Contributing

Geomstats is a community effort, and everyone is welcome to contribute.

The project is hosted on https://github.com/geomstats/geomstats.

Code is not the only way to help the project:

  • reviewing pull requests,

  • submitting an issue or a bug report,

  • submitting a thumb up on issues that are important for you,

  • answering questions to help others on issues,

  • requesting new features,

  • improving the coding style in the codebase,

  • improving the coding style guidelines,

  • organizing and teaching tutorials, organizing hackathons,

  • working on the website and improving the documentation,

  • reference the project in your articles,

  • or simply star it to say “I use it”,

are all priceless contributions.

If you have questions, do not hesitate to send an email to the mailing list hi@geomstats.ai.

In this contributing document, we give details on submitting issues, contributing code, writing documentation, following code style guidelines, and reviewing code. This document is largely inspired by the Scikit-Learn project.

Submitting a Bug Report or Feature Request

We use GitHub issues to track all bugs and feature requests; feel free to open an issue if you have found a bug or wish to see a feature implemented.

It is recommended to check that your issue complies with the following rules before submitting:

How to Write a Good Bug Report

When you submit an issue to Github, please do your best to follow these guidelines! This will make it a lot easier to provide you with good feedback:

  • The ideal bug report contains a short reproducible code snippet, this way anyone can try to reproduce the bug easily (see this for more details). If your snippet is longer than around 50 lines, please link to a gist or a github repo.

  • If not feasible to include a reproducible snippet, please be specific about what estimators and/or functions are involved and the shape of the data.

  • If an exception is raised, please provide the full traceback.

  • Please include your operating system type and version number, as well as your Python, geomstats, numpy, and scipy versions. This information can be found by running the following code snippet:

    >>> import geomstats
    >>> print('geomstats', geomstats.__version___)
    
  • Please ensure all code snippets and error messages are formatted in appropriate code blocks. See Creating and highlighting code blocks for more details.

Contributing: Code Workflow

To avoid duplicating work, it is highly advised that you search through the issue tracker and the PR list. If in doubt about duplicated work, or if you want to work on a non-trivial feature, it’s recommended to first open an issue in the issue tracker to get some feedbacks from core developers.

Contributing: GitHub Workflow

The preferred way to contribute to geomstats is to fork the main repository on GitHub, then submit a “pull request” (PR).

In the first few steps, we explain how to locally install geomstats, and how to set up your git repository:

  1. Create an account on GitHub if you do not already have one.

  2. Fork the project repository: click on the ‘Fork’ button near the top of the page. This creates a copy of the code under your account on the GitHub user account. For more details on how to fork a repository see this guide.

  3. Clone your fork of the geomstats repo from your GitHub account to your local disk:

    $ git clone git@github.com:YourLogin/geomstats.git
    $ cd geomstats
    
  4. Add the upstream remote. This saves a reference to the main geomstats repository, which you can use to keep your repository synchronized with the latest changes:

    $ git remote add upstream https://github.com/geomstats/geomstats.git
    

You should now have a working installation of geomstats, and your git repository properly configured. The next steps now describe the process of modifying code and submitting a PR:

  1. Synchronize your master branch with the upstream master branch:

    $ git checkout master
    $ git pull upstream master
    
  2. Create a feature branch to hold your development changes:

    $ git checkout -b my_feature
    

    and start making changes. Always use a feature branch. It’s good practice to never work on the master branch!

  3. Develop the feature on your feature branch on your computer, using Git to do the version control. When you’re done editing, add changed files using git add and then git commit:

    $ git add modified_files
    $ git commit -m "Add my feature"
    

    to record your changes in Git. Your commit message should respect the good commit messages guidelines. Then push the changes to your GitHub account with:

    $ git push -u origin my-feature
    
  4. Follow these instructions to create a pull request from your fork. This will send an email to the committers. You may want to consider sending an email to the mailing list hi@geomstats.ai for more visibility.

