Migrate to same linting and formatting as in aiida-core

We migrate to ruff for the linter and formatter with the settings of
aiida-core as well as the pre-commit hooks used for formatting. This
makes the repository more compatible with aiida-core and also allows
solves more linter problems automatically which should speed up
development

.pre-commit-config.yaml

@@ -1,24 +1,24 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.6.0
     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/pycqa/isort
-    rev: '5.12.0'
-    hooks:
-    - id: isort
-
-  - repo: https://github.com/psf/black
-    rev: '22.10.0'
-    hooks:
-    - id: black
-
+    - 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/pre-commit/mirrors-mypy
     rev: v1.10.0
     hooks:
@@ -34,25 +34,40 @@ repos:
             tests/.*|
             conftest.py
         )$
-
-  - repo: https://github.com/PyCQA/pylint
-    rev: v3.2.2
+  
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.28.6
     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: >
+    - id: check-github-workflows
+
+  - repo: https://github.com/ikamensh/flynt/
+    rev: 1.0.1
+    hooks:
+    - id: flynt
+      args: [--line-length=120, --fail-on-change]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.0
+    hooks:
+    - id: ruff-format
+      exclude: &exclude_ruff >
         (?x)^(
-            docs/.*|
+          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|
         )$

pyproject.toml

@@ -82,26 +82,36 @@ exclude = [
     'codecov.yml',
 ]
 
-[tool.isort]
-profile = 'black'
-
-[tool.pylint.master]
-extension-pkg-whitelist = ['pydantic']
-
-[tool.pylint.format]
-max-line-length = 125
-
-[tool.pylint.messages_control]
-disable = [
-    'duplicate-code',
-    'fixme',
-    'invalid-name',
-    'too-many-ancestors',
-    'too-many-arguments',
+[tool.ruff]
+line-length = 120
+
+[tool.ruff.format]
+quote-style = 'single'
+
+[tool.ruff.lint]
+ignore = [
+  'F403',  # Star imports unable to detect undefined names
+  'F405',  # Import may be undefined or defined from star imports
+  'PLR0911',  # Too many return statements
+  'PLR0912',  # Too many branches
+  'PLR0913',  # Too many arguments in function definition
+  'PLR0915',  # Too many statements
+  'PLR2004',  # Magic value used in comparison
+  'RUF005',  # Consider iterable unpacking instead of concatenation
+  'RUF012',  # Mutable class attributes should be annotated with `typing.ClassVar`
+]
+select = [
+  'E',  # pydocstyle
+  'W',  # pydocstyle
+  'F',  # pyflakes
+  'I',  # isort
+  'N',  # pep8-naming
+  'PLC',  # pylint-convention
+  'PLE',  # pylint-error
+  'PLR',  # pylint-refactor
+  'PLW',  # pylint-warning
+  'RUF'  # ruff
 ]
-
-[tool.pylint.similarities]
-ignore-imports = 'yes'
 
 [tool.pytest.ini_options]
 python_files = 'test_*.py example_*.py'