Lab 01: Introduction to Julia

This lab should get everyone up to speed in the basics of Julia's installation, syntax and basic coding. For more detailed introduction you can check out Lectures 1-3 of the bachelor course.

Testing Julia installation (custom setup)

In order to proceed further let's run a simple script to see, that the setup described in chapter Installation is working properly. After spawning a terminal/cmdline run this command:

julia ./test_setup.jl

The script does the following

• "Tests" if Julia is added to path and can be run with julia command from anywhere
• Prints Julia version info
• Checks Julia version.
• Checks git configuration (name + email)
• Creates an environment configuration files
• Installs a basic pkg called BenchmarkTools, which we will use for benchmarking a simple function later in the labs.

There are some quality of life improvements over long term support versions of Julia and thus throughout this course we will use the latest stable release of Julia 1.6.x.

Polynomial evaluation example

Let's consider a common mathematical example for evaluation of nth-degree polynomial

\[f(x) = a_{n}x^{n} + a_{n-1}x^{n-1} + \dots + a_{0}x^{0},\]

where $x \in \mathbb{R}$ and $\vec{a} \in \mathbb{R}^{n+1}$.

The simplest way of writing this in a generic fashion is realizing that essentially the function $f$ is really implicitly containing argument $\vec{a}$, i.e. $f \equiv f(\vec{a}, x)$, yielding the following Julia code

function polynomial(a, x)
    accumulator = 0
    for i in length(a):-1:1
        accumulator += x^(i-1) * a[i] # ! 1-based indexing for arrays
    end
    return accumulator
end

a = [-19, 7, -4, 6] # list coefficients a from a^0 to a^n
x = 3               # point of evaluation

julia> function polynomial(a, x)
           accumulator = 0
           for i in length(a):-1:1
               accumulator += x^(i-1) * a[i] # ! 1-based indexing for arrays
           end
           return accumulator
       endpolynomial (generic function with 1 method)

julia> a = [-19, 7, -4, 6]4-element Vector{Int64}:
 -19
   7
  -4
   6
julia> x = 33

julia> polynomial(a, x)    # function call128

Thanks to the high level nature of Julia language it is often the case that examples written in pseudocode are almost directly rewritable into the language itself without major changes and the code can be thus interpreted easily.

Due to the existence of the end keyword, indentation is not necessary as opposed to other languages such as Python, however it is strongly recommended to use it, see style guide.

Though there are libraries/IDEs that allow us to step through Julia code (Debugger.jl link and VSCode link), here we will explore the code interactively in REPL by evaluating pieces of code separately.

Basic types, assignments and variables

When defining a variable through an assignment we get the representation of the right side, again this is different from the default behavior in Python, where the output of assignments a = [-19, 7, -4, 6] or x = 3, prints nothing. Internally Julia returns the result of the display function.

julia> a = [-19, 7, -4, 6]4-element Vector{Int64}:
 -19
   7
  -4
   6
julia> display(a) # should return the same thing as the line above

As you can see, the string that is being displayed contains information about the contents of a variable along with it's type in this case this is a Vector/Array of Int types. If the output of display is insufficient the type of variable can be checked with the typeof function:

julia> typeof(a)Vector{Int64} (alias for Array{Int64, 1})

Additionally for collection/iterable types such as Vector there is also the eltype function, which returns the type of elements in the collection.

julia> eltype(a)Int64

In most cases variables store just a reference to a place in memory either stack/heap (exceptions are primitive types such as Int, Float) and therefore creating an array a, "storing" the reference in b with an assignment and changing elements of b, e.g. b[1] = 2, changes also the values in a.

julia> x = 3.03.0
julia> accumulator = 00
julia> typeof(x), typeof(accumulator)(Float64, Int64)

For cycles and ranges

Moving further into the polynomial function we encounter the definition of a for cycle, with the de facto standard syntax

for iteration_variable in iterator
    # do something
end

As an example of iterator we have used an instance of a range type

julia> r = length(a):-1:14:-1:1
julia> typeof(r)StepRange{Int64, Int64}

As opposed to Python, ranges in Julia are inclusive, i.e. they contain number from start to end - in this case running from 4 to 1 with negative step -1, thus counting down. This can be checked with the collect and/or length functions.

