CI: Restore coverage collection after test reorganization by falloficarus22 · Pull Request #3006 · mesa/mesa

falloficarus22 · 2025-12-24T05:47:48Z

Summary

Improves coverage collection after test reorganization in #2994 by adopting pytest's native coverage integration and measuring all code including tests.

Problem

After moving tests into nested subdirectories, coverage.py reported 0% coverage. The root cause was a combination of:

Path resolution issues with nested test packages
Tests not being measured in coverage reports

Solution

This PR implements reviewer feedback to adopt coverage best practices:

Configuration Changes (`pyproject.toml`):

Added source = ["."]: Measures all code in the project directory
Kept source_pkgs = ["mesa"]: Specifically tracks the mesa package
Added relative_files = true: Fixes path resolution for nested directories
Removed omit = ["tests/*"]: Now measures test coverage (critical for verifying all tests run)
Added [tool.coverage.paths]: Maps installed package paths for accurate coverage reporting

CI Changes (`.github/workflows/build_lint.yml`):

Replaced coverage run -m pytest + coverage xml (2 commands from CI: Split off separate coverage job #3005)
With python -Im pytest -p pytest_cov --cov --cov-report=xml --cov-report=markdown-append:"${GITHUB_STEP_SUMMARY}" --cov-context=test tests/ (single command)
Benefits:
- -Im flag ensures testing installed package, not git checkout
- -p pytest_cov loads plugin early to avoid import issues
- --cov (no value) measures everything per coverage config
- Markdown report appears in GitHub Actions summary (better UX)
- --cov-context=test enables per-test coverage tracking

Advantages Over PR #3005

Single command instead of two separate commands
Measures test coverage to verify all tests actually run
More accurate with source = ["."] + source_pkgs combination
Tests installed package using python -Im flag

Testing

Local verification shows 84.75% total coverage (up from 0%)
All 379 tests pass
Test files now measured in coverage
Coverage XML generated successfully
Branch coverage: 74.91%

Coverage by Package

Core modules: 94-99%
Discrete space: 96.55%
Experimental: 94%+
Visualization: 65.87%

