The is package provides a variety of common utilities that can be used by downstream automatic differentiation (AD) tools to define and execute forward-, reverse-, and mixed-mode primitives.

This package exports following operations over bit vectors with extremely fast speed while keeping extra memory usage small:

• getindex(bv::IndexableBitVectors, i::Integer): i-th element of bv

• rank(b::Bool, bv::AbstractIndexableBitVector, i::Integer): the number of occurrences of bit b in bv[1:i]

• select(b::Bool, bv::AbstractIndexableBitVector, i::Integer): the index of i-th occurrence of b in bv.

and other shortcuts or types.

Various special functions based on log and exp moved from StatsFuns.jl into a separate package, to minimize dependencies. These functions only use native Julia code, so there is no need to depend on librmath or similar libraries.

This package provides generic methods and modules used in many of the other BioJulia packages. This package defines IO, exceptions, and other types or methods used by other BioJulia packages.

This package provides information about the features of the host CPU in Julia.

This package provides a summary of available CPU features in Julia.

This package provides an interface to invert functions.

This package is intended as a lightweight foundation for tensor operations across the Julia ecosystem. Currently it exports three operations: hadamard, tensor, and boxdot.

BSON.jl is a Julia package for working with the Binary JSON serialisation format. It can be used as a general store for Julia data structures.

The @unpack and @pack! macros work to unpack types, modules, and dictionaries.

This package only contains and exports a single function realdot(x, y). It computes real(LinearAlgebra.dot(x, y)) while avoiding computing the imaginary part of LinearAlgebra.dot(x, y) if possible. The real dot product is useful when one treats complex numbers as embedded in a real vector space.

The Preferences package provides an integrated way for packages to store configuration switches to persistent TOML files, and use those pieces of information at both run time and compile time in Julia. This enables the user to modify the behavior of a package, and have that choice reflected in everything from run time algorithm choice to code generation at compile time.

Jive.jl is a Julia package to help with writing tests.

This package provides a convenient Julia interface for loading standard named test images and example images for the internal usage in JuliaImages. This can be used in conjunction with the Images package.

This package provides Julia implementation of C-style interface to CFITSIO functions with following features:

• Function names closely mirror the C interface (e.g., fits_open_file()).

• Functions operate on FITSFile, a thin wrapper for fitsfile C struct (FITSFile has concept of "current HDU", as in CFITSIO).

• Wrapper functions do check the return status from CFITSIO and throw an error with the appropriate message.

This package provides a combinatorics library for Julia, focusing mostly (as of now) on enumerative combinatorics and permutations.

This package provides a framework for implementing statically sized arrays in Julia, using the abstract type StaticArraySize,T,N <: AbstractArrayT,N. Subtypes of StaticArray will provide fast implementations of common array and linear algebra operations.

This package implements "lazy" in-place elementwise transformations of arrays for the Julia programming language. Explicitly, it provides a "view" M of an array A so that M[i] = f(A[i]) for a specified (but arbitrary) function f, without ever having to compute M explicitly (in the sense of allocating storage for M). The name of the package comes from the fact that M == map(f, A).

This package lazily represents matrices filled with a single entry, as well as identity matrices. This package exports the following types: Eye, Fill, Ones, Zeros, Trues and Falses.

This package provides a namespace for data-related generic function definitions to solve the optional dependency problem; packages wishing to share and/or extend functions can avoid depending directly on each other by moving the function definition to DataAPI.jl and each package taking a dependency on it.

ReferenceTests.jl is a Julia package that adds a couple of additional macros to your testing toolbox. In particular, it focuses on functionality for testing values against reference files, which in turn the package can help create and update if need be.

This package implements a trait-based framework for describing array layouts such as column major, row major, etc. that can be dispatched to appropriate BLAS or optimised Julia linear algebra routines. This supports a much wider class of matrix types than Julia's in-built StridedArray.

This package provides bit twiddling convenience functions in Julia. These are useful for going to the next or previous mask size or for calculating corresponding shifts.

Optimisers.jl defines many standard gradient-based optimisation rules, and tools for applying them to deeply nested models.