julia> collect(r)4-element Vector{Int64}:
 4
 3
 2
 1
julia> length(r)4

julia> c = collect(2:2:42)21-element Vector{Int64}:
  2
  4
  6
  8
 10
 12
 14
 16
 18
 20
  ⋮
 26
 28
 30
 32
 34
 36
 38
 40
 42
julia> d = copy(c)21-element Vector{Int64}:
  2
  4
  6
  8
 10
 12
 14
 16
 18
 20
  ⋮
 26
 28
 30
 32
 34
 36
 38
 40
 42
julia> d[7] = 1313
julia> d21-element Vector{Int64}:
  2
  4
  6
  8
 10
 12
 13
 16
 18
 20
  ⋮
 26
 28
 30
 32
 34
 36
 38
 40
 42

Functions and operators

Let us now move from the function body to the function definition itself. From the picture at the top of the page, we can infer the general syntax for function definition:

function function_name(arguments)
    # do stuff with arguments and define output value `something`
    return something
end

The return keyword can be omitted, if the last line being evaluated contains the result.

By creating the function polynomial we have defined a variable polynomial, that from now on always refers to a function and cannot be reassigned to a different type, like for example Int.

julia> polynomial = 42ERROR: invalid redefinition of constant Main.polynomial

This is caused by the fact that each function defines essentially a new type, the same like Int ~ Int64 or Vector{Int}.

julia> typeof(polynomial)typeof(Main.polynomial) (singleton type of function polynomial, subtype of Function)

You can check that it is a subtype of the Function abstract type, with the subtyping operator <:

julia> typeof(polynomial) <: Functiontrue

These concepts will be expanded further in the type system lecture, however for now note that this construction is quite useful for example if we wanted to create derivative rules for our function derivativeof(::typeof(polynomial), ...).

Looking at mathematical operators +, *, we can see that in Julia they are also standalone functions.

julia> ++ (generic function with 284 methods)
julia> ** (generic function with 407 methods)

The main difference from our polynomial function is that there are multiple methods, for each of these functions. Each one of the methods corresponds to a specific combination of arguments, for which the function can be specialized to using multiple dispatch. You can see the list by calling a methods function:

julia> methods(+)
# 190 methods for generic function "+":                                                                               
[1] +(x::T, y::T) where T<:Union{Int128, Int16, Int32, Int64, Int8, UInt128, UInt16, UInt32, UInt64, UInt8} in Base at
 int.jl:87                                                                                                            
[2] +(c::Union{UInt16, UInt32, UInt64, UInt8}, x::BigInt) in Base.GMP at gmp.jl:528                                   
[3] +(c::Union{Int16, Int32, Int64, Int8}, x::BigInt) in Base.GMP at gmp.jl:534
...

One other notable difference is that these functions allow using both infix and postfix notation a + b and +(a,b), which is a specialty of elementary functions such as arithmetic operators or set operation such as ∩, ∪, ∈.

The functionality of methods is complemented with the reverse lookup methodswith, which for a given type returns a list of methods that can be called with it as an argument.

julia> methodswith(Int)
[1] +(x::T, y::T) where T<:Union{Int128, Int16, Int32, Int64, Int8, UInt128, UInt16, UInt32, UInt64, UInt8} in Base at int.jl:87
[2] +(c::Union{Int16, Int32, Int64, Int8}, x::BigInt) in Base.GMP at gmp.jl:534
[3] +(c::Union{Int16, Int32, Int64, Int8}, x::BigFloat) in Base.MPFR at mpfr.jl:384
[4] +(x::BigFloat, c::Union{Int16, Int32, Int64, Int8}) in Base.MPFR at mpfr.jl:379
[5] +(x::BigInt, c::Union{Int16, Int32, Int64, Int8}) in Base.GMP at gmp.jl:533
...

julia> function addone(x)
           x + 1
       endaddone (generic function with 1 method)
julia> addone(1) == 2true

Calling for help

In order to better understand some keywords we have encountered so far, we can ask for help in the Julia's REPL itself with the built-in help terminal. Accessing help terminal can be achieved by writing ? with a query keyword after. This searches documentation of all the available source code to find the corresponding keyword. The simplest way to create documentation, that can be accessed in this way, is using so called docstrings, which are multiline strings written above function or type definition.

