Merge remote-tracking branch 'github/main' into 100-extend-to-chemprop-205

# Conflicts:
#	requirements_chemprop.txt

Author: c-w-feldmann

.github/workflows/linting.yml

@@ -12,46 +12,42 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: astral-sh/setup-uv@v5
       with:
-        python-version: "3.11"
+        python-version: "3.13"
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install $(find . -name "requirement*" -type f -printf ' -r %p')
-        pip install pylint
+        uv sync --all-extras
+        uv pip install torch --index-url https://download.pytorch.org/whl/cpu
     - name: Analysing the code with pylint
       run: |
-        pylint  -d C0301,R0913,W1202 $(git ls-files '*.py') --ignored-modules "rdkit"  --max-positional-arguments 10
+        uv run pylint  -d C0301,R0913,W1202 $(git ls-files '*.py') --ignored-modules "rdkit"  --max-positional-arguments 10
   mypy:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: astral-sh/setup-uv@v5
       with:
-        python-version: "3.11"
+        python-version: "3.13"
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install mypy
-        mypy . || exit_code=$?
-        mypy --install-types --non-interactive
+        uv run mypy . || exit_code=$?
+        uv run mypy --install-types --non-interactive
     - name: Analysing the code with mypy
       run: |
-        mypy --ignore-missing-imports --disallow-any-generics --disallow-untyped-defs --no-implicit-optional --disallow-incomplete-defs . 
+        uv run mypy --ignore-missing-imports --disallow-any-generics --disallow-untyped-defs --no-implicit-optional --disallow-incomplete-defs .
   pydocstyle:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python
       uses: actions/setup-python@v3
       with:
-        python-version: "3.11"
+        python-version: "3.13"
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install pydocstyle
+        python -m pip install pydocstyle
     - name: Analysing the code with pydocstyle
       run: |
         pydocstyle .
@@ -63,46 +59,28 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v3
       with:
-        python-version: "3.11"
+        python-version: "3.13"
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install docsig
+        python -m pip install docsig
     - name: Analysing the code with docsig
       run: |
         docsig --check-class-constructor --check-dunders --check-protected-class-methods --check-nested --check-overridden --check-protected .
 
-  black:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.11"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install black[jupyter]
-    - name: Analysing the code with black
-      run: |
-        black --check .
-
   flake8:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
-          python-version: "3.11"
+          python-version: "3.13"
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install flake8
+          python -m pip install flake8
       - name: Analysing the code with flake8
         run: |
-          flake8 --extend-ignore=D203,E203,E501,W503 .
+          flake8 --extend-ignore=D203,E203,E501,W503 --extend-exclude .venv .
 
   interrogate:
     runs-on: ubuntu-latest
@@ -111,11 +89,10 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
-          python-version: "3.11"
+          python-version: "3.13"
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install interrogate
+          python -m pip install interrogate
       - name: Analysing the code with interrogate
         run: |
          interrogate --ignore-overloaded-functions -vv .
@@ -127,46 +104,66 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
-          python-version: "3.11"
+          python-version: "3.13"
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install bandit
+          python -m pip install bandit
       - name: Analysing the code with bandit
         run: |
-         bandit -r --skip=B404,B603,B602 .
+         bandit -r --skip=B404,B603,B602 -c pyproject.toml .
 
-  isort:
+  pyright:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: "3.11"
-      - name: Install dependencies
+          python-version: "3.13"
+      - name: Analysing the code with pyright
         run: |
-          python -m pip install --upgrade pip
-          pip install isort
-      - name: Analysing the code with isort
+          uv run --all-extras pyright .
+
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.13"
+      - name: Analysing the code with ruff
+        run: |
+          uv run ruff check --config pyproject.toml
+
+  ruff-format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.13"
+      - name: Analysing the code with ruff
         run: |
-          isort --profile black --check-only .
+          uvx ruff format --check
 
   test_basis:
     needs:
         - pylint
         - mypy
         - pydocstyle
         - docsig
-        - black
         - flake8
         - interrogate
         - bandit
-        - isort
+        - ruff
+        - ruff-format
+        - pyright
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -189,39 +186,37 @@ jobs:
     needs:
       - test_basis
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: "3.11"
+          python-version: ${{ matrix.python-version }}
       - name: Install package
         run: |
-          python -m pip install --upgrade pip
-          pip install coverage
-          pip install torch
-          pip install .[chemprop]
+          uv sync --all-extras
+          uv pip install torch --index-url https://download.pytorch.org/whl/cpu
       - name: Run unit-tests for chemprop
         run: |
           # Run only the chemprop test suite.
-          coverage run --source=molpipeline,tests -m unittest discover test_extras/test_chemprop
+          uv run coverage run --source=molpipeline,tests -m unittest discover test_extras/test_chemprop
           # Create a coverage report. Fail if the coverage is below 85%. Include only chemprop files in the report.
-          coverage report --fail-under=85 --include="*chemprop*","*/*chemprop*/*"
+          uv run coverage report --fail-under=85 --include="*chemprop*","*/*chemprop*/*"
 
   test_notebooks:
     needs:
       - test_basis
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v3
-        with:
-          python-version: "3.11"
+      - name: Set up Python 3.13
+        uses: astral-sh/setup-uv@v5
       - name: Install package
         run: |
-          python -m pip install --upgrade pip
-          pip install .[notebooks]
+          uv sync --all-extras
       - name: Run unit-tests for notebooks
         run: |
-          python test_extras/test_notebooks/test_notebooks.py  --continue-on-failure
+          uv run python test_extras/test_notebooks/test_notebooks.py --continue-on-failure

.github/xai_example.png

@@ -0,0 +1,67 @@
+exclude: |
+  (?x)(
+    ^notebooks/|
+    ^$
+  )
+fail_fast: false
+default_stages: [pre-commit, pre-push]
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+        exclude_types: [tsv]
+        args: [--markdown-linebreak-ext=md]
+
+  - repo: https://github.com/commitizen-tools/commitizen
+    rev: v3.29.1
+    hooks:
+      - id: commitizen
+        stages: [commit-msg]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.2
+    hooks:
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [ --fix, --exit-non-zero-on-fix, --config, ruff.toml]
+
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        types:
+          - ts
+          - javascript
+          - yaml
+          - markdown
+          - json
+
+  - repo: https://github.com/RobertCraigie/pyright-python
+    rev: v1.1.398
+    hooks:
+      - id: pyright
+        args: [-p, pyproject.toml]
+        verbose: true
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        additional_dependencies:
+          - docsig==0.69.3
+        args:
+          - --extend-ignore=D203,E203,E501,F401,W5
+          - "--sig-check-class-constructor"
+          - "--sig-check-dunders"
+          - "--sig-check-protected-class-methods"
+          - "--sig-check-nested"
+          - "--sig-check-overridden"
+          - "--sig-check-protected"

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+# Development-Guidelines
+## Pre-commit Hooks
+Before committing any changes, make sure to enable the pre-commit hooks.
+This will help you to automatically format your code and check for any linting issues.
+You can enable the pre-commit hooks by running the following command:
+```bash
+pre-commit install
+```
+In case you want to run the pre-commit hooks manually, you can do so by running:
+```bash
+pre-commit run --all-files
+```
+> **_NOTE:_** Be aware that the code in its current state does not comply with the pre-commit hooks.
+> Hence, you might encounter errors in sections that are not related to your changes.
+> This is intended to slowly improve the code quality over time.
+> If fixing the errors would cause a massive overhead, you can ignore them via the `--no-verify` flag when committing.