  committed
  a1a5d2a
- Document `FastqFile.Offset` as the sole alternative to integer offsets
  padix-key
  committed
  af45afd
- Remove `verbose` parameter from `fetch()` functions
  padix-key
  committed
  b7c5978
- Make `fetch()` functions accept and return `Path` objects
  padix-key
  committed
  9b9c442
- Change default scoring scheme for alignment functions
  padix-key
  committed
  8c13c8d
- Represent secondary structure elements as `IntEnum`
  padix-key
  committed
  128231b
- Represent Compiled Graphics Objects using dedicated `CGO` class
  padix-key
  committed
  e57dd28
- Add `ColorScheme` dataclass
  padix-key
  committed
  84045c7
- Add `GFFRecord` dataclass
  padix-key
  committed
  7463169
- Add `GenBankLocus` dataclass
  padix-key
  committed
  c78eaa2
- Add `GenBankRecord` dataclass
  padix-key
  committed
  9ad425a
- Refactor `AffineTransformation` into `RigidTransformation`
  padix-key
  committed
  32e966f
- Use `label` fields by default in `biotite.structure.io.pdbx`
  padix-key
  committed
  3d90260
- Remove deprecated code
  padix-key
  committed
  d40a7e7
- Rename `biotite.application_v2` to `biotite.application`
  padix-key
  committed
  ea52625
- fixup! Represent secondary structure elements as `IntEnum`
  padix-key
  committed
  b42305a
- fixup! Add `GFFRecord` dataclass
  padix-key
  committed
  235b53b
- fixup! Use `label` fields by default in `biotite.structure.io.pdbx`
  padix-key
  committed
  a7be4be
- fixup! Add `ColorScheme` dataclass
  padix-key
  committed
  debd78d
- fixup! Refactor `AffineTransformation` into `RigidTransformation`
  padix-key
  committed
  13c0f2e
- Merge pull request #949 from padix-key/v2-finish
  padix-key
  authored
  c647245
- Support the standard ambiguous `J` amino acid symbol
  padix-key
  committed
  3a13834
Commits on Oct 15, 2026
- Merge pull request #958 from padix-key/j-support
  padix-key
  authored
  eeb3637
- Use `ColorScheme` in `rbs_identification.py`
  padix-key
  committed
  83b9dc5
- Merge branch 'main' into v2
  padix-key
  committed
  9c84779
- Merge pull request #965 from padix-key/color-scheme-example
  padix-key
  authored
  bb43f93
- Merge branch 'main' into v2
  padix-key
  committed
  0015cef

Commits

Commits on Jul 16, 2026

Commits on Jul 18, 2026

Commits on Sep 12, 2026

Commits on Sep 14, 2026

Commits on Sep 22, 2026

Commits on Sep 23, 2026

Commits on Sep 24, 2026

Commits on Oct 14, 2026

Commits on Oct 15, 2026