"""
    polynomial(a, x)

Returns value of a polynomial with coefficients `a` at point `x`.
"""
function polynomial(a, x)
    # function body
end

More on this in lecture 4 about pkg development.

  typeof(x)

  Get the concrete type of x.

  Examples
  ≡≡≡≡≡≡≡≡≡≡

  julia> a = 1//2;
  
  julia> typeof(a)
  Rational{Int64}
  
  julia> M = [1 2; 3.5 4];
  
  julia> typeof(M)
  Matrix{Float64} (alias for Array{Float64, 2})

Testing waters

As the arguments of the polynomial functions are untyped, i.e. they do not specify the allowed types like for example polynomial(a, x::Number) does, the following exercise explores which arguments the function accepts, while giving expected result.

af = [-19.0, 7.0, -4.0, 6.0]
at = (-19, 7, -4, 6)
ant = (a₀ = -19, a₁ = 7, a₂ = -4, a₃ = 6)
a2d = [-19 -4; 7 6]
ac = [2i^2 + 1 for i in -2:1]

julia> typeof(af), eltype(af)(Vector{Float64}, Float64)
julia> polynomial(af, x)128.0

julia> typeof(at), eltype(at)(NTuple{4, Int64}, Int64)
julia> polynomial(at, x)128.0

julia> typeof(ant), eltype(ant)(@NamedTuple{a₀::Int64, a₁::Int64, a₂::Int64, a₃::Int64}, Int64)
julia> polynomial(ant, x)128.0

julia> typeof(a2d), eltype(a2d)(Matrix{Int64}, Int64)
julia> polynomial(a2d, x)128.0

julia> typeof(ac), eltype(ac)(Vector{Int64}, Int64)
julia> polynomial(ac, x)108.0

So far we have seen that polynomial function accepts a wide variety of arguments, however there are some understandable edge cases that it cannot handle.

Consider first the vector/array of characters ach

ach = ['1', '2', '3', '4']

4-element Vector{Char}:
 '1': ASCII/Unicode U+0031 (category Nd: Number, decimal digit)
 '2': ASCII/Unicode U+0032 (category Nd: Number, decimal digit)
 '3': ASCII/Unicode U+0033 (category Nd: Number, decimal digit)
 '4': ASCII/Unicode U+0034 (category Nd: Number, decimal digit)

which themselves have numeric values (you can check by converting them to Int Int('1') or convert(Int, '1')). In spite of that, our untyped function cannot process such input, as there isn't an operation/method that would allow multiplication of Char and Int type. Julia tries to promote the argument types to some common type, however checking the promote_type(Int, Char) returns Any (union of all types), which tells us that the conversion is not possible automatically.

julia> typeof(ach), eltype(ach)(Vector{Char}, Char)
julia> polynomial(ach, x)ERROR: MethodError: no method matching *(::Float64, ::Char)

Closest candidates are:
  *(::Any, ::Any, ::Any, ::Any...)
   @ Base operators.jl:587
  *(::ChainRulesCore.NotImplemented, ::Any)
   @ ChainRulesCore ~/.julia/packages/ChainRulesCore/zgT0R/src/tangent_arithmetic.jl:37
  *(::Any, ::ChainRulesCore.NotImplemented)
   @ ChainRulesCore ~/.julia/packages/ChainRulesCore/zgT0R/src/tangent_arithmetic.jl:38
  ...

In the stacktrace we can see the location of each function call. If we include the function polynomial from some file poly.jl using include("poly.jl"), we will see that the location changes from REPL[X]:10 to the actual file name.