It is often helpful to keep your local feature branch synchronized with the latest changes of the main geomstats repository:

$ git fetch upstream
$ git rebase upstream/master

Subsequently, you might need to solve potential conflicts. Refer to the Git documentation related to resolving merge conflict using the command line. The Git documentation and http://try.github.io are excellent resources to get started with git, and understanding all of the commands shown here.

Pull Request Checklist

In order to ease the reviewing process, we recommend that your contribution complies with the following rules. The bolded ones are especially important:

  1. Give your pull request a helpful title that summarises what your contribution does. This title will often become the commit message once merged so it should summarise your contribution for posterity. In some cases “Fix <ISSUE TITLE>” is enough. “Fix #<ISSUE NUMBER>” is never a good title.

  2. Make sure that your code is vectorized.

  3. Submit your code with associated unit tests. High-quality unit testing is a corner-stone of the geomstats development process. The tests are functions appropriately named, located in the tests subdirectory, that check the validity of the algorithms and the different options of the code. For each function my_fun that you implement in a given my_module.py, you should add the corresponding test function test_my_fun in the file test_my_module.py. We expect code coverage of new features to be at least 90%, which is automatically verified by the codecov software when you submit a PR. You should also add test_my_fun_vect tests to ensure that your code is vectorized.

  4. Make sure your code passes all unit tests. First, run the tests related to your changes. For example, if you changed something in geomstats/spd_matrices_space.py:

    nose2 –verbose tests.test_spd_matrices_space

    and then run the tests of the whole codebase to check that your feature is not breaking any of them:

    nose2

    This way, further modifications on the code base are granted to be consistent with the desired behavior. Merging your PR should not break any test in any backend (numpy, tensorflow or pytorch).

  5. Make sure that your PR follows Python international style guidelines, PEP8, which you should read. The flake8 package automatically checks for style violations when you submit your PR. We recommend installing flake8 with its plugins on your machine by running

    pip3 install -r dev-requirements.txt

    Then you can run

    flake8 geomstats tests examples

    To prevent adding commits which fail to adhere to the PEP8 guidelines, we include a pre-commit <https://pre-commit.com/> config, which immediately invokes flake8 on all files staged for commit when running git commit. To enable the hook, simply run pre-commit install after installing pre-commit either manually via pip or as part of dev-requirements.txt.

    Please avoid reformatting parts of the file that your pull request doesn’t change, as it distracts during code reviews.

  6. Make sure that your PR follows geomstats coding style and API, see our coding-guidelines below. Ensuring style consistency throughout geomstats allows using tools to automatically parse the codebase, for example searching all instances where a given function is used, or use automatic find-and-replace during code’s refactorizations. It also speeds up the code review and acceptance of PR, as the maintainers do not spend time getting used to new conventions and coding preferences.

  7. Make sure your code is properly documented, and make sure the documentation renders properly. To build the documentation, please see our Documentation guidelines. The plugin flake8-docstrings automatically checks that your the documentation follows our guidelines when you submit a PR.

  8. Often pull requests resolve one or more other issues (or pull requests). If merging your pull request means that some other issues/PRs should be closed, you should use keywords to create link to them (e.g., Fixes #1234; multiple issues/PRs are allowed as long as each one is preceded by a keyword). Upon merging, those issues/PRs will automatically be closed by GitHub. If your pull request is simply related to some other issues/PRs, create a link to them without using the keywords (e.g., See Also #1234).

  9. PRs should often substantiate the change, through benchmarks of performance and efficiency or through examples of usage. Examples also illustrate the features and intricacies of the library to users. Have a look at other examples in the examples/ directory for reference. Examples should demonstrate why the new functionality is useful in practice and, if possible, compare it to other methods available in geomstats.

  10. The user guide should also include expected time and space complexity of the algorithm and scalability, e.g. “this algorithm can scale to a large number of samples > 100000, but does not scale in dimensionality: n_features is expected to be lower than 100”.

