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doc/developers/contributing.rst
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Thomas J. Fan
BLD Migrate away from distutils and only use setuptools (#24563)
03 ноя 2022, 20:30
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03 ноя 2022, 20:30
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.. _contributing: ============ Contributing ============ .. currentmodule:: sklearn This project is a community effort, and everyone is welcome to contribute. The project is hosted on https://github.com/scikit-learn/scikit-learn The decision making process and governance structure of scikit-learn is laid out in the governance document: :ref:`governance`. Scikit-learn is somewhat :ref:`selective <selectiveness>` when it comes to adding new algorithms, and the best way to contribute and to help the project is to start working on known issues. See :ref:`new_contributors` to get started. .. topic:: **Our community, our values** We are a community based on openness and friendly, didactic, discussions. We aspire to treat everybody equally, and value their contributions. We are particularly seeking people from underrepresented backgrounds in Open Source Software and scikit-learn in particular to participate and contribute their expertise and experience. Decisions are made based on technical merit and consensus. Code is not the only way to help the project. Reviewing pull requests, answering questions to help others on mailing lists or issues, organizing and teaching tutorials, working on the website, improving the documentation, are all priceless contributions. We abide by the principles of openness, respect, and consideration of others of the Python Software Foundation: https://www.python.org/psf/codeofconduct/ In case you experience issues using this package, do not hesitate to submit a ticket to the `GitHub issue tracker <https://github.com/scikit-learn/scikit-learn/issues>`_. You are also welcome to post feature requests or pull requests. Ways to contribute ================== There are many ways to contribute to scikit-learn, with the most common ones being contribution of code or documentation to the project. Improving the documentation is no less important than improving the library itself. If you find a typo in the documentation, or have made improvements, do not hesitate to send an email to the mailing list or preferably submit a GitHub pull request. Full documentation can be found under the doc/ directory. But there are many other ways to help. In particular helping to :ref:`improve, triage, and investigate issues <bug_triaging>` and :ref:`reviewing other developers' pull requests <code_review>` are very valuable contributions that decrease the burden on the project maintainers. Another way to contribute is to report issues you're facing, and give a "thumbs up" on issues that others reported and that are relevant to you. It also helps us if you spread the word: reference the project from your blog and articles, link to it from your website, or simply star to say "I use it": .. raw:: html <a class="github-button" href="https://github.com/scikit-learn/scikit-learn" data-icon="octicon-star" data-size="large" data-show-count="true" aria-label="Star scikit-learn/scikit-learn on GitHub">Star</a> <script async defer src="https://buttons.github.io/buttons.js"></script> In case a contribution/issue involves changes to the API principles or changes to dependencies or supported versions, it must be backed by a :ref:`slep`, where a SLEP must be submitted as a pull-request to `enhancement proposals <https://scikit-learn-enhancement-proposals.readthedocs.io>`_ using the `SLEP template <https://scikit-learn-enhancement-proposals.readthedocs.io/en/latest/slep_template.html>`_ and follows the decision-making process outlined in :ref:`governance`. .. topic:: Contributing to related projects Scikit-learn thrives in an ecosystem of several related projects, which also may have relevant issues to work on, including smaller projects such as: * `scikit-learn-contrib <https://github.com/search?q=org%3Ascikit-learn-contrib+is%3Aissue+is%3Aopen+sort%3Aupdated-desc&type=Issues>`__ * `joblib <https://github.com/joblib/joblib/issues>`__ * `sphinx-gallery <https://github.com/sphinx-gallery/sphinx-gallery/issues>`__ * `numpydoc <https://github.com/numpy/numpydoc/issues>`__ * `liac-arff <https://github.com/renatopp/liac-arff/issues>`__ and larger projects: * `numpy <https://github.com/numpy/numpy/issues>`__ * `scipy <https://github.com/scipy/scipy/issues>`__ * `matplotlib <https://github.com/matplotlib/matplotlib/issues>`__ * and so on. Look for issues marked "help wanted" or similar. Helping these projects may help Scikit-learn too. See also :ref:`related_projects`. Submitting a bug report or a 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. In case you experience issues using this package, do not hesitate to submit a ticket to the `Bug Tracker <https://github.com/scikit-learn/scikit-learn/issues>`_. You are also welcome to post feature requests or pull requests. It is recommended to check that your issue complies with the following rules before submitting: - Verify that your issue is not being currently addressed by other `issues <https://github.com/scikit-learn/scikit-learn/issues?q=>`_ or `pull requests <https://github.com/scikit-learn/scikit-learn/pulls?q=>`_. - If you are submitting an algorithm or feature request, please verify that the algorithm fulfills our `new algorithm requirements <http://scikit-learn.org/stable/faq.html#what-are-the-inclusion-criteria-for-new-algorithms>`_. - If you are submitting a bug report, we strongly encourage you to follow the guidelines in :ref:`filing_bugs`. .. _filing_bugs: How to make a good bug report ----------------------------- When you submit an issue to `Github <https://github.com/scikit-learn/scikit-learn/issues>`__, 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 :ref:`short reproducible code snippet <minimal_reproducer>`, this way anyone can try to reproduce the bug easily (see `this <https://stackoverflow.com/help/mcve>`_ for more details). If your snippet is longer than around 50 lines, please link to a `gist <https://gist.github.com>`_ 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, scikit-learn, numpy, and scipy versions**. This information can be found by running the following code snippet:: >>> import sklearn >>> sklearn.show_versions() # doctest: +SKIP - Please ensure all **code snippets and error messages are formatted in appropriate code blocks**. See `Creating and highlighting code blocks <https://help.github.com/articles/creating-and-highlighting-code-blocks>`_ for more details. If you want to help curate issues, read :ref:`the following <bug_triaging>`. Contributing code ================= .. note:: To avoid duplicating work, it is highly advised that you search through the `issue tracker <https://github.com/scikit-learn/scikit-learn/issues>`_ and the `PR list <https://github.com/scikit-learn/scikit-learn/pulls>`_. 