fix(ci): pre-commit — PR #459

[barneydobson]

Automated fix targeting ImperialCollegeLondon/SWMManywhere#459.

What failed (classification)

• Kind: pre_commit (pre-commit)
• Notes: pre-commit-style log; no hook id lines parsed

Reproduce locally

• Strategy: pre-commit all hooks (no hook ids parsed)

Command used for the final green verify:

pixi run --manifest-path /home/barney/Documents/GitHub/SWMManywhere/pixi.toml pre-commit run --all-files

Failing CI run

• Workflow run: 25048425954 (head 00e104c…)

Excerpt from downloaded Actions logs (may be truncated):

test session starts ==============================
2026-04-28T11:26:27.1490162Z platform linux -- Python 3.10.20, pytest-9.0.3, pluggy-1.6.0 -- /opt/hostedtoolcache/Python/3.10.20/x64/bin/python
2026-04-28T11:26:27.1490644Z cachedir: .pytest_cache
2026-04-28T11:26:27.1490921Z rootdir: /home/runner/work/SWMManywhere/SWMManywhere
2026-04-28T11:26:27.1491233Z configfile: pyproject.toml
2026-04-28T11:26:27.1491490Z plugins: mypy-1.0.1, mock-3.15.1, cov-7.1.0
2026-04-28T11:42:35.7042512Z collecting ... collected 110 items / 8 deselected / 102 selected
2026-04-28T11:42:35.7042960Z 
2026-04-28T11:42:35.7109139Z src/swmmanywhere/geospatial_utilities.py::swmmanywhere.geospatial_utilities.get_transformer PASSED [  0%]
2026-04-28T11:42:35.7995295Z src/swmmanywhere/geospatial_utilities.py::swmmanywhere.geospatial_utilities.get_utm_epsg PASSED [  1%]
2026-04-28T11:42:35.8082342Z src/swmmanywhere/post_processing.py::swmmanywhere.post_processing.explode_polygon PASSED [  2%]
2026-04-28T11:42:35.8835047Z src/swmmanywhere/post_processing.py::swmmanywhere.post_processing.format_to_swmm_dict PASSED [  3%]
2026-04-28T11:43:39.7026981Z tests/test_cli.py::test_swmmanywhere_cli PASSED                          [  4%]
2026-04-28T11:43:39.7044826Z tests/test_geospatial_utilities.py::test_interp_with_nans PASSED         [  5%]
2026-04-28T11:43:39.7087709Z tests/test_geospatial_utilities.py::test_interpolate_points_on_raster PASSED [  6%]
2026-04-28T11:43:39.8826182Z tests/test_geospatial_utilities.py::test_get_utm PASSED                  [  7%]
2026-04-28T11:43:39.9098211Z tests/test_geospatial_utilities.py::test_reproject_raster PASSED         [  8%]
2026-04-28T11:43:39.9114698Z tests/test_geospatial_utilities.py::test_get_transformer PASSED          [  9%]
2026-04-28T11:43:39.9135515Z tests/test_geospatial_utilities.py::test_reproject_graph PASSED          [ 10%]
2026-04-28T11:43:39.9152517Z tests/test_geospatial_utilities.py::test_nearest_node_buffer PASSED      [ 11%]
2026-04-28T11:43:39.9229292Z tests/test_geospatial_utilities.py::test_burn_shape_in_raster PASSED     [ 12%]
2026-04-28T11:43:49.2415995Z tests/test_geospatial_utilities.py::test_derive_subcatchments[True-pyflwdir-2498-0.1187-28.202] PASSED [ 13%]
2026-04-28T11:43:50.1655354Z tests/test_geospatial_utilities.py::test_derive_subcatchments[True-whitebox-2998-0.1102-30.894] PASSED [ 14%]
2026-04-28T11:43:50.1997357Z tests/test_geospatial_utilities.py::test_derive_subcatchments[False-pyflwdir-2498-0.1187-28.202] PASSED [ 15%]
2026-04-28T11:43:51.0680403Z tests/test_geospatial_utilities.py::test_derive_subcatchments[False-whitebox-2998-0.1102-30.894] PASSED [ 16%]
2026-04-28T11:43:51.3057869Z tests/test_geospatial_utilities.py::test_derive_rc PASSED                [ 17%]
2026-04-28T11:43:51.3070548Z tests/test_geospatial_utilities.py::test_calculate_angle PASSED          [ 18%]
2026-04-28T11:43:51.3191951Z tests/test_geospatial_utilities.py::test_remove_intersections PASSED     [ 19%]
2026-04-28T11:43:51.3523409Z tests/test_geospatial_utilities.py::test_graph_to_file[.geojson] PASSED  [ 20%]
2026-04-28T11:43:51.4431253Z tests/test_geospatial_utilities.py::test_graph_to_file[.geoparquet] PASSED [ 21%]
2026-04-28T11:43:51.4469538Z tests/test_geospatial_utilities.py::test_merge_points PASSED             [ 22%]
2026-04-28T11:43:51.4630182Z tests/test_graph_utilities.py::test_save_load PASSED                     [ 23%]
2026-04-28T11:43:51.4664613Z tests/test_graph_utilities.py::test_assign_id PASSED                     [ 24%]
2026-04-28T11:43:51.4724950Z tests/test_graph_utilities.py::test_double_directed PASSED               [ 25%]
2026-04-28T11:43:51.5162424Z tests/test_graph_utilities.py::test_calculate_streetcover PASSED         [ 26%]
2026-04-28T11:43:51.5380612Z tests/test_graph_utilities.py::test_split_long_edges PASSED              [ 27%]
2026-04-28T11:43:52.6445117Z tests/test_graph_utilities.py::test_derive_subcatchments PASSED          [ 28%]
2026-04-28T11:43:52.6574907Z tests/test_graph_utilities.py::test_set_elevation_and_slope PASSED       [ 29%]
2026-04-28T11:43:52.6622278Z tests/test_graph_utilities.py::test_chahinian_angle PASSED               [ 30%]
2026-04-28T11:43:52.6672730Z tests/test_graph_utilities.py::test_calculate_weights PASSED             [ 31%]
2026-04-28T11:43:52.6721681Z tests/test_graph_utilities.py::test_calculate_weights_novar PASSED       [ 32%]
2026-04-28T11:43:52.6990161Z tests/test_graph_utilities.py::test_identify_outfalls_no_river PASSED    [ 33%
... [session excerpt truncated to 4500 chars]

