From 5eb06a1dc25670d675e1d5e6555638e4111c3bcc Mon Sep 17 00:00:00 2001
From: Victor Lin <vlin@fredhutch.org>
Date: Tue, 29 Jul 2025 14:43:47 -0700
Subject: [PATCH] Configure Codecov
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Update CI to run pytest with coverage, generate a coverage report, and
upload it to Codecov.

Using default file paths for coverage results.

codecov.yml file copied from Augur.¹

¹ <https://github.com/nextstrain/augur/blob/8d1257463231079dd73aac609f0f7d1f692a9cb4/codecov.yml>
---
 .github/workflows/ci.yaml | 13 +++++++++++--
 .gitignore                |  5 ++++-
 codecov.yml               | 13 +++++++++++++
 pyproject.toml            |  4 ++++
 4 files changed, 32 insertions(+), 3 deletions(-)
 create mode 100644 codecov.yml

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 136a277..92d4c90 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -71,5 +71,14 @@ jobs:
       # Install project. 
       - run: poetry install --no-interaction
 
-      # Run tests.
-      - run: poetry run pytest
+      # Run tests with coverage.
+      - run: poetry run coverage run -m pytest
+
+      # Generate coverage report.
+      - run: poetry run coverage xml
+
+      # Upload coverage report to Codecov.
+      - uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
diff --git a/.gitignore b/.gitignore
index 0632f33..0a6f604 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,4 +2,7 @@ __pycache__/
 
 *.DS_Store
 
-notebooks/.ipynb_checkpointsdocs/_build/html
\ No newline at end of file
+notebooks/.ipynb_checkpointsdocs/_build/html
+
+.coverage
+coverage.xml
diff --git a/codecov.yml b/codecov.yml
new file mode 100644
index 0000000..c0a1e90
--- /dev/null
+++ b/codecov.yml
@@ -0,0 +1,13 @@
+comment:
+  # Only post a codecov comment if coverage changes.
+  require_changes: true
+
+coverage:
+  status:
+    # Disable GitHub checks for code coverage that make otherwise valid builds fail.
+    project: off
+    patch: off
+
+github_checks:
+  # Disable inline annotations of code coverage in pull requests.
+  annotations: false
diff --git a/pyproject.toml b/pyproject.toml
index c26aff9..8180cbb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,6 +33,7 @@ nbsphinx = "^0.9.4"
 pandoc = "^2.3"
 isort = "^5.13.2"
 pre-commit = "^3.7.1"
+coverage = "^7"
 
 [docs]
 jupyter = "^1.0.0"
@@ -41,6 +42,9 @@ sphinx-rtd-theme = "^2.0.0"
 nbsphinx = "^0.9.4"
 pandoc = "^2.3"
 
+[tool.coverage.run]
+source = ["evofr"]
+
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"