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 <https://github.com/scikit-learn/scikit-learn/issues>`_ to get some feedbacks from core developers. One easy way to find an issue to work on is by applying the "help wanted" label in your search. This lists all the issues that have been unclaimed so far. In order to claim an issue for yourself, please comment exactly ``/take`` on it for the CI to automatically assign the issue to you. Video resources --------------- These videos are step-by-step introductions on how to contribute to scikit-learn, and are a great companion to the following text guidelines. Please make sure to still check our guidelines below, since they describe our latest up-to-date workflow. - Crash Course in Contributing to Scikit-Learn & Open Source Projects: `Video <https://youtu.be/5OL8XoMMOfA>`__, `Transcript <https://github.com/data-umbrella/event-transcripts/blob/main/2020/05-andreas-mueller-contributing.md>`__ - Example of Submitting a Pull Request to scikit-learn: `Video <https://youtu.be/PU1WyDPGePI>`__, `Transcript <https://github.com/data-umbrella/event-transcripts/blob/main/2020/06-reshama-shaikh-sklearn-pr.md>`__ - Sprint-specific instructions and practical tips: `Video <https://youtu.be/p_2Uw2BxdhA>`__, `Transcript <https://github.com/data-umbrella/data-umbrella-scikit-learn-sprint/blob/master/3_transcript_ACM_video_vol2.md>`__ - 3 Components of Reviewing a Pull Request: `Video <https://youtu.be/dyxS9KKCNzA>`__, `Transcript <https://github.com/data-umbrella/event-transcripts/blob/main/2021/27-thomas-pr.md>`__ .. note:: In January 2021, the default branch name changed from ``master`` to ``main`` for the scikit-learn GitHub repository to use more inclusive terms. These videos were created prior to the renaming of the branch. For contributors who are viewing these videos to set up their working environment and submitting a PR, ``master`` should be replaced to ``main``. How to contribute ----------------- The preferred way to contribute to scikit-learn is to fork the `main repository <https://github.com/scikit-learn/scikit-learn/>`__ on GitHub, then submit a "pull request" (PR). In the first few steps, we explain how to locally install scikit-learn, and how to set up your git repository: 1. `Create an account <https://github.com/join>`_ on GitHub if you do not already have one. 2. Fork the `project repository <https://github.com/scikit-learn/scikit-learn>`__: 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 <https://help.github.com/articles/fork-a-repo/>`_. 3. Clone your fork of the scikit-learn repo from your GitHub account to your local disk: .. prompt:: bash $ git clone git@github.com:YourLogin/scikit-learn.git # add --depth 1 if your connection is slow cd scikit-learn 3. Follow steps 2-7 in :ref:`install_bleeding_edge` to build scikit-learn in development mode and return to this document. 4. Install the development dependencies: .. prompt:: bash $ pip install pytest pytest-cov flake8 mypy numpydoc black==22.3.0 .. _upstream: 5. Add the ``upstream`` remote. This saves a reference to the main scikit-learn repository, which you can use to keep your repository synchronized with the latest changes: .. prompt:: bash $ git remote add upstream git@github.com:scikit-learn/scikit-learn.git 6. Check that the `upstream` and `origin` remote aliases are configured correctly by running `git remote -v` which should display:: origin git@github.com:YourLogin/scikit-learn.git (fetch) origin git@github.com:YourLogin/scikit-learn.git (push) upstream git@github.com:scikit-learn/scikit-learn.git (fetch) upstream git@github.com:scikit-learn/scikit-learn.git (push) You should now have a working installation of scikit-learn, and your git repository properly configured. The next steps now describe the process of modifying code and submitting a PR: 7. Synchronize your ``main`` branch with the ``upstream/main`` branch, more details on `GitHub Docs <https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/syncing-a-fork>`_: .. prompt:: bash $ git checkout main git fetch upstream git merge upstream/main 8. Create a feature branch to hold your development changes: .. prompt:: bash $ git checkout -b my_feature and start making changes. Always use a feature branch. It's good practice to never work on the ``main`` branch! 9. (**Optional**) Install `pre-commit <https://pre-commit.com/#install>`_ to run code style checks before each commit: .. prompt:: bash $ pip install pre-commit pre-commit install pre-commit checks can be disabled for a particular commit with `git commit -n`. 10. 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``: .. prompt:: bash $ git add modified_files git commit to record your changes in Git, then push the changes to your GitHub account with: .. prompt:: bash $ git push -u origin my_feature 11. Follow `these <https://help.github.com/articles/creating-a-pull-request-from-a-fork>`_ 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 for more visibility. .. note:: If you are modifying a Cython module, you have to re-compile after modifications and before testing them: .. prompt:: bash $ pip install --no-build-isolation -e . Use the ``--no-build-isolation`` flag to avoid compiling the whole project each time, only the files you have modified. It is often helpful to keep your local feature branch synchronized with the latest changes of the main scikit-learn repository: .. prompt:: bash $ git fetch upstream git merge upstream/main Subsequently, you might need to solve the conflicts. You can refer to the `Git documentation related to resolving merge conflict using the command line <https://help.github.com/articles/resolving-a-merge-conflict-using-the-command-line/>`_. .. topic:: Learning git: The `Git documentation <https://git-scm.com/documentation>`_ and http://try.github.io are excellent resources to get started with git, and understanding all of the commands shown here. .. _pr_checklist: Pull request checklist ---------------------- Before a PR can be merged, it needs to be approved