  11. Each PR needs to be accepted by two core developpers before being merged.

You can also check our Code Review Guidelines to get an idea of what reviewers will expect.

Bonus points for contributions that include a performance analysis with a benchmark script and profiling output (please report on the mailing list hi@geomstats.ai or on the GitHub issue).

Note

The current state of the geomstats code base is not compliant with all of those guidelines, but we expect that enforcing those constraints on all new contributions will get the overall code base quality in the right direction.

Stalled Pull Requests

As contributing a feature can be a lengthy process, some pull requests appear inactive but unfinished. In such a case, taking them over is a great service for the project.

A good etiquette to take over is:

  • Determine if a PR is stalled

    • A pull request may have the label “stalled” or “help wanted” if we have already identified it as a candidate for other contributors.

    • To decide whether an inactive PR is stalled, ask the contributor if she/he plans to continue working on the PR in the near future. Failure to respond within 2 weeks with an activity that moves the PR forward suggests that the PR is stalled and will result in tagging that PR with “help wanted”.

      Note that if a PR has received earlier comments on the contribution that have had no reply in a month, it is safe to assume that the PR is stalled and to shorten the wait time to one day.

  • Taking over a stalled PR: To take over a PR, it is important to comment on the stalled PR that you are taking over and to link from the new PR to the old one. The new PR should be created by pulling from the old one.

Issues for New Contributors

New contributors should look for the following tags when looking for issues. We strongly recommend that new contributors tackle “easy” issues first: this helps the contributor become familiar with the contribution workflow, and for the core devs to become acquainted with the contributor; besides which, we frequently underestimate how easy an issue is to solve!

good first issue tag

A great way to start contributing to geomstats is to pick an item from the list of good first issues in the issue tracker. Resolving these issues allow you to start contributing to the project without much prior knowledge. If you have already contributed to geomstats, you should look at Easy issues instead.

starter project tag

If you have already contributed to geomstats, another great way to contribute to geomstats is to pick an item from the list of starter project in the issue tracker. Your assistance in this area will be greatly appreciated by the more experienced developers as it helps free up their time to concentrate on other issues.

help wanted tag

We often use the help wanted tag to mark issues regardless of difficulty. Additionally, we use the help wanted tag to mark Pull Requests which have been abandoned by their original contributor and are available for someone to pick up where the original contributor left off. The list of issues with the help wanted tag can be found here .

Note that not all issues which need contributors will have this tag.

Documentation

We are glad to accept any sort of documentation: function docstrings, reStructuredText documents (like this one), tutorials, etc. reStructuredText documents live in the source code repository under the docs/ directory.

Building the Documentation

Building the documentation requires installing sphinx:

pip3 install sphinx

To build the documentation, you need to be in the main geomstats folder. You can do this with:

sphinx-build docs/ docs/html

Writing Docstrings

Intro to Docstrings

A docstring is a well-formatted description of your function/class/module which includes its purpose, usage, and other information.

There are different markdown languages/formats used for docstrings in Python. The most common three are reStructuredText, numpy, and google docstring styles. For geomstats, we are using the numpy docstring standard. When writing up your docstrings, please review the NumPy docstring guidge to understand the role and syntax of each section. Following this syntax is important not only for readability, it is also required for automated parsing for inclusion into our generated API Reference.

You can look at these for any object by printing out the __doc__ attribute. Try this out with the np.array class and the np.mean function to see good examples:

>>> import numpy as np
>>> print(np.mean.__doc__)

The Anatomy of a Docstring

These are some of the most common elements for functions (and ones we’d like you to add where appropriate):

  1. Summary - a one-line (here <79 char) description of the object

    1. Begins immediately after the first “”” with a capital letter, ends with a period

    2. If describing a function, use a verb with the imperative mood (e.g. Compute vs Computes)

    3. Use a verb which is as specific as possible, but default to Compute when uncertain (as opposed to Calculate or Evaluate, for example)

  2. Description - a more informative multi-line description of the function

    1. Separated from the summary line by a blank line

    2. Begins with a capital letter and ends with period

  3. Parameters - a formatted list of arguments with type information and description

    1. On the first line, state the parameter name, type, and shape when appropriate. The parameter name should be separated from the rest of the line by a : (with a space on either side). If a parameter is optional, write Optional, default: default_value. as a separate line in the description.

