Merge remote-tracking branch 'upstream/main'

# Conflicts:
#	docs/source/notebooks/language_notebooks/language_model_game.ipynb
#	docs/source/notebooks/vision_notebooks/vision_transformer.ipynb
#	shapiq/approximator/__init__.py
#	shapiq/approximator/_base.py
#	shapiq/game_theory/indices.py
#	shapiq/games/benchmark/_setup/_vit_setup.py
#	shapiq/games/benchmark/local_xai/benchmark_image.py

Author: justinkang221

.coveragerc

@@ -1,21 +1,45 @@
 # ✌️ 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.
+This document outlines how to easily contribute to the project.
 For the code of conduct, please refer to the [CODE_OF_CONDUCT.md](./CODE_OF_CONDUCT.md).
 
 ## 🗺️ 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.
-
-### 🙏 Discussions
+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) which is just storing all the ideas
+and problems found on shapiq's [issues page](https://github.com/mmschlk/shapiq/issues). If you want
+to work on something, check out the roadmap or issues first to see if the feature is already
+planned or if there is a similar feature that you could contribute to.
+
+Here are some examples of what we are very happy to receive contributions for:
+
+### Approximators
+We are always looking for new approximators to add to `shapiq`. Approximators are always extending
+the base class `Approximator` and implementing `approximate` method. Make sure to create unit tests
+for the new approximator.
+
+### Explainers
+If you want to add a new explainer, you can extend the base class `Explainer` and implement the
+`explain_function` method. Make sure to create unit tests for the new explainer. Note that
+explainers are quite elaborate, so it is a very good idea to open a discussion before starting to
+work on a new explainer.
+
+### Model Support
+You like a particular machine learning model and it is not yet supported by `shapiq`? Maybe you can
+add support in the [transformation code](https://github.com/mmschlk/shapiq/blob/56e1ea4a41d185b8364ca8e6370a01646dd792c6/shapiq/explainer/utils.py#L1) or [tree/validation](https://github.com/mmschlk/shapiq/blob/56e1ea4a41d185b8364ca8e6370a01646dd792c6/shapiq/explainer/tree/validation.py).
+Make sure to add tests for the new model as part of the unit tests (you can find the tests of the
+other model types).
+
+### Visualizations
+If you have a nice idea to visualize Shapley values or Shapley interaction values, you can add a new
+visualization to the `shapiq.plot` package. Make sure that plots are also available through the
+`InteractionValues` object like the other plots (e.g. `InteractionValues.plot_force`). Make sure to
+add tests for the new visualization.
+
+### 🙏 Discussions and Issues
 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.
+[Discussions](https://github.com/mmschlk/shapiq/discussions/new/choose) section or open an [issues](https://github.com/mmschlk/shapiq/issues).
 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.
 
@@ -39,52 +63,37 @@ 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:
+[uv](https://docs.astral.sh/uv/getting-started/installation), which works extremely fast and helps
+to stay up-to-date with the latest Python versions. With `uv`, you can set up your development
+environment with the following command:
 
 ```sh
-pyenv install 3.10
+uv sync --all-extras --dev
 ```
 
-Then, create a virtual environment and install the development dependencies:
+Now you are all set up and ready to go.
 
-```sh
-cd shapiq
-python -m venv .venv
-source .venv/bin/activate
-pip install -e .[dev]
-```
 
----
-> 📝 **Note**: Since `shapiq` uses the `requests` library, you might need to install the
+> 📝 **Note**: `shapiq` uses the `requests` library, you might need to install the
 > certificates on your MacOS system ([more information](https://stackoverflow.com/a/53310545)).
 ```sh
 /Applications/Python\ 3.x/Install\ Certificates.command
 ```
----
 
-Finally, install the [pre-commit](https://pre-commit.com/) push hooks. This will run some code
-quality checks every time you push to GitHub.
+### 🛠️ Pre-Commit Hooks
+To ensure that the code quality is maintained, we use `pre-commit` hooks. You need to install the
+[pre-commit](https://pre-commit.com/)  hooks. This will run some code quality checks every time
+you push to GitHub. You can view the checks in the `.pre-commit-config.yaml` file and the setup in
+the `pyproject.toml` file.
 
 ```sh
-pre-commit install --hook-type pre-push
+uv run pre-commit install
 ```
 
