Development

This document explains how to set up a development environment for contributing to cleanlab.

Setting up a virtual environment

While this is not required, we recommend that you do development and testing in a virtual environment. There are a number of tools to do this, including virtualenv, pipenv, and venv. You can compare the tools and choose what is right for you. Here, we'll explain how to get set up with venv, which is built in to Python 3.

python3 -m venv ./ENV  # create a new virtual environment in the directory ENV
source ./ENV/bin/activate  # switch to using the virtual environment

You only need to create the virtual environment once, but you will need to activate it every time you start a new shell. Once the virtual environment is activated, the pip install commands below will install dependencies into the virtual environment rather than your system Python installation.

Installing dependencies and cleanlab

Run the following commands in the repository's root directory.

Install development requirements

pip install -r requirements-dev.txt

Install cleanlab as an editable package

pip install -e .

For Macs with Apple silicon: replace tensorflow in requirements-dev.txt with: tensorflow-macos==2.9.2 and tensorflow-metal==0.5.1

Handling optional dependencies

When designing a class that relies on an optional, domain-specific runtime dependency, it is better to use lazy-importing to avoid forcing users to install the dependency if they do not need it.

Depending on the coupling of your class to the dependency, you may want to consider importing it at the module-level or as an instance variable of the class or a function that uses the dependency.

If the dependency is used by many methods in the module or other classes, it is better to import it at the module-level. On the other hand, if the dependency is only used by a handful of methods, then it's better to import it inside the method. If the dependency is not installed, an ImportError should be raised when the method is called, along with instructions on how to install the dependency.

Here is an example of a class that lazily imports CuPy and has a sum method (element-wise) that can be used on both CPU and GPU devices.

Unless an alternative implementations of the sum method is available, an ImportError should be raised when the method is called with instructions on how to install the dependency.

Example code

def lazy_import_cupy():
  try:
    import cupy
  except ImportError as error:
    # If the dependency is required for the class to work,
    # replace this block with a raised ImportError containing instructions
    print("Warning: cupy is not installed. Please install it with `pip install cupy`.")
    cupy = None
  return cupy

class Summation:
  def __init__(self):
    self.cupy = lazy_import_cupy()
  def sum(self, x) -> float:
    if self.cupy is None:
      return sum(x)
    return self.cupy.sum(x)

For the build system to recognize the optional dependency, you should add it to the EXTRAS_REQUIRE constant in setup.py:

Example code

EXTRAS_REQUIRE = {
    ...
    "gpu": [
      # Explain why the dependency below is needed,
      # e.g. "for performing summation on GPU"
      "cupy",
    ],
}

Or assign to a separate variable and add it to EXTRAS_REQUIRE

GPU_REQUIRES = [
  # Explanation ...
  "cupy",
]

EXTAS_REQUIRE = {
    ...
    "gpu": GPU_REQUIRES,
}

The package can be installed with the optional dependency (here called gpu) via:

PyPI installation

pip install -r "cleanlab[gpu]"

Editable installation

pip install -e ".[gpu]"

Testing

Download test data The test data for cleanlab resides in the assets repository. Use the following commands to download test data before running tests.

git clone https://github.com/cleanlab/assets.git
mv assets/cleanlab_test_data cleanlab/tests/datalab/data

Run all the tests:

pytest

Run a specific file or test:

pytest -k <filename or filter expression>

Run with verbose output:

pytest --verbose

Run with code coverage:

pytest --cov=cleanlab/ --cov-config .coveragerc --cov-report=html

The coverage report will be available in coverage_html_report/index.html, which you can open with your web browser.

Type checking

Cleanlab uses mypy typing. Type checking happens automatically during CI but can be run locally.

Check typing in all files:

mypy cleanlab

The above is just a simplified command for demonstration, do NOT run this for testing your own type annotations! Our CI adds a few additional flags to the mypy command it uses in the file: .github/workflows/ci.yml. To exactly match the mypy command that is executed in CI, copy these flags, and also ensure your version of mypy and related packages like pandas-stubs match the latest released versions (used in our CI).

