Patrick Kunzmann

Unclarities in specification

3

While implementing a `BinaryCIF` file interface and I found some parts of the specification ambiguous: - What are the integer values a `mask` can hold and how do they map...

Currently `PDBFile.set_structure()` does not restrict the upper bound of float values in the atom annotations (e.g. coordinates). However the fixed columns in PDB only allow for a certain value range:...

Currently `MolFile` only supports `V2000` CTAB formats. However, there are also many V3000 MOL/SDF files out there. The authoring company [even recommends using V3000](https://discover.3ds.com/sites/default/files/2020-08/biovia_ctfileformats_2020.pdf).

Currently, `write_alignment_to_cigar()` omits terminal gaps in the segment sequence. However, there are use cases where it is practical to keep terminal gaps as deletions (`D` code). An optional parameter would...

This PR implements `ruff` as code formatter and linter and reformats the entire code base (except Cython https://github.com/astral-sh/ruff/issues/10250).

Implementing TRR/XTC support

2

Currently Biotite requires *MDTraj* as additional dependency only for reading coordinates from trajectory files. However, *MDTraj* does not support NumPy 2.0, yet, but Biotite 1.0 will require NumPy 2.0. Therefore...

Adding more tutorials

3

The new documentation #552 contains also a revamped tutorial. However, some important sets of functionalities miss a tutorial: - [ ] `tantan` application interface: `tutorial/application/tantan` - [ ] `sra-tools` application...

Resolves #569 .

Currently the default color scheme for protein sequence alignment and logo plots is `"rainbow"`. However `"flower"` is visually more appealing and depicts amino acid similarities better: https://doi.org/10.1186/s12859-020-3526-6

As the Biotite code base has become quite stable and well tested in recent years, a `1.0` release is reasonable. However, before all necessary backwards incompatible changes should be implemented...