Migrate formatter and linter to ruff #72

Migrate formatter and linter to ruff to be more compatible with aiida-core 2.6 version and simplify development as ruff can fix most linter errors.
aiidateam · Nov 20, 2024 · 3e0e5df · 3e0e5df
2 parents b7a57cb + 11d8aad
commit 3e0e5df
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Showing 57 changed files with 1,365 additions and 1,594 deletions.
diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml
@@ -1,49 +1,49 @@
 name: cd
 
 on:
-    push:
-        tags:
-        -   'v[0-9]+.[0-9]+.[0-9]+*'
+  push:
+    tags:
+    - v[0-9]+.[0-9]+.[0-9]+*
 
 jobs:
 
-    validate-release-tag:
+  validate-release-tag:
 
-        if: github.repository == 'aiidateam/aiida-restapi'
-        runs-on: ubuntu-latest
+    if: github.repository == 'aiidateam/aiida-restapi'
+    runs-on: ubuntu-latest
 
-        steps:
-        -   name: Checkout source
-            uses: actions/checkout@v2
+    steps:
+    - name: Checkout source
+      uses: actions/checkout@v2
 
-        -   name: Set up Python 3.9
-            uses: actions/setup-python@v2
-            with:
-                python-version: '3.9'
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.9'
 
-        -   name: Validate the tag version against the package version
-            run: python .github/workflows/validate_release_tag.py $GITHUB_REF
+    - name: Validate the tag version against the package version
+      run: python .github/workflows/validate_release_tag.py $GITHUB_REF
 
-    publish:
+  publish:
 
-        name: Publish to PyPI
-        needs: [validate-release-tag]
-        runs-on: ubuntu-latest
+    name: Publish to PyPI
+    needs: [validate-release-tag]
+    runs-on: ubuntu-latest
 
-        steps:
-        -   name: Checkout source
-            uses: actions/checkout@v2
+    steps:
+    - name: Checkout source
+      uses: actions/checkout@v2
 
-        -   name: Set up Python 3.9
-            uses: actions/setup-python@v2
-            with:
-                python-version: '3.9'
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.9'
 
-        -   name: Install flit
-            run: pip install flit~=3.4
+    - name: Install flit
+      run: pip install flit~=3.4
 
-        -   name: Build and publish
-            run: flit publish
-            env:
-                FLIT_USERNAME: __token__
-                FLIT_PASSWORD: ${{ secrets.pypi_token }}
+    - name: Build and publish
+      run: flit publish
+      env:
+        FLIT_USERNAME: __token__
+        FLIT_PASSWORD: ${{ secrets.pypi_token }}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -4,73 +4,73 @@ on: [push, pull_request]
 
 jobs:
 
-    pre-commit:
+  pre-commit:
 
-        runs-on: ubuntu-latest
+    runs-on: ubuntu-latest
 
-        steps:
-        -   uses: actions/checkout@v2
+    steps:
+    - uses: actions/checkout@v2
 
-        -   name: Set up Python 3.9
-            uses: actions/setup-python@v2
-            with:
-                python-version: '3.9'
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.9'
 
-        -   uses: pre-commit/[email protected]
+    - uses: pre-commit/[email protected]
 
-    tests:
+  tests:
 
-        runs-on: ubuntu-latest
-        timeout-minutes: 30
-        strategy:
-            matrix:
-                python-version: ['3.9', '3.10', '3.11']
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']
 
-        services:
-            postgres:
-                image: postgres:latest
-                env:
-                    POSTGRES_DB: test_db
-                    POSTGRES_PASSWORD: ''
-                    POSTGRES_HOST_AUTH_METHOD: trust
-                options: >-
-                    --health-cmd pg_isready
-                    --health-interval 10s
-                    --health-timeout 5s
-                    --health-retries 5
-                ports:
-                -   5432:5432
-            rabbitmq:
-                image: rabbitmq:latest
-                ports:
-                -   5672:5672
+    services:
+      postgres:
+        image: postgres:latest
+        env:
+          POSTGRES_DB: test_db
+          POSTGRES_PASSWORD: ''
+          POSTGRES_HOST_AUTH_METHOD: trust
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+        - 5432:5432
+      rabbitmq:
+        image: rabbitmq:latest
+        ports:
+        - 5672:5672
 
