From 9a22dda024f59624fe772658b5916801f24de89d Mon Sep 17 00:00:00 2001 From: Maximilian Date: Wed, 14 Feb 2024 09:55:10 +0100 Subject: [PATCH] adds a collaboration tutorial and code of conduct (closes #39). --- CODE_OF_CONDUCT.md | 134 ++++++++++++++++++++++++++++ CONTRIBUTING.md | 152 ++++++++++++++++++++++++++++++++ setup.py | 13 ++- shapiq/approximator/__init__.py | 3 + 4 files changed, 300 insertions(+), 2 deletions(-) create mode 100644 CODE_OF_CONDUCT.md create mode 100644 CONTRIBUTING.md diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 00000000..a0f77968 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,134 @@ + +# ✌️ Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or advances of + any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email address, + without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official email address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +`maximilian.muschalik"at"ifi.lmu.de`. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.1, available at +[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. + +Community Impact Guidelines were inspired by +[Mozilla's code of conduct enforcement ladder][Mozilla CoC]. + +For answers to common questions about this code of conduct, see the FAQ at +[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at +[https://www.contributor-covenant.org/translations][translations]. + +[homepage]: https://www.contributor-covenant.org +[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html +[Mozilla CoC]: https://github.com/mozilla/diversity +[FAQ]: https://www.contributor-covenant.org/faq +[translations]: https://www.contributor-covenant.org/translations + diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..171c8c45 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,152 @@ +# ✌️ Contributing Guidelines + +This document outlines the guidelines for contributing to the project. It should enable contributors +to understand the process for applying changes to the project and how to interact with the community. +For the code of conduct, please refer to the [CODE_OF_CONDUCT.md](./CODE_OF_CONDUCT.md). + +## πŸ—ΊοΈ What to Work On +First, we welcome contributions from everyone in every form. If you feel that something is missing +or could be improved, feel free to change it. However, to streamline the process of contributing +higher-tier changes or features to the project, we maintain an open +[roadmap](https://github.com/users/mmschlk/projects/4/views/4). There, we collect ideas and features +that we want to add to the project. If you want to work on something, please check the roadmap first +to see if the feature is already planned or if there is a similar feature that you could contribute +to. + +### πŸ™ Discussions +If you have an idea for a new feature or a change, we encourage everyone to open a discussion in the +[Discussions](https://github.com/mmschlk/shapiq/discussions/new/choose) section. +We encourage you to open a discussion so that we can align on the work to be done. It's generally a +good idea to have a quick discussion before opening a pull request that is potentially out-of-scope. + + +## πŸ“ Typical Setup: Fork, Clone, and Pull + +The typical workflow for contributing to `shapiq` is: + +1. Fork the `main` branch from the [GitHub repository](https://github.com/mmschlk/shapiq/). +2. Clone your fork locally. +3. Commit changes. +4. Push the changes to your fork. +5. Send a pull request from your fork back to the original `main` branch. + +## πŸ“¦ Development Setup + +Start by cloning the repository: + +```sh +git clone https://github.com/mmschlk/shapiq/ +``` + +Next you need a python environment with a supported version of python. We recommend using +[pyenv](https://github.com/pyenv/pyenv-installer). Once you have pyenv, you can install the latest +Python version `shapiq` supports: + +```sh +pyenv install 3.9 +``` + +Then, create a virtual environment and install the development dependencies: + +```sh +cd shapiq +python -m venv .venv +source .venv/bin/activate +pip install -e .