Coverage.py Path Collapsing Bug with pytest-cov

Minimal reproduction showing pytest --cov with relative_files=true incorrectly collapses files when a directory name appears at both root and nested levels, resulting in lost coverage data.

The Bug

When a directory name exists at both root and nested levels (e.g., features/ and pkg/features/), pytest-cov's auto-generated path mapping rules collapse both locations into a single entry:

features/templates.py → features/templates.py
pkg/features/templates.py → features/templates.py ❌ COLLAPSED

Result: Coverage data from pkg/features/templates.py is lost.

Note: The bug does NOT occur with coverage run -m pytest - only with pytest --cov.

Repository Structure

coverage-path-bug/
├── features/templates.py          # Root level
├── pkg/features/templates.py      # Nested level - TRIGGERS BUG
├── utils/helpers.py               # Root level (working comparison)
├── app1/utils/helpers.py          # Nested level (working comparison)
├── test_base_features.py
├── test_pkg_features.py
└── pyproject.toml

The utils/ pattern works correctly because the */app1 rule preserves app1/utils/helpers.py as separate. The features/ pattern fails because the */features rule matches both locations and collapses them.

Reproduction

Install dependencies:
```
uv sync
```

Run with pytest --cov:

COVERAGE_DEBUG=pathmap uv run pytest --cov=. --cov-report=term

Observe bug: pkg/features/templates.py is missing from the report:

features/templates.py        4      0      0      0   100%
utils/helpers.py             4      0      0      0   100%
app1/utils/helpers.py        4      0      0      0   100%
TOTAL                       44 (should be 48!)

Debug output shows path collapsing:

Matched path 'features/templates.py' to rule '*/features' -> 'features/', producing 'features/templates.py'
Matched path 'pkg/features/templates.py' to rule '*/features' -> 'features/', producing 'features/templates.py'

Compare with coverage run (no bug):

rm .coverage
COVERAGE_DEBUG=pathmap uv run coverage run -m pytest
COVERAGE_DEBUG=pathmap uv run coverage report

Output correctly shows both files:

features/templates.py         4      0      0      0   100%
pkg/features/templates.py     4      0      0      0   100%
TOTAL                        48

Expected vs Actual

Expected: All four files tracked separately (48 total statements) Actual with pytest --cov: Only three files appear - pkg/features/templates.py is missing (44 total statements)

Investigation

When relative_files=true, coverage.py auto-generates path mapping rules. The rule */features matches both:

features/templates.py → features/templates.py
pkg/features/templates.py → features/templates.py

Both collapse to the same destination.

The utils/ files work because */app1 catches app1/utils/helpers.py first, preserving the app1/ prefix before */utils can match it.

Rule Generation Order

The bug is triggered by the order in which pathmap rules are generated:

features/ discovered first → generates rule */features -> features/
features/templates.py matched → produces features/templates.py ✓
pkg/ discovered → generates rule */pkg -> pkg/
pkg/__init__.py matched → produces pkg/__init__.py ✓
pkg/features/templates.py encountered → matches existing */features rule ❌
Result: pkg/features/templates.py → features/templates.py (collapsed!)

The */features rule is too broad - it matches any path ending with /features/, regardless of what comes before it.

Debug output showing the issue:

Generating rule: '*/features' -> 'features/' using regex '^(.*[\\\\/])?features[\\\\/]'
Matched path 'features/__init__.py' to rule '*/features' -> 'features/', producing 'features/__init__.py'
Matched path 'features/templates.py' to rule '*/features' -> 'features/', producing 'features/templates.py'
Generating rule: '*/pkg' -> 'pkg/' using regex '^(.*[\\\\/])?pkg[\\\\/]'
Matched path 'pkg/__init__.py' to rule '*/pkg' -> 'pkg/', producing 'pkg/__init__.py'
Matched path 'pkg/features/__init__.py' to rule '*/features' -> 'features/', producing 'features/__init__.py'
Matched path 'pkg/features/templates.py' to rule '*/features' -> 'features/', producing 'features/templates.py'

Notice how pkg/features/templates.py matches the */features rule (generated earlier) instead of being preserved with its full path.

Configuration

pyproject.toml:

[tool.coverage.run]
relative_files = true
branch = true
source = ["."]

