Merge pull request #39 from niaid/add_pre-commit

Setting up pre-commit

.github/workflows/main.yml

@@ -15,21 +15,22 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.9
+      with:
+        fetch-depth: 0
+    - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
-    - name: Install tools
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements-dev.txt
-    - name: Lint with black
-      run: |
-        python -m black --check --diff .
-    - name: Lint with flake8
+        python-version: 3.11
+    - name: set PY
+      run: echo "PY=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
+    - uses: actions/cache@v4
+      with:
+        path: ~/.cache/pre-commit
+        key: pre-commit|${{ env.PY }}|${{ hashFiles('.pre-commit-config.yaml') }}
+    - name: Linting
       run: |
-        # stop the build for flake8 issues
-        python -m flake8 . --show-source --statistics
+        pip install pre-commit
+        pre-commit run --all-files
 
   test:
     needs: linting

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+# .pre-commit-config.yaml
+# for details see https://pre-commit.com
+# for list of available hooks see https://pre-commit.com/hooks.html
+#
+# Preclude commits that do not conform to various criteria.
+
+fail_fast: true
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.3.0
+  hooks: # check for large files, aws credentials and private key files
+   - id: check-added-large-files
+     args: ['--maxkb=200']
+   - id: detect-private-key
+- repo: https://github.com/pycqa/flake8
+  rev: 5.0.4
+  hooks:
+   - id: flake8
+     entry: pflake8
+     additional_dependencies: [pyproject-flake8]
+- repo: https://github.com/psf/black
+  rev: 23.1.0
+  hooks: # check conformance to black formatting
+   - id: black
+     args: ['--diff', '-v'] # if run without arguments, will fail and will format the files

pyproject.toml

@@ -11,3 +11,7 @@ junit_family="xunit2"
 [tool.black]
 line-length =  120
 exclude = '(docs/conf\.py)|venv*'
+
+[tool.flake8]
+max-line-length = 120
+extend-exclude = "docs/conf.py,venv*"