Exclude test source from coverage

[dmitriyrepin]

Closes#574

Remove the tests source code (tests/) from the codebase used for the mdio-python package code coverage calculations.

Notes:

• This PR reduces the package coverage codebase from 4,500 to 2,219 statements.
• The package code coverage might fall with this PR: removing almost 100%-covered tests code might reduce the figure for the overall package code coverage.

This PR:

• Adds pytest-cov to the dev dependency-groups in order to allow measuring code coverage with VS Code
• Excludes tests/ from the code coverage. (NOTE: setting source = ["src/mdio"] is not enough and omit needs to be used)

Before:

• NOX

Run nox --session=coverage
nox > Running session coverage
Installed Python 3.13.7 in 22ms
+ cpython-3.13.7-linux-x86_64-gnu (python3.13)
nox > Creating virtual environment (uv) using python3.13 in .nox/coverage
nox > uv export --only-dev --no-hashes -o .nox/coverage/tmp/requirements.txt
nox > uv pip install 'coverage[toml]' --constraint .nox/coverage/tmp/requirements.txt
nox > coverage combine
Combined data file .coverage.Mac-1758731966514.local.2022.XlBoVagx
Combined data file .coverage.runnervmbe3js.4092.XPJvtkDx
Combined data file .coverage.runnervmf4ws1.2191.XXnivYMx
Combined data file .coverage.runnervmf4ws1.2198.XUVVNufx
Skipping duplicate data .coverage.runnervmf4ws1.2342.XGtKsvMx
nox > coverage report
Name Stmts Miss Branch BrPart Cover Missing
------------------------------------------------------------------------------------------------------
src/mdio/__init__.py 10 2 0 0 80% 12-13
src/mdio/__main__.py 44 24 8 0 38% 40-47, 51-65, 72-73
...
src/mdio/segy/parsers.py 31 0 4 1 97% 68->77
src/mdio/segy/utilities.py 51 1 10 2 95% 77->80, 86
tests/__init__.py 0 0 0 0 100%
tests/conftest.py 41 9 10 4 71% 26, 40-41, 53, 60-62, 69-70
...
tests/unit/v1/test_dataset_serializer.py 154 7 10 1 95% 38, 250-255
------------------------------------------------------------------------------------------------------
TOTAL 4500 516 584 80 87%
nox > Session coverage was successful.

• VS Code

================================ tests coverage ================================
_______________ coverage: platform linux, python 3.13.5-final-0 ________________
Name Stmts Miss Branch BrPart Cover Missing
------------------------------------------------------------------------------------------------------
noxfile.py 132 132 40 0 0% 3-274
src/mdio/__init__.py 10 2 0 0 80% 12-13
src/mdio/__main__.py 44 24 8 0 38% 40-47, 51-65, 72-73
...
src/mdio/segy/parsers.py 31 0 4 1 97% 68->77
src/mdio/segy/utilities.py 51 1 10 2 95% 77->80, 86
tests/__init__.py 0 0 0 0 100%
tests/conftest.py 43 11 10 4 68% 26-28, 42-43, 55, 62-64, 71-72
...
tests/unit/v1/test_dataset_builder_helpers.py 15 0 0 0 100%
tests/unit/v1/test_dataset_serializer.py 154 7 10 1 95% 38, 250-255
------------------------------------------------------------------------------------------------------
TOTAL 4419 504 610 81 86%
Required test coverage of 85.0% reached. Total coverage: 86.14%
================== 178 passed, 12 skipped in 61.85s (0:01:01) ==================

After

• NOX

Run nox --session=coverage
nox > Running session coverage
Installed Python 3.13.7 in 22ms
+ cpython-3.13.7-linux-x86_64-gnu (python3.13)
nox > Creating virtual environment (uv) using python3.13 in .nox/coverage
nox > uv export --only-dev --no-hashes -o .nox/coverage/tmp/requirements.txt
nox > uv pip install 'coverage[toml]' --constraint .nox/coverage/tmp/requirements.txt
nox > coverage combine
Combined data file .coverage.runnervm3ublj.2233.XQoKNNhx
Skipping duplicate data .coverage.runnervm3ublj.2245.XQvtQbJx
Combined data file .coverage.runnervm3ublj.2246.XORxRNpx
Combined data file .coverage.runnervm747y6.1340.XzSeRsFx
Combined data file .coverage.sat12-bq152-da46c735-6d0d-4c5b-886a-f3b8cfcc49d0-DA37D04C399C.local.1492.XIXJhZVx
nox > coverage report
Name Stmts Miss Branch BrPart Cover Missing
-----------------------------------------------------------------------------------------------------
src/mdio/__init__.py 10 2 0 0 80% 12-13
src/mdio/__main__.py 44 24 8 0 38% 40-47, 51-65, 72-73
...
src/mdio/segy/utilities.py 51 1 10 2 95% 77->80, 86
-----------------------------------------------------------------------------------------------------
TOTAL 2219 416 426 63 79%
Coverage failure: total of 79 is less than fail-under=85
nox > Command coverage report failed with exit code 2
nox > Session coverage failed.
Error: Process completed with exit code 1.

• VS Code

================================ tests coverage ================================
_______________ coverage: platform linux, python 3.13.5-final-0 ________________
Name Stmts Miss Branch BrPart Cover Missing
-----------------------------------------------------------------------------------------------------
src/mdio/__init__.py 10 2 0 0 80% 12-13
src/mdio/__main__.py 44 24 8 0 38% 40-47, 51-65, 72-73
...
src/mdio/segy/parsers.py 31 0 4 1 97% 68->77
src/mdio/segy/utilities.py 51 1 10 2 95% 77->80, 86
-----------------------------------------------------------------------------------------------------
TOTAL 2099 270 414 64 84%
FAIL Required test coverage of 85.0% not reached. Total coverage: 84.08%
================== 178 passed, 12 skipped in 62.18s (0:01:02) ==================

[tasansal]

This is great but once we excluded the tests, the coverage falls below our threshold. Mainly because CLI code is not tested anymore since we need to re-implement it. Can you remove all the CLI code and CLI documentation for now. Then coverage should be fine. We can always get it back from the old tags if needed.