Merge branch 'develop' into 259-implement-class-wise-shapley

# Conflicts:
#	CHANGELOG.md
#	docs/30-data-valuation.rst
#	src/pydvl/value/shapley/montecarlo.py

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,7 +1,7 @@
 <!--
 Thanks for making a contribution! 
 Please make sure you have read the contributing guide: 
-https://github.com/appliedAI-Initiative/pyDVL/blob/develop/CONTRIBUTING.md
+https://github.com/aai-institute/pyDVL/blob/develop/CONTRIBUTING.md
 -->
 
 ### Description
@@ -17,4 +17,4 @@ This PR closes #XXX
 - [ ] Wrote Unit tests (if necessary)
 - [ ] Updated Documentation (if necessary)
 - [ ] Updated Changelog
-- [ ] If notebooks were added/changed, added boilerplate cells are tagged with `"nbsphinx":"hidden"`
+- [ ] If notebooks were added/changed, added boilerplate cells are tagged with `"tags": ["hide"]` or `"tags": ["hide-input"]`

.github/actions/deploy-docs/action.yml

@@ -0,0 +1,43 @@
+name: Deploy Docs
+description: Deploy documentation from develop or master branch
+inputs:
+  version:
+    description: Version number to use
+    required: true
+  alias:
+    description: Alias to use (latest or stable)
+    required: true
+  title:
+    description: Alternative title to use
+    required: false
+    default: ''
+  email:
+    description: Email to use for git config
+    required: true
+  username:
+    description: Username to use for git config
+    required: true
+  set-default:
+    description: Set alias as the default version
+    required: false
+    default: 'false'
+runs:
+  using: "composite"
+  steps:
+  - run: |
+      # https://github.com/jimporter/mike#deploying-via-ci
+      git fetch origin gh-pages --depth=1
+      git config --local user.email ${{ inputs.email }}
+      git config --local user.name ${{ inputs.username }}
+    shell: bash
+  - run: |
+      if [ -z "${{ inputs.title }}" ]
+      then
+        mike deploy ${{ inputs.version }} ${{ inputs.alias }} --push --update-aliases
+      else
+        mike deploy ${{ inputs.version }} ${{ inputs.alias }} --title=${{ inputs.title }} --push --update-aliases
+      fi
+    shell: bash
+  - if: ${{ inputs.set-default == 'true' }}
+    run: mike set-default ${{ inputs.alias }}
+    shell: bash

.github/actions/python/action.yml

@@ -0,0 +1,20 @@
+name: Setup Python
+description: Setup Python on GitHub Actions and install dev and docs requirements.
+inputs:
+  python_version:
+    description: Python version to use
+    required: true
+runs:
+  using: "composite"
+  steps:
+  - name: Set up Python ${{ inputs.python_version }}
+    uses: actions/setup-python@v4
+    with:
+      python-version: ${{ inputs.python_version }}
+      cache: 'pip'
+      cache-dependency-path: |
+        requirements-dev.txt
+        requirements-docs.txt
+  - name: Install Dev & Docs Requirements
+    run: pip install -r requirements-dev.txt -r requirements-docs.txt
+    shell: bash

.github/workflows/publish.yaml

@@ -58,15 +58,29 @@ jobs:
         run: |
           echo "Running action locally. Failing"
           exit -1
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+      - name: Setup Python 3.8
+        uses: ./.github/actions/python
         with:
-          python-version: 3.8
-          cache: 'pip'
-      - name: Install Dev Requirements
-        run: pip install -r requirements-dev.txt
+          python_version: 3.8
+      - name: Get Current Version
+        run: |
+          export CURRENT_VERSION=$(python setup.py --version --quiet | awk -F. '{print $1"."$2"."$3}')
+          # Make the version available as env variable for next steps
+          echo CURRENT_VERSION=$CURRENT_VERSION >> $GITHUB_ENV
+        shell: bash
+      - name: Deploy Docs
+        uses: ./.github/actions/deploy-docs
+        with:
+          version: ${{ env.CURRENT_VERSION }}
+          alias: latest
+          title: Latest
+          email: ${{ env.GITHUB_BOT_EMAIL }}
+          username: ${{ env.GITHUB_BOT_USERNAME }}
+          set-default: 'true'
       - name: Build and publish to PyPI
         env:
           TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
           TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: tox -e publish-release-package
+        run: |
+          python setup.py sdist bdist_wheel
+          twine upload --verbose --non-interactive dist/*

.github/workflows/run-tests-workflow.yaml

@@ -22,13 +22,10 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: Set up Python ${{ inputs.python_version }}
-      uses: actions/setup-python@v4
+    - name: Setup Python ${{ inputs.python_version }}
+      uses: ./.github/actions/python
       with:
-        python-version: ${{ inputs.python_version }}
-        cache: 'pip'
-    - name: Install Dev Requirements
-      run: pip install -r requirements-dev.txt
+        python_version: ${{ inputs.python_version }}
     - name: Cache Tox Directory for Tests
       uses: actions/cache@v3
       with:

