diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..f390822
--- /dev/null
+++ b/.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() }}
+
+
diff --git a/.github/workflows/run-code-checks.yaml b/.github/workflows/run-code-checks.yaml
deleted file mode 100644
index 5b38f17..0000000
--- a/.github/workflows/run-code-checks.yaml
+++ /dev/null
@@ -1,31 +0,0 @@
-name: run-code-checks
-
-on:
-  push:
-  workflow_dispatch:
-
-jobs:
-  run-checks:
-    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 unit tests 🧪
-        run: |
-          pytest -k unit
-
diff --git a/.github/workflows/run-integration-tests.yaml b/.github/workflows/run-integration-tests.yaml
deleted file mode 100644
index e4c7ce5..0000000
--- a/.github/workflows/run-integration-tests.yaml
+++ /dev/null
@@ -1,30 +0,0 @@
-name: run-integration-tests
-
-on:
-  push:
-    branches:
-      - main
-  pull_request:
-    types: [opened, ready_for_review, reopened]
-  workflow_dispatch:
-
-jobs:
-  run-checks:
-    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: Run integration tests 🧪
-        run: pytest -k integration
diff --git a/README.md b/README.md
index bb61c51..059bbd7 100644
--- a/README.md
+++ b/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