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Add FastqFile.Offset enum
…ue array elements only
Use NumPy 2.0 API
Trees are now represented as rooted `networkx.DiGraph` objects with integer leaf nodes and a `distance` edge attribute, replacing the Cython `Tree` and `TreeNode` classes. UPGMA and neighbor joining are implemented in Rust, with UPGMA tracking the row minima to avoid rescanning the entire distance matrix. The Newick parser is iterative, hence deeply nested trees no longer hit the recursion limit. Closes #903, closes #397
Remove `Tree` and `TreeNode` class
Remove license banner
The `IntEnum` already existed, but the docstrings and documentation still referred to the removed string offsets. Closes #923
`align_ungapped()`, `align_optimal()`, `align_banded()`, `align_local_gapped()`, `align_multiple()` and `score()` now default to a match score of 1, a mismatch score of -1 and a linear gap penalty of -1. To allow a default for `matrix`, the required `band` and `seed`/`threshold` parameters of `align_banded()` and `align_local_gapped()` now precede it. Closes #930
`annotate_sse()` and `pdbx.get_sse()` return `SecondaryStructure` values, `DsspApp` returns `DsspElement` values. Both enums provide conversion from/to the one-letter symbols. Closes #924
The former `CGO` enum listing the directives is now `CGO.Type`. Closes #909
`load_color_scheme()` returns a `ColorScheme` instead of an untyped dictionary and the plotting functions accept it as `color_scheme`. Closes #908
`GFFFile` entries are now represented by `GFFRecord` objects instead of 9-tuples. Closes #906
`get_locus()` returns a `GenBankLocus` and `set_locus()` accepts one instead of the 6-tuple of locus properties. Closes #925
`GenBankFile` fields are now represented by `GenBankRecord` objects instead of (name, content, subfields) tuples. Closes #907
- The transformation now consists of a single rotation and translation - Transformations can be combined via `*` and inverted via unary `-` - `align_vectors()` and `orient_principal_components()` return the transformation instead of transformed coordinates Closes #844
- `use_author_fields` defaults to `False` in `get_structure()`, `get_assembly()` and `get_unit_cell()` - `get_sequence()` keys the sequences by `label_asym_id` (via `struct_asym`) - `get_sse()` uses `label_asym_id` as chain ID - Tests and documentation that rely on author fields (PDB, PDBQT, PyMOL, foldseek references and hard-coded author IDs) request them explicitly Closes #773
- Remove the `biotite.application` package in favor of `biotite.application_v2` - Remove `align_local_ungapped()`, `set_font_size_in_coord()` and `get_symmetry_mates()` - Remove the deprecated parameters `as_bytes` (`LetterAlphabet.decode*()`), `distance_range` (`connect_via_distances()`), `float_tolerance` (`pdbx.compress()`), `include_bonds` (`pdbx.set_structure()`) and `as_mask` (`CellList.get_atoms*()`) - Remove the `label_entity_id` annotation fallback in `pdbx.set_structure()`
`biotite.application_v2` remains as deprecated shim that forwards to `biotite.application`.
Implement backwards incompatible changes
Support the standard ambiguous `J` amino acid symbol
Since #949 `plot_sequence_logo()` does not accept a plain list of colors anymore.
# Conflicts: # src/biotite/sequence/io/fasta/file.py # src/biotite/structure/io/pdbx/convert.py
Hotfix: Use `ColorScheme` in `rbs_identification.py` example
# Conflicts: # doc/examples/scripts/sequence/homology/genome_search.py # doc/examples/scripts/sequence/sequencing/genome_assembly.py
Merging this PR will regress 1 benchmark
|
| Benchmark | BASE |
HEAD |
Efficiency | |
|---|---|---|---|---|
| ❌ | benchmark_structural_alphabet_methods[to_protein_blocks] |
6.7 ms | 10.1 ms | -34.12% |
| ⚡ | benchmark_set_structure[cif-False] |
92.7 ms | 31.6 ms | ×2.9 |
| ⚡ | benchmark_set_structure[cif-True] |
103.3 ms | 41.6 ms | ×2.5 |
| ⚡ | benchmark_connect[connect_via_distances] |
3.2 ms | 1.7 ms | +86.86% |
| ⚡ | benchmark_superimpose_multi_model[superimpose] |
9.1 ms | 5.6 ms | +60.86% |
| ⚡ | benchmark_superimpose[superimpose] |
1.9 ms | 1.3 ms | +53.37% |
| ⚡ | benchmark_serialize_pdbx[cif] |
177.4 ms | 120.5 ms | +47.2% |
| ⚡ | benchmark_infer_bond_types |
1,199.3 µs | 828.9 µs | +44.68% |
| ⚡ | benchmark_clustering[neighbor_joining] |
554.7 µs | 396.5 µs | +39.89% |
| ⚡ | benchmark_set_structure |
9.4 ms | 7 ms | +35.46% |
| ⚡ | benchmark_set_structure_with_bonds |
9.7 ms | 7.2 ms | +34.88% |
| ⚡ | benchmark_superimpose_multi_model[superimpose_homologs] |
36 ms | 32.1 ms | +12.17% |
| ⚡ | benchmark_superimpose_multi_model[superimpose_without_outliers] |
86.7 ms | 78.2 ms | +10.89% |
Tip
Investigate this regression by commenting @codspeedbot fix this regression on this PR, or directly use the CodSpeed MCP with your agent.
Comparing v2 (0015cef) with main (8fa052e)2
Footnotes
-
14 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩
-
No successful run was found on
main(0015cef) during the generation of this report, so 8fa052e was used instead as the comparison base. There might be some changes unrelated to this pull request in this report. ↩
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With Biotite
1.8.0published, we can include the backwards incompatible changes fromv2inmainand release Biotite2.0.0.