Code cleanup: Apply Ruff for formatting and linting by sy-cui · Pull Request #173 · SophT-Team/SophT

sy-cui · 2026-04-01T00:17:35Z

Summary

The goal of this PR is to use Ruff to reformat the code. This includes:

Reformat the code
Converge on a reasonable set of lint rules that the code should comply to

Several fixes related to this change:

Circular import problems in sopht/simulator
isort is handled natively by ruff Add isort for sorting imports #83

Work in progress

The following compiles a list of rules listed by Ruff that sopht has yet to comply to. This PR may not resolve all of them

Additional notes

Lint checks for all docstrings are disabled at this moment. In the future, it should be enabled at least for the sopht package (we can be lenient with examples and tests). This should be resolved together with Documentation for SophT #115

…s usually handled directly in elasticapp itself

…ed to be built as packages

Copilot

Pull request overview

This PR applies Ruff formatting/linting across the repository and includes a handful of small refactors needed to satisfy the chosen Ruff ruleset (notably around imports, logging, test determinism, and shell-out usage).

Changes:

Standardize formatting/linting via Ruff (including import sorting) and add per-folder Ruff configs for tests/ and examples/.
Refactor several modules/tests for determinism and safer operations (e.g., pytest RNG fixture, avoid os.system, structured logging).
Restructure/clarify public exports via __all__ in key packages and adjust some simulator factory entrypoints.

