• Lectures
• Code
• Notebooks
• Community

# Julia Tools and Editors¶

## Contents¶

Co-authored with Arnav Sood

While Jupyter notebooks are a great way to get started with the language, eventually you will want to use more powerful tools.

We’ll discuss a few of them here, such as

• Text editors like Atom, which come with rich Julia support for debugging, documentation, git integration, plotting and inspecting data, and code execution.
• The Julia REPL, which has specialized modes for package management, shell commands, and help.

Note that we assume you’ve already completed the getting started and interacting with Julia lectures.

## Preliminary Setup¶

### Creating a Startup File (Recommended)¶

Whenever the Julia compiler or REPL starts, it will look for a file called startup.jl (see Julia Manual).

We provide a file here which does two things

• Makes the REPL shell mode “sticky,” so you don’t need to keep running ; for new commands.
• Loads the Revise.jl package on startup, which lets you see changes you make to a package in real-time (i.e., no need to quit the REPL, open again, and load again).

The location for the file is relative to your default Julia environment (e.g. ~/.julia/config/startup.jl or C:\Users\USERNAME\.julia\config\startup.jl on Windows).

Recall that you can find the location of the ~/.julia directory by running

In [1]:
DEPOT_PATH[1]

Out[1]:
"/home/ubuntu/.julia"

Note: On Mac, this won’t be visible in the Finder unless you specifically enable that option, but you can get to it by running cd .julia; open . from a new terminal.

• In the julia terminal, type the following
] add  Revise REPL; precompile

• Create the ~/.julia/config/ directory if necessary in the terminal or file explorer.
• For convenience, you may find it useful on your operating system to change the directory where the REPL starts.

On Windows, if you have a shortcut on your desktop or on the taskbar, you could: (1) right-click on the icon; (2) right click on the “julia” text; (3) choose “Properties”, and (4) change the “Start In” to be something such as C:\Users\YOURUSERNAME\Documents.

## The REPL¶

Previously, we discussed basic use of the Julia REPL (“Read-Evaluate-Print Loop”).

Here, we’ll consider some more advanced features.

### Shell Mode¶

Hitting ; brings you into shell mode, which lets you run bash commands (PowerShell on Windows)

In [2]:
; pwd

/home/ubuntu/repos/lecture-source-jl/_build/website/jupyter/executed/more_julia


You can also use Julia variables from shell mode

In [3]:
x = 2

Out[3]:
2
In [4]:
; echo $x  2  ### Package Mode¶ Hitting ] brings you into package mode. • ] add Expectations will add a package (here, Expectations.jl). • Likewise, ] rm Expectations will remove that package. • ] st will show you a snapshot of what you have installed. • ] up will (intelligently) upgrade versions of your packages. • ] precompile will precompile everything possible. • ] build will execute build scripts for all packages. • Running ] preview before a command (i.e., ] preview up) will display the changes without executing. You can get a full list of package mode commands by running In [5]: ] ?   Welcome to the Pkg REPL-mode. To return to the julia> prompt, either press backspace when the input line is empty or press Ctrl+C. Synopsis pkg> cmd [opts] [args] Multiple commands can be given on the same line by interleaving a ; between the commands. Commands activate: set the primary environment the package manager manipulates add: add packages to project build: run the build script for packages develop: clone the full package repo locally for development free: undoes a pin, develop, or stops tracking a repo gc: garbage collect packages not used for a significant time generate: generate files for a new project help: show this message instantiate: downloads all the dependencies for the project pin: pins the version of packages precompile: precompile all the project dependencies redo: redo the latest change to the active project remove: remove packages from project or manifest resolve: resolves to update the manifest from changes in dependencies of developed packages status: summarize contents of and changes to environment test: run tests for packages undo: undo the latest change to the active project update: update packages in manifest registry add: add package registries registry remove: remove package registries registry status: information about installed registries registry update: update package registries On some operating systems (such as OSX) REPL pasting may not work for package mode, and you will need to access it in the standard way (i.e., hit ] first and then run your commands). ### Help Mode¶ Hitting ? will bring you into help mode. The key use case is to find docstrings for functions and macros, e.g. ? print  Note that objects must be loaded for Julia to return their documentation, e.g. ? @test  will fail, but using Test  ? @test  will succeed. ## Atom¶ As discussed previously, eventually you will want to use a fully fledged text editor. The most feature-rich one for Julia development is Atom, with the Juno package. There are several reasons to use a text editor like Atom, including • Git integration (more on this in the next lecture). • Painless inspection of variables and data. • Easily run code blocks, and drop in custom snippets of code. • Integration with Julia documentation and plots. ### Installation and Configuration¶ #### Installing Atom¶ 1. Download and Install Atom from the Atom website. 2. (Optional, but recommended): Change default Atom settings • Use Ctrl-, to get the Settings pane • Choose the Packages tab • Type line-ending-selector into the Filter and then click “Settings” for that package • Change the default line ending to LF (only necessary on Windows) • Choose the Editor tab • Turn on Soft Wrap • Set the Tab Length default to 4 #### Installing Juno¶ 1. Use Ctrl-, to get the Settings pane. 2. Go to the Install tab. 3. Type uber-juno into the search box and then click Install on the package that appears. 4. Wait while Juno installs dependencies. 5. When it asks you whether or not to use the standard layout, click yes. At that point, you should see a built-in REPL at the bottom of the screen and be able to start using Julia and Atom. #### Troubleshooting¶ Sometimes, Juno will fail to find the Julia executable (say, if it’s installed somewhere nonstandard, or you have multiple). To do this 1. Ctrl-, to get Settings pane, and select the Packages tab. 2. Type in julia-client and choose Settings. 3. Find the Julia Path, and fill it in with the location of the Julia binary. • To find the binary, you could run Sys.BINDIR in the REPL, then add in an additional /julia to the end of the screen. • e.g. C:\Users\YOURUSERNAME\AppData\Local\Julia-1.0.1\bin\julia.exe on Windows as /Applications/Julia-1.0.app/Contents/Resources/julia/bin/julia on OSX. See the setup instructions for Juno if you have further issues. If you upgrade Atom and it breaks Juno, run the following in a terminal. apm uninstall ink julia-client apm install ink julia-client  If you aren’t able to install apm in your PATH, you can do the above by running the following in PowerShell: cd$ENV:LOCALAPPDATA/atom/bin


