Documentation, testing, and continuous integration (CI) are some of the key ingredients to make software maintainable and reliable in the long term. During the first part of my (short) career in academia, when my daily software tools were C, Fortran and IDL, I barely knew these practices (probably didn’t know continuous integration at all), and never applied them in practice. Some time around 5 years ago I started my journey with the Julia programming language, and I learned to value and use these principles.
I have the general feeling that Julia makes documentation and testing very simple and lowers the entry barriers for newcomers. Today, the Julia ecosystem offers many tools about this:
Documenter.jl: a package to generate HTML and PDF versions of the documentation
Teststandard library provides very basic tools for testing, but it’s also extremely simple to use: you don’t have a good reason for not testing your code
- in addition to
Test, there are third-party packages which offer more advanced testing frameworks. Some of them are:
- packages like
PkgSkeleton.jllets you easily generate a new package with minimal setup for documentation, testing, and continuous integration.
If you’re looking for tips about testing workflow in Julia, see these best testing practices with Julia by Erik Engheim.
Analysing Julia packages in the General registry
Is my feeling that Julia makes documentation and testing easy actually true?
Prompted by the recent analysis of the prevalence of continuous integration in
JOSS made by my colleague
Jamie Quinn, I decided to look how Julia packages in the General
registry fare with regard to
documentation, testing and continuous integration. I quickly wrote a Julia
for this task: it clones all packages in the registry (only the last commit of
the default branch, to save time and bandwidth) and looks for some specific
files to decide whether a package uses documentation, testing and, continuous
The usage of the package is described in its
(yes, I haven’t set up proper documentation, yet!). I ran the analysis with 8
threads, it took less than 30 minutes to analyse the entire General registry (I
was mainly limited by my Internet connection, using some threads less wouldn’t
have changed much):
julia> using AnalyzeRegistry julia> @time report = analyze(find_packages()); 1567.008404 seconds (7.41 M allocations: 857.636 MiB, 0.01% gc time, 0.00% compilation time)
analyze returns a vector of a data structure,
Package, which describes a
- URL of the git repository
- can the repository be cloned? Some repositories have been deleted or made private, so it can be accessed from the public anymore
- does it have documentation? This is the hardest criterion: I looked for the
doc/make.jl, which is used to generate the documentation with
Documenter.jl, but many packages may do something else, see more in the comments below
- does it have the
test/runtests.jlfile? This is what the
Teststandard library uses to launch the tests
- does it use GitHub Actions?
- does it use Travis CI?
- does it use AppVeyor?
- does it use Cirrus CI?
- does it use Circle CI?
- does it use Drone CI?
- does it use Buildkite?
- does it use Azure Pipelines?
- does it use GitLab Pipeline?
Report of the analysis on 2021-01-23
Now, some statistics:
- total number of packages: 4312 (note: I excluded JLL packages, which are automatically generated, and not very useful to measure whether humans follow best programming practices);
- packages hosted on GitHub: 4296
- packages hosted on GitLab: 16
- packages that could be cloned: 4287 (99.4% of the total). The rest of percentages will refer to this number, since I could look for documentation and testing only if I could actually clone the repository of a package;
- packages using
Documenter.jlto publish documentation: 1887 (44%)
- packages with testing: 4139 (96.5%)
- packages using any of the CI services below: 4105 (95.8%)
- packages using GitHub Actions: 3240 (75.6%)
- packages using Travis CI: 2512 (58.6%)
- packages using AppVeyor: 783 (18.3%)
- packages using Cirrus CI: 60 (1.4%)
- packages using Circle CI: 13 (0.3%)
- packages using Drone CI: 43 (1%)
- packages using Buildkite: 29 (0.7%)
- packages using Azure Pipelines: 7 (0.2%)
- packages using GitLab Pipeline: 85 (1.9%)
I ran the analysis on 2020-01-23, on this revision of the General registry.