-        steps:
-        -   uses: actions/checkout@v2
+    steps:
+    - uses: actions/checkout@v2
 
-        -   name: Set up Python ${{ matrix.python-version }}
-            uses: actions/setup-python@v2
-            with:
-                python-version: ${{ matrix.python-version }}
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
 
-        -   name: Install Python dependencies
-            run: |
-                pip install --upgrade pip
-                pip install -e .[testing,auth]
+    - name: Install Python dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -e .[testing,auth]
 
-        -   name: Run test suite
-            env:
+    - name: Run test suite
+      env:
                 # show timings of tests
-                PYTEST_ADDOPTS: "--durations=0"
-                AIIDA_WARN_v3: true
-            run: pytest --cov aiida_restapi --cov-report=xml
+        PYTEST_ADDOPTS: --durations=0
+        AIIDA_WARN_v3: true
+      run: pytest --cov aiida_restapi --cov-report=xml
 
-        -   name: Upload to Codecov
-            if: matrix.python-version == 3.8
-            uses: codecov/codecov-action@v4
-            with:
-                name: pytests
-                flags: pytests
-                file: ./coverage.xml
-                token: ${{ secrets.CODECOV_TOKEN }}
-                fail_ci_if_error: true
+    - name: Upload to Codecov
+      if: matrix.python-version == 3.8
+      uses: codecov/codecov-action@v4
+      with:
+        name: pytests
+        flags: pytests
+        file: ./coverage.xml
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: true
diff --git a/.github/workflows/validate_release_tag.py b/.github/workflows/validate_release_tag.py
@@ -1,5 +1,5 @@
-# -*- coding: utf-8 -*-
 """Validate that the version in the tag label matches the version of the package."""
+
 import argparse
 import ast
 from pathlib import Path
@@ -13,33 +13,27 @@ def get_version_from_module(content: str) -> str:
     try:
         module = ast.parse(content)
     except SyntaxError as exception:
-        raise IOError("Unable to parse module.") from exception
+        raise IOError('Unable to parse module.') from exception
 
     try:
         return next(
             ast.literal_eval(statement.value)
             for statement in module.body
             if isinstance(statement, ast.Assign)
             for target in statement.targets
-            if isinstance(target, ast.Name) and target.id == "__version__"
+            if isinstance(target, ast.Name) and target.id == '__version__'
         )
     except StopIteration as exception:
-        raise IOError(
-            "Unable to find the `__version__` attribute in the module."
-        ) from exception
+        raise IOError('Unable to find the `__version__` attribute in the module.') from exception
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     parser = argparse.ArgumentParser()
-    parser.add_argument("GITHUB_REF", help="The GITHUB_REF environmental variable")
+    parser.add_argument('GITHUB_REF', help='The GITHUB_REF environmental variable')
     args = parser.parse_args()
-    tag_prefix = "refs/tags/v"
-    assert args.GITHUB_REF.startswith(
-        tag_prefix
-    ), f'GITHUB_REF should start with "{tag_prefix}": {args.GITHUB_REF}'
+    tag_prefix = 'refs/tags/v'
+    assert args.GITHUB_REF.startswith(tag_prefix), f'GITHUB_REF should start with "{tag_prefix}": {args.GITHUB_REF}'
     tag_version = args.GITHUB_REF.removeprefix(tag_prefix)
-    package_version = get_version_from_module(
-        Path("aiida_restapi/__init__.py").read_text(encoding="utf-8")
-    )
-    error_message = f"The tag version `{tag_version}` is different from the package version `{package_version}`"
+    package_version = get_version_from_module(Path('aiida_restapi/__init__.py').read_text(encoding='utf-8'))
+    error_message = f'The tag version `{tag_version}` is different from the package version `{package_version}`'
     assert tag_version == package_version, error_message
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,58 +1,73 @@
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
-    hooks:
-      - id: end-of-file-fixer
-      - id: fix-encoding-pragma
-      - id: mixed-line-ending
-      - id: trailing-whitespace
-      - id: check-json
-      - id: check-yaml
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+  - id: check-merge-conflict
+  - id: check-yaml
+  - id: double-quote-string-fixer
+  - id: end-of-file-fixer
+    exclude: &exclude_pre_commit_hooks >
+      (?x)^(
+        tests/.*(?<!\.py)$|
+        docs/source/.+\.aiida/repo/.+|
+        CHANGELOG.md|
+      )$
+  - id: fix-encoding-pragma
+    args: [--remove]
+  - id: mixed-line-ending
+    args: [--fix=lf]
+  - id: trailing-whitespace
+    exclude: *exclude_pre_commit_hooks
 
