Merge pull request #371 from kenibrewer/refactor/code-quality-updates

Apply ruff formatting and linting along with relevant refactoring

.devcontainer/devcontainer.json

@@ -25,7 +25,11 @@
       },
 
       // Add the IDs of extensions you want installed when the container is created.
-      "extensions": ["ms-python.python", "ms-python.vscode-pylance"]
+      "extensions": [
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "charliermarsh.ruff"
+      ]
     }
   }
 }

.pre-commit-config.yaml

@@ -1,9 +1,10 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.1.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.1.6"
     hooks:
-      - id: black
-        language_version: python3.9
+      - id: ruff
+        exclude: tutorials/nbconverted/
+      - id: ruff-format
         exclude: tutorials/nbconverted/
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v2.7.1"

CONTRIBUTING.md

@@ -23,8 +23,10 @@ If you are stuck, please feel free to ask any questions or ask for help.
 - [Dev environments](#dev-environments)
 - [Releases](#releases)
 
-[Style guides](#style-guides)
+[Code Quality](#code-quality)
 
+- [Formatting](#formatting)
+- [Linting](#linting)
 - [Git commit messages](#git-commit-messages)
 - [Python style guide](#python-style-guide)
 - [Documentation style guide](#documentation-style-guide)
@@ -189,23 +191,33 @@ Creating a new release includes the following steps:
 11. The release will be automatically published to [PyPI](https://pypi.org/project/pycytominer/) via Github Actions.
 12. Manually create the release at [conda-forge](https://anaconda.org/conda-forge/pycytominer).
 
-## Style guides
+## Code Quality
 
-Please follow all style guides to the best of your abilities.
+Please follow the below quality guides to the best of your abilities.
+If you have configured your [dev environment](#dev-environments) as described above, the formatting and linting rules will also be enforced automatically using the installed [pre-commit](https://pre-commit.com/) hooks.
+
+### Formatting
+
+We use [ruff](https://docs.astral.sh/ruff/) for formatting Python code, and [prettier](https://prettier.io/) for formatting markdown, json and yaml files.
+Ruff includes a python code formatter similar to Black.
+We include `ruff` in the poetry dev dependencies so it can be run manually using `ruff format`
+Prettier (which is not python-based) is not included in the poetry dev dependencies, but can be installed and run manually.
+Alternately, both `ruff format` and `prettier` will be run automatically at commit time with the pre-commit hooks installed.
+
+### Linting
+
+For python code linting, we also use [ruff](https://docs.astral.sh/ruff/), which can perform same linting checks as Flake8.
+You can use the command `ruff check` to check for linting errors.
+The list of linting rules and exceptions are defined in the `pyproject.toml` file under the `[tool.ruff.lint]` section.
+We also include some commented-out rules in that section that we are working towards enabling in the future.
+All linting checks will also be run automatically at commit time with the pre-commit hooks as described above.
 
 ### Git commit messages
 
 Pycytominer uses [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/) standard for commit messages to aid in automatic changelog generation.
 We prepare commit messages that follow this standard using [commitizen](https://commitizen-tools.github.io/commitizen/), which comes with the poetry dev dependencies.
 
-### Python style guide
-
-For python code style, we use [black](https://github.com/psf/black).
-Please use black before committing any code.
-We will not accept code contributions that do not use black.
-Configuring your [dev environment](#dev-environments) as described above will ensure your code is formatted correctly automatically (using a tool called [pre-commit](https://pre-commit.com/)).
-
 ### Documentation style guide
 
 We use the [numpy documentation style guide](https://numpydoc.readthedocs.io/en/latest/format.html).
-We also use [prettier](https://prettier.io/) for automatic formatting of markdown, json and yaml files.
+When writing markdown documentation, please also ensure that each sentence is on a new line.

README.md

@@ -4,7 +4,7 @@
 
 [![Build Status](https://github.com/cytomining/pycytominer/actions/workflows/integration-test.yml/badge.svg?branch=main)](https://github.com/cytomining/pycytominer/actions/workflows/integration-test.yml?query=branch%3Amain)
 [![Coverage Status](https://codecov.io/gh/cytomining/pycytominer/branch/main/graph/badge.svg)](https://codecov.io/github/cytomining/pycytominer?branch=main)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![RTD](https://readthedocs.org/projects/pycytominer/badge/?version=latest&style=flat)](https://pycytominer.readthedocs.io/)
 [![DOI](https://img.shields.io/badge/DOI-10.48550/arXiv.2311.13417-blue)](https://doi.org/10.48550/arXiv.2311.13417)
 

docs/conf.py

@@ -12,21 +12,19 @@
 #
 import os
 import sys
-import pathlib
 import dunamai
 from datetime import date
 
 sys.path.insert(0, os.path.abspath(".."))
 
-import pycytominer
+# Ignore rules regarding import order which is required for sphinx build process
+import pycytominer  # noqa: E402, RUF100
 
 # -- Project information -----------------------------------------------------
 
 project = pycytominer.__about__.__project__
 author = pycytominer.__about__.__author__
-copyright = "Copyright 2019 - {date} {author}".format(
-    date=date.today().year, author=author
-)
+project_copyright = f"Copyright 2019 - {date.today().year} {author}"
 
 # Get the version from dunamai (the backend of poetry-dynamic-versioning)
 auto_version = dunamai.Version.from_git()