Then navigating to a folder like C:\Users\USERNAME\AppData\Local\atom\bin (which will contain the apm tool), and running:

./apm uninstall ink julia-client
./apm install ink julia-client


To get a new release working with Jupyter, run (in the new version’s REPL)

] add IJulia
] build IJulia


This will install (and build) the IJulia kernel.

To get it working with Atom, open the command palette and type “Julia Client: Settings.”

Then, in the box labelled “Julia Path,” enter the path to yor Julia executabe.

You can find the folder by running Sys.BINDIR in a new REPL, and then add the /julia at the end to give the exact path.

For example:

### Standard Layout¶

If you follow the instructions, you should see something like this when you open a new file.

If you don’t, simply go to the command palette and type “Julia standard layout”

The bottom pane is a standard REPL, which supports the different modes above.

The “workspace” pane is a snapshot of currently-defined objects.

For example, if we define an object in the REPL

In [6]:
x = 2

Out[6]:
2

The ans variable simply captures the result of the last computation.

The Documentation pane simply lets us query Julia documentation

The Plots pane captures Julia plots output (the code is as follows)

using Plots
gr(fmt = :png);
data = rand(10, 10)
h = heatmap(data)


Note: The plots feature is not perfectly reliable across all plotting backends, see the Basic Usage page.

### Other Features¶

• Shift + Enter will evaluate a highlighted selection or line (as above).
• The run symbol in the left sidebar (or Ctrl+Shift+Enter) will run the whole file.

See basic usage for an exploration of features, and the FAQ for more advanced steps.

## Package Environments¶

Julia’s package manager lets you set up Python-style “virtualenvs,” or subsets of packages that draw from an underlying pool of assets on the machine.

This way, you can work with (and specify) the dependencies (i.e., required packages) for one project without worrying about impacts on other projects.

• An environment is a set of packages specified by a Project.toml (and optionally, a Manifest.toml).
• A registry is a git repository corresponding to a list of (typically) registered packages, from which Julia can pull (for more on git repositories, see version control).
• A depot is a directory, like ~/.julia, which contains assets (compile caches, registries, package source directories, etc.).

Essentially, an environment is a dependency tree for a project, or a “frame of mind” for Julia’s package manager.

