build: Upgrade precommits (#115)

* build: Update pre commit configuration

* refactor: Update code to support new pre-commits

* build: Upgrade version

* refactor: Solve test issues for python 3.9

* build: Upgrade mlflow version

* docs: Update changelog

* docs: Update readme

* build: Remove black from dev dependencies

* build: Replace certain pylint checks with ruff

* refactor: Apply updated pre-commits

* build: Fix wrong pylintrc file

* fix: Fix wrong variable used in function

* build: Reformat pylintrc to use tabs

* build: Replace mlflow requirement with mlflow-skinny

.github/ISSUE_TEMPLATE/1_bug_report.yaml

@@ -38,4 +38,4 @@ body:
     attributes:
       label: Relevant log output
       description: Please copy and paste any relevant log output. This will be automatically formatted into code, so no need for backticks.
-      render: shell
+      render: shell

.pre-commit-config.yaml

@@ -1,14 +1,6 @@
 fail_fast: true
 
 repos:
-  - repo: local
-    hooks:
-      - id: ruff
-        name: ruff
-        files: \.py$
-        entry: ruff
-        language: python
-        exclude: ^(tests|scripts|notebooks|quadra/utils/tests)/
   - repo: local
     hooks:
       - id: jupyter-nb-clear-output
@@ -23,47 +15,16 @@ repos:
       - id: prettier
         name: (prettier) Reformat YAML files with prettier
         types: [yaml]
-
-  - repo: https://github.com/myint/autoflake
-    rev: v1.4
-    hooks:
-      - id: autoflake
-        name: Remove unused variables and imports
-        language: python
-        entry: autoflake
-        types: [python]
-        args:
-          [
-            "--in-place",
-            "--remove-all-unused-imports",
-            "--remove-unused-variables",
-            "--expand-star-imports",
-            "--ignore-init-module-imports",
-          ]
-        files: \.py$
-  - repo: local
-    hooks:
-      - id: isort
-        name: (isort) Sorting import statements
-        args: [--settings-path=pyproject.toml]
-        language: python
-        types: [python]
-        files: \.py$
-        entry: isort
-  - repo: local
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.1
     hooks:
-      - id: black
-        name: (black) Format Python code
-        args: [--config=pyproject.toml]
-        language: python
-        types: [python]
-        entry: black
-      - id: black-jupyter
-        name: (black-jupyter) Format jupyter notebooks
-        args: [--config=pyproject.toml]
-        language: python
-        types: [jupyter]
-        entry: black
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: ["--config", "pyproject.toml", "--fix"]
+        exclude: ^(tests|scripts|notebooks|quadra/utils/tests)/
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+        args: ["--config", "pyproject.toml"]
   - repo: local
     hooks:
       - id: pylint

CHANGELOG.md

@@ -2,6 +2,17 @@
 # Changelog
 All notable changes to this project will be documented in this file.
 
+### [2.1.4]
+
+#### Updated
+
+- Remove black from pre-commit hooks
+- Use ruff as the main formatter and linting tool
+- Upgrade mypy version
+- Upgrade mlflow version
+- Apply new pre-commits to all tests
+- Update most of typing to py310 style
+
 ### [2.1.3]
 
 #### Updated

README.md

@@ -10,7 +10,11 @@
 </p>
 
 <div align="center">
-
+  <a href="https://github.com/astral-sh/ruff">
+    <img 
+    src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" 
+    alt="ruff"
+  ></a>
   <a href="https://github.com/pre-commit/pre-commit"><img
     src="https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white"
     alt="pre-commit"
@@ -27,14 +31,6 @@
     src="https://www.mypy-lang.org/static/mypy_badge.svg"
     alt="Checked with mypy"
   /></a>
-  <a href="https://github.com/psf/black"><img
-    src="https://img.shields.io/badge/code%20style-black-000000.svg"
-    alt="black"
-  /></a>
-  <a href="https://pycqa.github.io/isort/"><img
-    src="https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336"
-    alt="isort"
-  /></a>
 
 </div>
 
@@ -251,7 +247,7 @@ First clone the repository from `Github`, then we need to install the package wi
 
 Now you can start developing and the pre-commit hooks will run automatically to prevent you from committing code that does not pass the linting and formatting checks.
 
-We rely on a combination of `Black`, `Pylint`, `Mypy`, `Ruff` and `Isort` to enforce code quality.
+We rely on a combination of `Pylint`, `Mypy` and `Ruff` to enforce code quality.
 
 ## Building Documentations
 
@@ -273,7 +269,7 @@ This project is based on many open-source libraries and frameworks, we would lik
 - Documentation website is using [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/) and [MkDocs](https://www.mkdocs.org/). For code documentation we are using [Mkdocstrings](https://mkdocstrings.github.io/). For releasing software versions we combine [Bumpver](https://github.com/mbarkhau/bumpver) and [Mike](https://github.com/jimporter/mike).
 - Models can be exported in different ways (`torchscript` or `torch` file). We have also added [ONNX](https://onnx.ai/) support for some models.
 - Testing framework is based on [Pytest](https://docs.pytest.org/en/) and related plug-ins.
-- Code quality is ensured by [pre-commit](https://pre-commit.com/) hooks. We are using [Black](https://github.com/psf/black) for formatting, [Pylint](https://www.pylint.org/) for linting, [Mypy](https://mypy.readthedocs.io/en/stable/) for type checking, [Isort](https://pycqa.github.io/isort/) for sorting imports, and [Ruff](https://github.com/astral-sh/ruff) for checking futher code and documentation quality.
+- Code quality is ensured by [pre-commit](https://pre-commit.com/) hooks. We are using [Ruff](https://github.com/astral-sh/ruff) for linting, enforcing code quality and formatting, [Pylint](https://www.pylint.org/) for in depth linting and [Mypy](https://mypy.readthedocs.io/en/stable/) for type checking.
 
 ## FAQ
 

docs/gen_ref_pages.py

@@ -17,7 +17,7 @@ def init_file_imports(init_file: Path) -> bool:
     Returns:
         True if the file imports anything, False otherwise.
     """
-    with open(init_file, "r") as fd:
+    with open(init_file) as fd:
         return any(line.startswith("__all__") for line in fd.readlines())
 
 
@@ -61,7 +61,7 @@ def add_submodules_as_list(parent_folder: Path) -> str:
         full_doc_path = full_doc_path.with_name("index.md")
         readme_file = path.parent / "README.md"
         if readme_file.exists():
-            with open(readme_file, "r") as rfd:
+            with open(readme_file) as rfd:
                 MARKDOWN_CONTENTS += f"{rfd.read()}\n"
         if not init_file_imports(path):
             MARKDOWN_CONTENTS += add_submodules_as_list(path.parent)
@@ -76,14 +76,14 @@ def add_submodules_as_list(parent_folder: Path) -> str:
 
     mkdocs_gen_files.set_edit_path(full_doc_path, path)
 
-with open(Path("README.md"), "r") as read_fd:
+with open(Path("README.md")) as read_fd:
     readme = read_fd.read()
     readme = readme.replace("# Quadra: Deep Learning Experiment Orchestration Library", "# Home")
     readme = readme.replace("docs/", "")
     with mkdocs_gen_files.open("getting_started.md", "w") as nav_file:  # (2)
         nav_file.write(readme)
 
-with open("CHANGELOG.md", "r") as change_fd:
+with open("CHANGELOG.md") as change_fd:
     changelog = change_fd.read()
     changelog = changelog.replace("All notable changes to this project will be documented in this file.", "")
     with mkdocs_gen_files.open("reference/CHANGELOG.md", "w") as nav_file:  # (2)