Credits

Implementation incorporates excellent feedback from @webknjaz

Replace pytest-cov plugin with direct coverage.py invocation to resolve 0% coverage reporting issue that occurred after moving tests into nested subdirectories. Changes: - Update CI workflow to use ============================= test session starts ============================== platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 rootdir: /root/mesa configfile: pyproject.toml plugins: mock-3.15.1, anyio-4.12.0, base-url-2.1.0, playwright-0.7.2, cov-7.0.0, ipywidgets-1.55.1 collected 379 items tests/discrete_space/test_discrete_space.py ............................ [ 7%] .. [ 7%] tests/discrete_space/test_grid.py ...................................... [ 17%] . [ 18%] tests/discrete_space/test_hexgrid_torus_validation.py . [ 18%] tests/examples/test_examples.py .......... [ 21%] tests/examples/test_examples_viz.py ......... [ 23%] tests/experimental/test_continuous_space.py ....... [ 25%] tests/experimental/test_devs.py ..... [ 26%] tests/experimental/test_mesa_signals.py ..... [ 27%] tests/experimental/test_meta_agents.py ............... [ 31%] tests/test_agent.py ...................... [ 37%] tests/test_batch_run.py ........ [ 39%] tests/test_datacollector.py ............... [ 43%] tests/test_import_namespace.py . [ 44%] tests/test_lifespan.py .. [ 44%] tests/test_mesa_logging.py .. [ 45%] tests/test_model.py ........... [ 48%] tests/test_space.py s................................................... [ 61%] .............................................. [ 73%] tests/visualization/test_backends.py .............. [ 77%] tests/visualization/test_components_matplotlib.py ....... [ 79%] tests/visualization/test_portrayal_components.py ............. [ 82%] tests/visualization/test_solara_viz.py ......... [ 85%] tests/visualization/test_solara_viz_updated.py .......... [ 87%] tests/visualization/test_space_drawer.py .............................. [ 95%] tests/visualization/test_space_renderer.py ................ [100%] =============================== warnings summary =============================== tests/visualization/test_space_renderer.py::test_property_layer_style_instance /root/mesa/tests/visualization/test_space_renderer.py:200: PendingDeprecationWarning: Passing propertylayer_portrayal to draw_propertylayer() is deprecated. Use setup_propertylayer(propertylayer_portrayal) before calling draw_propertylayer(). sr.draw_propertylayer(style) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================================ tests coverage ================================ _______________ coverage: platform linux, python 3.13.11-final-0 _______________ Name Stmts Miss Branch BrPart Cover ------------------------------------------------------------------------------------------------- mesa/__init__.py 14 0 0 0 100% mesa/agent.py 194 1 78 3 99% mesa/batchrunner.py 88 2 36 4 95% mesa/datacollection.py 157 4 78 4 97% mesa/discrete_space/__init__.py 9 0 0 0 100% mesa/discrete_space/cell.py 82 1 18 0 99% mesa/discrete_space/cell_agent.py 52 0 12 0 100% mesa/discrete_space/cell_collection.py 56 3 18 1 95% mesa/discrete_space/discrete_space.py 57 3 4 1 93% mesa/discrete_space/grid.py 125 6 48 5 94% mesa/discrete_space/network.py 29 0 6 0 100% mesa/discrete_space/property_layer.py 141 11 44 3 89% mesa/discrete_space/voronoi.py 144 0 46 1 99% mesa/examples/__init__.py 11 0 0 0 100% mesa/examples/advanced/__init__.py 0 0 0 0 100% mesa/examples/advanced/alliance_formation/agents.py 8 0 0 0 100% mesa/examples/advanced/alliance_formation/app.py 23 10 0 0 57% mesa/examples/advanced/alliance_formation/model.py 74 2 34 4 94% mesa/examples/advanced/epstein_civil_violence/__init__.py 0 0 0 0 100% mesa/examples/advanced/epstein_civil_violence/agents.py 68 0 18 1 99% mesa/examples/advanced/epstein_civil_violence/app.py 28 5 6 2 79% mesa/examples/advanced/epstein_civil_violence/model.py 48 9 20 5 76% mesa/examples/advanced/pd_grid/__init__.py 0 0 0 0 100% mesa/examples/advanced/pd_grid/agents.py 28 3 6 3 82% mesa/examples/advanced/pd_grid/app.py 11 0 0 0 100% mesa/examples/advanced/pd_grid/model.py 