 If you want, you can optionally run `pre-commit` at any time as so:
 
 ```sh
-pre-commit run --all-files
-```
-
-## 📝 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
+uv run pre-commit run --all-files
 ```
 
 ## 🛠️ Making Changes
@@ -102,7 +111,7 @@ To build the documentation on your end and to check if your changes are document
 need to install the documentation dependencies:
 
 ```sh
-pip install -e .[docs]
+uv sync --all-extras --dev --docs
 ```
 
 Then, you can build the documentation from the root of the repository with:
@@ -116,18 +125,18 @@ 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.
+We use `pytest` for running unit tests and coverage.
 
 #### 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:
+Unit tests are located in the `tests` directory. To run the tests with `pytest`, you can use the
+following command and replace `n_jobs` with the number of jobs you want to run in parallel:
 
 ```sh
-pytest
+uv run pytest -n n_jobs
 ```
 
 #### Coverage
@@ -138,7 +147,7 @@ We use `pytest-cov` to measure the test coverage. To run the tests with coverage
 following command:
 
 ```sh
-pytest --cov=shapiq
+uv run pytest --cov=shapiq
 ```
 
 #### Static Type Checking and Code Quality
@@ -147,14 +156,5 @@ Currently, we do not have static type checking in place. We use `pre-commit` to
 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
+uv run pre-commit run --all-files
 ```

.dev-pre-commit-config.yaml

@@ -8,14 +8,15 @@ updates:
   - package-ecosystem: "pip"
     directory: "/"
     schedule:
-      interval: "monthly"
+      interval: "weekly"
     open-pull-requests-limit: 12
     groups:
       pip-all-updates:
         patterns:
           - "*"
+
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-        interval: "monthly"
+        interval: "weekly"
     open-pull-requests-limit: 12

.github/CONTRIBUTING.md

@@ -17,18 +17,21 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
         python-version: "3.10"
-        cache: 'pip'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+          enable-cache: true
+
     - name: Install pre-commit
       run: |
-        pip install pre-commit
-        pre-commit install
+        uv sync --only-group lint
+        uv run pre-commit install
+
     - name: Run code-quality checks
-      run: SKIP=mypy pre-commit run --all-files
+      run: uv run pre-commit run --all-files

.github/dependabot.yml

@@ -19,19 +19,31 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
-        cache: 'pip'
+        python-version: "3.11"
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        enable-cache: true
+
+    - name: Cache UV packages
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/uv
+        key: uv-${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml', 'uv.lock') }}
+        restore-keys: |
+          uv-${{ runner.os }}-${{ matrix.python-version }}-
+
     - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
-    - name: Test with pytest
-      run: |
-        pip install pytest pytest-cov
-        pytest --cov=shapiq --cov-report=xml
+      run: uv sync --all-extras --dev
+
+    - name: Measure coverage
+      run: uv run pytest --cov=shapiq --cov-report=xml -n logical
+
     - name: Coveralls
       uses: coverallsapp/github-action@v2
       with:

.github/workflows/code-quality.yml

@@ -0,0 +1,27 @@
+name: Install & Import shapiq
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  install-and-import:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install uv and Python
+        uses: astral-sh/setup-uv@v6
+        with:
+          python-version: "3.11"
+          activate-environment: true
+      - name: Install package using uv
+        run: uv pip install .
+
+      - name: Test import
+        run: uv run python -c "import shapiq; print('✅ shapiq imported successfully')"

.github/workflows/publish-coverage.yml .github/workflows/coverage.yml.github/workflows/publish-coverage.yml renamed to .github/workflows/coverage.yml

@@ -23,18 +23,22 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
         python-version: '3.10'
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install build
+
     - name: Build package
       run: python -m build
+
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc
+      uses: pypa/gh-action-pypi-publish@v1.12.4
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}