Environment

Tested with:

Python: 3.11.10
coverage.py: 7.11.0
pytest: 8.4.2
pytest-cov: 7.0.0
uv: for dependency management

Detailed Output Comparison

With `pytest --cov` (BUG - Missing File)

$ COVERAGE_DEBUG=pathmap uv run pytest --cov=. --cov-report=term

Output:

test_app1_helpers.py ..                                                  [ 25%]
test_base_features.py ..                                                 [ 50%]
test_base_helpers.py ..                                                  [ 75%]
test_pkg_features.py ..                                                  [100%]

================================ tests coverage ================================
______________ coverage: platform darwin, python 3.11.10-final-0 _______________

Name                     Stmts   Miss Branch BrPart  Cover   Missing
--------------------------------------------------------------------
app1/__init__.py             0      0      0      0   100%
app1/utils/__init__.py       0      0      0      0   100%
app1/utils/helpers.py        4      0      0      0   100%
features/__init__.py         0      0      0      0   100%
features/templates.py        4      0      0      0   100%
pkg/__init__.py              0      0      0      0   100%
test_app1_helpers.py         8      0      0      0   100%
test_base_features.py        8      0      0      0   100%
test_base_helpers.py         8      0      0      0   100%
test_pkg_features.py         8      0      0      0   100%
utils/__init__.py            0      0      0      0   100%
utils/helpers.py             4      0      0      0   100%
--------------------------------------------------------------------
TOTAL                       44      0      0      0   100%
============================== 8 passed in 0.03s ===============================

❌ Notice: pkg/features/__init__.py and pkg/features/templates.py are MISSING! Total statements: 44 (should be 48)

With `coverage run` (WORKS - All Files Present)

$ COVERAGE_DEBUG=pathmap coverage run -m pytest
$ COVERAGE_DEBUG=pathmap coverage report

Output:

============================= test session starts ==============================
platform darwin -- Python 3.11.10, pytest-8.4.2, pluggy-1.6.0
rootdir: /private/tmp/coverage-path-bug
configfile: pyproject.toml
plugins: cov-7.0.0
collected 8 items

test_app1_helpers.py ..                                                  [ 25%]
test_base_features.py ..                                                 [ 50%]
test_base_helpers.py ..                                                  [ 75%]
test_pkg_features.py ..                                                  [100%]

============================== 8 passed in 0.02s ===============================

Name                        Stmts   Miss Branch BrPart  Cover   Missing
-----------------------------------------------------------------------
app1/__init__.py                0      0      0      0   100%
app1/utils/__init__.py          0      0      0      0   100%
app1/utils/helpers.py           4      0      0      0   100%
features/__init__.py            0      0      0      0   100%
features/templates.py           4      0      0      0   100%
pkg/__init__.py                 0      0      0      0   100%
pkg/features/__init__.py        0      0      0      0   100%
pkg/features/templates.py       4      0      0      0   100%
test_app1_helpers.py            8      0      0      0   100%
test_base_features.py           8      0      0      0   100%
test_base_helpers.py            8      0      0      0   100%
test_pkg_features.py            8      0      0      0   100%
utils/__init__.py               0      0      0      0   100%
utils/helpers.py                4      0      0      0   100%
-----------------------------------------------------------------------
TOTAL                          48      0      0      0   100%

✓ Notice: ALL files including pkg/features/__init__.py and pkg/features/templates.py are present! Total statements: 48 (correct)

Key Difference

With COVERAGE_DEBUG=pathmap:

pytest --cov: Generates pathmap rules, applies them, causes file collapsing
coverage run: Does NOT generate or apply pathmap rules at all, even with debug flag enabled

Navigation Menu

Repository navigation

About

Repository files navigation

Coverage.py Path Collapsing Bug with pytest-cov

The Bug

Repository Structure

Reproduction

Expected vs Actual

Investigation

Rule Generation Order

Configuration

Environment

Detailed Output Comparison

With `pytest --cov` (BUG - Missing File)

With `coverage run` (WORKS - All Files Present)

Key Difference

About

Releases

Packages

Contributors

Languages

Name		Name	Last commit message	Last commit date
app1		app1
features		features
pkg		pkg
utils		utils
.gitignore		.gitignore
README.md		README.md
pyproject.toml		pyproject.toml
test_app1_helpers.py		test_app1_helpers.py
test_base_features.py		test_base_features.py
test_base_helpers.py		test_base_helpers.py
test_pkg_features.py		test_pkg_features.py
uv.lock		uv.lock

Latest commit

History

Folders and files

Repository files navigation

Coverage.py Path Collapsing Bug with pytest-cov

The Bug

Repository Structure

Reproduction

Expected vs Actual

Investigation

Rule Generation Order

Configuration

Environment

Detailed Output Comparison

With pytest --cov (BUG - Missing File)

With coverage run (WORKS - All Files Present)

Key Difference

About

Resources

Stars

Watchers

Forks

Releases

Packages

Contributors

Languages

With `pytest --cov` (BUG - Missing File)

With `coverage run` (WORKS - All Files Present)