Reviewed changes

Copilot reviewed 171 out of 173 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
uv.lock	Lockfile updated for new deps (e.g., `ffmpeg-python`, `future`, `typing-extensions`).
pyproject.toml	Adds deps (`ffmpeg-python`, `typing-extensions`), expands Ruff to `select=["ALL"]`, and adjusts line length/excludes.
justfile	Adds `format`/`check` tasks and makes pytest invocation more verbose.
README.md	Adds MacOS-specific pystencils/OpenMP troubleshooting section.
.gitignore	Ignores `.vscode/`.
.coveragerc	Adjusts omit list (no longer omits `rod_viz.py`).
tests/ruff.toml	Ruff config for tests (extends root; ignores docstyle/namespace/assert rules).
tests/conftest.py	Adds deterministic `rng` fixture for tests.
tests/test_utils/test_restart.py	Uses helper cleanup, f-strings, and formatting updates.
tests/test_utils/test_precision.py	Formatting-only update to `pytest.raises`.
tests/test_simulator/test_immersed_body/test_immersed_body_forcing_grid.py	Strengthens logging assertions by checking emitted logger records.
tests/test_simulator/test_immersed_body/rigid_body/test_derived_rigid_bodies.py	Avoids mutable default args; asserts warnings via log records; formatting updates.
tests/test_simulator/test_immersed_body/cosserat_rod/test_cosserat_rod_flow_interaction.py	Import order formatting.
tests/test_simulator/test_flow/test_passive_transport_flow_simulators.py	Uses `rng` fixture instead of global `np.random`; minor formatting.
tests/test_simulator/test_flow/test_flow_simulators_3d.py	Switches to `create_unbounded_flow_simulator_3d`, adds `rng` usage, and updates `cfl` kwarg.
tests/test_simulator/test_flow/test_flow_simulators_2d.py	Switches to `create_unbounded_flow_simulator_2d` and adds `rng` usage.
tests/test_numeric/test_immersed_boundary_ops/test_brinkmann_boundary_forcing.py	Uses `rng` fixture; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_3d/test_vorticity_stretching_flux_3d.py	Uses injected RNG; reshapes random generation; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_3d/test_update_vorticity_from_velocity_forcing_3d.py	Uses injected RNG; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_3d/test_laplacian_filter_3d.py	Uses injected RNG; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_3d/test_elementwise_ops_3d.py	Import ordering and formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_3d/test_divergence_3d.py	Uses injected RNG; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_3d/test_diffusion_timestep_3d.py	Uses injected RNG; small refactors/formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_3d/test_diffusion_flux_3d.py	Uses injected RNG; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_3d/test_curl_3d.py	Uses injected RNG; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_3d/test_char_func_from_level_set_3d.py	Uses injected RNG; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_3d/test_brinkmann_penalise_3d.py	Uses injected RNG; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_2d/test_update_vorticity_from_velocity_forcing_2d.py	Uses injected RNG; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_2d/test_penalise_field_boundary_2d.py	Uses injected RNG; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_2d/test_outplane_field_curl_2d.py	Uses injected RNG; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_2d/test_inplane_field_curl_2d.py	Uses injected RNG; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_2d/test_elementwise_ops_2d.py	Import ordering and formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_2d/test_diffusion_timestep_2d.py	Uses injected RNG; refactors helper solution signature; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_2d/test_diffusion_flux_2d.py	Uses injected RNG; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_2d/test_char_func_from_level_set_2d.py	Uses injected RNG; refactors solution signature; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_2d/test_advection_timestep_2d.py	Uses injected RNG; refactors solution signature; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_stencil_ops_2d/test_advection_flux_2d.py	Uses injected RNG; refactors solution signature; formatting cleanup.
tests/test_numeric/test_eulerian_grid_ops/test_poisson_solver_3d/test_fft_kernel_3d.py	Uses injected RNG; import cleanup and formatting.
tests/test_numeric/test_eulerian_grid_ops/test_poisson_solver_2d/test_fft_kernel_2d.py	Uses injected RNG; type annotations; formatting cleanup.
sopht/init.py	Adds `NullHandler` to avoid “No handler found” warnings.
sopht/utils/restart_sim.py	Uses `pathlib` and module logger; avoids `print`; improves exception messages.
sopht/utils/pyst_kernel_config.py	Improves error messages/types; minor signature typing; formatting cleanup.
sopht/utils/precision.py	Simplifies control flow; improves error message handling; formatting cleanup.
