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Documenting OSCAR code

The general philosophy of the OSCAR documentation is to put as much of the information as possible into the docstrings and only use the doc pages for collecting this information and provide some additional general context. Exceptions to this philosophy are the developer and general pages.

Docstrings of exported functions

Exported function should have docstrings, which look like

@doc raw"""
    functionname(x::ArgumentType, b::OtherArgument; c::Keyword = default) -> Int, Int

A short description of the function. It is allowed to use $\LaTeX$.
"""
functionname(x...,b...; c = ...)

If the signature is too long, use linebreaks to fit 80 characters.

Please also do provide an example within the docstring if possible, preferably as a jldoctest, i.e.

@doc raw"""
    functionname(x::ArgumentType, b::OtherArgument; c::Keyword = default) -> Int, Int

A short description of the function. It is allowed to use $\LaTeX$.

# Examples
This shows that `functionname` does the right thing for input `input`
```jldoctest
julia> input = ...

julia> functionname(input)
output
```
"""
functionname(x...,b...; c = ...)

This allows the user to immediately see how the function can be used, gives them some code that they can copy-paste and manipulate, and, as a bonus, provides a testcase as well.

The folder docs

The folder docs/src contains the OSCAR documentation website. Most of the pages are relatively sparse and consist of

```@docs
some_function
some_other_function
[...]
```

blocks that simply pull in the docstring from the corresponding source file. If you add a new page in docs/src, you will have to modify docs/doc.main to include your new page in the appropriate place.

Building the OSCAR documentation with Oscar.build_doc

!!! note "Previewing the documentation" Once you have created a pull request it is possible to preview the documentation on github using the link https://docs.oscar-system.org/previews/PR/ where you insert the number of your PR for prnumber. Alternatively you can look at the github actions tab of your PR and click the details link next to the documenter/deploy action. There are a few conditions for this to work: - No conflicts with the master branch. - Documentation action is successful, i.e. no doctest errors. - The branch for the PR is in the main oscar-system/Oscar.jl repository. You can still build the documentation locally with the commands described below.

build_doc

Please also read the section below on repairing the jldoctests using build_doc. !!! note "Browser reports denied access" Depending on your system, it might happen that the browser opens after a successful build, but only informs you that the access to the file was denied. This happens, for example, on Ubuntu which comes with a sandboxed Firefox. In this case, using build_doc with start_server = true should circumvent this problem.

Automatically repairing jldoctests

It is possible to have julia fix the output of all jldoctests when your changes to the code entail changes to the output. Just run the following command:

build_doc(doctest = :fix)

If you just want to fix some of the jldoctests, and do not want to build the documentation, you can also use Oscar.doctest_fix:

Oscar.doctest_fix

!!! danger Please use these commands carefully: - Make sure to only commit the changes to the doctests originating from your changes to the code. - The doctests also serve as actual tests, so make absolutely sure that the output is still mathematically correct.

!!! tip If these commands fail with an error message indicating lacking permissions to change AbstractAlgebra.jl related docs, it may help to run the following command: ]dev AbstractAlgebra

Updating the bibliography

When editing docs/oscar_references.bib please follow the style of the existing entries. An easy way to do that is to add your new BibTeX entry, then run bibtool by invoking it as follows from the root directory of the Oscar.jl repository:

bibtool docs/oscar_references.bib -o docs/oscar_references.bib

For every pull request on github, the CI checks if running bibtool leads to changes in the bibliography. If so, this test fails and indicates that the (recently) added bibliography entries are not standardized. For a merge, it is not required that this test is passed. Still, please feel encouraged to fix this failure by running bibtool locally as explained above.

Please follow the additional guidelines below, that are not checked by bibtool:

  • Do not escape special characters like umlauts or accented characters. Instead, use the unicode character directly.
  • You do not need to use braces to preserve capitalization as DocumenterCitations.jl keeps entries as is (in contrast to bibtex). In some cases, braces can even be harmful, i.e., show up in the output.
  • If a DOI is available for your reference, please add it as a doi field to the BibTeX entry. In this case, please refrain from adding an additional url field.
  • If your reference has no DOI or the paper is not open-access, but is available as an arXiv preprint, you can add the arXiv link as a eprint field (even additionally to a doi field). For other preprint servers (e.g. HAL), please refer to the DocumenterCitations.jl docs.
  • Documents available only as an arXiv preprint should be added as @Article entries with, e.g., arXiv:2003.10132 in the journal field, and, e.g., 10.48550/arxiv.2003.10132 in the doi field, but without an eprint field.