31 9 10 3 61% mesa/examples/advanced/sugarscape_g1mt/__init__.py 0 0 0 0 100% mesa/examples/advanced/sugarscape_g1mt/agents.py 101 3 22 0 94% mesa/examples/advanced/sugarscape_g1mt/app.py 20 2 2 0 91% mesa/examples/advanced/sugarscape_g1mt/model.py 52 5 10 2 85% mesa/examples/advanced/wolf_sheep/__init__.py 0 0 0 0 100% mesa/examples/advanced/wolf_sheep/agents.py 60 1 14 1 97% mesa/examples/advanced/wolf_sheep/app.py 34 5 10 2 84% mesa/examples/advanced/wolf_sheep/model.py 34 0 6 2 95% mesa/examples/basic/__init__.py 0 0 0 0 100% mesa/examples/basic/boid_flockers/__init__.py 0 0 0 0 100% mesa/examples/basic/boid_flockers/agents.py 28 0 2 0 100% mesa/examples/basic/boid_flockers/app.py 22 1 4 1 92% mesa/examples/basic/boid_flockers/model.py 34 2 4 1 92% mesa/examples/basic/boltzmann_wealth_model/__init__.py 0 0 0 0 100% mesa/examples/basic/boltzmann_wealth_model/agents.py 18 0 4 0 100% mesa/examples/basic/boltzmann_wealth_model/app.py 19 2 0 0 89% mesa/examples/basic/boltzmann_wealth_model/model.py 22 0 0 0 100% mesa/examples/basic/boltzmann_wealth_model/st_app.py 47 47 10 0 0% mesa/examples/basic/conways_game_of_life/__init__.py 0 0 0 0 100% mesa/examples/basic/conways_game_of_life/agents.py 31 2 6 0 95% mesa/examples/basic/conways_game_of_life/app.py 16 3 0 0 81% mesa/examples/basic/conways_game_of_life/model.py 13 0 2 0 100% mesa/examples/basic/conways_game_of_life/st_app.py 40 40 10 0 0% mesa/examples/basic/schelling/__init__.py 0 0 0 0 100% mesa/examples/basic/schelling/agents.py 22 0 6 0 100% mesa/examples/basic/schelling/app.py 24 1 6 0 97% mesa/examples/basic/schelling/model.py 24 0 4 0 100% mesa/examples/basic/virus_on_network/__init__.py 0 0 0 0 100% mesa/examples/basic/virus_on_network/agents.py 34 0 12 0 100% mesa/examples/basic/virus_on_network/app.py 23 6 0 0 74% mesa/examples/basic/virus_on_network/model.py 36 0 2 0 100% mesa/experimental/__init__.py 2 0 0 0 100% mesa/experimental/continuous_space/__init__.py 3 0 0 0 100% mesa/experimental/continuous_space/continuous_space.py 112 4 14 1 96% mesa/experimental/continuous_space/continuous_space_agents.py 45 0 4 0 100% mesa/experimental/devs/__init__.py 3 0 0 0 100% mesa/experimental/devs/eventlist.py 78 2 20 1 97% mesa/experimental/devs/simulator.py 112 6 28 4 93% mesa/experimental/mesa_signals/__init__.py 3 0 0 0 100% mesa/experimental/mesa_signals/mesa_signal.py 190 10 66 10 92% mesa/experimental/mesa_signals/observable_collections.py 41 2 0 0 95% mesa/experimental/mesa_signals/signals_util.py 19 2 2 0 90% mesa/experimental/meta_agents/__init__.py 2 0 0 0 100% mesa/experimental/meta_agents/meta_agent.py 128 3 60 6 95% mesa/mesa_logging.py 82 2 14 1 95% mesa/model.py 97 5 16 2 94% mesa/space.py 584 40 222 17 92% mesa/visualization/__init__.py 8 0 0 0 100% mesa/visualization/backends/__init__.py 3 0 0 0 100% mesa/visualization/backends/abstract_renderer.py 29 1 4 1 94% mesa/visualization/backends/altair_backend.py 139 11 40 8 89% mesa/visualization/backends/matplotlib_backend.py 186 20 68 9 87% mesa/visualization/command_console.py 191 155 48 0 15% mesa/visualization/components/__init__.py 18 6 8 1 58% mesa/visualization/components/altair_components.py 190 82 66 11 55% mesa/visualization/components/matplotlib_components.py 59 13 18 4 73% mesa/visualization/components/portrayal_components.py 37 2 12 2 92% mesa/visualization/mpl_space_drawing.py 346 83 122 31 72% mesa/visualization/solara_viz.py 378 187 160 21 48% mesa/visualization/space_drawers.py 291 7 74 10 95% mesa/visualization/space_renderer.py 180 50 74 12 66% mesa/visualization/user_param.py 23 2 4 1 89% mesa/visualization/utils.py 4 1 0 0 75% ------------------------------------------------------------------------------------------------- TOTAL 5815 885 1762 202 82% ============= 378 passed, 1 skipped, 1 warning in 98.00s (0:01:38) ============= with - Change pyproject.toml to use instead of - Add to coverage configuration The pytest-cov plugin had conflicts with the new nested test package structure introduced in PR mesa#2994. Using coverage.py directly with the --cov-context flag resolves the tracing issues.

