[BUG] XML generated from coverage.py `.coverage` doesn’t respect config

Describe the bug
In my project, I configured coverage.py using pyproject.toml to

• write all files into a test-files folder (idk if that’s relevant)
• skip coverage for if TYPE_CHECKING: blocks

The reported coverage reflects that (see table below), and when I run coverage xml, the test-files/coverage.xml file is also correct.

Name                                           Stmts   Miss  Cover
------------------------------------------------------------------
src/fast_array_utils/__init__.py                   4      0   100%
src/fast_array_utils/_patches.py                   2      0   100%
src/fast_array_utils/conv/__init__.py              3      0   100%
src/fast_array_utils/conv/_asarray.py             25      3    88%
src/fast_array_utils/conv/scipy/__init__.py        3      0   100%
src/fast_array_utils/conv/scipy/_to_dense.py      12      0   100%
src/fast_array_utils/stats/__init__.py             3      0   100%
src/fast_array_utils/stats/_sum.py                33      0   100%
src/fast_array_utils/types.py                     25      2    92%
------------------------------------------------------------------
TOTAL                                            110      5    95%

But when the codecov CLI runs coverage xml via its coveragepy plugin, the lines are not skipped and codecov reports a 82.87% coverage instead of the expected 95.45% (see codecov report for the linked run below)

See also Additional context below for a workaround I’m using

To Reproduce

1. set coverage.py’s report.exclude_also setting in a pyproject.toml to ignore some lines
2. collect coverage in .coverage file and run coverage xml
3. run codecov CLI’s upload (which will re-generate the XML)
4. compare the XML you created with the one codecov’s CLI created

Expected behavior
either

• coverage xml run from the codecov CLI uses the same config as when I run it, or
• when the file passed via --file already exists, have the codecov CLI skip running coverage xml

Regression
This probably worked using the old coverage PyPI package, but IDK.

Screenshots
NA

Product Area
coverage

Versions

• OS: linux
• Git Host: GitHub
• CI/CD: GitHub Actions
• Uploader: codecov-action@v5.3.1, codecov-cli@v10.1.0

Commit and CI link
scverse/fast-array-utils@13436951846

https://github.com/scverse/fast-array-utils/actions/runs/13436951846/job/37541444988

Additional context
I can manually work around this by generating the XML myself and then deleting the test-files/.coverage file, but this should be fixed on your side.

See https://github.com/scverse/fast-array-utils/pull/29 for the workaround, which results in the correct coverage of 95.45% being reported.