Skip to content

Latest commit

 

History

History
572 lines (429 loc) · 16.7 KB

julia.md

File metadata and controls

572 lines (429 loc) · 16.7 KB

Julia @ IHI Code Club

The REPL

Julia comes with a REPL (Read-Eval-Print-Loop) where you can interactively run commands.

2 + 2
sin(3.14)

You can define simple functions with the one-line syntax

f(x) = 4 * x - 2.5

or with the longer, equivalent, syntax

function g(x)
    return 4 * x - 2.5
end
f(log(57) / 4)
g(log(57) / 4)

You can assign a value to a variable, like the speed of light in vacuum in m/s (underscores are ignored, but make the number more readable)

c = 299_792_458
f(c)

Use the semicolon ; at the end of the line to hide the output of the result

c ^ 4;

Do you note something strange? Can you guess what happened? Read the Frequently Asked Questions in the documentation to know more.

Julia has full support for Unicode

println("人人生而自由,在尊严和权利上一律平等。他们赋有理性和良心,并应以兄弟关系的精神相对待。")

including in identifiers (tip: you can use LaTeX-like commands \alpha + TAB and \beta + TAB to get these symbols)

α = 1.2
β = 3.4
α / β

or even emoji, if your font supports them (tip: use \:apple: + TAB and \:tangerine: + TAB for these). Who said you can't sum apples and oranges?

🍎 = 5
🍊 = 7
🍎 + 🍊

Julia has by default other REPL modes: the package manager mode (that you can enter with ]), the shell-mode (enter with ;) and the help mode (enter with ?).

Arrays and statistics

Julia has native support for arrays

v = [7.43, 5.05, 1.7, 6.68]
length(v)
v[1]
v[3]

You can apply functions or operators with the broadcasting syntax: the dot:

4 .* v .- 2.5

Broadcasting is completely generic and works with user-defined functions:

f.(v)

Nested broadcasted expressions are fused into a single loop. To know more about broadcasting, read the blog post More Dots: Syntactic Loop Fusion in Julia.

We can define a simple function implementing a naive summation algorithm:

function mysum(vector)
    result = 0.0
    for x in vector
        result = result + x # or result += x
    end
    return result
end
mysum(v)

You can generate random numbers with rand and randn:

rand()
randn()

or random arrays by specifying the dimension:

r = randn(1000)
A = rand(4, 4)

Statistical functions are defined in the Statistics.jl standard library

using Statistics

mean(r)
median(r)
std(r)
quantile(r, 0.01)

More advanced statistical functions are provided in third-party packages, like StatsBase.jl.

Rock-paper-scissors: playing with multiple dispatch

We can write a simple implementatio of the popular hand game rock-paper-scissors in less than 10 lines of code in Julia. This implementation will give use the opportunity to have a closer look to one of Julia's main features: multiple dispatch.

Note: this section is based on the blog post Rock–paper–scissors game in less than 10 lines of code.

The game

Here we go:

abstract type Shape end
struct Rock     <: Shape end
struct Paper    <: Shape end
struct Scissors <: Shape end
play(::Type{Paper}, ::Type{Rock}) = "Paper wins"
play(::Type{Paper}, ::Type{Scissors}) = "Scissors wins"
play(::Type{Rock}, ::Type{Scissors}) = "Rock wins"
play(::Type{T}, ::Type{T}) where {T<: Shape} = "Tie, try again"
play(a::Type{<:Shape}, b::Type{<:Shape}) = play(b, a); # Commutativity

That's all. Nine lines of code, as promised.

Play the game

Now that we’ve implemented the game we can play it in the Julia REPL:

play(Paper, Scissors)
play(Rock, Rock)
play(Rock, Paper)

There was no explicit method for the combination of arguments Rock-Paper, but the commutative rule has been used here.

Data science with Julia

Dataframes

DataFrames.jl provides the tools to work with tabular data. This section is largely based on its documentation

using DataFrames
df = DataFrame(A = 1:4, B = ["M", "F", "F", "M"])

Columns can be accessed via df.col, df."col", df[:, "col"] and and a few more options not mentioned here for brevity.

df.A
df[:, "A"]
names(df)

Constructing from another table type

DataFrames.jl can also interact with other packages:

df = DataFrame(a=[1, 2, 3], b=[:a, :b, :c])

# write DataFrame out to CSV file
CSV.write("dataframe.csv", df)

# store DataFrame in an SQLite database table
SQLite.load!(df, db, "dataframe_table")

# transform a DataFrame through Query.jl package
df = df |> @map({a=_.a + 1, _.b}) |> DataFrame

Working with dataframes

df = DataFrame(A = 1:2:40, B = repeat(1:4, inner=5), C = 1:20)
describe(df)
df[7:12, :]
df[:, ["A", "B"]]
df[6:10, ["A", "C"]]
df[iseven.(df.B), :]
df[df.A .> 20, :]
df[(df.A .> 20) .& (iseven.(df.B)), :]

This is only the tip of what you can do with DataFrames.jl. For a more in-depth guide, besides the official documentation of the package check out this tutorial on DataFrames

An alternative stack to deal with tabular data is the Queryverse.

Dataframes and CSV files

For reading and writing tabular data from CSV and other delimited text files, use the CSV.jl package.

using CSV
# Read a dataframe from a CSV file
df = DataFrame(CSV.File(input))
# Create a dataframe to be written to a CSV file
df = DataFrame(x = 1, y = 2)
CSV.write(output, df)

Databases

There are a few packages to access different flavours of databases:

Coming from other languages?

