⚒️ Reduce package clutter and adds uv (mmschlk#348)

* Bump numpy from 1.26.4 to 2.1.2

Bumps [numpy](https://github.com/numpy/numpy) from 1.26.4 to 2.1.2.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v1.26.4...v2.1.2)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

* updated python project structure

* removed setup.py

* adjusted toml

* adjusted toml

* adjusted toml

* adjusted toml

* adjusted toml

* updated tests to get setup with uv

* updated tests to get setup with uv

* fixed np.nan to np.NaN

* excludes test

* test numpy

* fixed np.NaN

* fixed np.NaN

* updated test run

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Author: mmschlk

.coveragerc

@@ -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@v5
+      with:
+          enable-cache: true
+
     - name: Install pre-commit
       run: |
-        pip install pre-commit
+        uv pip install --system pre-commit ruff
         pre-commit install
+
     - name: Run code-quality checks
       run: SKIP=mypy pre-commit run --all-files

.dev-pre-commit-config.yaml

@@ -19,19 +19,27 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
         python-version: "3.10"
-        cache: 'pip'
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: true
+
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
-    - name: Test with pytest
+        uv pip install --system --no-deps .
+        uv pip install --system -r requirements.txt
+        uv pip install --system pytest pytest-cov
+
+    - name: Measure coverage
       run: |
-        pip install pytest pytest-cov
         pytest --cov=shapiq --cov-report=xml
+
     - name: Coveralls
       uses: coverallsapp/github-action@v2
       with:

.github/workflows/code-quality.yml

@@ -23,16 +23,20 @@ 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
       with:

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

@@ -22,11 +22,17 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: "3.10"
-        cache: 'pip'
 
-    - name: Install current dependencies
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: true
+
+    - name: Install dependencies
       run: |
-        pip install -r requirements.txt
+        uv pip install --system --no-deps .
+        uv pip install --system -r requirements.txt
+        uv pip install --system pytest
 
     - name: Test with pytest
       run: |

.github/workflows/python-publish.yml

@@ -25,12 +25,18 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-        cache: 'pip'
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: true
 
     - name: Install dependencies
       run: |
-        pip install -r tests/requirements/requirements.txt
+        uv pip install --system --no-deps .
+        uv pip install --system -r tests/requirements/requirements.txt
+        uv pip install --system pytest
 
     - name: Test with pytest
       run: |
-        pytest
+        pytest tests/

.github/workflows/unit-tests-current.yml

@@ -10,18 +10,6 @@ repos:
       - id: mixed-line-ending
       - id: check-merge-conflict
 
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.2
-    hooks:
-      - id: black
-        name: black
-        entry: black
-        language: python
-      - id: black-jupyter
-        name: black-jupyter
-        entry: black
-        language: python
-
   - repo: local
     hooks:
       - id: ruff

.github/workflows/unit-tests.yml

@@ -0,0 +1,40 @@
+cff-version: 1.2.0
+message: "If you use ``shapiq`` and enjoy it, please consider citing our paper or consider starring this repository."
+authors:
+  - family-names: Muschalik
+    given-names: Maximilian
+  - family-names: Baniecki
+    given-names: Hubert
+  - family-names: Fumagalli
+    given-names: Fabian
+  - family-names: Kolpaczki
+    given-names: Patrick
+  - family-names: Hammer
+    given-names: Barbara
+  - family-names: H\"ullermeier
+    given-names: Eyke
+title: 'shapiq: Shapley Interactions for Machine Learning'
+version: 1.2.0
+url: https://openreview.net/forum?id=knxGmi6SJi
+date-released: '2024-11-15'
+preferred-citation:
+  authors:
+  - family-names: Muschalik
+    given-names: Maximilian
+  - family-names: Baniecki
+    given-names: Hubert
+  - family-names: Fumagalli
+    given-names: Fabian
+  - family-names: Kolpaczki
+    given-names: Patrick
+  - family-names: Hammer
+    given-names: Barbara
+  - family-names: H\"ullermeier
+    given-names: Eyke
+  title: 'shapiq: Shapley Interactions for Machine Learning'
+  url: https://openreview.net/forum?id=knxGmi6SJi
+  type: conference-paper
+  year: '2024'
+  collection-title: The Thirty-eight Conference on Neural Information Processing Systems Datasets and Benchmarks Track
+  conference: {}
+  publisher: {}