Fix test coverage (zarr-developers#3334)

* Fix test coverage

* Run GPU tests in GPU CI

Author: dstansby

.github/workflows/gpu_test.yml

@@ -63,7 +63,7 @@ jobs:
         hatch env run -e gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} list-env
     - name: Run Tests
       run: |
-        hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-coverage
+        hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-coverage-gpu
 
     - name: Upload coverage
       uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3  # v5.3.1

pyproject.toml

@@ -150,6 +150,12 @@ dependencies = [
 ]
 features = ["test"]
 
+[tool.hatch.envs.test.env-vars]
+# Required to test with a pytest plugin; see https://pytest-cov.readthedocs.io/en/latest/plugins.html
+COV_CORE_SOURCE = "src"
+COV_CORE_CONFIG = ".coveragerc"
+COV_CORE_DATAFILE = ".coverage.eager"
+
 [[tool.hatch.envs.test.matrix]]
 python = ["3.11", "3.12", "3.13"]
 numpy = ["1.26", "2.2"]
@@ -161,25 +167,18 @@ matrix.deps.dependencies = [
 ]
 
 [tool.hatch.envs.test.scripts]
-run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
-run-coverage-html = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report html --cov=src"
+run-coverage = "pytest --cov-config=pyproject.toml --cov=src --cov-append --cov-report xml --junitxml=junit.xml -o junit_family=legacy"
+run-coverage-html = "pytest --cov-config=pyproject.toml --cov=src --cov-append --cov-report html"
+run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pyproject.toml --cov=src --cov-append --cov-report xml --junitxml=junit.xml -o junit_family=legacy"
 run = "run-coverage --no-cov"
 run-pytest = "run"
 run-verbose = "run-coverage --verbose"
 run-mypy = "mypy src"
 run-hypothesis = "run-coverage -nauto --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful*"
 list-env = "pip list"
 
-[tool.hatch.envs.doctest]
-features = ["test", "optional", "remote", "remote_tests"]
-description = "Test environment for doctests"
-
-[tool.hatch.envs.doctest.scripts]
-run = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst'"
-fix = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst' --accept"
-list-env = "pip list"
-
 [tool.hatch.envs.gputest]
+template = "test"
 dependencies = [
     "numpy~={matrix:numpy}",
     "universal_pathlib",
@@ -191,22 +190,8 @@ python = ["3.11", "3.12", "3.13"]
 numpy = ["1.26", "2.2"]
 version = ["minimal"]
 
-[tool.hatch.envs.gputest.scripts]
-run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
-run = "run-coverage --no-cov"
-run-verbose = "run-coverage --verbose"
-run-mypy = "mypy src"
-run-hypothesis = "run-coverage --hypothesis-profile ci --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful*"
-list-env = "pip list"
-
-[tool.hatch.envs.docs]
-features = ['docs']
-
-[tool.hatch.envs.docs.scripts]
-build = "cd docs && make html"
-serve = "sphinx-autobuild docs docs/_build --host 0.0.0.0"
-
 [tool.hatch.envs.upstream]
+template = 'test'
 python = "3.13"
 dependencies = [
     'packaging @ git+https://github.com/pypa/packaging',
@@ -226,20 +211,12 @@ PIP_INDEX_URL = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simp
 PIP_EXTRA_INDEX_URL = "https://pypi.org/simple/"
 PIP_PRE = "1"
 
-[tool.hatch.envs.upstream.scripts]
-run = "pytest --verbose"
-run-mypy = "mypy src"
-run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*"
-run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
-run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
-run-coverage-html = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report html --cov=src"
-list-env = "pip list"
-
 [tool.hatch.envs.min_deps]
 description = """Test environment for minimum supported dependencies
 
 See Spec 0000 for details and drop schedule: https://scientific-python.org/specs/spec-0000/
 """
+template = "test"
 python = "3.11"
 dependencies = [
     'zarr[remote]',
@@ -257,13 +234,22 @@ dependencies = [
     'zarr[remote_tests]',
 ]
 
-[tool.hatch.envs.min_deps.scripts]
-run = "pytest --verbose"
-run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*"
+
+[tool.hatch.envs.doctest]
+features = ["test", "optional", "remote", "remote_tests"]
+description = "Test environment for doctests"
+
+[tool.hatch.envs.doctest.scripts]
+run = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst'"
+fix = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst' --accept"
 list-env = "pip list"
-run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
-run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
-run-coverage-html = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report html --cov=src"
+
+[tool.hatch.envs.docs]
+features = ['docs']
+
+[tool.hatch.envs.docs.scripts]
+build = "cd docs && make html"
+serve = "sphinx-autobuild docs docs/_build --host 0.0.0.0"
 
 [tool.ruff]
 line-length = 100