By swapping square brackets for round in the array comprehension ac above, we have defined so called generator/iterator, which as opposed to original variable ac does not allocate an array, only the structure that produces it.

ag = (2i^2 + 1 for i in -2:1)
typeof(ag), eltype(ag)

(Base.Generator{UnitRange{Int64}, Main.var"#3#4"}, Any)

You may notice that the element type in this case is Any, which means that a function using this generator as an argument cannot specialize based on the type and has to infer it every time an element is generated/returned. We will touch on how this affects performance in one of the later lectures.

julia> polynomial(ag, x)ERROR: MethodError: no method matching getindex(::Base.Generator{UnitRange{Int64}, Main.var"#3#4"}, ::Int64)

The problem that we face during evaluation is that generator type is missing the getindex operation, as they are made for situations where the size of the collection may be unknown and the only way of obtaining particular elements is through sequential iteration. Generators can be useful for example when creating batches of data for a machine learning training. We can "fix" the situation using collect function, mentioned earlier, however that again allocates an array.

Extending/limiting the polynomial example

Following up on the polynomial example, let's us expand it a little further in order to facilitate the arguments, that have been throwing exceptions. The first direction, which we will move forward to, is providing the user with more detailed error message when an incorrect type of coefficients has been provided.

if condition
    println("true") # true branch code
else
    println("false") # false branch code
end

julia> function polynomial(a, x)
           if eltype(a) != Char
               accumulator = 0
               for i in length(a):-1:1
                   accumulator += x^(i-1) * a[i] # ! 1-based indexing for arrays
               end
               return accumulator
           else
               throw(ArgumentError("Invalid coefficients $(a) of type Char!"))
           end
       endpolynomial (generic function with 1 method)

julia> polynomial(ach, x)ERROR: ArgumentError: Invalid coefficients ['1', '2', '3', '4'] of type Char!

julia> polynomial(a, x)128.0
julia> polynomial(af, x)128.0
julia> polynomial(at, x)128.0
julia> polynomial(ant, x)128.0
julia> polynomial(a2d, x)128.0
julia> polynomial(ac, x)108.0

The second direction concerns the limitation to index-able structures, which the generator example is not. For this we will have to rewrite the whole loop in a more functional programming approach using map, anonymous function and other concepts.

accumulator = 0
for i in length(a):-1:1
    accumulator += x^(i-1) * a[i] # ! 1-based indexing for arrays
end

julia> x -> x + 1              # unless the reference is stored it cannot be called#1 (generic function with 1 method)
julia> plusone = x -> x + 1    # the reference can be stored inside a variable#3 (generic function with 1 method)
julia> plusone(x)              # calling with the same syntaxERROR: UndefVarError: `x` not defined

function polynomial(a, x)
    powers = map(enumerate(a)) do (i, aᵢ)
        x^(i-1) * aᵢ
    end
    accumulator = sum(powers)
    return accumulator
end

function polynomial(a, x)
    polypow(i,aᵢ) = x^(i-1) * aᵢ
    powers = map(polypow, enumerate(a))
    return sum(powers)
end

function polynomial(a, x)
    powers = map(((i,aᵢ),) -> x^(i-1) * aᵢ, enumerate(a))
    sum(powers)
end

julia> polynomial(a, x)128.0
julia> polynomial(af, x)128.0
julia> polynomial(at, x)128.0
julia> polynomial(ant, x)128.0
julia> polynomial(a2d, x)128.0
julia> polynomial(ach, x)ERROR: MethodError: no method matching *(::Float64, ::Char)

Closest candidates are:
  *(::Any, ::Any, ::Any, ::Any...)
   @ Base operators.jl:587
  *(::ChainRulesCore.NotImplemented, ::Any)
   @ ChainRulesCore ~/.julia/packages/ChainRulesCore/zgT0R/src/tangent_arithmetic.jl:37
  *(::Any, ::ChainRulesCore.NotImplemented)
   @ ChainRulesCore ~/.julia/packages/ChainRulesCore/zgT0R/src/tangent_arithmetic.jl:38
  ...
julia> polynomial(ac, x)108.0
julia> polynomial(ag, x)108.0

polynomial(a, x) = mapreduce(+, enumerate(a), init=zero(x)) do (i, aᵢ)
    x^(i-1) * aᵢ
end

polynomial(a, x)

128.0

julia> polynomial(a, x) = sum(ia -> x^(ia[1]-1) * ia[2], enumerate(a))polynomial (generic function with 1 method)

How to use code from other people

The script that we have run at the beginning of this lab has created two new files inside the current folder:

./
 ├── Manifest.toml
 └── Project.toml

Every folder with a toml file called Project.toml, can be used by Julia's pkg manager into setting so called environment, which contains a list of pkgs to be installed. Setting up or more often called activating an environment can be done either before starting Julia itself by running julia with the --project XXX flag or from within the Julia REPL, by switching to Pkg mode with ] key (similar to the help mode activated by pressing ?) and running command activate.

