feat(black)

.github/workflows/black.yml

@@ -0,0 +1,21 @@
+name: Black
+
+on: [pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out git repository
+        uses: actions/[email protected]
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Set up Black
+        uses: psf/black@stable
+        with:
+          options: ". --check --line-length 100"
+          version: "~=24.1.0"

.github/workflows/merge_master_ci.yml

@@ -23,26 +23,26 @@ jobs:
     name: Create staging image
     steps:
       - name: Check out git repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4.1.1
 
       - name: Extract branch name and remove illegal chars
         id: get_branch_name
         shell: bash
         run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3.0.0
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3.1.0
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5.1.0
         with:
           context: ./
           file: ./Dockerfile
@@ -54,12 +54,12 @@ jobs:
     name: Test and coveralls
     steps:
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5.0.0
         with:
           python-version: "3.10"
 
       - name: Check out genotype-api
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4.1.1
         with:
           repository: "Clinical-Genomics/genotype-api"
 

.github/workflows/pull_request_ci.yml

@@ -9,8 +9,8 @@ jobs:
     runs-on: ubuntu-latest
     name: Black
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4.1.1
+      - uses: actions/setup-python@v5.0.0
       - uses: psf/black@stable
         with:
           black_args: ". --check --line-length 100"
@@ -20,26 +20,26 @@ jobs:
     name: Create staging docker image
     steps:
      - name: Check out git repository
-       uses: actions/checkout@v2
+       uses: actions/checkout@v4.1.1
 
      - name: Extract branch name and remove illegal chars
        id: get_branch_name
        shell: bash
        run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
 
      - name: Login to Docker Hub
-       uses: docker/login-action@v1
+       uses: docker/login-action@v3.0.0
        with:
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_PASSWORD }}
 
      - name: Set up Docker Buildx
        id: buildx
-       uses: docker/setup-buildx-action@v1
+       uses: docker/setup-buildx-action@v3.1.0
 
      - name: Build and push
        id: docker_build
-       uses: docker/build-push-action@v2
+       uses: docker/build-push-action@v5.1.0
        with:
          context: ./
          file: ./Dockerfile
@@ -51,12 +51,12 @@ jobs:
     name: Test and coveralls
     steps:
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5.0.0
         with:
           python-version: "3.10"
 
       - name: Check out genotype-api
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4.1.1
         with:
           repository: "Clinical-Genomics/genotype-api"
 

.github/workflows/release_ci.yml

@@ -12,26 +12,26 @@ jobs:
     name: Push production docker image to dockerhub
     steps:
       - name: Check out git repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4.1.1
 
       - name: Extract branch name and remove illegal chars
         id: get_branch_name
         shell: bash
         run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3.0.0
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3.1.0
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5.1.0
         with:
           context: ./
           file: ./Dockerfile

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 24.1.0
+    hooks:
+      - id: black
+        args: [--line-length=100]
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.7
+    hooks:
+      - id: ruff
+

genotype_api/api/app.py

@@ -2,6 +2,7 @@
 Main functions for the genotype api
 
 """
+
 from fastapi import FastAPI, status, Request
 from fastapi.responses import JSONResponse
 from fastapi.middleware.cors import CORSMiddleware

genotype_api/api/endpoints/analyses.py

@@ -1,4 +1,5 @@
 """Routes for analysis"""
+
 from pathlib import Path
 from typing import List
 

genotype_api/api/endpoints/plates.py

@@ -1,4 +1,5 @@
 """Routes for plates"""
+
 from datetime import datetime
 from io import BytesIO
 from pathlib import Path

genotype_api/api/endpoints/snps.py

@@ -1,4 +1,5 @@
 """Routes for the snps"""
+
 from genotype_api.models import SNP, User
 from typing import List
 

genotype_api/constants.py

@@ -1,4 +1,5 @@
 """Constants used over the package"""
+
 from enum import Enum
 from pydantic import BaseModel
 

genotype_api/database.py

@@ -1,4 +1,5 @@
 """Hold the database information"""
+
 from sqlmodel import Session, SQLModel, create_engine
 
 from genotype_api.config import settings

requirements-dev.txt

@@ -1,5 +1,6 @@
-pytest>=5.2
-pytest-cov
+bump2version
 coveralls
+pre-commit
 pylint
-bump2version
+pytest-cov
+pytest>=5.2<

requirements.txt

@@ -1,5 +1,3 @@
-
-# server stuff
 SQLAlchemy==1.4.30
 aiofiles
 bcrypt