Basic CI (#36)

Fixes #35.

Adds a GHA job with steps:

* linting check using `pre-commit`
* `pytest` run of all collectable `pytest` compatible tests in the
package
* `dependabot` automation

Author: fkiraly

.github/dependabot.yml

@@ -0,0 +1,20 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    commit-message:
+      prefix: "[MNT] [Dependabot]"
+      include: "scope"
+    labels:
+      - "maintenance"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    commit-message:
+      prefix: "[MNT] [Dependabot]"
+      include: "scope"
+    labels:
+      - "maintenance"

.github/workflows/test.yml

@@ -0,0 +1,97 @@
+name: Test
+
+on:
+  push:
+    paths-ignore:
+      - 'docs/**'
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - 'docs/**'
+    types: [opened, synchronize]
+
+  # Allows workflows to be manually triggered
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  code-quality:
+    name: code-quality
+    runs-on: ubuntu-latest
+    steps:
+      - name: repository checkout step
+        uses: actions/checkout@v4
+
+      - name: python environment step
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: install pre-commit
+        run: python3 -m pip install pre-commit
+
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Get changed files
+        id: changed-files
+        run: |
+          CHANGED_FILES=$(git diff --name-only ${{ github.event.pull_request.base.sha }} ${{ github.sha }} | tr '\n' ' ')
+          echo "CHANGED_FILES=${CHANGED_FILES}" >> $GITHUB_ENV
+
+      - name: Print changed files
+        run: |
+          echo "Changed files: $CHANGED_FILES"
+
+      - name: Run pre-commit on changed files
+        run: |
+          if [ -n "$CHANGED_FILES" ]; then
+            pre-commit run --color always --files $CHANGED_FILES --show-diff-on-failure
+          else
+            echo "No changed files to check."
+          fi
+
+  run-tests-no-extras:
+    needs: code-quality
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - run: git remote set-branches origin 'main'
+
+      - run: git fetch --depth 1
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
+      - name: Install package and dependencies
+        run: |
+          python -m pip install .[dev] --no-cache-dir
+
+      - name: Show dependencies
+        run: python -m pip list
+
+      - name: Show available branches
+        run: git branch -a
+
+      - name: Run tests
+        run: |
+          python -m pytest pyaptamer -p no:warnings

pyaptamer/__init__.py

@@ -0,0 +1,3 @@
+"""pyaptamer: Python library for aptamer design."""
+
+__version__ = "0.0.1.dev0"

pyaptamer/tests/__init__.py

@@ -0,0 +1 @@
+"""Tests for the pyaptamer package."""

pyaptamer/tests/test_dummy.py

@@ -0,0 +1,6 @@
+"""Single dummy test to ensure pytest is working."""
+
+
+def test_dummy():
+    """A dummy test that always passes."""
+    assert True, "This is a dummy test that should always pass."

pyproject.toml

@@ -9,7 +9,7 @@ description = "Python library for aptamer simulation"
 readme = "README.md"
 requires-python = ">=3.10"
 authors = [
-    { name="Your Name", email="your@email.com" }
+    {name="German Center for Open Source AI", email="info@gcos.ai"}
 ]
 
 dependencies = [