From 2c623c769d41926e75f0505a5f90eb6067df8dd2 Mon Sep 17 00:00:00 2001
From: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date: Mon, 30 Mar 2026 12:00:47 -0400
Subject: [PATCH 1/5] chore: improve code coverage reporting

---
 codecov.yml    | 1 -
 pyproject.toml | 6 +++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/codecov.yml b/codecov.yml
index ef535fd8fe..745d1f503c 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -10,7 +10,6 @@ coverage:
         threshold: 0.1
 codecov:
   notify:
-    after_n_builds: 10 # Wait for all 10 reports before updating the status
     wait_for_ci: yes
 comment:
   layout: "diff, files"
diff --git a/pyproject.toml b/pyproject.toml
index 8277c3f752..c69a3e4869 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -157,7 +157,7 @@ dependency-groups = ["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_CONFIG = "pyproject.toml"
 COV_CORE_DATAFILE = ".coverage.eager"
 
 [[tool.hatch.envs.test.matrix]]
@@ -175,8 +175,8 @@ matrix.deps.dependency-groups = [
 ]
 
 [tool.hatch.envs.test.scripts]
-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 = "pytest --cov-config=pyproject.toml --cov=src --cov-report xml --junitxml=junit.xml -o junit_family=legacy"
+run-coverage-html = "pytest --cov-config=pyproject.toml --cov=src --cov-report html"
 run = "run-coverage --no-cov --ignore tests/benchmarks"
 run-verbose = "run-coverage --verbose"
 run-mypy = "mypy src"

From da174e3fc917bdb554887bc4a1adbb83eb27eb44 Mon Sep 17 00:00:00 2001
From: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date: Mon, 30 Mar 2026 12:11:39 -0400
Subject: [PATCH 2/5] update after_n_builds

---
 .github/workflows/gpu_test.yml    |  1 +
 .github/workflows/hypothesis.yaml |  1 +
 .github/workflows/test.yml        |  2 ++
 codecov.yml                       | 17 +++++++++++++++--
 4 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/gpu_test.yml b/.github/workflows/gpu_test.yml
index 4fdffab057..d3aa03d2f6 100644
--- a/.github/workflows/gpu_test.yml
+++ b/.github/workflows/gpu_test.yml
@@ -72,4 +72,5 @@ jobs:
       uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3  # v5.3.1
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
+        flags: gpu
         verbose: true # optional (default = false)
diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml
index 1ec6b4806d..a6a5ebbe6a 100644
--- a/.github/workflows/hypothesis.yaml
+++ b/.github/workflows/hypothesis.yaml
@@ -81,6 +81,7 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
+        flags: tests
         verbose: true # optional (default = false)
 
     - name: Generate and publish the report
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 8c55c7e93d..d0e244f507 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -71,6 +71,7 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
+        flags: tests
         verbose: true # optional (default = false)
 
   test-upstream-and-min-deps:
@@ -110,6 +111,7 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
+        flags: tests
         verbose: true # optional (default = false)
 
   doctests:
diff --git a/codecov.yml b/codecov.yml
index 745d1f503c..bfeb8e1169 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -6,10 +6,23 @@ coverage:
         informational: true
     project:
       default:
-        target: auto
-        threshold: 0.1
+        target: 90%
+        threshold: 1%
+        flags:
+          - tests
+flags:
+  tests:
+    paths:
+      - src/
+    carryforward: true
+  gpu:
+    paths:
+      - src/
+    carryforward: true
 codecov:
   notify:
+    # 6 = test.yml: 3 (optional+ubuntu) + 2 (upstream + min_deps), hypothesis: 1
+    after_n_builds: 6
     wait_for_ci: yes
 comment:
   layout: "diff, files"

From 7e47998e0f51c265d3148588f5ee2ae0a0b4c4fa Mon Sep 17 00:00:00 2001
From: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date: Mon, 30 Mar 2026 21:03:56 -0400
Subject: [PATCH 3/5] fix: use `coverage run` instead of `pytest --cov` for
 accurate import-time coverage

The pytest11 entry point (`zarr = "zarr.testing"`) imports 76 zarr modules
during plugin loading, before pytest-cov starts measuring. This caused all
module-level code (class definitions, imports, decorators) to appear uncovered,
dropping reported coverage well below actual test coverage.