sopht/utils/post_process.py	Replaces shelling-out with `ffmpeg-python` + `pathlib` cleanup/moves.
sopht/utils/lab_cmap.py	Import order + small return simplification.
sopht/utils/field.py	Normalizes TODO comment formatting.
sopht/utils/init.py	Adds `__all__` and reorganizes exports.
sopht/simulator/immersed_body/rigid_body/rigid_body_flow_interaction.py	Uses explicit imports, typing updates, and `override`.
sopht/simulator/immersed_body/rigid_body/derived_rigid_bodies.py	Logging cleanup, `override`, `super()` modernization, and message formatting.
sopht/simulator/immersed_body/rigid_body/init.py	Removes re-exports; replaces with module docstring.
sopht/simulator/immersed_body/immersed_body_forcing_grid.py	Uses module logger; updates warning formatting.
sopht/simulator/immersed_body/immersed_body_flow_interaction.py	Logging restructuring; typing updates; minor return simplification.
sopht/simulator/immersed_body/flow_forces.py	Import refactor and `override` usage; formatting cleanup.
sopht/simulator/immersed_body/cosserat_rod/cosserat_rod_flow_interaction.py	Uses explicit imports, typing updates, and `override`.
sopht/simulator/immersed_body/cosserat_rod/init.py	Removes re-exports; replaces with module docstring.
sopht/simulator/immersed_body/cosserat_rod_cpp/cosserat_rod_cpp_forcing_grids.py	Removes unused/dead module content.
sopht/simulator/immersed_body/cosserat_rod_cpp/cosserat_rod_cpp_flow_interaction.py	Removes unused/dead module content.
sopht/simulator/immersed_body/cosserat_rod_cpp/init.py	Removes re-exports for deleted CPP modules.
sopht/simulator/immersed_body/init.py	Replaces star exports with explicit exports and `__all__`.
sopht/simulator/flow/flow_simulators_3d.py	Renames factory to `create_unbounded_flow_simulator_3d` and switches `CFL`→`cfl`.
sopht/simulator/flow/flow_simulators_2d.py	Renames factory to `create_unbounded_flow_simulator_2d` and switches `CFL`→`cfl`.
sopht/simulator/flow/init.py	Reworks exports and adds `__all__`.
sopht/simulator/init.py	Replaces star exports with explicit exports and `__all__`.
sopht/numeric/immersed_boundary_ops/VirtualBoundaryForcing.py	Replaces `assert` with `ValueError`; formatting cleanup.
sopht/numeric/immersed_boundary_ops/experimental/BrinkmannBoundaryForcing.py	Replaces `assert` with `ValueError`; formatting cleanup.
sopht/numeric/immersed_boundary_ops/experimental/init.py	Adds module docstring.
sopht/numeric/immersed_boundary_ops/init.py	Adds explicit `__all__` and export ordering.
sopht/numeric/eulerian_grid_ops/stencil_ops_3d/vorticity_stretching_timestep_3d.py	Imports cleanup + typing (`collections.abc.Callable`) + formatting.
sopht/numeric/eulerian_grid_ops/stencil_ops_3d/vorticity_stretching_flux_3d.py	Imports cleanup + formatting improvements.
sopht/numeric/eulerian_grid_ops/stencil_ops_3d/divergence_3d.py	Imports cleanup + formatting improvements.
sopht/numeric/eulerian_grid_ops/stencil_ops_3d/diffusion_timestep_3d.py	Imports cleanup + formatting improvements.
sopht/numeric/eulerian_grid_ops/stencil_ops_3d/diffusion_flux_3d.py	Imports cleanup + improved error message handling.
sopht/numeric/eulerian_grid_ops/stencil_ops_3d/curl_3d.py	Imports cleanup + formatting improvements.
sopht/numeric/eulerian_grid_ops/stencil_ops_3d/char_func_from_level_set_3d.py	Simplifies to direct `return` of compiled kernel; imports cleanup.
sopht/numeric/eulerian_grid_ops/stencil_ops_3d/brinkmann_penalise_3d.py	Imports cleanup + improved error message handling.
sopht/numeric/eulerian_grid_ops/stencil_ops_3d/advection_timestep_3d.py	Imports cleanup + improved error message handling.
sopht/numeric/eulerian_grid_ops/stencil_ops_3d/advection_flux_3d.py	Imports cleanup + comment formatting updates.
sopht/numeric/eulerian_grid_ops/stencil_ops_3d/init.py	Removes re-export surface (keeps docstring only).
sopht/numeric/eulerian_grid_ops/stencil_ops_2d/update_vorticity_from_velocity_forcing_2d.py	Imports cleanup + TODO comment normalization.
sopht/numeric/eulerian_grid_ops/stencil_ops_2d/penalise_field_boundary_2d.py	Replaces `assert` with `ValueError`; imports/formatting cleanup.
sopht/numeric/eulerian_grid_ops/stencil_ops_2d/outplane_field_curl_2d.py	Imports cleanup + TODO comment normalization.
sopht/numeric/eulerian_grid_ops/stencil_ops_2d/inplane_field_curl_2d.py	Minor signature formatting and kernel expression formatting.
sopht/numeric/eulerian_grid_ops/stencil_ops_2d/diffusion_timestep_2d.py	Imports cleanup + formatting improvements.
sopht/numeric/eulerian_grid_ops/stencil_ops_2d/diffusion_flux_2d.py	Imports cleanup + formatting improvements.
sopht/numeric/eulerian_grid_ops/stencil_ops_2d/char_func_from_level_set_2d.py	Simplifies to direct `return` of compiled kernel; imports cleanup.
sopht/numeric/eulerian_grid_ops/stencil_ops_2d/brinkmann_penalise_2d.py	Improved error message handling; formatting cleanup.
