SageMath Development Checklist

When developing a new package for SageMath, it can feel daunting, especially because your code is subject to public review and needs to meet a myriad of standards. The definitive guide for these standards is the official developer guide. Another helpful resource is the reviewer’s checklist. You should always try to go ahead and do a review of your own code. You probably will not catch everything, but it is good to know what reviewers will be looking for!

Most notably, SageMath packages are expected to adhere to general Python coding conventions as well as extra SageMath conventions. The Developer’s Guide does a good job enumerating all of these, but I want to list a few key things developed by my former colleague Matthew Lancellotti when he was migrating code into SageMath. Original source.

Even as someone who has contributed multiple bits of Sage code, I can have a hard time keeping track of all these conventions. So, this list is primarily made for my reference but publicly available in case it might help you, too.

Coding

Sage is built on top of Python, so it is important to follow general Python best practices. In addition, Sage has its own best practices. Some of them to keep in mind are the following.

  1. (Required) Follow PEP 8 coding conventions. A handy tool to help you is autopep8. Another good document on Python coding conventions, with some overlap, is here.
  2. (Required) When implementing new algebraic structures, look at these guides. Implementing Algebraic Structures, How to implement new algebraic structures in Sage. In particular,

    • make sure you understand the “Parent” and “Element” design pattern in SageMath,
    • make sure your “Parent” is unique, easily done by inheriting from UniqueRepresentation,
    • implement single underscore methods instead of double underscore methods. For instance, _repr_, as well as _add_, _mul_, etc.
    • make sure your algebraic object fits into Sage’s category framework.
  3. (Required) If a function has multiple different ways of computing its output, the user should be able to specify which algorithm to use with an optional parameter algorithm.
  4. (Required) When verifying that input parameters for an object are “correct”, use a check method.

Documenting

Sage documentation is compiled by Sphynx and uses reStructuredText (reST) formatting. Some things to keep in mind.

  1. (Required) Make sure every class, method (except an __init__ method), and function has a docstring and, at minimum,…

    • that they conform to PEP 257,
    • that the first sentence concisely describes the function in a declarative form. Eg, for the add_cell method of the Partition class, the beginning line of the docstring says Return a partition corresponding to "self" with a cell added in row "i". (This does not change "self".),
    • that further exposition defining any new terms or providing references for curious users is given after the opening sentence and a blank line,
    • that they include an example in an EXAMPLES block with insightful examples that also test the code well.
  2. (Required) Update the file header correctly with your real name and email address, year of edits, and a brief description of what you did.
  3. (Required) While older SageMath code may not follow this convention, references should go in the master bibliography file. In the SageMath source tree, this file is located at src/doc/en/reference/references/index.rst at the time of this writing. You can cite anything in the master bibliography using the Sphynx reST syntax.
  4. (Recommended) Just make all docstrings multi-line raw docstrings. In otherwords, always wrap them in r""" ... """. Sage does not require this, but most docstrings in Sage do it.
  5. (Recommended) Include a .. SEELALSO: block when relevant. You can reference other classes anywhere in your docstrings via the convention :class:Foo, other methods via :meth:foo_bar, and functions via :func:foo_var.
  6. (Required, but a last order of business) Sage requires that all lines in your source file are broken at 80 characters except in certain special cases. If you do not adhere to this convention in your posted code, someone will most certainly comment on your Trac ticket telling you to do so. However, I recommend to simply not take offense, safely backlog the comment, address all other outstanding issues, and save this cleaning up for last because it is annoying to constantly redo it.

Contributing code via Trac

  1. Make sure you have a Trac account / log into Trac with your GitHub account. Be sure to add your ssh-keys to the account.
  2. Create a new ticket for your addition, label the ticket as an enhancement, and put your real name in the Author section.
  3. Make sure your changes are added on top of the current state of the develop branch for Sage.
  4. Push your code to a new branch with a descriptive name, and either with convention u/username/ticket-num-and-short-desc or public/ticket-num-and-short-desc. To accomplish this, you have two options. You may use the git-trac command and use the Sage git-trac tutorial or, if you are comfortable with git, you may use the git the hard way tutuorial, which is my preferred method.
  5. Make sure the branch is linked to your Trac ticket.
  6. Change ticket status to “Needs Review” and CC potential reviewers or other people who may be interested. If you are modifying an existing file, then people who have worked on the file in the past may be a helpful place to start.

Reviewing

  1. If you have not built Sage from source, you should run make on Sage with the changes you are reviewing. You can build in parallel using MAKE='make -j4' make where you replace 4 with however many threads you want to use. This may take awhile.
  2. Make sure your additions can compile by running sage -b.
  3. Then, run sage -t file.py on all relevant files to make sure doctests pass.
  4. Run sage -covereage file.py on all relevant files to make sure every method is documented.
  5. Make sure the documentation can build. You can use sage --docbuild reference html to do this, but if you run into problems, you might have to start from scratch. To do this, do make doc-clean followed by make doc. This may take awhile.
  6. Look at the Reviewer’s checklist.

Weird headaches/cornercases I have run into

  1. When adding a new file to the source code, make sure you add relevant import statements to the all.py file in the directory so that the important functions and classes are added to the namespace.
  2. When adding a new file specifically to the combinat module, make sure to add a line to the src/doc/en/reference/combinat/module_list.rst file so the documentation is added to Sage.
  3. As mentioned above, Sage requires that every line be no longer than 80 characters. There are some exceptions to this rule, as far as I can tell.

    • In codeblocks inside documentation, such as inside EXAMPLES and TESTS blocks, code seems to not limited to 80 characters.
    • I have seen that long strings in the Sage library, such as error statements, are often not forced to be line wrapped. I believe this happens because, although this functionality is possible, it disagrees with indentation structure. For example,
       >>> if True:
       ...     raise ValueError("Oh no! You have triggered a very very \
       ... very very very very very long error!")
       ... 
       Traceback (most recent call last):
      File "<stdin>", line 3, in <module>
       ValueError: Oh no! You have triggered a very very very very very very very long error!
      

      but

       >>> if True:
       ...     raise ValueError("Oh no! You have triggered a very very \
       ...                       very very very very very long error!")
       ... 
       Traceback (most recent call last):
      File "<stdin>", line 3, in <module>
       ValueError: Oh no! You have triggered a very very 			  very very very very very long error!
      

      However, probably the best thing to do to avoid this altogether is

       >>> error_msg = "oh no! You have triggered a very very very very \
       very very very very long error!"
       >>> if True:
       ...     raise ValueError(error_msg)
       ... 
       Traceback (most recent call last):
      File "<stdin>", line 2, in <module>
       ValueError: oh no! You have triggered a very very very very very very very very long error!
      

      or

       >>> error_msg = ("oh no! You have triggered a very very very very"
       ... "very very very very long error!")
       >>> if True:
       ...     raise ValueError(error_msg)
       ... 
       Traceback (most recent call last):
      File "<stdin>", line 2, in <module>
       ValueError: oh no! You have triggered a very very very veryvery very very very long error!
      
  4. When meeting the 80 character line limit, you must make sure bulleted lists follow an indentation structure like so:

    INPUT:

    - ``directed`` -- (default: ``False``) whether to have the dual
      equivalence graph be directed (where we have a directed edge
      `S \to T` if `i` appears to the left of `i+1` in the
      reading word of `T`; otherwise we have the directed edge
      `T \to S`)