cicd: update style checks and test coverage dependencies, init

.github/workflows/checks.yml

@@ -50,30 +50,11 @@ jobs:
 
   lint:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
-    env:
-      AWS_ACCESS_KEY_ID: ${{ secrets.DUMMY_AWS_ACCESS_KEY_ID }}
-      AWS_SECRET_ACCESS_KEY: ${{ secrets.DUMMY_AWS_SECRET_ACCESS_KEY }}
-      AWS_DEFAULT_REGION: us-east-2
-      AWS_DEFAULT_OUTPUT: text
     steps:
     - uses: actions/checkout@v3
 
-    - name: Setup Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install dependencies
-      run: python3 -m pip install ".[dev]"
-
-    - name: flake8 check
-      run: flake8 disease/ tests/ setup.py
-
-    - name: black check
-      run: black --check disease/ tests/ setup.py
+    - name: black
+      uses: psf/black@stable
 
-    - name: isort check
-      run: isort --profile black --check disease/ tests/ setup.py
+    - name: ruff
+      uses: chartboost/ruff-action@v1

.pre-commit-config.yaml

@@ -1,22 +1,18 @@
-# See https://pre-commit.com for more information
-# See https://pre-commit.com/hooks.html for more hooks
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v1.4.0
-    hooks:
-      - id: flake8
-        additional_dependencies: [flake8-docstrings]
-      - id: check-added-large-files
-        args: ['--maxkb=2500']
-      - id: detect-private-key
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
-    hooks:
-      - id: black
-        args: ["--check"]
-        language_version: python3.10
-  - repo: https://github.com/pycqa/isort
-    rev: 5.6.4
-    hooks:
-      - id: isort
-        args: ["--profile", "black", "--check"]
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v1.4.0
+  hooks:
+  - id: check-added-large-files
+  - id: detect-private-key
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+- repo: https://github.com/psf/black
+  rev: 23.7.0
+  hooks:
+    - id: black
+      language_version: python3.11
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.0.280
+  hooks:
+    - id: ruff
+      args: [ --fix, --exit-non-zero-on-fix ]

Pipfile

@@ -11,18 +11,14 @@ owlready2 = "*"
 rdflib = "*"
 pytest = "*"
 pytest-cov = "*"
-flake8 = "*"
-flake8-docstrings = "*"
-black = "*"
-isort = "*"
 pre-commit = "*"
-coveralls = "*"
-coverage = "*"
 ipykernel = "*"
 matplotlib = "*"
 lxml = "*"
 xmlformatter = "*"
 psycopg = {version = "*", extras=["binary"]}
+black = "*"
+ruff = "*"
 
 [packages]
 pydantic = "*"

README.md

@@ -128,16 +128,15 @@ pip install -e ".[pg,etl,dev,test]"
 
 ### Init coding style tests
 
-Code style is managed by [flake8](https://github.com/PyCQA/flake8) and checked prior to commit.
+Code style is managed by [Ruff](https://github.com/astral-sh/ruff) and [Black](https://github.com/psf/black) and checked prior to commit.
 
-We use [pre-commit](https://pre-commit.com/#usage) to run conformance tests.
+This performs checks for:
 
-This ensures:
-
-* Check code style
-* Check for added large files
-* Detect AWS Credentials
-* Detect Private Key
+* Code style
+* File endings
+* Added large files
+* AWS credentials
+* Private keys
 
 Before first commit run:
 

disease/cli.py

@@ -1,4 +1,4 @@
-"""This module provides a CLI util to make updates to normalizer database."""
+"""Provides a CLI util to make updates to normalizer database."""
 import os
 from pathlib import Path
 from timeit import default_timer as timer
@@ -89,7 +89,7 @@ def update_from_remote(data_url: Optional[str], db_url: str) -> None:
     type=click.Path(exists=True, path_type=Path),
 )
 @click.option("--db_url", help="URL endpoint for the application database.")
-def dump_database(output_directory: Path, db_url: str):
+def dump_database(output_directory: Path, db_url: str) -> None:
     """Dump data from database into file.
 
     \f
@@ -176,7 +176,7 @@ def _load_source(
     start_load = timer()
 
     # used to get source class name from string
-    SourceClass = eval(n.value)
+    SourceClass = eval(n.value)  # noqa: N806
 
     source = SourceClass(database=db)
     processed_ids += source.perform_etl(use_existing=from_local)