by two core developers. Please prefix the title of your pull request with ``[MRG]`` if the contribution is complete and should be subjected to a detailed review. An incomplete contribution -- where you expect to do more work before receiving a full review -- should be prefixed ``[WIP]`` (to indicate a work in progress) and changed to ``[MRG]`` when it matures. WIPs may be useful to: indicate you are working on something to avoid duplicated work, request broad review of functionality or API, or seek collaborators. WIPs often benefit from the inclusion of a `task list <https://github.com/blog/1375-task-lists-in-gfm-issues-pulls-comments>`_ in the PR description. In order to ease the reviewing process, we recommend that your contribution complies with the following rules before marking a PR as ``[MRG]``. The **bolded** ones are especially important: 1. **Give your pull request a helpful title** that summarizes what your contribution does. This title will often become the commit message once merged so it should summarize your contribution for posterity. In some cases "Fix <ISSUE TITLE>" is enough. "Fix #<ISSUE NUMBER>" is never a good title. 2. **Make sure your code passes the tests**. The whole test suite can be run with `pytest`, but it is usually not recommended since it takes a long time. It is often enough to only run the test related to your changes: for example, if you changed something in `sklearn/linear_model/_logistic.py`, running the following commands will usually be enough: - `pytest sklearn/linear_model/_logistic.py` to make sure the doctest examples are correct - `pytest sklearn/linear_model/tests/test_logistic.py` to run the tests specific to the file - `pytest sklearn/linear_model` to test the whole :mod:`~sklearn.linear_model` module - `pytest doc/modules/linear_model.rst` to make sure the user guide examples are correct. - `pytest sklearn/tests/test_common.py -k LogisticRegression` to run all our estimator checks (specifically for `LogisticRegression`, if that's the estimator you changed). There may be other failing tests, but they will be caught by the CI so you don't need to run the whole test suite locally. For guidelines on how to use ``pytest`` efficiently, see the :ref:`pytest_tips`. 3. **Make sure your code is properly commented and documented**, and **make sure the documentation renders properly**. To build the documentation, please refer to our :ref:`contribute_documentation` guidelines. The CI will also build the docs: please refer to :ref:`generated_doc_CI`. 4. **Tests are necessary for enhancements to be accepted**. Bug-fixes or new features should be provided with `non-regression tests <https://en.wikipedia.org/wiki/Non-regression_testing>`_. These tests verify the correct behavior of the fix or feature. In this manner, further modifications on the code base are granted to be consistent with the desired behavior. In the case of bug fixes, at the time of the PR, the non-regression tests should fail for the code base in the ``main`` branch and pass for the PR code. 5. Run `black` to auto-format your code. .. prompt:: bash $ black . See black's `editor integration documentation <https://black.readthedocs.io/en/stable/integrations/editors.html>`_ to configure your editor to run `black`. 6. Run `flake8` to make sure you followed the project coding conventions. .. prompt:: bash $ flake8 . 7. Follow the :ref:`coding-guidelines`. 8. When applicable, use the validation tools and scripts in the ``sklearn.utils`` submodule. A list of utility routines available for developers can be found in the :ref:`developers-utils` page. 9. 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 <https://github.com/blog/1506-closing-issues-via-pull-requests/>`_ (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``). 10. PRs should often substantiate the change, through benchmarks of performance and efficiency (see :ref:`monitoring_performances`) 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/ <https://github.com/scikit-learn/scikit-learn/tree/main/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 scikit-learn. 11. New features have some maintenance overhead. We expect PR authors to take part in the maintenance for the code they submit, at least initially. New features need to be illustrated with narrative documentation in the user guide, with small code snippets. If relevant, please also add references in the literature, with PDF links when possible. 12. 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". You can also check our :ref:`code_review` to get an idea of what reviewers will expect. You can check for common programming errors with the following tools: * Code with a good unittest coverage (at least 80%, better 100%), check with: .. prompt:: bash $ pip install pytest pytest-cov pytest --cov sklearn path/to/tests_for_package see also :ref:`testing_coverage` Run static analysis with `mypy`: .. prompt:: bash $ mypy sklearn must not produce new errors in your pull request. Using `# type: ignore` annotation can be a workaround for a few cases that are not supported by mypy, in particular, - when importing C or Cython modules - on properties with decorators Bonus points for contributions that include a performance analysis with a benchmark script and profiling output (see :ref:`monitoring_performances`). Also check out the :ref:`performance-howto` guide for more details on profiling and Cython optimizations. .. note:: The current state of the scikit-learn 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. .. note:: For two very well documented and more detailed guides on development workflow, please pay a visit to the `Scipy Development Workflow <http://scipy.github.io/devdocs/dev/dev_quickstart.html>`_ - and the `Astropy Workflow for Developers <https://astropy.readthedocs.io/en/latest/development/workflow/development_workflow.html>`_ sections. Continuous Integration (CI) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Azure pipelines are used for testing scikit-learn on Linux, Mac and Windows, with different dependencies and settings. * CircleCI is used to build the docs for viewing, for linting with flake8, and for testing with ARM64 / aarch64 on Linux Please note that if one of the following markers appear in the latest commit message, the following actions are taken. ====================== =================== Commit Message Marker Action Taken by CI ---------------------- ------------------- [ci skip] CI is skipped completely [cd build] CD is run (wheels and source distribution are