Nithin9585 · 2025-12-24T07:03:08Z

Nice fix @falloficarus22! Small note: original CI used coverage run -m pytest, not pytest-cov. So root cause was path resolution (fixed by relative_files = true), not a plugin conflict. Works great!

falloficarus22 · 2025-12-24T08:55:16Z

Nice fix @falloficarus22! Small note: original CI used coverage run -m pytest, not pytest-cov. So root cause was path resolution (fixed by relative_files = true), not a plugin conflict. Works great!

Yeah but this is still a workaround, works until maintainers find the fix for the root cause.

EwoutH · 2025-12-24T08:59:08Z

Thanks for the PR. What are the main advantages of this workaround over the other one?

falloficarus22 · 2025-12-24T09:30:28Z

Thanks for the PR. What are the main advantages of this workaround over the other one?

The key advantage is this workaround will do the same thing in a single command rather than 2 seperate commands.
Also added --cov-context=test to enable per-test coverage tracking which might help in debugging.
I think it may be better to use the standard pytest command rather than directly using coverage.py.

webknjaz

Here's a few notes from me.

webknjaz · 2025-12-25T08:44:07Z

pyproject.toml

 omit = ["tests/*"]

+[tool.coverage.report]
+omit = ["tests/*"]
+


Best not to skip collecting coverage of the test modules, nor hide it from reports.

Suggested change

omit = ["tests/*"]

[tool.coverage.report]

omit = ["tests/*"]

https://nedbatchelder.com/blog/202008/you_should_include_your_tests_in_coverage.html / https://nedbatchelder.com/blog/201908/dont_omit_tests_from_coverage.html / https://nedbatchelder.com/blog/201106/running_coverage_on_your_tests.html

In fact, it'd be a good idea to include an additional reported check in the Codecov config, requiring 100% code coverage on the test folder: https://github.com/ansible/awx-plugins/blob/274b32a/.codecov.yml#L33-L38.

One might argue that this is out of the scope of this PR and request a follow-up PR but can you prove that all the tests actually run in CI w/o that?

webknjaz · 2025-12-25T08:56:03Z

.github/workflows/build_lint.yml

-      - run: |
-          coverage run -m pytest tests/
-          coverage xml
+      - run: pytest --cov=mesa --cov-report=xml --cov-context=test tests/


Use --cov w/o a value to enable the plugin but not limit what's measured. It's actually a bit messy since it corresponds to source in the coveragepy config and there's no corresponding flag for source_pkgs, which means it probably refereces a folder and not an importable. Plus, as I mentioned elsewhere, test modules should really be measured too.

It's a good idea to also add -p pytest_cov which makes pytest load the plugin earlier than the standard entry point-based auto-discovery mechanism.

Finally, I'm adding --cov-report=markdown-append:"${GITHUB_STEP_SUMMARY}" since it's a nice touch to have this integrated in GHA:

Suggested change

- run: pytest --cov=mesa --cov-report=xml --cov-context=test tests/

- run: pytest -p pytest_cov --cov --cov-report=xml --cov-report=markdown-append:"${GITHUB_STEP_SUMMARY}" --cov-context=test tests/

Follow-up PR action items:

Move tests/ into a dedicated testpaths setting in .pytest.toml

Move --cov and --cov-context=test into addopts in the pytest config too — these would be useful to be auto-added for both local contributors and in CI

Keep --cov-report=xml and --cov-report=markdown-append:"${GITHUB_STEP_SUMMARY}" in CI since locally contributors don't need those reports

Configure html coverage explicitly so that the contributors could pass --cov-report=html locally and have everything show up nicely by default: https://github.com/ansible/awx-plugins/blob/274b32a/.coveragerc#L1-L3

Look into replacing pytest with python -Im pytest (-I disables auto-adding the current working directory to $PYTHONPATH/sys.path so you'd be sure you're testing what's in site-packages/ and not the Git checkout copy)

webknjaz · 2025-12-25T08:58:01Z

pyproject.toml

You may want to play with hiding less important things in all reports: https://github.com/ansible/awx-plugins/blob/274b32a/.coveragerc#L17-L19. But it's best to do so combined with setting up HTML as I mentioned in another comment — this one should show everything because it's to be used interactively.

pyproject.toml

webknjaz · 2025-12-25T09:04:51Z

pyproject.toml

When the copy of the library in site-packages is tested correctly, you might need to set up mappings in [paths]: https://github.com/ansible/awx-plugins/blob/274b32a/.coveragerc#L5-L12.

webknjaz · 2025-12-25T09:07:53Z

Also added --cov-context=test to enable per-test coverage tracking which might help in debugging.