So far we have used the general environment (depending on your setup), which by default does not come with any 3rd party packages and includes only the base and standard libraries - already quite powerful on its own.

In order to find which environment is currently active, run the following:

pkg> status

The output of such command usually indicates the general environment located at .julia/ folder (${HOME}/.julia/ or ${APPDATA}/.julia/ in case of Unix/Windows based systems respectively)

pkg> status
Status `~/.julia/environments/v1.6/Project.toml` (empty project)

Generally one should avoid working in the general environment, with the exception of some generic pkgs, such as PkgTemplates.jl, which is used for generating library templates/folder structure like the one above (link), more on this in the lecture on pkg development.

aexp = ones(10) ./ factorial.(0:9)
x = 1.1

julia> using BenchmarkTools

julia> @btime polynomial(aexp, x)
  97.119 ns (1 allocation: 16 bytes)
3.004165230550543

julia> polynomial(aexp, x) - exp(x)-7.933958903194593e-7

Discussion & future directions

Instead of if-else statements that would throw an error for different types, in Julia, we generally see the pattern of typing the function in a way, that for other than desirable types MethodError is emitted with the information about closest matching methods. This is part of the design process in Julia of a function and for the particular functionality of the polynomial example, we can look into the Julia itself, where it has been implemented in the evalpoly function

julia> methods(evalpoly)# 5 methods for generic function "evalpoly" from Base.Math:
 [1] evalpoly(z::Complex, p::AbstractVector)
     @ math.jl:239
 [2] evalpoly(z::Complex, p::Tuple{Any})
     @ math.jl:236
 [3] evalpoly(z::Complex, p::Tuple)
     @ math.jl:211
 [4] evalpoly(x, p::AbstractVector)
     @ math.jl:199
 [5] evalpoly(x, p::Tuple)
     @ math.jl:186

Another avenue, that we have only touched with the BenchmarkTools, is performance and will be further explored in the later lectures.

With the next lecture focused on typing in Julia, it is worth noting that polynomials lend themselves quite nicely to a definition of a custom type, which can help both readability of the code as well further extensions.

struct Polynom{C}
    coefficients::{C}
end

function (p:Polynom)(x)
    polynomial(p.coefficients, x)
end

Useful resources

• Getting Started tutorial from JuliaLang documentation - Docs
• Converting syntax between MATLAB ↔ Python ↔ Julia - Cheatsheet
• Bachelor course for refreshing your knowledge - Course
• Stylistic conventions - Style Guide
• Reserved keywords - List
• Official cheatsheet with basic syntax - link

Various errors and how to read them

This section summarizes most commonly encountered types of errors in Julia and how to resolve them or at least understand, what has gone wrong. It expands a little bit the official documentation, which contains the complete list with examples. Keep in mind again, that you can use help mode in the REPL to query error types as well.

MethodError

This type of error is most commonly thrown by Julia's multiple dispatch system with a message like no method matching X(args...), seen in two examples bellow.

julia> 2 * 'a'                       # many candidatesERROR: MethodError: no method matching *(::Int64, ::Char)

Closest candidates are:
  *(::Any, ::Any, ::Any, ::Any...)
   @ Base operators.jl:587
  *(::ChainRulesCore.NotImplemented, ::Any)
   @ ChainRulesCore ~/.julia/packages/ChainRulesCore/zgT0R/src/tangent_arithmetic.jl:37
  *(::Any, ::ChainRulesCore.NotImplemented)
   @ ChainRulesCore ~/.julia/packages/ChainRulesCore/zgT0R/src/tangent_arithmetic.jl:38
  ...
julia> getindex((i for i in 1:4), 3) # no candidatesERROR: MethodError: no method matching getindex(::Base.Generator{UnitRange{Int64}, typeof(identity)}, ::Int64)

