Igor Sfiligoi
Igor Sfiligoi
DIsk IO can be overlapped with compute, avoiding artificial serialization. Since true async IO does not exist, I add a dedicated thread that reads for the compute threads in parallel...
On small thread count, the polling LockedQueue add substantial overhead to bowtie2, so we revert back to using the lightweight condition_variable based solution there. See #465 for details. We keep...
Currently, the DistanceMatrix supports only the redundant, square in-memory representation of the data. For memory constrained setups, we should support non-redundant representation, too. The most obvious alternative is SciPy's condensed...
We currently only support fp64 and fp32 values in distance matrices. However, many problems do not need neither that much precision nor that much dynamic range. Indeed, the semantics of...
The unifrac implementation in the unifrac-binaries library has been extensively used by several communities, but it is currently not directly accessible through the scikit-bio interface (relying instead on a separate...
Update unifrac-binaries to v1.6.1 and add ARM linux support ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions * If this PR...
Most libraries and tools these days automatically detect and use all the CPU cores that are available. To properly play with node sharing, e.g. in batch systems but not only,...