Add github bot to run precommit linting

.github/workflows/dev_tests.yml

@@ -1,12 +1,14 @@
 name: dev tests
 
 on:
+  push:
+    branches: [ main ]
   pull_request:
+    types: [opened, synchronize, reopened]
   workflow_dispatch:
   schedule:
     - cron: '0 0 * * *'
 
-
 permissions:
   contents: write
   issues: write
@@ -34,7 +36,7 @@ jobs:
           CLIENT_ID: ${{ secrets.CLIENT_ID }}
           CLIENT_SECRET: ${{ secrets.CLIENT_SECRET }}
           ENV : "dev"
-        run: pytest -r nmdc_api_utilities/test/
+        run: pytest -x nmdc_api_utilities/test/
       - name: Create Issue
         if: failure() && github.event.pull_request == null && github.event_name == 'schedule'
         uses: actions/github-script@v6

.github/workflows/documentation.yml

@@ -1,6 +1,10 @@
 name: documentation
 
-on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+  workflow_dispatch:
 
 permissions:
   contents: write

.github/workflows/precommit.yml

@@ -0,0 +1,48 @@
+name: Run pre-commit hooks & push changes
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    types: [opened, synchronize, reopened]
+    paths:
+      - '**.py'
+
+
+permissions:
+  contents: write
+
+
+jobs:
+  run-hooks:
+    name: Run Pre-Commit hooks and push changes back
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout the code
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.event.pull_request.head.ref }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.12
+
+      - name: Install pre-commit
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pre-commit
+
+      - name: Run pre-commit hooks
+        run: |
+          pre-commit run --all-files || true
+
+      - name: Commit and push changes if pre-commit made any modifications
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          if [ -n "$(git status --porcelain)" ]; then
+            git add .
+            git commit -m "precommit: reformat"
+            git push
+          fi

.github/workflows/prod_tests.yml

@@ -1,7 +1,10 @@
 name: prod tests
 
 on:
+  push:
+    branches: [ main ]
   pull_request:
+    types: [opened, synchronize, reopened]
   workflow_dispatch:
   schedule:
     - cron: '0 0 * * *'
@@ -33,7 +36,7 @@ jobs:
           CLIENT_ID: ${{ secrets.CLIENT_ID }}
           CLIENT_SECRET: ${{ secrets.CLIENT_SECRET }}
           ENV : "prod"
-        run: pytest -r nmdc_api_utilities/test/
+        run: pytest -x nmdc_api_utilities/test/
       - name: Create Issue
         if: failure() && github.event.pull_request == null && github.event_name == 'schedule'
         uses: actions/github-script@v6

pyproject.toml

@@ -17,5 +17,7 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Operating System :: OS Independent",
 ]
-dependencies = ["pandas~=2.2.3", "requests~=2.32.3", "matplotlib~=3.10.0"]
 license-files = ["LICENSE"]
+dynamic = ["dependencies"]
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}