chore: Update pre-commit hooks [review required]

[PasteurBot]

Pre-commit is unable to automatically update the hooks due to unresolvable conflicts.
Please review the changes and merge manually.

Log:

check for added large files..............................................Passed
check json...........................................(no files to check)Skipped
check toml...............................................................Passed
check yaml...............................................................Passed
detect private key.......................................................Passed
fix end of files.........................................................Passed
trim trailing whitespace.................................................Passed
ruff (legacy alias)......................................................Failed
- hook id: ruff
- exit code: 1

EXE001 Shebang is present but file is not executable
 --> .github/scripts/detect-changed-solvers.py:1:1
  |
1 | #!/usr/bin/env python3
  | ^^^^^^^^^^^^^^^^^^^^^^
2 |
3 | # Copyright 2026 Pasteur Labs. All Rights Reserved.
  |

EXE001 Shebang is present but file is not executable
 --> .github/scripts/filter-problems-by-solver.py:1:1
  |
1 | #!/usr/bin/env python3
  | ^^^^^^^^^^^^^^^^^^^^^^
2 |
3 | # Copyright 2026 Pasteur Labs. All Rights Reserved.
  |

S112 `try`-`except`-`continue` detected, consider logging the exception
  --> .github/scripts/filter-problems-by-solver.py:51:9
   |
49 |           try:
50 |               names = {s.name for s in get_config(p).solvers}
51 | /         except Exception:
52 | |             continue
   | |____________________^
53 |           if wanted & names:
54 |               hits.append(p)
   |

BLE001 Do not catch blind exception: `Exception`
  --> .github/scripts/filter-problems-by-solver.py:51:16
   |
49 |         try:
50 |             names = {s.name for s in get_config(p).solvers}
51 |         except Exception:
   |                ^^^^^^^^^
52 |             continue
53 |         if wanted & names:
   |

EXE001 Shebang is present but file is not executable
 --> .github/scripts/generate-benchmark-matrix.py:1:1
  |
1 | #!/usr/bin/env python3
  | ^^^^^^^^^^^^^^^^^^^^^^
2 |
3 | # Copyright 2026 Pasteur Labs. All Rights Reserved.
  |

EXE001 Shebang is present but file is not executable
 --> .github/scripts/merge-results.py:1:1
  |
1 | #!/usr/bin/env python3
  | ^^^^^^^^^^^^^^^^^^^^^^
2 |
3 | # Copyright 2026 Pasteur Labs. All Rights Reserved.
  |

S112 `try`-`except`-`continue` detected, consider logging the exception
   --> .github/scripts/merge-results.py:117:9
    |
115 |                       # overwritten; per-solver keys accumulate.
116 |                       merged[key] = np.asarray(data[key])
117 | /         except Exception:
118 | |             continue
    | |____________________^
119 |       if merged:
120 |           out_path.parent.mkdir(parents=True, exist_ok=True)
    |

BLE001 Do not catch blind exception: `Exception`
   --> .github/scripts/merge-results.py:117:16
    |
115 |                     # overwritten; per-solver keys accumulate.
116 |                     merged[key] = np.asarray(data[key])
117 |         except Exception:
    |                ^^^^^^^^^
118 |             continue
119 |     if merged:
    |

BLE001 Do not catch blind exception: `Exception`
   --> .github/scripts/merge-results.py:173:24
    |
171 |                 try:
172 |                     results.append(_load_json(src))
173 |                 except Exception as e:
    |                        ^^^^^^^^^
174 |                     print(f"  warning: failed to load {src}: {e}", file=sys.stderr)
175 |             if not results:
    |

EXE001 Shebang is present but file is not executable
 --> .github/scripts/overlay-results.py:1:1
  |
1 | #!/usr/bin/env python3
  | ^^^^^^^^^^^^^^^^^^^^^^
2 |
3 | # Copyright 2026 Pasteur Labs. All Rights Reserved.
  |

BLE001 Do not catch blind exception: `Exception`
   --> .github/scripts/overlay-results.py:273:20
    |
271 |                 _save_json(merged, out_path)
272 |                 n_merged += 1
273 |             except Exception as e:
    |                    ^^^^^^^^^
274 |                 print(f"  warning: merge failed for {relpath}: {e}", file=sys.stderr)
275 |                 # Fall back to PR version.
    |

BLE001 Do not catch blind exception: `Exception`
   --> .github/scripts/overlay-results.py:284:20
    |
282 |                 _merge_npz_pair(baseline_files[relpath], pr_files[relpath], out_path)
283 |                 n_npz_merged += 1
284 |             except Exception as e:
    |                    ^^^^^^^^^
285 |                 print(
286 |                     f"  warning: npz merge failed for {relpath}: {e}", file=sys.stderr
    |

EXE001 Shebang is present but file is not executable
 --> .github/scripts/pull-solver-images.py:1:1
  |
1 | #!/usr/bin/env python3
  | ^^^^^^^^^^^^^^^^^^^^^^
2 |
3 | # Copyright 2026 Pasteur Labs. All Rights Reserved.
  |

PLW1510 `subprocess.run` without explicit `check` argument
  --> .github/scripts/pull-solver-images.py:45:8
   |
43 |     """Pull *remote* and retag it to *local_tag*. Returns True on success."""
44 |     print(f"Pulling {remote}")
45 |     if subprocess.run(["docker", "pull", remote]).returncode != 0:
   |        ^^^^^^^^^^^^^^
46 |         return False
47 |     subprocess.run(["docker", "tag", remote, local_tag])
   |
help: Add explicit `check=False`

