Project dependencies in Julia
When you work on a project using the Julia language most likely you will use some packages that are available in the Julia ecosystem. In particular, JuliaHub is a great place to look for packages that might be useful for you.
Most likely the first thing you start doing is adding the package to your default environment. This is the easiest thing to do, but has one significant downside — Julia package ecosystem is evolving very fast. This, in particular, means that during your project life cycle the versions of the packages provided by their maintainers can go up and introduce breaking changes. In consequence your code might suddenly stop working for no apparent reason.
In this post I have collected some practices I find useful to avoid such problems. Even if you do not end up using the functionalities of the Julia package manager I discuss on daily basis I think it is worth to be aware of their existence.
All examples were tested under Julia 1.4.1.
For every project keep a separate project environment
This is a basic rule. Unless I do quick-and-dirty interactive calculations I always create a project environment for my work.
Fortunately this is really easy. Just use
generate command in the Julia
package manager. The steps to achieve it are easy:
juliain the folder in which you want to create a project
]character to enter package manager mode
generate [target folder name]and press enter
- press backspace to leave this mode
Here is a screen shot of the session where I executed these steps:
~$ julia _ _ _ _(_)_ | Documentation: https://docs.julialang.org (_) | (_) (_) | _ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help. | | | | | | |/ _` | | | | |_| | | | (_| | | Version 1.4.1 (2020-04-14) _/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release |__/ | (@v1.4) pkg> generate test_project Generating project test_project: test_project/Project.toml test_project/src/test_project.jl julia> exit() ~$
Alternatively you can achieve this by running the following command:
~$ julia -e 'using Pkg; Pkg.generate("test_project")' Generating project test_project: test_project/Project.toml test_project/src/test_project.jl ~$
When I use
-e command Julia executes the commands that I pass and quits.
In this case I loaded the
Pkg module and executed
Pkg.generate function that
is a part of
Pkg module API.
Let us check what is the contents of the
~$ cd test_project/ ~/test_project$ ls -R .: Project.toml src ./src: test_project.jl ~/test_project$
You can see that two files were created: a
Project.toml file in the top-level
directory that specifies the dependencies of our project
src/test_project.jl which is a placeholder for our code.
Let us quickly inspect their contents:
~/test_project$ cat Project.toml name = "test_project" uuid = "d78710ad-1861-4169-903b-684d2f77c7fa" authors = ["Bogumił Kamiński <firstname.lastname@example.org>"] version = "0.1.0" ~/test_project$ cat src/test_project.jl module test_project greet() = print("Hello World!") end # module ~/test_project$
You can change the contents or rename the
test_project.jl file in whatever
way you like, but do not touch
Project.toml file as it contains the list
of dependencies of your project (currently there are none). Here
you can find the details of the specification of
Project.toml file contents.
Now — a crucial step is that whenever you want to work with your project
activate the project environment specified by
when starting Julia.
The easiest way to do it is to make sure that you are in the folder that
Project.toml file and write:
~/test_project$ julia --project=. _ _ _ _(_)_ | Documentation: https://docs.julialang.org (_) | (_) (_) | _ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help. | | | | | | |/ _` | | | | |_| | | | (_| | | Version 1.4.1 (2020-04-14) _/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release |__/ | julia>
--project=. part tells Julia to start the interpreter using
file from the current working directory as a specification of your dependencies.
I this post I discuss how to make Julia automatically activate the project environment in your current working directory on startup.
Now we can check that indeed we are in a correct project environment that is empty:
In the next section I discuss how to add packages to your project.
When adding packages use
preserve=PRESERVE_DIRECT keyword argument
You can add dependencies to your project using the
Pkg.add function in the
project manager. You can find the list of the available options by running the
help for the
Pkg.add function (I omit the output here as it is long).
It is crucial that the
Pkg.add function has a
preserve keyword argument that
tells Julia what it is allowed to do with the already installed packages. In
this post I have discussed potential problems when multiple
packages you install have conflicting dependencies. Therefore my practice is to
preserve=PRESERVE_DIRECT keyword argument. I do not want the packages that
my code depends on to change versions (and if there is some conflict generated
due to this restriction I prefer to get an error rather than a package version
change). However, I typically allow changing versions of recursive dependencies
as normally it should not affect my code.
Let me give an example how one can run such a command (in this case it does not
really matter if we add the
preserve=PRESERVE_DIRECT keyword argument as we do
not have any packages installed):
If you are curious what Pipe.jl package does you can check it out here.
We are informed that
Manifest.toml were updated.
Let us inspect their contents from within Julia as an exercise:
Manifest.toml contains the exact specification of all dependencies
of our project (direct and recursive) and
Project.toml lists only essential
information about direct dependencies.
Before we move on let me stress in what cases using
is most important. Assume you have worked on some project for some time already.
It had several packages as its dependencies. Now you decide that you need to add
some new package to its direct dependencies. The potential problem is that it is
possible (as you have worked on your project already for some time) that the
packages that you have installed previously have new versions available. Most
likely you do not want these packages to change their versions when you add
a new package as your code might stop working. This is exactly what
preserve=PRESERVE_DIRECT keyword argument safeguards you against.
When updating packages use
However, if you work on a project for some time the packages that you depend on, might have released patches (e.g. bug fixes or documentation enhancements) that you want to allow in your project.
You can achieve such an update by running
Here is an example of this command run:
In this case nothing happened as we have just installed that package. To check
out all the options of the
Pkg.update function run its help. In particular, it is
OK to allow changing major or minor versions of your dependencies when running
Pkg.update function, but remember that in this case your code might stop
working correctly, so if you do this please make sure to test that your code
produces the expected results after the update (and if it fails you can use the
Pkg.undo() function to undo the latest change to the active project).
Final notes on using package manager
In this post I used the
Pkg module API by calling functions. All this
functionality is also available via a package manager, which you enter by
] in the Julia command line. The names of the commands are the same,
and you can get help on them by writing e.g.
Finally, let me add one more comment, as this issue has raised some discussion.
The methods I describe for adding packages (with
updating them (with
level=UPDATELEVEL_PATCH) are meant to be a safe way to
perform these operations (so as I have written in the introduction this is an
option to be aware of). The core idea is that when working with production
code you want to:
- separate steps of adding new packages and updating packages you already have in your project;
- avoid package updates to introduce breaking changes in your dependencies unless you explicitly allow for this.