Both of these examples have a short stacktrace, showing that the execution failed on the top most level in REPL, however if this code is a part of some function in a separate file, the stacktrace will reflect it. What this error tells us is that the dispatch system could not find a method for a given function, that would be suitable for the type of arguments, that it has been given. In the first case Julia offers also a list of candidate methods, that match at least some of the arguments

When dealing with basic Julia functions and types, this behavior can be treated as something given and though one could locally add a method for example for multiplication of Char and Int, there is usually a good reason why Julia does not support such functionality by default. On the other hand when dealing with user defined code, this error may suggest the developer, that either the functions are too strictly typed or that another method definition is needed in order to satisfy the desired functionality.

InexactError

This type of error is most commonly thrown by the type conversion system (centered around convert function), informing the user that it cannot exactly convert a value of some type to match arguments of a function being called.

julia> Int(1.2)                      # root causeERROR: InexactError: Int64(1.2)
julia> append!([1,2,3], 1.2)         # same as above but shows the root cause deeper in the stack traceERROR: InexactError: Int64(1.2)

In this case the function being Int and the value a floating point. The second example shows InexactError may be caused deeper inside an inconspicuous function call, where we want to extend an array by another value, which is unfortunately incompatible.

ArgumentError

As opposed to the previous two errors, ArgumentError can contain user specified error message and thus can serve multiple purposes. It is however recommended to throw this type of error, when the parameters to a function call do not match a valid signature, e.g. when factorial were given negative or non-integer argument (note that this is being handled in Julia by multiple dispatch and specific DomainError).

This example shows a concatenation of two 2d arrays of incompatible sizes 3x3 and 2x2.

julia> hcat(ones(3,3), zeros(2,2))ERROR: DimensionMismatch: number of rows of each array must match (got (3, 2))

KeyError

This error is specific to hash table based objects such as the Dict type and tells the user that and indexing operation into such structure tried to access or delete a non-existent element.

julia> d = Dict(:a => [1,2,3], :b => [1,23])Dict{Symbol, Vector{Int64}} with 2 entries:
  :a => [1, 2, 3]
  :b => [1, 23]
julia> d[:c]ERROR: KeyError: key :c not found

TypeError

Type assertion failure, or calling an intrinsic function (inside LLVM, where code is strictly typed) with incorrect argument type. In practice this error comes up most often when comparing value of a type against the Bool type as seen in the example bellow.

julia> if 1 end                # calls internally typeassert(1, Bool)ERROR: TypeError: non-boolean (Int64) used in boolean context
julia> typeassert(1, Bool)ERROR: TypeError: non-boolean (Int64) used in boolean context

In order to compare inside conditional statements such as if-elseif-else or the ternary operator x ? a : b the condition has to be always of Bool type, thus the example above can be fixed by the comparison operator: if 1 == 1 end (in reality either the left or the right side of the expression contains an expression or a variable to compare against).

UndefVarError

While this error is quite self-explanatory, the exact causes are often quite puzzling for the user. The reason behind the confusion is to do with code scoping, which comes into play for example when trying to access a local variable from outside of a given function or just updating a global variable from within a simple loop.

In the first example we show the former case, where variable is declared from within a function and accessed from outside afterwards.

julia> function plusone(x)
           uno = 1
           return x + uno
       endplusone (generic function with 1 method)
julia> uno # defined only within plusoneERROR: UndefVarError: `uno` not defined

Unless there is variable I_am_not_defined in the global scope, the following should throw an error.

julia> I_am_not_definedERROR: UndefVarError: `I_am_not_defined` not defined

Often these kind of errors arise as a result of bad code practices, such as long running sessions of Julia having long forgotten global variables, that do not exist upon new execution (this one in particular has been addressed by the authors of the reactive Julia notebooks Pluto.jl).

For more details on code scoping we recommend particular places in the bachelor course lectures here and there.

ErrorException & error function

ErrorException is the most generic error, which can be thrown/raised just by calling the error function with a chosen string message. As a result developers may be inclined to misuse this for any kind of unexpected behavior a user can run into, often providing out-of-context/uninformative messages.