Add code coverage check to CI (#78)

* Combine GitHub actions test runs into a single ci file

Setting the groundwork to add a coverage report to Cladetime. We'll want to
run integration tests and unit tests at the same time to get a full report
of test coverage, so do that (but not on every push).

* Add test coverage check and report

The coverage job will fail if if code coverage is >= 80%

* Add status badge for the CI workflow

This doesn't give us an actual coverage percentage, but a successful
workflow run does mean that coverage is at or above the stated minimum
(in this case 80%, to match Hubverse standards).

* Rename run-code-checks to ci

This is a common pattern I've seen when looking at other python projects
(and also, the workflow does more than run tests now)

* Also run CI workflow on merge to main branch

* Fix typo

.github/workflows/ci.yaml

@@ -0,0 +1,98 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+env:
+  FORCE_COLOR: "1"
+  PIP_DISABLE_PIP_VERSION_CHECK: "1"
+  PIP_NO_PYTHON_VERSION_WARNING: "1"
+
+jobs:
+  run-checks:
+    name: Run linter and tests
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v4
+
+      - name: Set up Python 🐍
+        uses: actions/setup-python@v5
+        with:
+          cache: pip
+
+      - name: Install dependencies 📦️
+        run: |
+          pip install --upgrade pip
+          pip install -r requirements/requirements-dev.txt
+          pip install -e .
+
+      - name: Lint 🧹
+        run: ruff check
+
+      - name: Run tests 🧪
+        run: |
+          pip install --upgrade pip
+          pip install -r requirements/requirements-dev.txt
+          pip install -e .
+          coverage run -m pytest
+
+      - name: Upload coverage data 📤
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage
+          path: .coverage
+          include-hidden-files: true
+          if-no-files-found: ignore
+
+  coverage:
+    # https://hynek.me/articles/ditch-codecov-python/
+    name: Generate coverage report
+    runs-on: ubuntu-latest
+    needs: run-checks
+    if: always()
+
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+
+      - name: Set up Python 🐍
+        uses: actions/setup-python@v5
+        with:
+          cache: pip
+
+      - name: Install uv 🌟
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: ">=0.0.1"
+
+      - name: Download coverage data 📥
+        uses: actions/download-artifact@v4
+        with:
+          name: coverage
+          merge-multiple: true
+
+      - name: Generate coverage report 📊
+        run: |
+          uv tool install coverage
+          coverage html --skip-covered --skip-empty
+          coverage report --format=markdown >> $GITHUB_STEP_SUMMARY
+
+          # Generate report again, this time with a fail-under threshold
+          coverage report --fail-under=80
+
+      - name: Upload HTML report if coverage check fails
+        uses: actions/upload-artifact@v4
+        with:
+            name: html-cov-report
+            path: htmlcov
+        if: ${{ failure() }}
+
+

README.md

@@ -1,3 +1,5 @@
+![cladetime CI status](https://github.com/reichlab/cladetime/actions/workflows/ci.yaml/badge.svg)
+
 # User Guide
 
 Cladetime is a wrapper around Nextstrain's GenBank-based SARS-CoV-2 genome