add codecov to repository (#233)

* add test.yaml

* coverage for r package

* change working directory

* change order of steps

* Update .github/workflows/test.yaml

Co-authored-by: Damon Bayer <[email protected]>

* add path in covr run

* add a test

* fix errors

* debug

* fix incorrect module name, changed to pyrenew_hew

* pre-commit

* review suggestions

* more names

---------

Co-authored-by: Damon Bayer <[email protected]>

.github/workflows/test.yaml

@@ -0,0 +1,99 @@
+name: test
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  python-test:
+    name: Run python tests and collect coverage
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: cache poetry
+        uses: actions/cache@v4
+        with:
+          path: ~/.local
+          key: ${{ runner.os }}-poetry
+
+      - name: install poetry
+        run: pip install poetry
+
+      - name: install package
+        run: poetry install --with test
+
+      - name: run tests
+        run: |
+          poetry run pytest \
+            --mpl --mpl-default-tolerance=10 \
+            --cov=pyrenew_hew --cov-report=term --cov-report=xml .
+
+      - name: Upload results to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          env_vars: OS,PYTHON
+          fail_ci_if_error: true
+          flags: python-tests
+          files: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true
+
+  r-test:
+    name: Run R tests and collect coverage
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+          working-directory: hewr
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            path = "hewr",
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v5
+        with:
+          fail_ci_if_error: true
+          files: ./cobertura.xml
+          plugins: noop
+          flags: r-tests
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -216,6 +216,8 @@ cython_debug/
 # https://github.com/github/gitignore/blob/main/R.gitignore
 
 .Rprofile
+renv/
+renv.lock
 
 # History files
 .Rhistory

pyproject.toml

@@ -20,6 +20,14 @@ pygit2 = "^1.16.0"
 azuretools = {git = "https://github.com/cdcgov/cfa-azuretools"}
 forecasttools = {git = "https://github.com/CDCgov/forecasttools-py"}
 
+[tool.poetry.group.test]
+optional = true
+
+[tool.poetry.group.test.dependencies]
+pytest = "^8.3.2"
+pytest-cov = "^5.0.0"
+pytest-mpl = "^0.17.0"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"

tests/test_utils.py

@@ -0,0 +1,27 @@
+"""
+Tests for the pyrenew-hew utils.
+"""
+
+import jax.numpy as jnp
+import pytest
+
+from pyrenew_hew.utils import convert_to_logmean_log_sd
+
+
+@pytest.mark.parametrize(
+    ["mean", "sd"],
+    [
+        [
+            jnp.array([10]),
+            jnp.array([0]),
+        ]
+    ],
+)
+def test_convert_to_logmean_log_sd_edge_case_zero_sd(mean, sd):
+    logmean, logsd = convert_to_logmean_log_sd(mean, sd)
+
+    expected_logmean = jnp.log(10.0)
+    expected_logsd = 0.0
+
+    assert jnp.isclose(logmean, expected_logmean)
+    assert jnp.isclose(logsd, expected_logsd)