Local verify (after agent edits)

Final successful run of the same repro command (truncated if long):

check for merge conflicts.....................................................Passed
debug statements (python).....................................................Passed
ruff (legacy alias)...........................................................Passed
ruff format...................................................................Passed
mypy..........................................................................Passed
markdownlint..................................................................Passed
Check common misspellings in text files with codespell........................Passed
Apply a consistent format to pyproject.toml...................................Passed
Modernizing Python codebases using Refurb.....................................Passed

Mechanical CI context

• Local reproduction command: pixi run --manifest-path /home/barney/Documents/GitHub/SWMManywhere/pixi.toml pre-commit run --all-files
• CI command inferred from logs: pytest
• Suggested sanity command(s): pixi run --manifest-path /home/barney/Documents/GitHub/SWMManywhere/pixi.toml pytest --lf -q /home/barney/.pr-maintainer/worktrees/ImperialCollegeLondon_SWMManywhere-pr459-1777467204/tests
• Failure mode signals: normal_assertion
• Confidence: high
• Mechanical risk notes:
  • Local reproduction command differs from the apparent CI command.

Review required (agent-flagged)

The automated agent flagged changes that a human should double-check before merging:

1. 🟡 LOW — PR only updates GitHub Actions checkout from v5 to v6 — no code or dependency changes. CI log shows pytest passed entirely. Failure labeled 'pre_commit' is likely a CI misclassification. Human review recommended to confirm no action needed.
   • Files: .github/workflows/check-links.yml, .github/workflows/ci_template.yml, .github/workflows/publish.yml

Upstream changelog / release notes (cross-reference)

https://github.com/actions/checkout

GitHub - actions/checkout: Action for checking out a repo · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS <a href="https://github.com/features/actions" data-analytics-event="{"action":"actions","tag":"link","context":"platform","location":"na

https://github.com/actions/checkout/releases

Releases · actions/checkout · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY <a href="https://github.com/security/advanced-security" data-analytics-event="{"action":"github_advanced_

Run metadata

• Agent: provider deepinfra, model Qwen/Qwen3-Next-80B-A3B-Instruct
• Succeeded on maintainer round: 1 (of automated rounds)

Session debug files under maintainer_state/ are omitted from this branch by default; they are summarised above when relevant.

[Codecov Comments Bot (codecov-commenter)]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 87.41%. Comparing base (e8f20f9) to head (00e104c).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #485   +/-   ##
=======================================
  Coverage   87.41%   87.41%           
=======================================
  Files          23       23           
  Lines        2352     2352           
  Branches      301      301           
=======================================
  Hits         2056     2056           
  Misses        205      205           
  Partials       91       91           

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