`coverage run -m pytest` starts tracing before any imports, resolving the issue.
---
 pyproject.toml | 30 ++++++++++++++++++++----------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index c69a3e4869..ac16436917 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -142,6 +142,7 @@ exclude_also = [
 [tool.coverage.run]
 omit = [
     "bench/compress_normal.py",
+    "src/zarr/_version.py",  # auto-generated by setuptools-scm
     "src/zarr/testing/conftest.py",  # only for downstream projects
 ]
 
@@ -155,10 +156,6 @@ hooks.vcs.version-file = "src/zarr/_version.py"
 dependency-groups = ["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 = "pyproject.toml"
-COV_CORE_DATAFILE = ".coverage.eager"
 
 [[tool.hatch.envs.test.matrix]]
 python = ["3.12", "3.13", "3.14"]
@@ -175,13 +172,23 @@ matrix.deps.dependency-groups = [
 ]
 
 [tool.hatch.envs.test.scripts]
-run-coverage = "pytest --cov-config=pyproject.toml --cov=src --cov-report xml --junitxml=junit.xml -o junit_family=legacy"
-run-coverage-html = "pytest --cov-config=pyproject.toml --cov=src --cov-report html"
-run = "run-coverage --no-cov --ignore tests/benchmarks"
+run-coverage = [
+    "coverage run --source=src -m pytest --junitxml=junit.xml -o junit_family=legacy {args:}",
+    "coverage xml",
+]
+run-coverage-html = [
+    "coverage run --source=src -m pytest {args:}",
+    "coverage html",
+]
+run = "pytest --ignore tests/benchmarks"
 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*"
+run-hypothesis = [
+    "coverage run --source=src -m pytest -nauto --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful* {args:}",
+    "coverage xml",
+]
 run-benchmark = "pytest --benchmark-enable tests/benchmarks"
+serve-coverage-html = "python -m http.server -d htmlcov 8000"
 list-env = "pip list"
 
 [tool.hatch.envs.gputest]
@@ -195,8 +202,11 @@ features = ["gpu"]
 python = ["3.12", "3.13"]
 
 [tool.hatch.envs.gputest.scripts]
-run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=src --cov-report xml --junitxml=junit.xml -o junit_family=legacy --ignore tests/benchmarks"
-run = "run-coverage --no-cov"
+run-coverage = [
+    "coverage run --source=src -m pytest -m gpu --junitxml=junit.xml -o junit_family=legacy --ignore tests/benchmarks {args:}",
+    "coverage xml",
+]
+run = "pytest -m gpu --ignore tests/benchmarks"
 
 [tool.hatch.envs.upstream]
 template = 'test'

From b695fe167f0196fa67760f28f11fcc444444b068 Mon Sep 17 00:00:00 2001
From: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date: Mon, 30 Mar 2026 21:10:26 -0400
Subject: [PATCH 4/5] Revert changes

---
 codecov.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/codecov.yml b/codecov.yml
index bfeb8e1169..a3783cc39a 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -6,8 +6,8 @@ coverage:
         informational: true
     project:
       default:
-        target: 90%
-        threshold: 1%
+        target: auto
+        threshold: 0.1
         flags:
           - tests
 flags:

From 50a4db5400c47c8eb1dd407ec78be78484261ed9 Mon Sep 17 00:00:00 2001
From: Max Jones <14077947+maxrjones@users.noreply.github.com>
Date: Mon, 30 Mar 2026 21:11:54 -0400
Subject: [PATCH 5/5] Revert change

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ac16436917..96932a9611 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -142,7 +142,6 @@ exclude_also = [
 [tool.coverage.run]
 omit = [
     "bench/compress_normal.py",
-    "src/zarr/_version.py",  # auto-generated by setuptools-scm
     "src/zarr/testing/conftest.py",  # only for downstream projects
 ]