    2. On the next line, indent and write a summary of the parameter beginning with a capital letter and ending with a period.

    3. See Docstring Examples below

  4. Returns (esp. for functions) - a formatted list of returned objects type information and description

    1. The syntax here is the same as in the parameters section above.

    2. See Docstring Examples below

If documenting a class, you would also want to include an Attributes section. There are many other optional sections you can include which are very helpful. For example: Raises, See Also, Notes, Examples, References, etc.

N.B. Within Notes, you can
  • include LaTex code

  • cite references in text using ids placed in References

Docstring Examples

Here’s a generic docstring template:

def my_method(self, my_param_1, my_param_2='vector'):
   """Write a one-line summary for the method.

   Write a description of the method, including "big O"
   (:math:`O\left(g\left(n\right)\right)`) complexities.

   Parameters
   ----------
   my_param_1 : array-like, shape=[..., dim]
      Write a short description of parameter my_param_1.
   my_param_2 : str, {'vector', 'matrix'}
      Write a short description of parameter my_param_2.
      Optional, default: 'vector'.

   Returns
   -------
   my_result : array-like, shape=[..., dim, dim]
      Write a short description of the result returned by the method.

   Notes
   -----
   If relevant, provide equations with (:math:)
   describing computations performed in the method.

   Example
   -------
   Provide code snippets showing how the method is used.
   You can link to scripts of the examples/ directory.

   Reference
   ---------
   If relevant, provide a reference with associated pdf or
   wikipedia page.
   """

And here’s a filled-in example from the Scikit-Learn project, modified to our syntax:

def fit_predict(self, X, y=None, sample_weight=None):
   """Compute cluster centers and predict cluster index for each sample.

   Convenience method; equivalent to calling fit(X) followed by
   predict(X).

   Parameters
   ----------
   X : {array-like, sparse_matrix} of shape=[..., n_features]
      New data to transform.
   y : Ignored
      Not used, present here for API consistency by convention.
   sample_weight : array-like, shape [...,], optional
      The weights for each observation in X. If None, all observations
      are assigned equal weight (default: None).

   Returns
   -------
   labels : array, shape=[...,]
      Index of the cluster each sample belongs to.
   """
   return self.fit(X, sample_weight=sample_weight).labels_

In general, have the following in mind:

  1. Use built-in Python types. (bool instead of boolean)

  2. Use [ for defining shapes: array-like, shape=[..., dim]

  3. If a shape can vary, use a list-like notation: array-like, shape=[dimension[:axis], n, dimension[axis:]]

  4. For strings with multiple options, use brackets: input: str, {'log', 'squared', 'multinomial'}

  5. 1D or 2D data can be a subset of {array-like, ndarray, sparse matrix, dataframe}. Note that array-like can also be a list, while ndarray is explicitly only a numpy.ndarray.

  6. Add “See Also” in docstrings for related classes/functions. “See Also” in docstrings should be one line per reference, with a colon and an explanation.

For Class and Module Examples see the scikit-learn _weight_boosting.py module. The class AdaBoost has a great example using the elements we’ve discussed here. Of course, these examples are rather verbose, but they’re good for understanding the components.

When editing reStructuredText (.rst) files, try to keep line length under 80 characters (exceptions include links and tables).

Coding Style Guidelines

The following are some guidelines on how new code should be written. Of course, there are special cases and there will be exceptions to these rules. However, following these rules when submitting new code makes the review easier so new code can be integrated in less time. Uniformly formatted code makes it easier to share code ownership.