[dev] +``` + +Finally, install the [pre-commit](https://pre-commit.com/) push hooks. This will run some code +quality checks every time you push to GitHub. + +```sh +pre-commit install --hook-type pre-push +``` + +If you want, you can optionally run `pre-commit` at any time as so: + +```sh +pre-commit run --all-files +``` + +## πŸ“ Commit Messages + +We do not enforce a strict commit message format, but we encourage you to follow good practices. +We recommend to use action-words to automatically close issues or pull requests (example: `closes #123`). +For example, start the commit message with a verb in the imperative mood, and keep the message short +and concise. For example: + +``` +add feature-xyz and closes #123 +``` + +## πŸ› οΈ Making Changes + +Now, you're ready to make changes to the code. We recommend that you check out `shapiq`'s source +code for inspiration before getting started. How you make changes is, of course, up to you. However, +we can give you some tips on how to document and test your changes. + +### πŸ“– Documenting Changes +If you are adding a new class of function, you will need to add a docstring to the class or +function. With `shapiq`, we use the [Google Style Convention](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). +Please add a docstring in the same style. + +To build the documentation on your end and to check if your changes are documented correctly, you +need to install the documentation dependencies: + +```sh +pip install -e .[docs] +``` + +Then, you can build the documentation from the root of the repository with: + +```sh +sphinx-build docs/source docs/build +``` + +This will render the documentation in the `docs/build` directory. You can open the `index.html` file +in your browser to see the rendered documentation. + +### 🎯 Testing Changes + +We use `pytest` for running unit tests and coverage. In the near future we will add `mypy` to the +static type checking. + +#### Unit Tests + +Unit tests **absolutely need to pass**. Write unit tests for your changes. If you are adding a new +feature, you need to add tests for the new feature. If you are fixing a bug it is a good idea to add +a test that shows the bug and that your fix works. +Unit tests are located in the `tests` directory. To run the tests, you can use the following command: + +```sh +pytest +``` + +#### Coverage + +With `shapiq`, we aim to have a high test coverage (95% -100%). We aim that every pull request does +not decrease the test coverage. +We use `pytest-cov` to measure the test coverage. To run the tests with coverage, you can use the +following command: + +```sh +pytest --cov=shapiq +``` + +#### Static Type Checking and Code Quality + +Currently, we do not have static type checking in place. We use `pre-commit` to run some code quality +checks. These checks **absolutely need to pass**. You can run the checks with the following command: + +```sh +pre-commit run --all-files +``` + +In the near future we aim to use `mypy` for type checking. Once added this will also be part of the +pre-commit pipeline and hence **absolutely need to pass**. + +If you want, you can run `mypy` with the following command: + +```sh +mypy shapiq +``` \ No newline at end of file diff --git a/setup.py b/setup.py index e1d181d8..ebc6dba2 100644 --- a/setup.py +++ b/setup.py @@ -18,7 +18,7 @@ with io.open(os.path.join(work_directory, "README.md"), encoding="utf-8") as f: long_description = "\n" + f.read() -base_packages = ["numpy", "scipy", "pandas"] +base_packages = ["numpy", "scipy", "pandas", "tqdm"] plotting_packages = ["matplotlib", "colour", "networkx"] @@ -76,6 +76,15 @@ "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", ], - keywords=["python", "machine learning", "shap", "xai", "interaction"], + keywords=[ + "python", + "machine learning", + "shap", + "xai", + "interaction", + "shapley interactions", + "shapley values", + "feature interaction", + ], zip_safe=True, ) diff --git a/shapiq/approximator/__init__.py b/shapiq/approximator/__init__.py index 4b9e0bc6..ef1f236b 100644 --- a/shapiq/approximator/__init__.py +++ b/shapiq/approximator/__init__.py @@ -1,4 +1,5 @@ """This module contains the approximators to estimate the Shapley interaction values.""" +from .k_sii import convert_ksii_into_one_dimension, transforms_sii_to_ksii from .permutation.sii import PermutationSamplingSII from .permutation.sti import PermutationSamplingSTI from .regression import KernelSHAP, RegressionFSI, RegressionSII @@ -11,4 +12,6 @@ "RegressionFSI", "RegressionSII", "ShapIQ", + "transforms_sii_to_ksii", + "convert_ksii_into_one_dimension", ]