Examples

You can check that the examples still work with changes you make to cleanlab by manually running the notebooks. You can also run all example notebooks as follows:

git clone https://github.com/cleanlab/examples.git

Then specify your local version of cleanlab source in the first line of: examples/requirements.txt. E.g. you can edit this line to point to your local version of cleanlab as a relative path such as ../cleanlab if the cleanlab and examples repos are sibling directories on your computer.

Finally execute the bash script:

examples/run_all_notebooks.sh

How to style new code contributions

cleanlab follows the Black code style (see pyproject.toml). This is enforced by CI, so please format your code by invoking black before submitting a pull request.

Generally aim to follow the PEP-8 coding style. Please do not use wildcard import * in any files, instead you should always import the specific functions that you need from a module.

All cleanlab code should have a maximum line length of 100 characters.

Pre-commit hook

This repo uses the pre-commit framework to easily set up code style checks that run automatically whenever you make a commit. You can install the git hook scripts with:

pre-commit install

EditorConfig

This repo uses EditorConfig to keep code style consistent across editors and IDEs. You can install a plugin for your editor, and then your editor will automatically ensure that indentation and line endings match the project style.

Adding new modules into the source code

You should go through the following checklist if you intend to add new functionality to the package in a separate module.

Add brief description of the module’s purpose in a comment at the top of file and docstrings for every function.
Import the module my_module.py into main __init__.py
Create detailed unit tests (typically in a new file tests/test_my_module.py)
Add new module to docs index pages (docs/source/index.rst) and create .rst file in docs/source/cleanlab/ (so that module appears on docs.cleanlab.ai -- please verify its documentation also looks good there)
Create a QuickStart (docs/source/tutorials) notebook that runs main module functionality in 5min or less and add it to index pages (docs/source/tutorials/index.rst, docs/source/index.rst). Clear cell output before pushing.
Create an examples notebook that runs more advanced module functionality with a more real-world application (can have a longer run time). Push with printed cell output.

Contributing new issue types to Datalab

To contribute a new type of issue that Datalab can automatically detect in any dataset, refer to our guide on Creating Your Own Issues Manager.

Do not add your new issue type to the set of issues that Datalab detects by default, our team can add it to this default set later on once it's utility has been thoroughly validated.

Don't forget to update the issue type descriptions guide with a brief description of your new issue type. It is ideal to stick to a format that maintains consistency and readability. Generally, the format includes a title, explanation of the issue, required arguments, then any additional information. It would be helpful to include a tip for users on how to detect the issue using Datalab.

Try to add tests for this new issue type. It's a good idea to start with some tests in a separate module in the issue manager test directory.

Documentation

You can build the docs from your local cleanlab version by following these instructions.

If editing existing docs or adding new tutorials, please first read through our guidelines.

Documentation style

cleanlab uses NumPy style docstrings (example).

Aspects that are not covered in the NumPy style or that are different from the NumPy style are documented below:

Referring to the cleanlab package: we refer to cleanlab without any special formatting, so no cleanlab, just cleanlab.
Cross-referencing: when mentioning functions/classes/methods, always cross-reference them to create a clickable link. Cross-referencing code from Jupyter notebooks is not currently supported.
Variable, module, function, and class names: when not cross-references, should be written between single back-ticks, like `pred_probs`. Such names in Jupyter notebooks (Markdown) can be written between single back-ticks as well.
Math: We support LaTeX math with the inline :math:`x+y` or the block:
```
.. math::

   \sum_{0}^{n} 2n+1
```
Pseudocode vs math: Prefer pseudocode in double backticks over LaTeX math.
Bold vs italics: Use italics when defining a term, and use bold sparingly for extra emphasis.
Shapes: Do not include shapes in the type of parameters, instead use np.array or array_like as the type and specify allowed shapes in the description. See, for example, the documentation for cleanlab.classification.CleanLearning.fit(). Format for 1D shape: (N,1)
Optional arguments: for the most part, just put , optional in the type.
Type unions: if a parameter or return type is something like "a numpy array or None", you can use "or" to separate types, e.g. np.array or None, and it'll be parsed correctly.
Parameterized types: Use standard Python type hints for referring to parameters and parameterized types in docs, e.g. Iterable[int] or list[float].