- The General registry is not a curated list of Julia packages and at the moment there is no requirement to have documentation, nor testing, nor continuous integration to be accepted. The question here is: do Julia users apply these principles even if they aren’t mandatory?
- The results are biased by the criteria I’ve chosen to determine whether a
package “has documentation”, or “has tests” and should be taken cum grano
salis: these criteria aren’t bullet-proof, also an empty
test/runtests.jlwould count as “has tests”, but see below. If you change the criteria a bit you may find different numbers, but I hope I got the orders of magnitude right;
- the goal of this analysis was not to measure the goodness of documentation or testing, but rather to see whether users apply these principles at all. It’s also very difficult to accurately measure them. Line code coverage is often used to measure degree of testing of the code, but I don’t think it’s says the whole story: it’s often easy to have 100% lines coverage, but have a poor paths coverage (if you have many conditionals, loops, etc… you can hit the same lines from different directions), also, in very elaborated code-bases it may be good enough to have high coverage of the core of the software, while some other extra features may be less important to test, or may be too complicated to test because require sophisticated external setups;
- about 44% of packages are set up to use
Documenter.jlto publish documentation. While this fraction doesn’t look particularly high, consider that many packages don’t keep the documentation within the repository but it may be stored somewhere else (very notable examples are
Plots.jl), or they are so simple that the entire documentation is written down in the
READMEfile (for example
Tar.jl) or the wiki.
- I looked at a random sample of 43 packages (1% of total) “without
documentation”, of this
- 4 didn’t have any documentation, docstrings, or examples of uses whatsoever (but 2 of them still had meaningful tests!)
- 1 didn’t have documentation nor examples, but only docstrings
- 1 only had an
examplesdirectory, with poorly commented samples of code
- all the others had documentation in the
README, in the wiki, or anyway published on a different website.
To summarise, 6 packages out of 43 (14%) had a very poor or completely missing meaningful documentation for users. Assuming this was a representative sample, my conclusion is that about 8% of packages in the registry have a lacking documentation, while the rest of the packages (92%) have some documentation to get users started, and a bit less than half of the total are set up to use
Documenter.jlto publish documentation;
- I looked at a random sample of 43 packages (1% of total) “without documentation”, of this
- an overwhelming majority of packages, 96.5%, have tests!
- packages like the above mentioned
PkgSkeleton.jlcreates for you a
test/runtests.jlfile when you generate a new package, but this script doesn’t actually contain any test at all, or just a dummy assertion like
@test 1 == 1. I looked at a random sample of 43 packages “with tests”, to check whether they actually run some real tests, related to package: only two of them (4.7%) had a dummy
test/runtests.jlfile. As already explained above, here I’m not judging the goodness of the tests or whether they cover enough code of the package, but most of the packages I’ve seen had very extensive test suites. If the sample I analysed was representative of all Julia packages in the General registry, we can say that about 92% of Julia packages do test their code. Interestingly enough, this is about the same fraction of packages with some documentation;
- packages like the above mentioned
- almost all packages with testing also set up continuous integration (95.8%), even though a small fraction is probably running dummy tests. If compared to the about 80% of papers in JOSS found by Jamie not to have any obvious CI setup, the uptake of CI among Julia packages is remarkable (the audience of authors of JOSS paper and Julia packages has a large overlap, so I believe it makes sense to look at them together);
- GitHub Actions is the most used CI service (75.6%), followed by Travis (58.6%). Note that measuring usage of GitHub Actions for CI is tricky, because, differently from all the other services, there isn’t a single standard name for the configuration script, and GitHub Actions is also often used for other tasks than pure CI. For example, I didn’t consider files for CompatHelper or TagBot. It would have been interesting to look at these statistics before last November, when the new Travis pricing model pushed many open-source users away from their services.
My take-away message is that despite the General registry not being curated and not enforcing specific styles or best practices, a large fraction of Julia packages does embrace documentation, testing, and continuous integration, showing that the ecosystem provides easy-to-use tools for these practices.