Julia has got you covered! It has a good interoperability with other programming languages, which makes it easier to move to Julia from other languages but still keep using your current toolbox.

Note: all languages are different from each other and of course Julia is no special, so make sure to read the noteworthy differences between Julia and the other languages.

C/Fortran

If you are C or Fortran programmer, calling function in a C/Fortran libraries (in particular, the libraries should be "shared libraries") is as easy as running the ccall function, without writing wrapper code. For example, with this command we can run the function getenv in the standard C library

path = ccall(:getenv, Cstring, (Cstring,), "SHELL")

As you may expect, dealing with C is rather low-level. The output is quite unreadable for a human being, but can be converted to a standard string with

unsafe_string(path)

I will not indulge more into interfacing C libraries, but those interested can read more in the Calling C and Fortran Code section of the manual.

Python and R

Calling Python libraries is made simple by the PyCall.jl package. Simple packages requires little or no effort, The classes in the Python standard library or in the popular NumPy package are naturally translated to their equivalent Julia data types, to make the experience as seamless as possible:

using PyCall

const math = pyimport("math")
const np = pyimport("numpy")

math.sin(pi) - sin(math.pi)

Here we have mixed Python and Julia functions and variables: Python math.sin and math.pi with sin and pi from Julia. The syntax used by PyCall closely resembles that of Python.

Non-standard Python packages can also be called with PyCall and they mostly work without extra work, but you may encounter some quirks. For example, we can play a bit with pandas:

const pd = pyimport("pandas")

df = pd.DataFrame(Dict(:age=>[27, 29, 27], :name=>["James", "Jill", "Jake"]))
df.describe()
df.age

You can note in this case that the custom Python class used by pandas shows here an annoying PyObject text in the output. If you want to use a more integrated interface to pandas, consider the package Pandas.jl.

To call R package, check out RCall.jl.

RCall example

What about plotting?

That's a great question! Plotting is not a field where Julia shines currently. There are several nice plotting packages, with many different features, but a common problem is compilation latency, leading to coining the term "time to first plot". I will list here some of the options:

  • PyPlot.jl: interface to Python's Matplotlib, this is reasonably quick
  • Plots.jl: this is one of the most popular plotting packages in Julia, as it can use to many different plotting backends always using the same interface. It is also extensible: it allows to define "recipes" for custom Julia types. On the other end, it has a large compilation latency. After loading the package, the first plot in a session can take ~20-30 seconds, but this is improving!
  • Makie.jl: it aims to replace Plots.jl in the future, adding many more interactive and 3D features, but it has similar issues in terms of initial plot
  • Gadfly.jl: heavily inspired by "The Grammar of Graphics" book. Kind of quick
  • UnicodePlots.jl: simple plots directly in terminal. Super fast!

More advanced topics

So far we have relatively simple applications of Julia, but if you are interested you can have a look to more advanced ones. Even though the environment is young when compared with established languages like Python and R, many high-quality packages are being used to do avanced scientific research. Here is a summary of some of the most popular ones, classified by topic:

Beyond scientific computing

Julia is mainly employed for scientific computing, but more and more users are realising that its syntax and packages are equally good for general programming, too. The Administrative Scripting with Julia repository is a guide about how to use Julia for system administration. This also rightly points out the shortcomings of Julia in this field: its JIT-compilation model favours launching a single long-running script, rather than many small ones: the latter case can be exceedingly slow as compilation of each script may take much longer than actually running them. Many ways to tackle the issue of the compilation latency are currently being worked out.

Environments and reproducibility

Reproducibility

A great attention is dedicated to reproducibility in the Julia community. The built-in package manager, Pkg.jl, allows you to create environments, which are controlled by two files:

  • Project.toml: it records the list of the packages required in the environment — the direct dependencies — and you can also optioanlly specify the compatibility bounds of these packages, according to Semantic Versioning
  • Manifest.toml: it takes a snapshot al all packages in the environment, with the exact version number of all packages — both direct and indirect dependencies of the environment.

When compatibility bounds are properly used in the Project.toml file, it lets you instantiate at any point in the future a "compatible" environment — "compatible" in the SemVer sense. The Manifest.toml, instead, lets you recreate exactly the same environment.

In its top-level, this repository provides an example of Project.toml with the full specification of compatible versions for all non-standard libraries. The accompanying Manifest.toml lists all packages in the environment. This, for example, allows binder to generate a container with the same set of packages as me.

You can read more about working with environments in the documentation of Pkg.jl.

Also binary package or data can become a "package" with the artifact system: you can add an "artifact", with a version, as dependency to your package or environment to ensure full reproducibility.

Notebooks and literate programming

Julia is fully supported by the popular Jupyter notebooks. In fact, the "Ju" in its names stands for "Julia", alongside with Python and R. Julia kernels for Jupyter notebooks are provided by the IJulia.jl package.

Pluto.jl is a lightweight alternative to Jupyter notebooks. Pluto notebooks are reactive, which means that the values of the cells don't depend on their order of execution, which is a common gripe in Jupyter notebooks.

Pluto notebook

There are different tools for literate programming in Julia. This tutorial was created with Literate.jl, which allows you to generate a Markdown file and a Jupyter noetbook from a simple commented Julia script. Another option is Weave.jl. Similar to Pweave, knitr, R Markdown, and Sweave, Weave.jl supports multiple input and output formats, including HTML and PDF.

Keep in touch

There are several ways to engage the Julia community online:

You can find more resources in the community page of the official website.

This page was generated using Literate.jl.