simplifying workflows yml file, adding flake8

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+extend-ignore = E203,E501,W503
+max-line-length = 99

.github/workflows/linting.yml

@@ -0,0 +1,32 @@
+name: Linters
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 black isort
+      - name: Flake8 Lint
+        run: |
+          flake8 --ignore=E501,W503,E203
+      - name: Black Lint
+        run: |
+          black --line-length 99 --check --verbose
+      - name: isort Lint
+        run: |
+          isort --profile black --check-only --diff

.gitignore

@@ -1,5 +1,4 @@
 .vscode/
-.flake8
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

README.md

@@ -7,14 +7,15 @@ This repository contains plug-in tests for use during validation of submissions.
 ### Branches
 
 - Make new feature branches from `devel`.
-- Before submitting a PR, make sure your code is black and isort compliant. Run the following from the base `ingest-validation-tests` directory:
+- Before submitting a PR, make sure your code is black, isort, and flake8 compliant. Run the following from the base `ingest-validation-tests` directory:
 
   ```
   black --line-length 99 .
   isort --profile black --multi-line 3 .
+  flake8
   ```
 
-  (You can integrate black and potentially isort with your editor to skip this step, see Setup section below)
+  (Integrating black and potentially isort/flake8 with your editor may allow you to skip this step, see Setup section below.)
 
 - Make PRs to `devel`. (This is the default branch.)
 - The last reviewer to approve a PR should merge it.
@@ -32,6 +33,7 @@ This repository contains plug-in tests for use during validation of submissions.
 - (optional) Integrate black with your editor.
   - [Instructions for black.](https://black.readthedocs.io/en/stable/integrations/editors.html)
 - (optional) Integrate [isort](https://pycqa.github.io/isort/) with your editor.
+- (optional) Integrate [flake8](https://flake8.pycqa.org/en/latest/index.html) with your editor.
 
 ### Testing
 

requirements-dev.txt

@@ -1,4 +1,5 @@
 black==23.12.1
+flake8==7.0.0
 git+https://github.com/hubmapconsortium/fastq-utils.git@v0.2.5#egg=hubmap-fastq-utils
 imagecodecs>=2023.3.16
 isort==5.13.2