• We can see the default (v1.1) environment as such
In [7]:
] st

Status ~/repos/lecture-source-jl/_build/website/jupyter/executed/Project.toml
[2169fc97] AlgebraicMultigrid v0.2.2
[28f2ccd6] ApproxFun v0.11.13
[7d9fca2a] Arpack v0.4.0
[aae01518] BandedMatrices v0.15.7
[6e4b80f9] BenchmarkTools v0.5.0
[a134a8b2] BlackBoxOptim v0.5.0
[ffab5731] BlockBandedMatrices v0.8.4
[324d7699] CategoricalArrays v0.8.0
[34da2185] Compat v2.2.0
[a93c6f00] DataFrames v0.21.0
[1313f7d8] DataFramesMeta v0.5.1
[39dd38d3] Dierckx v0.4.1
[9fdde737] DiffEqOperators v4.10.0
[31c24e10] Distributions v0.23.2
[2fe49d83] Expectations v1.1.1
[a1e7a1ef] Expokit v0.2.0
[d4d017d3] ExponentialUtilities v1.6.0
[1a297f60] FillArrays v0.8.9
[9d5cd8c9] FixedEffectModels v0.10.7
[c8885935] FixedEffects v0.7.3
[587475ba] Flux v0.10.4
[f6369f11] ForwardDiff v0.10.10
[38e38edf] GLM v1.3.9
[28b8d3ca] GR v0.49.1
[40713840] IncompleteLU v0.1.1
[a98d9a8b] Interpolations v0.12.9
[b6b21f68] Ipopt v0.6.1
[42fd0dbc] IterativeSolvers v0.8.4
[4076af6c] JuMP v0.21.2
[5ab0869b] KernelDensity v0.5.1
[ba0b0d4f] Krylov v0.5.1
[0b1a1467] KrylovKit v0.4.2
[b964fa9f] LaTeXStrings v1.1.0
[5078a376] LazyArrays v0.16.9
[0fc2ff8b] LeastSquaresOptim v0.7.5
[093fc24a] LightGraphs v1.3.3
[7a12625a] LinearMaps v2.6.1
[5c8ed15e] LinearOperators v1.1.0
[961ee093] ModelingToolkit v3.3.0
[76087f3c] NLopt v0.6.0
[2774e3e8] NLsolve v4.3.0
[429524aa] Optim v0.20.1
[1dea7af3] OrdinaryDiffEq v5.38.1
[d96e819e] Parameters v0.12.1
[14b8a8f1] PkgTemplates v0.6.4
[91a5bcdd] Plots v1.2.5
[f27b6e38] Polynomials v1.0.6
[af69fa37] Preconditioners v0.3.0
[92933f4c] ProgressMeter v1.2.0
[fcd29c91] QuantEcon v0.16.2
[1a8c2f83] Query v0.12.2
[ce6b1742] RDatasets v0.6.8
[d519eb52] RegressionTables v0.4.0
[295af30f] Revise v2.6.6
[f2b01f46] Roots v1.0.1
[47a9eef4] SparseDiffTools v1.8.0
[684fba80] SparsityDetection v0.3.1
[90137ffa] StaticArrays v0.12.3
[2913bbd2] StatsBase v0.32.2
[3eaba693] StatsModels v0.6.11
[f3b207a7] StatsPlots v0.14.6
[789caeaf] StochasticDiffEq v6.20.0
[a759f4b9] TimerOutputs v0.5.5 #master (https://github.com/KristofferC/TimerOutputs.jl)
[112f6efa] VegaLite v2.1.3
[e88e6eb3] Zygote v0.4.20
[37e2e46d] LinearAlgebra
[9a3f8284] Random
[2f01184e] SparseArrays
[10745b16] Statistics
[8dfed614] Test

• We can also create and activate a new environment
In [8]:
] generate ExampleEnvironment

 Generating  project ExampleEnvironment:
ExampleEnvironment/Project.toml
ExampleEnvironment/src/ExampleEnvironment.jl

• And go to it
In [9]:
; cd ExampleEnvironment

/home/ubuntu/repos/lecture-source-jl/_build/website/jupyter/executed/more_julia/ExampleEnvironment

• To activate the directory, simply
In [10]:
] activate .

 Activating environment at ~/repos/lecture-source-jl/_build/website/jupyter/executed/more_julia/ExampleEnvironment/Project.toml


where “.” stands in for the “present working directory”.