built) [cd build gh] CD is run only for GitHub Actions [lint skip] Azure pipeline skips linting [scipy-dev] Build & test with our dependencies (numpy, scipy, etc ...) development builds [nogil] Build & test with the nogil experimental branches of CPython, Cython, NumPy, SciPy... [pypy] Build & test with PyPy [float32] Run float32 tests by setting `SKLEARN_RUN_FLOAT32_TESTS=1`. See :ref:`environment_variable` for more details [doc skip] Docs are not built [doc quick] Docs built, but excludes example gallery plots [doc build] Docs built including example gallery plots (very long) ====================== =================== Note that, by default, the documentation is built but only the examples that are directly modified by the pull request are executed. .. _stalled_pull_request: 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. After a sprint, follow-up for un-merged PRs opened during sprint will be communicated to participants at the sprint, and those PRs will be tagged "sprint". PRs tagged with "sprint" can be reassigned or declared stalled by sprint leaders. * **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. Stalled and Unclaimed Issues ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Generally speaking, issues which are up for grabs will have a `"help wanted" <https://github.com/scikit-learn/scikit-learn/labels/help%20wanted>`_. tag. However, not all issues which need contributors will have this tag, as the "help wanted" tag is not always up-to-date with the state of the issue. Contributors can find issues which are still up for grabs using the following guidelines: * First, to **determine if an issue is claimed**: * Check for linked pull requests * Check the conversation to see if anyone has said that they're working on creating a pull request * If a contributor comments on an issue to say they are working on it, a pull request is expected within 2 weeks (new contributor) or 4 weeks (contributor or core dev), unless an larger time frame is explicitly given. Beyond that time, another contributor can take the issue and make a pull request for it. We encourage contributors to comment directly on the stalled or unclaimed issue to let community members know that they will be working on it. * If the issue is linked to a :ref:`stalled pull request <stalled_pull_request>`, we recommend that contributors follow the procedure described in the :ref:`stalled_pull_request` section rather than working directly on the issue. .. _new_contributors: 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! .. topic:: good first issue tag A great way to start contributing to scikit-learn is to pick an item from the list of `good first issues <https://github.com/scikit-learn/scikit-learn/labels/good%20first%20issue>`_ 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 scikit-learn, you should look at Easy issues instead. .. topic:: Easy tag If you have already contributed to scikit-learn, another great way to contribute to scikit-learn is to pick an item from the list of `Easy issues <https://github.com/scikit-learn/scikit-learn/labels/Easy>`_ 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. .. topic:: 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 <https://github.com/scikit-learn/scikit-learn/labels/help%20wanted>`_. Note that not all issues which need contributors will have this tag. .. _contribute_documentation: Documentation ============= We are glad to accept any sort of documentation: * **function/method/class docstrings** (also known as "API documentation") - these describe what the object does and details any parameters, attributes and methods. Docstrings live alongside the code in `sklearn/ <https://github.com/scikit-learn/scikit-learn/tree/main/sklearn>`_. * **user guide** - these provide more detailed information about the algorithms implemented in scikit-learn and generally live in the root `doc/ <https://github.com/scikit-learn/scikit-learn/tree/main/doc>`_ directory and `doc/modules/ <https://github.com/scikit-learn/scikit-learn/tree/main/doc/modules>`_. * **tutorials** - these introduce various statistical learning and machine learning concepts and are located in `doc/tutorial <https://github.com/scikit-learn/scikit-learn/tree/main/doc/tutorial>`_. * **examples** - these provide full code examples that may demonstrate the use of scikit-learn modules, compare different algorithms or discuss their interpretation etc. Examples live in `examples/ <https://github.com/scikit-learn/scikit-learn/tree/main/examples>`_ * **other reStructuredText documents** (like this one) - provide various other useful information (e.g., our guide to contributing) and live in `doc/ <https://github.com/scikit-learn/scikit-learn/tree/main/doc>`_. You can edit the documentation using any text editor, and then generate the HTML output by following :ref:`building_documentation`. The resulting HTML files will be placed in ``_build/html/stable`` and are viewable in a web browser, for instance by opening the local ``_build/html/stable/index.html`` file. .. _building_documentation: Building the documentation -------------------------- First, make sure you have :ref:`properly installed <install_bleeding_edge>` the development version. .. packaging is not needed once setuptools starts shipping packaging>=17.0 Building the documentation requires installing some additional packages: .. prompt:: bash $ pip install sphinx sphinx-gallery numpydoc matplotlib Pillow pandas \ scikit-image packaging seaborn sphinx-prompt \ sphinxext-opengraph plotly To build the documentation, you need to be in the ``doc`` folder: .. prompt:: bash $ cd doc In the vast majority of cases, you only need to generate the full web site, without the example gallery: .. prompt:: bash $ make The documentation will be generated in the ``_build/html/stable`` directory and are viewable in a web browser, for instance by opening the local ``_build/html/stable/index.html`` file. To also generate the example gallery you can use: .. prompt:: bash $ make html This will run all the examples, which takes a while. If you only want to generate a few examples, you can use: .. prompt:: bash $ EXAMPLES_PATTERN=your_regex_goes_here make html This is particularly useful if you are modifying a few examples. Set the environment variable `NO_MATHJAX=1` if you intend to view the documentation in an offline setting. To build the PDF manual, run: .. prompt:: bash $ make latexpdf .. warning:: **Sphinx version** While we do our best to have the documentation build under as many versions of