.github/workflows/tox.yaml

@@ -16,60 +16,49 @@ env:
   GITHUB_BOT_USERNAME: github-actions[bot]
   GITHUB_BOT_EMAIL: 41898282+github-actions[bot]@users.noreply.github.com
   PY_COLORS: 1
+  MYPY_FORCE_COLOR: 1
+  PANDOC_VERSION: '3.1.6.2'
 
 jobs:
-  lint:
+  code-quality:
     name: Lint code and check type hints
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+    - name: Setup Python 3.8
+      uses: ./.github/actions/python
       with:
-        python-version: 3.8
-        cache: 'pip'
-    - name: Install Dev Requirements
-      run: pip install -r requirements-dev.txt
-    - name: Cache Tox Directory for Linting
-      uses: actions/cache@v3
+        python_version: 3.8
+    - uses: actions/cache@v3
       with:
-        key: tox-${{ github.ref }}-${{ runner.os }}-${{ hashFiles('tox.ini') }}
-        path: .tox
+        path: ~/.cache/pre-commit
+        key: pre-commit-${{ env.pythonLocation }}-${{ hashFiles('.pre-commit-config.yaml') }}
     - name: Lint Code
-      run: tox -e linting
+      run: |
+        pre-commit run --all --show-diff-on-failure
+        python build_scripts/run_pylint.py | (pylint-json2html -f jsonextended -o pylint.html)
+      shell: bash
     - name: Check Type Hints
-      run: tox -e type-checking
+      run: mypy src/
   docs:
     name: Build Docs
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+    - name: Setup Python 3.8
+      uses: ./.github/actions/python
       with:
-        python-version: 3.8
-        cache: 'pip'
-    - name: Install Dev Requirements
-      run: pip install -r requirements-dev.txt
+        python_version: 3.8
     - name: Install Pandoc
-      run: sudo apt-get install --no-install-recommends --yes pandoc
-    - name: Cache Tox Directory for Docs
-      uses: actions/cache@v3
+      uses: r-lib/actions/setup-pandoc@v2
       with:
-        key: tox-${{ github.ref }}-${{ runner.os }}-${{ hashFiles('tox.ini') }}
-        path: .tox
+        pandoc-version: ${{ env.PANDOC_VERSION }}
     - name: Build Docs
-      run: tox -e docs
-    - name: Save built docs
-      uses: actions/upload-artifact@v3
-      with:
-        name: docs
-        path: ./docs/_build
-        retention-days: 1
+      run: mkdocs build
   base-tests:
     strategy:
       matrix:
@@ -79,7 +68,7 @@ jobs:
     with:
       tests_to_run: base
       python_version: ${{ matrix.python_version }}
-    needs: [lint]
+    needs: [code-quality]
   torch-tests:
     strategy:
       matrix:
@@ -89,7 +78,7 @@ jobs:
     with:
       tests_to_run: torch
       python_version: ${{ matrix.python_version }}
-    needs: [lint]
+    needs: [code-quality]
   notebook-tests:
     strategy:
       matrix:
@@ -99,50 +88,41 @@ jobs:
     with:
       tests_to_run: notebooks
       python_version: ${{ matrix.python_version }}
-    needs: [lint]
+    needs: [code-quality]
   push-docs-and-release-testpypi:
     name: Push Docs and maybe release Package to TestPyPI
     runs-on: ubuntu-latest
     needs: [docs, base-tests, torch-tests, notebook-tests]
+    if: ${{ github.ref == 'refs/heads/develop' }}
     concurrency:
-      group: push-docs-and-release-testpypi
+      group: publish
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.8
-          cache: 'pip'
-      - name: Install Dev Requirements
-        run: pip install -r requirements-dev.txt
-      - name: Cache Tox Directory
-        uses: actions/cache@v3
+      - name: Setup Python 3.8
+        uses: ./.github/actions/python
         with:
-          key: tox-${{ github.ref }}-${{ runner.os }}-${{ hashFiles('tox.ini') }}
-          path: .tox
-      - name: Download built docs
-        uses: actions/download-artifact@v3
+          python_version: 3.8
+      - name: Install Pandoc
+        uses: r-lib/actions/setup-pandoc@v2
         with:
-          name: docs
-          path: ./docs/_build
+          pandoc-version: ${{ env.PANDOC_VERSION }}
       - name: Deploy Docs
-        uses: peaceiris/actions-gh-pages@v3
-        if: ${{ github.ref == 'refs/heads/develop' }}
+        uses: ./.github/actions/deploy-docs
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./docs/_build/html
-          user_name: ${{ env.GITHUB_BOT_USERNAME }}
-          user_email: ${{ env.GITHUB_BOT_EMAIL }}
+          version: devel
+          alias: develop
+          title: Development
+          email: ${{ env.GITHUB_BOT_EMAIL }}
+          username: ${{ env.GITHUB_BOT_USERNAME }}
       - name: Build and publish to TestPyPI
-        if: ${{ github.ref == 'refs/heads/develop' }}
         env:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.TEST_PYPI_PASSWORD }}
         run: |
           set -x
-          export CURRENT_VERSION=$(python setup.py --version)
           export BUILD_NUMBER=$GITHUB_RUN_NUMBER
-          tox -e bump-dev-version
-          tox -e publish-test-package
+          bump2version --no-tag --no-commit --verbose --serialize '\{major\}.\{minor\}.\{patch\}.\{release\}\{$BUILD_NUMBER\}' boguspart
+          python setup.py sdist bdist_wheel
+          twine upload -r testpypi --verbose --non-interactive dist/*

.gitignore

@@ -139,3 +139,6 @@ pylint.html
 # Saved data
 runs/
 data/models/
+
+# Docs
+docs_build