Note that this is only displayed in the HTML report and Codecov doesn't know how to show such contexts (it only shows own platform-specific flags you pass when uploading).

I think it may be better to use the standard pytest command rather than directly using coverage.py.

This is often considered controversial but I tend to like this way too.

DipayanDasgupta · 2025-12-25T11:37:01Z

@falloficarus22 I was looking into the root cause based on webknjaz's feedback in the issue. I verified locally that we can solve this without a workaround by updating pyproject.toml to handle the path resolution correctly.

If you apply these changes, it should fix the coverage reporting comprehensively:

pyproject.toml
[tool.coverage.run]
source_pkgs = ["mesa"]  # Targets the package specifically
branch = true
relative_files = true   # Fixes the path mapping from subdirectories
# omit = ["tests/*"]    # Removed to ensure tests are measured
And then in the workflow, simply use:
pytest -p pytest_cov --cov --cov-report=xml --cov-report=markdown-append:"${GITHUB_STEP_SUMMARY}" --cov-context=test tests/

@webknjaz

- Remove omit = [tests/*] to measure test coverage (as per @webknjaz) - Add source = [.] alongside source_pkgs for complete coverage - Update CI to use -p pytest_cov for early plugin loading - Add markdown coverage report to GitHub Actions summary - Use --cov without value to measure all code This ensures all tests are actually running and provides better visibility into coverage metrics.

falloficarus22 · 2025-12-25T13:10:19Z

@webknjaz Thanks for the detailed review and suggestions. As I have mentioned earlier this is supposed to be a temporary workaround (an improvement over #3004). I'll work on moving tests/ into dedicated test paths but doing so is out of scope for this PR. I guess there will be follow-up PRs coming up by me.

webknjaz · 2025-12-25T15:06:32Z

@falloficarus22 almost. You keep adding an empty report section which is not necessary w/o any settings in it.

I usually recommend accepting suggestions via GH UI – it is likely that you'll get them committed exactly as they were meant to be, and the added bonus is that it's easier to credit people this way. Otherwise, trying to reproduce that locally is rather manual and thus error-prone: https://hynek.me/til/easier-crediting-contributors-github/.

With this, you'd click commit in-browser and then pull the changes locally. Afterwards, you'd be able to make corrections/rebasing/cleanups as needed.

pyproject.toml

webknjaz · 2025-12-25T19:05:07Z

I thought that https://github.com/mesa/mesa/pull/3006/files#r2646764846 can wait but now I realized that it must be included into this PR.

Look at https://github.com/mesa/mesa/actions/runs/20505498180?pr=3006#summary-58919356331 — it lists both relative paths (with 0% for anything starting with mesa/) and absolute coverage (with something actually measured under ..../site-packages/mesa/). And because the modules from both locations are listed, that 0% ends up contributing to low overall coverage number.

You can take https://github.com/ansible/awx-plugins/blob/274b32a/.coveragerc#L5-L12 as is and convert it from INI into TOML, integrate that into pyproject.toml and this will fix the problem. You should end up with all paths being relative and CWD merged with site-packages.

As a side note, I noticed that some test modules don't have 100% coverage. This means that there's dead code in tests that's never exercised (but people may think that it's being run in CI, which would be misleading). This is a good candidate for figuring out in another follow-up PR — maybe, some code can be deleted, otherwise some of it might need to be marked with nocover pragma comments.