Common variable names / terminology used throughout codebase

N - the number of examples/datapoints in a dataset.
- num_examples may also be used when additional clarity is needed.
K - the number of classes (unique labels) for a dataset.
- num_classes may also be used when additional clarity is needed.
labels - a label for each example, length should be N (sample-size of dataset)
classes - set of possible labels for any one example, length should be K (number of possible categories in classification problem)

Try to adhere to this standardized terminology unless you have good reason not to!

Relative Link Formatting Instructions

Use relative linking to connect information between docs and jupyter notebooks, and make sure links will remain valid in the future as new cleanlab versions are released! Sphinx/html works with relative paths so try to specify relative paths if necessary. For specific situations:

Link another function or class from within a source code docstring:
- If you just want to specify the function/class name (ie. the function/class is unique throughout our library): `~cleanlab.file.function_or_class_name`.
  
  This uses the Sphinx's default_role = "py:obj" setting, so the leading tilde shortens the link to only display function_or_class_name.
- If you want to additionally specify the module which the function belongs to:
  - :py:func:`file.function_name <cleanlab.file.function_name>` for functions
  - :py:class:`file.class_name <cleanlab.file.class_name>` for classes
  Here you have more control over the text that is displayed to display the module name. When referring to a function that is alternatively defined in other modules as well, always use this option to be more explicit about which module you are referencing.
Link a tutorial (rst file) from within a source code docstring or rst file: :ref:`tutorial_name <tutorial_name>`
Link a tutorial notebook (ipynb file) from within a source code docstring or rst file: `notebook_name <tutorials/notebook_name.ipynb>`_ . (If the notebook is not the in the same folder as the source code, use a relative path)
Link a function from within a tutorial notebook: [function_name](../cleanlab/file.html#cleanlab.file.function_name)

Links from master branch tutorials will reference master branch functions, similarly links from tutorials in stable branch will reference stable branch functions since we are using relative paths.
Link a specific section of a notebook from within the notebook: [section title](#section-title)
Link a different tutorial notebook from within a tutorial notebook: [another notebook](another_notebook.html). (Note this only works when the other notebook is in same folder as this notebook, otherwise may need to try relative path)
Link another specific section of different notebook from within a tutorial notebook: [another notebook section title](another_notebook.html#another-notebook-section-title)
Linking examples notebooks from inside tutorial notebooks can be simply done by linking global url of the example notebook in master branch of github.com/cleanlab/examples/

Packaging and releasing

The release process is automated using GitHub Actions. When a release is published on the main cleanlab repository, the following workflows are triggered:

Docs are built and pushed to the cleanlab-docs depository within the same organization, which handles the deployment to docs.cleanlab.ai.
A new release is created on PyPI with the same version number as the release on GitHub.

There are other workflows that need to be handled manually in other repositories, but that is outside the score of this section. This section will focus on the PyPI release process.

Developing the PyPI release process

It's important to test the release process on a separate PyPI project before releasing to the main cleanlab project. For the remainder of this section, we'll refer to the test project as test-cleanlab-<username>, where <username> is your GitHub username. This name should be unique to avoid conflicts with other users' test projects.

Prerequisites

PyPI Prerequisites

Create separate user accounts on PyPI and Test PyPI.
- Register here on PyPI.
- Register here on Test PyPI.
- Ideally, these accounts should have the same username, but this is not strictly necessary.
Add a "Trusted Publisher" on both PyPI accounts (i.e. Publishing with OpenID Connect).
- This will allow you to publish packages to PyPI and Test PyPI using GitHub Actions, without needing to store your PyPI credentials in the repository.
- Walk through the steps in "Creating a PyPI project with a trusted publisher" for both PyPI and Test PyPI.
  - The PyPI Project name is: test-cleanlab-<username>.
  - The owner is: <username> (your GitHub username).
  - The repository name is: cleanlab (your fork of the cleanlab repository).
  - The workflow file name is: release-build-publish.yml
  - ATTENTION: The environment name should be left empty in the Test PyPI project, and set to pypi in the PyPI project.
    - See discussion on the environment in the GitHub Prerequisites section.