sopht/numeric/eulerian_grid_ops/stencil_ops_2d/advection_timestep_2d.py	Imports cleanup + formatting improvements.
sopht/numeric/eulerian_grid_ops/stencil_ops_2d/advection_flux_2d.py	Imports cleanup + TODO comment normalization.
sopht/numeric/eulerian_grid_ops/stencil_ops_2d/init.py	Removes re-export surface (keeps docstring only).
sopht/numeric/eulerian_grid_ops/poisson_solver_3d/UnboundedPoissonSolverPYFFTW3D.py	Formatting cleanup + TODO comment normalization.
sopht/numeric/eulerian_grid_ops/poisson_solver_3d/scipy_fft_3d.py	Formatting cleanup.
sopht/numeric/eulerian_grid_ops/poisson_solver_3d/FFTPyFFTW3D.py	Formatting cleanup.
sopht/numeric/eulerian_grid_ops/poisson_solver_3d/FastDiagPoissonSolver3D.py	Typing import cleanup + formatting improvements.
sopht/numeric/eulerian_grid_ops/poisson_solver_3d/init.py	Removes re-export surface (keeps docstring only).
sopht/numeric/eulerian_grid_ops/poisson_solver_2d/UnboundedPoissonSolverPYFFTW2D.py	Formatting cleanup + TODO comment normalization.
sopht/numeric/eulerian_grid_ops/poisson_solver_2d/scipy_fft_2d.py	Formatting cleanup.
sopht/numeric/eulerian_grid_ops/poisson_solver_2d/FFTPyFFTW2D.py	Formatting cleanup.
sopht/numeric/eulerian_grid_ops/poisson_solver_2d/FastDiagPoissonSolver2D.py	Typing import cleanup + formatting improvements.
sopht/numeric/eulerian_grid_ops/poisson_solver_2d/init.py	Removes re-export surface (keeps docstring only).
scripts/cluster/submit.py	Formatting-only whitespace tweak.
examples/ruff.toml	Ruff config for examples (extends root; ignores docstyle/namespace/print rules).
examples/3d_examples/PointSourceAdvectAndDiffuseCase/point_source_helpers.py	Formatting-only cleanup.
examples/3d_examples/PointSourceAdvectAndDiffuseCase/point_source_advection_diffusion.py	Uses f-strings for filenames/progress; import ordering.
examples/3d_examples/OctopusSwimming/oscillation_activation_functions.py	Signature cleanup (drops unused `system` arg) + formatting.
examples/3d_examples/OctopusSwimming/octopus_initializer_functions.py	Formatting-only cleanup.
examples/3d_examples/OctopusArmCase3D/arm_functions_3d.py	Signature cleanup (drops unused `system` arg) + formatting.
examples/3d_examples/HillSphericalVortexCase/hill_sphere_vortex_helpers.py	Formatting cleanup + minor variable unused cleanup.
examples/3d_examples/HillSphericalVortexCase/hill_sphere_vortex_case.py	Adds `noqa` for private member access; formatting cleanup.
examples/3d_examples/FlowThroughPipeCase/flow_through_circular_pipe_case.py	Formatting cleanup + f-string filenames/progress.
examples/3d_examples/FlowPastSphereCase/flow_past_sphere_case.py	Formatting cleanup + f-string filenames/progress.
examples/3d_examples/FishSwimmingCase/elastic_fish_utils/fish_geometry.py	Replaces `assert` with explicit `ValueError`; formatting cleanup.
examples/3d_examples/FishSwimmingCase/elastic_fish_utils/fish_connection.py	`super()` modernization + `override` usage + formatting.
examples/3d_examples/FishSwimmingCase/elastic_fish_utils/carling_fish_bc.py	Import order cleanup.
examples/2d_examples/OctopusArmCase/run_coupling_tapered_arm_and_cylinder.py	Formatting cleanup + f-string filenames/progress; drops unused vars.
examples/2d_examples/OctopusArmCase/arm_functions_2d.py	Signature cleanup (drops unused `system` arg) + formatting.
examples/2d_examples/LidDrivenCavityCase/lid_driven_cavity_grid.py	Formatting cleanup; simplifies assignments; removes redundant `pass` statements.
examples/2d_examples/LidDrivenCavityCase/lid_driven_cavity_case.py	Formatting cleanup + f-string filenames/progress.
examples/2d_examples/LambOseenVortexCase/lamb_oseen_vortex.py	Formatting cleanup + f-string filenames/progress.
examples/2d_examples/LambOseenVortexCase/lamb_oseen_helpers.py	Formatting cleanup.
examples/2d_examples/ImmersedFlexiblePendulumCases/immersed_flexible_pendulum_with_rigid_cylinder.py	Formatting cleanup + f-string filenames/progress.
examples/2d_examples/ImmersedContinuumSnakeCase/immersed_continuum_snake.py	Formatting cleanup + minor step loop simplification.
examples/2d_examples/FlowPastRodCase/flow_past_rod.py	Formatting cleanup + f-string filenames/progress.
examples/2d_examples/FlowPastCylinderCase/flow_past_cylinder.py	Import order cleanup + f-string filenames/progress.
examples/2d_examples/FishSwimmingCase/elastic_fish_utils/fish_geometry_2d.py	Replaces `assert` with explicit `ValueError`; formatting cleanup.
examples/2d_examples/FishSwimmingCase/elastic_fish_utils/fish_connection_2d.py	`super()` modernization + `override` usage + formatting.
examples/2d_examples/FishSwimmingCase/elastic_fish_utils/carling_fish_bc_2d.py	Import order cleanup.
examples/2d_examples/FishSwimmingCase/elastic_fish_swimming_case_2d.py	Switches to new 2D flow factory; formatting cleanup + f-string filenames/progress.