.github/workflows/build_lint.yml

Co-authored-by: 🇺🇦 Sviatoslav Sydorenko (Святослав Сидоренко) <[email protected]>

webknjaz

This should address the last missing piece: #3006 (comment) / https://github.com/mesa/mesa/pull/3006/files#r2646764846

pyproject.toml

falloficarus22 · 2025-12-26T17:18:06Z

coverage build has failed but has nothing to do with this PR. The problem is in tests/examples/test_examples_viz.py and can be fixed in another PR.

webknjaz · 2025-12-26T18:04:24Z

@falloficarus22 if that's the case, could you please close and then reopen the PR right away? This will trigger a new CI run. Or ask the maintainers to restart that one job. I'd like to see it post the coverage report on the CI run web page (that job Markdown summary as a table). The diff looks good but it's a good idea to double-check that the mapping works correctly before finally green-lighting the merge.

falloficarus22 · 2025-12-27T03:45:15Z

Weird, but I think the PR is now good enough to be merged.

webknjaz

Not weird, really. When the tests themselves are flaky, this is expected. They can usually be make more reliable or the easiest hack would be adding a pytest plugin for auto-restarting the unstable tests.

Anyway.. I see that the report looks like what I'd expect (within the context I learned): https://github.com/mesa/mesa/actions/runs/20526264823#summary-58974397795.

You're good to go now. No more notes from me.

EwoutH · 2025-12-27T10:25:21Z

Thanks for both your effort!

@falloficarus22 could you update the PR description to be fully up to date with the current diff and everything we’ve learned? I would like to have it as a reference for if we ever need to revisit it. Focus on helping us understand what every option does and how they interact.

falloficarus22 · 2025-12-27T11:00:49Z

@EwoutH updated the PR description. Please tell me if you would like to make any changes in this PR.

webknjaz · 2025-12-27T11:22:20Z

-Im flag ensures testing installed package, not git checkout

This is partially accurate. -m is the flag that invokes the target module through the runpy interface (pytest.__main__), but it also adds . (CWD) to the import paths. And -I counters that bit of the side effect, making the interpreter ignore any PYTHON* env vars, including PYTHONPATH which influences sys.path.

pytest itself may also manipulate sys.path internally and this ability is not suppressed by -I — the relevant behavior usually depends on the presence of the __init__.py modules in the test dirs (this also affects whether it's possible to have relative imports in tests or absolute ones).

EwoutH

Great, thanks!

falloficarus22 added 2 commits December 24, 2025 05:34

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Coverage reporting 0% after test reorganization #3004

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Merge branch 'mesa:main' into fix-cov-coverage-collection

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ci: restore coverage reporting and adopt best practices #3013

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Update .github/workflows/build_lint.yml

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Co-authored-by: 🇺🇦 Sviatoslav Sydorenko (Святослав Сидоренко) <[email protected]>

Update pyproject.toml

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Co-authored-by: 🇺🇦 Sviatoslav Sydorenko (Святослав Сидоренко) <[email protected]>

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Merge branch 'main' into fix-cov-coverage-collection

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EwoutH changed the title ~~Restore coverage collection after test reorganization~~ CI: Restore coverage collection after test reorganization Dec 27, 2025

EwoutH merged commit 5ffee4a into mesa:main Dec 27, 2025
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falloficarus22 deleted the fix-cov-coverage-collection branch December 28, 2025 13:29

	- run: pytest --cov=mesa --cov-report=xml --cov-context=test tests/
	- run: pytest -p pytest_cov --cov --cov-report=xml --cov-report=markdown-append:"${GITHUB_STEP_SUMMARY}" --cov-context=test tests/

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Summary

Problem

Solution

Configuration Changes (pyproject.toml):

CI Changes (.github/workflows/build_lint.yml):

Advantages Over PR #3005

Testing

Coverage by Package

Credits

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falloficarus22 commented Dec 24, 2025 •

edited

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Configuration Changes (`pyproject.toml`):

CI Changes (`.github/workflows/build_lint.yml`):

webknjaz commented Dec 26, 2025 •

edited

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