In addition to the PEP8 standards, geomstats follows the following guidelines:

  1. Use underscores to separate words in non class names: n_samples rather than nsamples.

  2. Avoid single-character variable names. This prevents using automatic tools to find-and-replace code, as searching for x in geomstats will return the whole database. At least 3 characters are advised for a variable name.

  3. Use understandable function and variable names. The naming should help the maintainers reading faster through your code. Thus, my_array, aaa, result, res are generally bad variable names, whereas rotation_vec or symmetric_mat read well.

  4. Avoid comment in the code, the documentation goes in the docstrings. This allows the explanations to be included in the documentation generated automatically on the website. Furthermore, forbidding comments forces us to write clean code, and clean docstrings.

  5. Follow geomstats’ API. For example, points on manifolds are denoted point, tangent vectors tangent_vec, matrices mat, exponential exp and logarithms log.

  6. Avoid multiple statements on one line. Divide complex computations on several lines. Prefer a line return after a control flow statement (if/for).

  7. Don’t use import * in any case. It is considered harmful by the official Python recommendations. It makes the code harder to read as the origin of symbols is no longer explicitly referenced, but most important, it prevents using a static analysis tool like pyflakes to automatically find bugs in geomstats.

  8. Avoid the use of import ... as and of from ... import foo, bar, i.e. do not rename modules or modules’ functions, because you would create objects living in several namespaces which creates confusion, see https://docs.python.org/2/howto/doanddont.html#language-constructs-you-should-not-use. Keeping the original namespace ensures naming consistency in the codebase and speeds up the code reviews: co-developpers and maintainers do not have to check if you are using the original module’s method or if you have overwritten it.

  9. Use single quotes ‘ and not double quotes ” for strings.

10. If you need several lines for a function call, use the syntax

my_function_with_a_very_long_name(
   my_param_1=value_1, my_param_2=value_2)

and not

my_function_with_a_very_long_name(my_param_1=value_1,
                                  my_param_2=value_2)

as the indentation will break and raise a flake8 error if the name of the function is changed.

These guidelines can be revised and modified at any time, the only constraint is that they should remain consistent through the codebase. To change geomstats style guidelines, submit a PR to this contributing file, together with the corresponding changes in the codebase.

Code Review Guidelines

Reviewing code contributed to the project as PRs is a crucial component of geomstats development. We encourage anyone to start reviewing code of other developers. The code review process is often highly educational for everybody involved. This is particularly appropriate if it is a feature you would like to use, and so can respond critically about whether the PR meets your needs. While each pull request needs to be signed off by two core developers, you can speed up this process by providing your feedback.

Here are a few important aspects that need to be covered in any code review, from high-level questions to a more detailed check-list.

  • Do we want this in the library? Is it likely to be used? Do you, as a geomstats user, like the change and intend to use it? Is it in the scope of geomstats? Will the cost of maintaining a new feature be worth its benefits?

  • Is the code consistent with the API of geomstats? Are public functions/classes/parameters well named and intuitively designed?

  • Are all public functions/classes and their parameters, return types, and stored attributes named according to geomstats conventions and documented clearly?

  • Is every public function/class tested? Are a reasonable set of parameters, their values, value types, and combinations tested? Do the tests validate that the code is correct, i.e. doing what the documentation says it does? If the change is a bug-fix, is a non-regression test included? Look at this to get started with testing in Python.

  • Do the tests pass in the continuous integration build? If appropriate, help the contributor understand why tests failed.

  • Do the tests cover every line of code (see the coverage report in the build log)? If not, are the lines missing coverage good exceptions?

  • Is the code easy to read and low on redundancy? Should variable names be improved for clarity or consistency?

  • Could the code easily be rewritten to run much more efficiently for relevant settings?

  • Will the new code add any dependencies on other libraries? (this is unlikely to be accepted)

  • Does the documentation render properly (see the Documentation section for more details), and are the plots instructive?

  • Upon merging, use the Rebase and Merge option to keep git history clean.