Merge pull request #91 from Materials-Data-Science-and-Informatics/fe…

…ature/update_hooks

update pre-commit hooks and dependencies

.pre-commit-config.yaml

@@ -1,68 +1,68 @@
 repos:
-  # Various general + format-specific helpers
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
-    hooks:
-      - id: check-symlinks
-      - id: trailing-whitespace
-      - id: mixed-line-ending
-        args: [--fix=lf]
-      - id: check-yaml
-        exclude: "mkdocs.yml"
-      - id: check-toml
-      - id: check-json
-      - id: check-ast
-      - id: debug-statements
-      - id: check-merge-conflict
-      - id: check-shebang-scripts-are-executable
-      - id: check-added-large-files
-        args: [--maxkb=10000]
-  - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: "0.22.0"
-    hooks:
-      - id: check-github-workflows
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: v0.1.6
-    hooks:
-      # Run the linter.
-      - id: ruff
-        types_or: [python, pyi, jupyter]
-        args: [--fix]
-      # Run the formatter.
-      - id: ruff-format
-        types_or: [python, pyi, jupyter]
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.1.1"
-    hooks:
-      - id: mypy
-        args: [--no-strict-optional, --ignore-missing-imports]
-        # NOTE: you might need to add some deps here:
-        additional_dependencies: []
+    # Various general + format-specific helpers
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.6.0
+      hooks:
+          - id: check-symlinks
+          - id: trailing-whitespace
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: check-yaml
+            exclude: 'mkdocs.yml'
+          - id: check-toml
+          - id: check-json
+          - id: check-ast
+          - id: debug-statements
+          - id: check-merge-conflict
+          - id: check-shebang-scripts-are-executable
+          - id: check-added-large-files
+            args: [--maxkb=10000]
+    - repo: https://github.com/python-jsonschema/check-jsonschema
+      rev: '0.29.0'
+      hooks:
+          - id: check-github-workflows
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      # Ruff version.
+      rev: v0.5.4
+      hooks:
+          # Run the linter.
+          - id: ruff
+            types_or: [python, pyi, jupyter]
+            args: [--fix]
+          # Run the formatter.
+          - id: ruff-format
+            types_or: [python, pyi, jupyter]
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: 'v1.11.0'
+      hooks:
+          - id: mypy
+            args: [--no-strict-optional, --ignore-missing-imports]
+            # NOTE: you might need to add some deps here:
+            additional_dependencies: []
 
-  # Metadata
-  - repo: https://github.com/citation-file-format/cff-converter-python
-    rev: "44e8fc9"
-    hooks:
-      - id: validate-cff
-  - repo: https://github.com/fsfe/reuse-tool
-    rev: "v1.1.2"
-    hooks:
-      - id: reuse
+    # Metadata
+    - repo: https://github.com/citation-file-format/cff-converter-python
+      rev: '054bda51dbe278b3e86f27c890e3f3ac877d616c'
+      hooks:
+          - id: validate-cff
+    - repo: https://github.com/fsfe/reuse-tool
+      rev: 'v4.0.3'
+      hooks:
+          - id: reuse
 
-  - repo: local
-    hooks:
-      # NOTE: copy from .pre-commit-hooks.yaml, for technical reasons
-      - id: somesy-sync
-        name: Run somesy sync
-        entry: somesy sync
-        language: python
-        files: '^\.somesy\.toml|pyproject\.toml$'
-        pass_filenames: false
+    - repo: local
+      hooks:
+          # NOTE: copy from .pre-commit-hooks.yaml, for technical reasons
+          - id: somesy-sync
+            name: Run somesy sync
+            entry: somesy sync
+            language: python
+            files: '^\.somesy\.toml|pyproject\.toml$'
+            pass_filenames: false
 
-      - id: somesy-fill
-        name: Update AUTHORS.md
-        entry: somesy fill -t docs/_template_authors.md -o AUTHORS.md
-        language: python
-        files: '^\.somesy\.toml|pyproject\.toml$'
-        pass_filenames: false
+          - id: somesy-fill
+            name: Update AUTHORS.md
+            entry: somesy fill -t docs/_template_authors.md -o AUTHORS.md
+            language: python
+            files: '^\.somesy\.toml|pyproject\.toml$'
+            pass_filenames: false

docs/scripts/coverage_status.py

@@ -1,4 +1,5 @@
 """Mkdocs hook to run tests with coverage collection and generate a badge."""
+
 import logging
 from io import StringIO
 from pathlib import Path

pyproject.toml

@@ -35,45 +35,45 @@ include = [
 
 [tool.poetry.dependencies]
 python = "^3.8"
-pydantic = {extras = ["email"], version = "^2.4.2"}
-ruamel-yaml = "^0.17.21"
-tomlkit = "^0.11.6"
-importlib-metadata = "^4.11.0"
-typer = {extras = ["all"], version = "^0.7.0"}
+pydantic = {extras = ["email"], version = "^2.8.2"}
+ruamel-yaml = "^0.18.6"
+tomlkit = "^0.13.0"
+importlib-metadata = "^8.0.0"
+typer = {extras = ["all"], version = "^0.12.3"}
 cffconvert = "^2.0.0"
-wrapt = "^1.15.0"
-packaging = "^23.1"
-jinja2 = "^3.1.2"
+wrapt = "^1.16.0"
+packaging = "^24.1"
+jinja2 = "^3.1.4"
 defusedxml = "^0.7.1"
 