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sy-cui added 4 commits March 31, 2026 18:04

chore: add .vscode to .gitignore

a917149

refactor: remove cosserat_rod_cpp immersed body interaction as this i…

c6fc270

…s usually handled directly in elasticapp itself

chore: add format and lint directivese to justfile

0c463da

fix: format the code using ruff and fixes several import issues

1f86642

sy-cui self-assigned this Apr 1, 2026

sy-cui added prio:low Low priority refactor Refactor existing codebase labels Apr 1, 2026

sy-cui added 23 commits March 31, 2026 19:32

doc: add __all__ to sopht.simulator package

8f62562

refactor: slightly adjust numeric subpackage imports to avoid wildcards

81e887f

chore: add __all__ to sopht.utils package

8e84cae

refactor: __init__.py enhancement in simulator.immersed_body module

94637b3

chore: add colon after TODO

1a09c13

chore: fix UP035 issues (deprecated imports)

aaf1c4a

chore: fix isort and RUF022 undered __all__

288a575

chore: fix RET issues (flake8-return)

acb51dc

chore: add extended ruff.toml to tests and examples directories

22f6a5a

chore: fix EM101 issues (raw-string-in-exception)

3579aa8

chore: fix EM102 issues (f-string-in-exception)

48a3bf8

chore: remove unused noqa directives

dc59153

chore: fix S101 issues (use of assert)

b488bee

chore: fix PIE issues (flake8-pie)

cd6d3fc

fix: fixed incomplete __init__.py docs for sopht.simulator

76e43aa

chore: fix SIM issues (flake8-simplify)

e78887f

chore: fix C408 (unnecessary-collection-call)

86f7cd5

chore: fix issues due to B007, B008, and B905

ff6c510

chore: reformat and apply isort

ce18095

build: new rules for format and lint in pyproject.toml

91ea9b8

chore: Add INP001 to examples/ and tests ignore list since they do ne…

8bc443c

…ed to be built as packages

build: add ffmpeg-python to dependency list

d904784

refactor: replace several shell invocations with python functions

d77e60d

sy-cui added 3 commits April 2, 2026 22:34

chore: mark two SLF001 errors with noqa

488e577

chore: fix ARG002 (unused-method-argument)

a9f01f4

fix: eliminate references to removed function in rod_viz

7a1bd8b

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sy-cui marked this pull request as ready for review April 3, 2026 03:58

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Comment thread sopht/simulator/flow/flow_simulators_2d.py

Comment thread sopht/simulator/flow/flow_simulators_3d.py

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Copilot started work on behalf of sy-cui April 3, 2026 04:09 View session

Fix grammar in sopht/simulator/__init__.py docstring

ec9de79

Agent-Logs-Url: https://github.com/SophT-Team/SophT/sessions/4b8e5733-6675-44c9-b3e5-1dfc0dc76438 Co-authored-by: sy-cui <47127977+sy-cui@users.noreply.github.com>

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fix: replace Path.rename with shutil.move

a5e6e0e

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Comment thread sopht/simulator/immersed_body/flow_forces.py

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sy-cui added 2 commits April 2, 2026 23:40

fix: testing for log messages are replaced by direct tuple comparisons

d4f2b98

refactor: remove old pattern with super() in FlowForces

15bcce7

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sy-cui added 2 commits April 2, 2026 23:53

fix: restore missing plot_video_of_rod_surface function

6f2e95f

chore: mark matplotlib scatter plot _offset3d with noqa to avoid SLF0…

b0ef750

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sy-cui mentioned this pull request Apr 3, 2026

Add isort for sorting imports #83

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sy-cui merged commit ffd5354 into main Apr 3, 2026
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sy-cui deleted the format/lint branch April 3, 2026 05:15

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Code cleanup: Apply Ruff for formatting and linting - #173

Code cleanup: Apply Ruff for formatting and linting#173
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sy-cui commented Apr 1, 2026 •

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sy-cui commented Apr 1, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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sy-cui commented Apr 1, 2026 •

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