-  - repo: https://github.com/pycqa/isort
-    rev: '5.12.0'
-    hooks:
-    - id: isort
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v1.10.0
+  hooks:
+  - id: mypy
+    additional_dependencies:
+    - pydantic~=2.0
+    - types-python-dateutil
+    - types-docutils
+    exclude: >
+      (?x)^(
+          docs/.*|
+          examples/.*|
+          tests/.*|
+          conftest.py
+      )$
 
-  - repo: https://github.com/psf/black
-    rev: '22.10.0'
-    hooks:
-    - id: black
+- repo: https://github.com/python-jsonschema/check-jsonschema
+  rev: 0.28.6
+  hooks:
+  - id: check-github-workflows
 
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.0
-    hooks:
-    - id: mypy
-      additional_dependencies:
-      - pydantic~=2.0
-      - types-python-dateutil
-      - types-docutils
-      exclude: >
-        (?x)^(
-            docs/.*|
-            examples/.*|
-            tests/.*|
-            conftest.py
-        )$
+- repo: https://github.com/ikamensh/flynt/
+  rev: 1.0.1
+  hooks:
+  - id: flynt
+    args: [--line-length=120, --fail-on-change]
 
-  - repo: https://github.com/PyCQA/pylint
-    rev: v3.2.2
-    hooks:
-    - id: pylint
-      additional_dependencies:
-      - aiida-core~=2.0
-      - fastapi~=0.115.5
-      - uvicorn[standard]~=0.19.0
-      - pydantic~=2.0
-      - graphene~=3.0
-      - lark
-      - python-dateutil~=2.0
-      - python-jose
-      - python-multipart
-      - passlib
-      - pytest~=3.6,<5.0.0
-      - sphinx<4
-      exclude: >
-        (?x)^(
-            docs/.*|
-        )$
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.5.0
+  hooks:
+  - id: ruff-format
+    exclude: &exclude_ruff >
+      (?x)^(
+        docs/source/topics/processes/include/snippets/functions/parse_docstring_expose_ipython.py|
+        docs/source/topics/processes/include/snippets/functions/signature_plain_python_call_illegal.py|
+      )$
+  - id: ruff
+    exclude: *exclude_ruff
+    args: [--fix, --exit-non-zero-on-fix, --show-fixes]
+
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  rev: v2.13.0
+  hooks:
+  - id: pretty-format-toml
+    args: [--autofix]
+  - id: pretty-format-yaml
+    args: [--autofix]
+    exclude: >-
+      (?x)^(
+        tests/.*|
+        environment.yml|
+      )$
diff --git a/aiida_restapi/__init__.py b/aiida_restapi/__init__.py
@@ -1,6 +1,5 @@
-# -*- coding: utf-8 -*-
 """AiiDA REST API for data queries and workflow managment."""
 
-__version__ = "0.1.0a1"
+__version__ = '0.1.0a1'
 
-from .main import app
+from .main import app  # noqa: F401