Sphinx as possible, the different versions tend to behave slightly differently. To get the best results, you should use the same version as the one we used on CircleCI. Look at this `github search <https://github.com/search?utf8=%E2%9C%93&q=sphinx+repo%3Ascikit-learn%2Fscikit-learn+extension%3Ash+path%3Abuild_tools%2Fcircle&type=Code>`_ to know the exact version. Guidelines for writing documentation ------------------------------------ It is important to keep a good compromise between mathematical and algorithmic details, and give intuition to the reader on what the algorithm does. Basically, to elaborate on the above, it is best to always start with a small paragraph with a hand-waving explanation of what the method does to the data. Then, it is very helpful to point out why the feature is useful and when it should be used - the latter also including "big O" (:math:`O\left(g\left(n\right)\right)`) complexities of the algorithm, as opposed to just *rules of thumb*, as the latter can be very machine-dependent. If those complexities are not available, then rules of thumb may be provided instead. Secondly, a generated figure from an example (as mentioned in the previous paragraph) should then be included to further provide some intuition. Next, one or two small code examples to show its use can be added. Next, any math and equations, followed by references, can be added to further the documentation. Not starting the documentation with the maths makes it more friendly towards users that are just interested in what the feature will do, as opposed to how it works "under the hood". Finally, follow the formatting rules below to make it consistently good: * 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 example:: See Also -------- SelectKBest : Select features based on the k highest scores. SelectFpr : Select features based on a false positive rate test. * When documenting the parameters and attributes, here is a list of some well-formatted examples:: n_clusters : int, default=3 The number of clusters detected by the algorithm. some_param : {'hello', 'goodbye'}, bool or int, default=True The parameter description goes here, which can be either a string literal (either `hello` or `goodbye`), a bool, or an int. The default value is True. array_parameter : {array-like, sparse matrix} of shape (n_samples, n_features) or (n_samples,) This parameter accepts data in either of the mentioned forms, with one of the mentioned shapes. The default value is `np.ones(shape=(n_samples,))`. list_param : list of int typed_ndarray : ndarray of shape (n_samples,), dtype=np.int32 sample_weight : array-like of shape (n_samples,), default=None multioutput_array : ndarray of shape (n_samples, n_classes) or list of such arrays In general have the following in mind: 1. Use Python basic types. (``bool`` instead of ``boolean``) 2. Use parenthesis for defining shapes: ``array-like of shape (n_samples,)`` or ``array-like of shape (n_samples, n_features)`` 3. For strings with multiple options, use brackets: ``input: {'log', 'squared', 'multinomial'}`` 4. 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``. 5. Specify ``dataframe`` when "frame-like" features are being used, such as the column names. 6. When specifying the data type of a list, use ``of`` as a delimiter: ``list of int``. When the parameter supports arrays giving details about the shape and/or data type and a list of such arrays, you can use one of ``array-like of shape (n_samples,) or list of such arrays``. 7. When specifying the dtype of an ndarray, use e.g. ``dtype=np.int32`` after defining the shape: ``ndarray of shape (n_samples,), dtype=np.int32``. You can specify multiple dtype as a set: ``array-like of shape (n_samples,), dtype={np.float64, np.float32}``. If one wants to mention arbitrary precision, use `integral` and `floating` rather than the Python dtype `int` and `float`. When both `int` and `floating` are supported, there is no need to specify the dtype. 8. When the default is ``None``, ``None`` only needs to be specified at the end with ``default=None``. Be sure to include in the docstring, what it means for the parameter or attribute to be ``None``. * For unwritten formatting rules, try to follow existing good works: * When bibliographic references are available with `arxiv <https://arxiv.org/>`_ or `Digital Object Identifier <https://www.doi.org/>`_ identification numbers, use the sphinx directives `:arxiv:` or `:doi:`. For example, see references in :ref:`Spectral Clustering Graphs <spectral_clustering_graph>`. * For "References" in docstrings, see the Silhouette Coefficient (:func:`sklearn.metrics.silhouette_score`). * When editing reStructuredText (``.rst``) files, try to keep line length under 80 characters when possible (exceptions include links and tables). * In scikit-learn reStructuredText files both single and double backticks surrounding text will render as inline literal (often used for code, e.g., `list`). This is due to specific configurations we have set. Single backticks should be used nowadays. * Before submitting your pull request check if your modifications have introduced new sphinx warnings and try to fix them. Cross-referencing ----------------- It is often useful to cross-reference to other pages in the scikit-learn documentation. This should be done with reStructuredText cross-referencing syntax: * Section - to link to an arbitrary section in the documentation, use reference labels (see `Sphinx docs <https://www.sphinx-doc.org/en/master/usage/restructuredtext/roles.html#ref-role>`_). For example: .. code-block:: rst .. _my-section: My section ---------- This is the text of the section. To refer to itself use :ref:`my-section`. You should not modify existing sphinx reference labels as this would break existing cross references and external links pointing to specific sections in the scikit-learn documentation. * Glossary - linking to a term in the :ref:`glossary`: .. code-block:: rst :term:`cross_validation` * Function - to link to the documentation of a function, use the full import path to the function: .. code-block:: rst :func:`~sklearn.model_selection.cross_val_score` However, if there is a 'currentmodule' directive above you in the document, you will only need to use the path to the function succeeding the current module specified. For example: .. code-block:: rst .. currentmodule:: sklearn.model_selection :func:`cross_val_score` * Class - to link to documentation of a class, use the full import path to the class, unless there is a 