Joshua Klein
Joshua Klein
#### What does this implement/fix? The computationally intensive part of the `scipy.stats.gaussian_kde.evaluate` involves calling `gaussian_kernel_estimate`, which has a triply nested for-loop, but does not release the GIL. This loop could...
This adds the following methods to the `File` type in the Python bindings: - `flush` - `readable` - `writable` - `seekable` - `closed` - `readinto` For `AsyncFile`, the following were...
- Describe the issue or question: Enabling writing sub-mzML fails with FragPipe v21 when the source MS data file is not an mzML file, but does work on v20. The...
This PR adds a new optional dependency on [mzdata](https://github.com/mobiusklein/mzdata) to read the mzMLb file format. mzMLb support was recently added to ProteoWizard, and it provides fast random access to compressed...
`cargo fmt` and `cargo rustfmt` crash when processing https://github.com/mobiusklein/mzdata/blob/34b2d6feb3201140991fa66b53960ab8141c7ed7/src/io/infer_format.rs. See below for traceback. Toolchain: stable-x86_64-pc-windows-msvc Version: rustc 1.76.0 (07dca489a 2024-02-04) Platform: Windows 10 ## Supposition This file specifically started to...
`Glycan.label_branches` curently assigns letter labels based on the order it visits a branch, but it should assign labels closer to `a` to the longer branch. It is hard to know...
`plot`'s current layout algorithm doesn't know about substituents, and they are just drawn on the corner of their parent residue. This causes residues with multiple substituents to be drawn with...
`plot` currently adapts the algorithm from `Improving Walker's algorithm to run in linear time` as implemented by [Bill Mill](http://billmill.org/pymag-trees/) which lays the tree out nicely, but ignores topological information. Create...
Convert `identity.identify` from a linear search to a tree search using `residue_list_to_tree`. Currently the function calls `identity.is_a` on every monosaccharide in the index, which is costly. Instead, it should try...