• Let’s make some changes to this
In [11]:
] add Expectations Parameters

   Updating registry at ~/.julia/registries/General


   Updating git-repo https://github.com/JuliaRegistries/General.git


  Resolving package versions...
Updating ~/repos/lecture-source-jl/_build/website/jupyter/executed/more_julia/ExampleEnvironment/Project.toml
[2fe49d83] + Expectations v1.4.0
[d96e819e] + Parameters v0.12.1
Updating ~/repos/lecture-source-jl/_build/website/jupyter/executed/more_julia/ExampleEnvironment/Manifest.toml
[7d9fca2a] + Arpack v0.4.0
[68821587] + Arpack_jll v3.5.0+3
[9e28174c] + BinDeps v1.0.1
[b99e7846] + BinaryProvider v0.5.9
[34da2185] + Compat v3.10.0
[e66e0078] + CompilerSupportLibraries_jll v0.3.3+0
[9a962f9c] + DataAPI v1.3.0
[864edb3b] + DataStructures v0.17.16
[31c24e10] + Distributions v0.22.6
[2fe49d83] + Expectations v1.4.0
[1a297f60] + FillArrays v0.8.9
[e1d29d7a] + Missings v0.4.3
[4536629a] + OpenBLAS_jll v0.3.9+4
[bac558e1] + OrderedCollections v1.2.0
[90014a1f] + PDMats v0.9.12
[d96e819e] + Parameters v0.12.1
[79098fc4] + Rmath v0.6.1
[f50d1b31] + Rmath_jll v0.2.2+0
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.8.0
[2913bbd2] + StatsBase v0.32.2
[4c63d2b9] + StatsFuns v0.9.5
[30578b45] + URIParser v0.4.1
[3a884ed6] + UnPack v1.0.1
[2a0f44e3] + Base64
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[4607b0f0] + SuiteSparse
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode


Note the lack of commas

• To see the changes, simply open the ExampleEnvironment directory in an editor like Atom.

The Project TOML should look something like this

name = "ExampleEnvironment"
uuid = "14d3e79e-e2e5-11e8-28b9-19823016c34c"
authors = ["QuantEcon User <quanteconuser@gmail.com>"]
version = "0.1.0"

[deps]
Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"


We can also

In [12]:
] precompile

Precompiling project...
┌ Warning: Package Expectations does not have LinearAlgebra in its dependencies:
│ - If you have Expectations checked out for development and have
│   environment's manifest file, try Pkg.resolve().
│ - Otherwise you may need to report an issue with Expectations
└ Loading LinearAlgebra into Expectations from project dependency, future warnings for Expectations are suppressed.
┌ Info: Precompiling ExampleEnvironment [317e9c5c-46a8-4568-875d-15e748cb39c8]


Note The TOML files are independent of the actual assets (which live in ~/.julia/packages, ~/.julia/dev, and ~/.julia/compiled).

You can think of the TOML as specifying demands for resources, which are supplied by the ~/.julia user depot.

In [13]:
] activate

 Activating environment at ~/repos/lecture-source-jl/_build/website/jupyter/executed/Project.toml


without any arguments.

• Lastly, let’s clean up
In [14]:
; cd ..

/home/ubuntu/repos/lecture-source-jl/_build/website/jupyter/executed/more_julia

In [15]:
; rm -rf ExampleEnvironment


### InstantiateFromURL¶

With this knowledge, we can explain the operation of the setup block

In [16]:
using InstantiateFromURL
# optionally add arguments to force installation: instantiate = true, precompile = true
github_project("QuantEcon/quantecon-notebooks-julia", version = "0.7.0")


What this github_project function does is activate (and if necessary, download, instantiate and precompile) a particular Julia environment.

• Share page
{"extraction_info": {"found_math": true, "script_math_tex": 0, "script_math_asciimath": 0, "math_annotations": 0, "math_alttext": 0, "mathml": 0, "mathjax_tag": 0, "mathjax_inline_tex": 1, "mathjax_display_tex": 0, "mathjax_asciimath": 1, "img_math": 0, "codecogs_latex": 0, "wp_latex": 0, "mimetex.cgi": 0, "/images/math/codecogs": 0, "mathtex.cgi": 0, "katex": 0, "math-container": 0, "wp-katex-eq": 0, "align": 0, "equation": 0, "x-ck12": 0, "texerror": 0, "math_score": 0.556041955947876, "perplexity": 27678.36230256323}, "config": {"markdown_headings": true, "markdown_code": true, "boilerplate_config": {"ratio_threshold": 0.18, "absolute_threshold": 10, "end_threshold": 15, "enable": true}, "remove_buttons": true, "remove_image_figures": true, "remove_link_clusters": true, "table_config": {"min_rows": 2, "min_cols": 3, "format": "plain"}, "remove_chinese": true, "remove_edit_buttons": true, "extract_latex": true}, "warc_path": "s3://commoncrawl/crawl-data/CC-MAIN-2020-24/segments/1590347388427.15/warc/CC-MAIN-20200525095005-20200525125005-00481.warc.gz"}