'currentmodule' directive in the document above (see above): .. code-block:: rst :class:`~sklearn.preprocessing.StandardScaler` .. _generated_doc_CI: Generated documentation on GitHub Actions ----------------------------------------- When you change the documentation in a pull request, GitHub Actions automatically builds it. To view the documentation generated by GitHub Actions, simply go to the bottom of your PR page, look for the item "Check the rendered docs here!" and click on 'details' next to it: .. image:: ../images/generated-doc-ci.png :align: center .. _testing_coverage: Testing and improving test coverage =================================== High-quality `unit testing <https://en.wikipedia.org/wiki/Unit_testing>`_ is a corner-stone of the scikit-learn development process. For this purpose, we use the `pytest <https://docs.pytest.org>`_ package. The tests are functions appropriately named, located in `tests` subdirectories, that check the validity of the algorithms and the different options of the code. Running `pytest` in a folder will run all the tests of the corresponding subpackages. For a more detailed `pytest` workflow, please refer to the :ref:`pr_checklist`. We expect code coverage of new features to be at least around 90%. Writing matplotlib related tests -------------------------------- Test fixtures ensure that a set of tests will be executing with the appropriate initialization and cleanup. The scikit-learn test suite implements a fixture which can be used with ``matplotlib``. ``pyplot`` The ``pyplot`` fixture should be used when a test function is dealing with ``matplotlib``. ``matplotlib`` is a soft dependency and is not required. This fixture is in charge of skipping the tests if ``matplotlib`` is not installed. In addition, figures created during the tests will be automatically closed once the test function has been executed. To use this fixture in a test function, one needs to pass it as an argument:: def test_requiring_mpl_fixture(pyplot): # you can now safely use matplotlib Workflow to improve test coverage --------------------------------- To test code coverage, you need to install the `coverage <https://pypi.org/project/coverage/>`_ package in addition to pytest. 1. Run 'make test-coverage'. The output lists for each file the line numbers that are not tested. 2. Find a low hanging fruit, looking at which lines are not tested, write or adapt a test specifically for these lines. 3. Loop. .. _monitoring_performances: Monitoring performance ====================== *This section is heavily inspired from the* `pandas documentation <https://pandas.pydata.org/docs/development/contributing_codebase.html#running-the-performance-test-suite>`_. When proposing changes to the existing code base, it's important to make sure that they don't introduce performance regressions. Scikit-learn uses `asv benchmarks <https://github.com/airspeed-velocity/asv>`_ to monitor the performance of a selection of common estimators and functions. You can view these benchmarks on the `scikit-learn benchmark page <https://scikit-learn.org/scikit-learn-benchmarks>`_. The corresponding benchmark suite can be found in the `scikit-learn/asv_benchmarks` directory. To use all features of asv, you will need either `conda` or `virtualenv`. For more details please check the `asv installation webpage <https://asv.readthedocs.io/en/latest/installing.html>`_. First of all you need to install the development version of asv: .. prompt:: bash $ pip install git+https://github.com/airspeed-velocity/asv and change your directory to `asv_benchmarks/`: .. prompt:: bash $ cd asv_benchmarks/ The benchmark suite is configured to run against your local clone of scikit-learn. Make sure it is up to date: .. prompt:: bash $ git fetch upstream In the benchmark suite, the benchmarks are organized following the same structure as scikit-learn. For example, you can compare the performance of a specific estimator between ``upstream/main`` and the branch you are working on: .. prompt:: bash $ asv continuous -b LogisticRegression upstream/main HEAD The command uses conda by default for creating the benchmark environments. If you want to use virtualenv instead, use the `-E` flag: .. prompt:: bash $ asv continuous -E virtualenv -b LogisticRegression upstream/main HEAD You can also specify a whole module to benchmark: .. prompt:: bash $ asv continuous -b linear_model upstream/main HEAD You can replace `HEAD` by any local branch. By default it will only report the benchmarks that have change by at least 10%. You can control this ratio with the `-f` flag. To run the full benchmark suite, simply remove the `-b` flag : .. prompt:: bash $ asv continuous upstream/main HEAD However this can take up to two hours. The `-b` flag also accepts a regular expression for a more complex subset of benchmarks to run. To run the benchmarks without comparing to another branch, use the `run` command: .. prompt:: bash $ asv run -b linear_model HEAD^! You can also run the benchmark suite using the version of scikit-learn already installed in your current Python environment: .. prompt:: bash $ asv run --python=same It's particularly useful when you installed scikit-learn in editable mode to avoid creating a new environment each time you run the benchmarks. By default the results are not saved when using an existing installation. To save the results you must specify a commit hash: .. prompt:: bash $ asv run --python=same --set-commit-hash=<commit hash> Benchmarks are saved and organized by machine, environment and commit. To see the list of all saved benchmarks: .. prompt:: bash $ asv show and to see the report of a specific run: .. prompt:: bash $ asv show <commit hash> When running benchmarks for a pull request you're working on please report the results on github. The benchmark suite supports additional configurable options which can be set in the `benchmarks/config.json` configuration file. For example, the benchmarks can run for a provided list of values for the `n_jobs` parameter. More information on how to write a benchmark and how to use asv can be found in the `asv documentation <https://asv.readthedocs.io/en/latest/index.html>`_. .. _issue_tracker_tags: Issue Tracker Tags ================== All issues and pull requests on the `GitHub issue tracker <https://github.com/scikit-learn/scikit-learn/issues>`_ should have (at least) one of the following tags: :Bug / Crash: Something is happening that clearly shouldn't happen. Wrong results as well as unexpected errors from estimators go here. :Cleanup / Enhancement: Improving performance, usability, consistency. :Documentation: Missing, incorrect or sub-standard documentations and examples. :New Feature: Feature requests and pull requests implementing a new feature. There are four other tags to help new contributors: :good first issue: This issue is ideal for a first contribution to scikit-learn. Ask for help if the formulation is unclear. If you have already contributed to scikit-learn, look at Easy issues instead. :Easy: This issue can be tackled without much prior experience. :Moderate: Might need some knowledge of machine learning or the package, but is still approachable for someone new to the project. :help wanted: This tag marks an issue which currently lacks a contributor or a PR that needs another contributor to take over the work. These issues can range in difficulty, and may not be approachable for new contributors. Note that not all issues which need contributors will have this tag. .. _backwards-compatibility: Maintaining backwards compatibility =================================== .. _contributing_deprecation: Deprecation ----------- If any publicly accessible method, function, attribute or parameter is renamed, we still support the old one for two releases and issue a deprecation warning when it is called/passed/accessed. E.g., if the function ``zero_one`` is renamed to ``zero_one_loss``, we add the decorator ``deprecated`` (from ``sklearn.utils``) to ``zero_one`` and call ``zero_one_loss`` from that function:: from ..utils import deprecated def zero_one_loss(y_true, y_pred, normalize=True): # actual implementation pass @deprecated("Function 'zero_one' was renamed to 'zero_one_loss' " "in version 0.13 and will be removed in release 0.15. " "Default behavior is changed from 'normalize=False' to " "'normalize=True'") def zero_one(y_true, y_pred, normalize=False): return zero_one_loss(y_true, y_pred, normalize) If an attribute is to be deprecated, use the decorator ``deprecated`` on a property. Please note that the ``property`` decorator should be placed before the ``deprecated`` decorator for the docstrings to be rendered properly. E.g., renaming an attribute ``labels_`` to ``classes_`` can be done as:: @deprecated("Attribute `labels_` was deprecated in version 0.13 and " "will be removed in 0.15. Use `classes_` instead") @property def labels_(self): return self.classes_ If a parameter has to be deprecated, a ``FutureWarning`` warning must be raised too. In the following example, k is deprecated and renamed to n_clusters:: import warnings def example_function(n_clusters=8, k='deprecated'): if k != 'deprecated': warnings.warn("'k' was renamed to n_clusters in version 0.13 and " "will be removed in 0.15.", FutureWarning) n_clusters = k When the change is in a class, we validate and raise warning in ``fit``:: import warnings class ExampleEstimator(BaseEstimator): def __init__(self, n_clusters=8, k='deprecated'): self.n_clusters = n_clusters self.k = k def fit(self, X, y): if self.k != 'deprecated': warnings.warn("'k' was renamed to n_clusters in version 0.13 and " "will be removed in 0.15.", FutureWarning) self._n_clusters = self.k else: self._n_clusters = self.n_clusters As in these examples, the warning message should always give both the version in which the deprecation happened and the version in which the old behavior will be removed. If the deprecation happened in version 0.x-dev, the message should say deprecation occurred in version 0.x and the removal will be in 0.(x+2), so that users will have enough time to adapt their code to the new behaviour. For example, if the deprecation happened in version 0.18-dev, the message should say it happened in version 0.18 and the old behavior will be removed in version 0.20. In addition, a deprecation note should be added in the docstring, recalling the same information as the deprecation warning as explained above. Use the ``.. deprecated::`` directive:: .. deprecated:: 0.13 ``k`` was renamed to ``n_clusters`` in version 0.13 and will be removed in 0.15. What's more, a deprecation requires a test which ensures that the warning is raised in relevant cases but not in other cases. The warning should be caught in all other tests (using e.g., ``@pytest.mark.filterwarnings``), and there should be no warning in the examples. Change the default value of a parameter --------------------------------------- If the default value of a parameter needs to be changed, please replace the default value with a specific value (e.g., ``warn``) and raise ``FutureWarning`` when users are using the default value. The following example assumes that the current version is 0.20 and that we change the default value of ``n_clusters`` from 5 (old default for 0.20) to 10 (new default for 0.22):: import warnings def example_function(n_clusters='warn'): if n_clusters == 'warn': warnings.warn("The default value of n_clusters will change from " "5 to 10 in 0.22.", FutureWarning) n_clusters = 5 When the change is in a class, we validate and raise warning in ``fit``:: import warnings class ExampleEstimator: def __init__(self, n_clusters='warn'): self.n_clusters = n_clusters def fit(self, X, y): if self.n_clusters == 'warn': warnings.warn("The default value of n_clusters will change from " "5 to 10 in 0.22.", FutureWarning) self._n_clusters = 5 Similar to deprecations, the warning message should always give both the version in which the change happened and the version in which the old behavior will be removed. The parameter description in the docstring needs to be updated accordingly by adding a `versionchanged` directive with the old and new default value, pointing to the version when the change will be effective:: .. versionchanged:: 0.22 The default value for `n_clusters` will change from 5 to 10 in version 0.22. Finally, we need a test which ensures that the warning is raised in relevant cases but not in other cases. The warning should be caught in all other tests (using e.g., ``@pytest.mark.filterwarnings``), and there should be no warning in the examples. .. currentmodule:: sklearn .. _code_review: Code Review Guidelines ====================== Reviewing code contributed to the project as PRs is a crucial component of scikit-learn 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. .. note:: The difference between an objective improvement and a subjective nit isn't always clear. Reviewers should recall that code review is primarily about reducing risk in the project. When reviewing code, one should aim at preventing situations which may require a bug fix, a deprecation, or a retraction. Regarding docs: typos, grammar issues and disambiguations are better addressed immediately. 