GitHub Prerequisites

Fork the cleanlab repository to your GitHub account.
- This will allow you to test the release process on your fork, on a separate PyPI project.
On your fork of the cleanlab repository, create two environments called testpypi and pypi in the "Environments" tab, under the repository "Settings".
- For the testpypi environment, add a wait timer of 1 minute to allow TestPyPI uploads to complete processing before testing installation.
- For the pypi environment, add a protection rule for requiring a review from a maintainer. For extra security, you may disallow a self-review so that a second maintainer must approve the release.
- You may wish to limit which tags can trigger a release in these environment, to avoid accidental releases.
- Github Docs provides instructions on how to create a new environment with these considerations.

Local Prerequisites

In pyproject.toml replace the project.name configuration with the value test-cleanlab-<username>, where <username> is your GitHub username.

Testing the release process

Push a commit with an updated version number in cleanlab/version.py.
- Ideally, this should be a patch version bump, e.g. 0.1.0 to 0.1.1 or a minor version bump, e.g. 0.1.X to 0.2.0.
- This is typically done via a standalone PR to the cleanlab/cleanlab repository.
```
# Bump the version number in cleanlab/version.py
- __version__ = "2.6.0"
+ __version__ = "2.6.1"
```
On the repository's GitHub page, navigate to the "Releases" page and click "Draft a new release".
- Choose a tag version that matches the version number in cleanlab/version.py, it should follow the format vX.Y.Z, e.g. v2.6.1 or v2.7.0.
  - This kind of format will be automatically checked by the release workflow.
  - This tag may not exist yet, but Github allows you to create it upon publishing the release.
- Target the master branch.
- Select the previous tag to compare against, if it exists. Usually this is the previous release tag, e.g. the previous patch version.
  - GitHub should allow you to generate release notes based on this information.
- When you've finalized the release notes and are ready to publish the release, click "Publish release".
- This will kick off the release workflow, which will build and publish the package to Test PyPI, test the package installation, and then publish the package to PyPI.
Open up the "Actions" tab on your fork of the cleanlab repository and monitor the progress of the release workflow.
- A "Release Build Publish" workflow should be triggered by the release, and you can monitor its progress there.
- It will check for the project name (for uploading to the proper PyPI project), and validate the version name/tag.
- When these steps pass, it will build the distribution and check the contents.
- Passing the build step, it will upload the distribution to Test PyPI.
- After the upload, it will kick off several test jobs to install the package from Test PyPI and run various tests.
  - Adding more kinds of tests at this stage in the workflow is a good idea, to ensure the package is working as expected. Just create a new job that needs the verify-version job, and runs the tests you want to add.
- After all the tests pass, it will trigger the final job. However, the environment should be configure to require a review from a maintainer before the final job can be run.
  - View the deployment and approve it it everything looks good so far. This will trigger the final job to publish the package to PyPI.

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DEVELOPMENT.md

DEVELOPMENT.md

Development

Setting up a virtual environment

Installing dependencies and cleanlab

Handling optional dependencies

Testing

Type checking

Examples

How to style new code contributions

Pre-commit hook

EditorConfig

Adding new modules into the source code

Contributing new issue types to Datalab

Documentation

Documentation style

Common variable names / terminology used throughout codebase

Relative Link Formatting Instructions

Packaging and releasing

Developing the PyPI release process

Prerequisites

PyPI Prerequisites

GitHub Prerequisites

Local Prerequisites

Testing the release process

Files

DEVELOPMENT.md

Latest commit

History

DEVELOPMENT.md

File metadata and controls

Development

Setting up a virtual environment

Installing dependencies and cleanlab

Handling optional dependencies

Testing

Type checking

Examples

How to style new code contributions

Pre-commit hook

EditorConfig

Adding new modules into the source code

Contributing new issue types to Datalab

Documentation

Documentation style

Common variable names / terminology used throughout codebase

Relative Link Formatting Instructions

Packaging and releasing

Developing the PyPI release process

Prerequisites

PyPI Prerequisites

GitHub Prerequisites

Local Prerequisites

Testing the release process