 [tool.poetry.group.dev.dependencies]
-poethepoet = "^0.18.1"
-pre-commit = "^3.1.1"
-pytest = "^7.2.2"
-pytest-cov = "^4.0.0"
-hypothesis = "^6.68.2"
-licensecheck = "^2023.1.1"
-pytest-mock = "^3.10.0"
+poethepoet = "^0.27.0"
+pre-commit = "^3.5.0"
+pytest = "^8.3.1"
+pytest-cov = "^5.0.0"
+hypothesis = "^6.108.4"
+licensecheck = "^2024.2"
+pytest-mock = "^3.14.0"
 
 [tool.poetry.group.docs]
 optional = true
 
 [tool.poetry.group.docs.dependencies]
-mkdocs = "^1.4.2"
-mkdocstrings = {extras = ["python"], version = "^0.24.0"}
-mkdocs-material = "^9.4"
+mkdocs = "^1.6.0"
+mkdocstrings = {extras = ["python"], version = "^0.25.1"}
+mkdocs-material = "^9.5.30"
 mkdocs-gen-files = "^0.5.0"
-mkdocs-literate-nav = "^0.6.0"
-mkdocs-section-index = "^0.3.5"
-mkdocs-macros-plugin = "^0.7.0"
+mkdocs-literate-nav = "^0.6.1"
+mkdocs-section-index = "^0.3.9"
+mkdocs-macros-plugin = "^1.0.5"
 markdown-include = "^0.8.1"
-pymdown-extensions = "^10.2"
-markdown-exec = {extras = ["ansi"], version = "^1.6.0"}
-mkdocs-coverage = "^1.0.0"
-mike = "^2.0.0"
+pymdown-extensions = "^10.8.1"
+markdown-exec = {extras = ["ansi"], version = "^1.9.3"}
+mkdocs-coverage = "^1.1.0"
+mike = "^2.1.2"
 anybadge = "^1.14.0"
-interrogate = "^1.5.0"
-black = "^23.3.0"
+interrogate = "^1.7.0"
+black = "^24.4.2"
 mkdocs-exclude = "^1.0.2"
 
 [tool.poetry.scripts]

src/somesy/__init__.py

@@ -1,4 +1,5 @@
 """somesy package."""
+
 import importlib_metadata
 from typing_extensions import Final
 

src/somesy/cff/__init__.py

@@ -1,4 +1,5 @@
 """CFF module."""
+
 from .writer import CFF
 
 __all__ = ["CFF"]

src/somesy/cff/writer.py

@@ -1,4 +1,5 @@
 """Citation File Format (CFF) parser and saver."""
+
 import json
 from pathlib import Path
 from typing import Optional

src/somesy/cli/fill.py

@@ -1,4 +1,5 @@
 """Fill command of somesy."""
+
 import logging
 from pathlib import Path
 from sys import stdin

src/somesy/cli/init.py

@@ -1,4 +1,5 @@
 """Set config files for somesy."""
+
 import logging
 from pathlib import Path
 

src/somesy/cli/sync.py

@@ -1,4 +1,5 @@
 """Sync command for somesy."""
+
 import logging
 from pathlib import Path
 

src/somesy/cli/util.py

@@ -1,4 +1,5 @@
 """Utility functions for CLI commands."""
+
 import logging
 import traceback
 from typing import Optional

src/somesy/codemeta/__init__.py

@@ -1,4 +1,5 @@
 """Integration with codemeta.json (to re-generate codemeta as part of somesy sync)."""
+
 from .writer import CodeMeta
 
 __all__ = ["CodeMeta"]

src/somesy/codemeta/writer.py

@@ -1,4 +1,5 @@
 """codemeta.json creation module."""
+
 import logging
 from collections import OrderedDict
 from pathlib import Path
@@ -158,6 +159,7 @@ def _sync_person_list(self, old: List[Any], new: List[Person]) -> List[Any]:
 
         Returns:
             List[Any]: _description_
+
         """
         return new
 

src/somesy/commands/__init__.py

@@ -1,4 +1,5 @@
 """Commands for somesy."""
+
 from .init_config import init_config
 from .sync import sync
 

src/somesy/commands/init_config.py

@@ -1,4 +1,5 @@
 """CLI command to initialize somesy configuration file."""
+
 import logging
 from pathlib import Path
 
@@ -16,6 +17,7 @@ def init_config(input_path: Path, options: dict) -> None:
     Args:
         input_path (Path): Path to somesy file (will be created/overwritten).
         options (dict): CLI options.
+
     """
     logger.info(f"Updating input file ({input_path}) with CLI configurations...")
 

src/somesy/commands/sync.py

@@ -1,4 +1,5 @@
 """Sync selected metadata files with given input file."""
+
 import logging
 from pathlib import Path
 from typing import Type

src/somesy/core/core.py

@@ -1,4 +1,5 @@
 """Core somesy functions."""
+
 import json
 import logging
 from pathlib import Path
@@ -31,6 +32,7 @@ def discover_input(input_file: Optional[Path] = None) -> Path:
 
     Returns:
         somesy configuration file path.
+
     """
     if input_file:
         if input_file.is_file():
@@ -71,6 +73,7 @@ def get_input_content(path: Path, *, no_unwrap: bool = False) -> Dict[str, Any]:
     Raises:
         ValueError: if the input file is not a valid somesy input file or if the file is not a TOML file.
         RuntimeError: if the input file does not contain a somesy input section at expected key
+
     """
     logger.debug(f"Path {path}")
     # somesy.toml / .somesy.toml

src/somesy/core/log.py

@@ -1,4 +1,5 @@
 """Somesy log configuration."""
+
 import logging
 from enum import Enum, auto
 from typing import Optional