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 scikit-learn user, like the change and intend to use it? Is it in the scope of scikit-learn? Will the cost of maintaining a new feature be worth its benefits? - Is the code consistent with the API of scikit-learn? 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 scikit-learn conventions and documented clearly? - Is any new functionality described in the user-guide and illustrated with examples? - 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 <https://jeffknupp.com/blog/2013/12/09/improve-your-python-understanding-unit-testing>`__ 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? Should comments be added? Should comments be removed as unhelpful or extraneous? - Could the code easily be rewritten to run much more efficiently for relevant settings? - Is the code backwards compatible with previous versions? (or is a deprecation cycle necessary?) - Will the new code add any dependencies on other libraries? (this is unlikely to be accepted) - Does the documentation render properly (see the :ref:`contribute_documentation` section for more details), and are the plots instructive? :ref:`saved_replies` includes some frequent comments that reviewers may make. .. _communication: Communication Guidelines ------------------------ Reviewing open pull requests (PRs) helps move the project forward. It is a great way to get familiar with the codebase and should motivate the contributor to keep involved in the project. [1]_ - Every PR, good or bad, is an act of generosity. Opening with a positive comment will help the author feel rewarded, and your subsequent remarks may be heard more clearly. You may feel good also. - Begin if possible with the large issues, so the author knows they've been understood. Resist the temptation to immediately go line by line, or to open with small pervasive issues. - Do not let perfect be the enemy of the good. If you find yourself making many small suggestions that don't fall into the :ref:`code_review`, consider the following approaches: - refrain from submitting these; - prefix them as "Nit" so that the contributor knows it's OK not to address; - follow up in a subsequent PR, out of courtesy, you may want to let the original contributor know. - Do not rush, take the time to make your comments clear and justify your suggestions. - You are the face of the project. Bad days occur to everyone, in that occasion you deserve a break: try to take your time and stay offline. .. [1] Adapted from the numpy `communication guidelines <https://numpy.org/devdocs/dev/reviewer_guidelines.html#communication-guidelines>`_. Reading the existing code base ============================== Reading and digesting an existing code base is always a difficult exercise that takes time and experience to main. Even though we try to write simple code in general, understanding the code can seem overwhelming at first, given the sheer size of the project. Here is a list of tips that may help make this task easier and faster (in no particular order). - Get acquainted with the :ref:`api_overview`: understand what :term:`fit`, :term:`predict`, :term:`transform`, etc. are used for. - Before diving into reading the code of a function / class, go through the docstrings first and try to get an idea of what each parameter / attribute is doing. It may also help to stop a minute and think *how would I do this myself if I had to?* - The trickiest thing is often to identify which portions of the code are relevant, and which are not. In scikit-learn **a lot** of input checking is performed, especially at the beginning of the :term:`fit` methods. Sometimes, only a very small portion of the code is doing the actual job. For example looking at the ``fit()`` method of :class:`~linear_model.LinearRegression`, what you're looking for might just be the call the ``scipy.linalg.lstsq``, but it is buried into multiple lines of input checking and the handling of different kinds of parameters. - Due to the use of `Inheritance <https://en.wikipedia.org/wiki/Inheritance_(object-oriented_programming)>`_, some methods may be implemented in parent classes. All estimators inherit at least from :class:`~base.BaseEstimator`, and from a ``Mixin`` class (e.g. :class:`~base.ClassifierMixin`) that enables default behaviour depending on the nature of the estimator (classifier, regressor, transformer, etc.). - Sometimes, reading the tests for a given function will give you an idea of what its intended purpose is. You can use ``git grep`` (see below) to find all the tests written for a function. Most tests for a specific function/class are placed under the ``tests/`` folder of the module - You'll often see code looking like this: ``out = Parallel(...)(delayed(some_function)(param) for param in some_iterable)``. This runs ``some_function`` in parallel using `Joblib <https://joblib.readthedocs.io/>`_. ``out`` is then an iterable containing the values returned by ``some_function`` for each call. - We use `Cython <https://cython.org/>`_ to write fast code. Cython code is located in ``.pyx`` and ``.pxd`` files. Cython code has a more C-like flavor: we use pointers, perform manual memory allocation, etc. Having some minimal experience in C / C++ is pretty much mandatory here. - Master your tools. - With such a big project, being efficient with your favorite editor or IDE goes a long way towards digesting the code base. Being able to quickly jump (or *peek*) to a function/class/attribute definition helps a lot. So does being able to quickly see where a given name is used in a file. - `git <https://git-scm.com/book/en>`_ also has some built-in killer features. It is often useful to understand how a file changed over time, using e.g. ``git blame`` (`manual <https://git-scm.com/docs/git-blame>`_). This can also be done directly on GitHub. ``git grep`` (`examples <https://git-scm.com/docs/git-grep#_examples>`_) is also extremely useful to see every occurrence of a pattern (e.g. a function call or a variable) in the code base. - Configure `git blame` to ignore the commit that migrated the code style to `black`. .. prompt:: bash $ git config blame.ignoreRevsFile .git-blame-ignore-revs Find out more information in black's `documentation for avoiding ruining git blame <https://black.readthedocs.io/en/stable/guides/introducing_black_to_your_project.html#avoiding-ruining-git-blame>`_.