PLW1510 `subprocess.run` without explicit `check` argument
  --> .github/scripts/pull-solver-images.py:47:5
   |
45 |     if subprocess.run(["docker", "pull", remote]).returncode != 0:
46 |         return False
47 |     subprocess.run(["docker", "tag", remote, local_tag])
   |     ^^^^^^^^^^^^^^
48 |     print(f"  Tagged as {local_tag}")
49 |     return True
   |
help: Add explicit `check=False`

S112 `try`-`except`-`continue` detected, consider logging the exception
   --> .github/scripts/pull-solver-images.py:109:9
    |
107 |           try:
108 |               cfg = get_config(p)
109 | /         except Exception:
110 | |             continue
    | |____________________^
111 |           for spec in cfg.solvers:
112 |               # --solvers filter: skip solvers not in the requested set
    |

BLE001 Do not catch blind exception: `Exception`
   --> .github/scripts/pull-solver-images.py:109:16
    |
107 |         try:
108 |             cfg = get_config(p)
109 |         except Exception:
    |                ^^^^^^^^^
110 |             continue
111 |         for spec in cfg.solvers:
    |

EXE001 Shebang is present but file is not executable
 --> .github/scripts/validate-problem-configs.py:1:1
  |
1 | #!/usr/bin/env python3
  | ^^^^^^^^^^^^^^^^^^^^^^
2 |
3 | # Copyright 2026 Pasteur Labs. All Rights Reserved.
  |

EXE001 Shebang is present but file is not executable
 --> .github/scripts/validate-tesseract-configs.py:1:1
  |
1 | #!/usr/bin/env python3
  | ^^^^^^^^^^^^^^^^^^^^^^
2 |
3 | # Copyright 2026 Pasteur Labs. All Rights Reserved.
  |

BLE001 Do not catch blind exception: `Exception`
  --> .github/scripts/validate-tesseract-configs.py:63:12
   |
61 |             if val is not None and not isinstance(val, bool):
62 |                 errors.append(f"{p}: mosaic.{bool_field}={val!r} must be a boolean")
63 |     except Exception as e:
   |            ^^^^^^^^^
64 |         errors.append(f"{p}: {e}")
   |

EXE001 Shebang is present but file is not executable
 --> docs/generate.py:1:1
  |
1 | #!/usr/bin/env python3
  | ^^^^^^^^^^^^^^^^^^^^^^
2 |
3 | # Copyright 2026 Pasteur Labs. All Rights Reserved.
  |

PLW0602 Using global for `_CATEGORY_LABELS` but no assignment is done
  --> docs/generate.py:50:27
   |
48 |     are sourced from the problem configs rather than from this file.
49 |     """
50 |     global _SOLVER_SPECS, _CATEGORY_LABELS
   |                           ^^^^^^^^^^^^^^^^
51 |     if _SOLVER_SPECS is not None:
52 |         return _SOLVER_SPECS
   |

S112 `try`-`except`-`continue` detected, consider logging the exception
  --> docs/generate.py:63:9
   |
61 |           try:
62 |               cfg = get_config(prob)
63 | /         except Exception:
64 | |             continue
   | |____________________^
65 |           domain_dir = cfg.tesseract_dir.name
66 |           # First non-empty category_label per tesseract dir wins. Multiple
   |

BLE001 Do not catch blind exception: `Exception`
  --> docs/generate.py:63:16
   |
61 |         try:
62 |             cfg = get_config(prob)
63 |         except Exception:
   |                ^^^^^^^^^
64 |             continue
65 |         domain_dir = cfg.tesseract_dir.name
   |

S110 `try`-`except`-`pass` detected, consider logging the exception
   --> docs/generate.py:128:17
    |
126 |                   try:
127 |                       return ast.literal_eval(raw)
128 | /                 except Exception:
129 | |                     pass
    | |________________________^
130 |               return raw
131 |       return ""
    |

BLE001 Do not catch blind exception: `Exception`
   --> docs/generate.py:128:24
    |
126 |                 try:
127 |                     return ast.literal_eval(raw)
128 |                 except Exception:
    |                        ^^^^^^^^^
129 |                     pass
130 |             return raw
    |

EXE001 Shebang is present but file is not executable
 --> docs/generate_results.py:1:1
  |
1 | #!/usr/bin/env python3
  | ^^^^^^^^^^^^^^^^^^^^^^
2 |
3 | # Copyright 2026 Pasteur Labs. All Rights Reserved.
  |

BLE001 Do not catch blind exception: `Exception`
   --> docs/generate_results.py:281:12
    |
279 |             return cfg.get_ic_description(experiment)
280 |         return cfg.get_plot_description(suite, experiment)
281 |     except Exception:
    |            ^^^^^^^^^
282 |         return ""
    |

BLE001 Do not catch blind exception: `Exception`
   --> docs/generate_results.py:289:12
    |
287 |     try:
288 |         return _get_config(problem).get_experiment_description(suite, experiment)
289 |     except Exception:
    |            ^^^^^^^^^
290 |         return ""
    |

S110 `try`-`except`-`pass` detected, consider logging the exception
   --> docs/generate_results.py:299:5
    |
297 |           if desc:
298 |               return desc
299 | /     except Exception:
300 | |         pass
    | |____________^
301 |       return PROBLEM_DESCRIPTIONS.get(problem, "")
    |

BLE001 Do not catch blind exception: `Exception`
   --> docs/generate_results.py:299:12
    |
297 |         if desc:
298 |             return desc
299 |     except Exception:
    |            ^^^^^^^^^
300 |         pass
301 |     return PROBLEM_DESCRIPTIONS.get(problem, "")
    |

S110 `try`-`except`-`pass` detected, consider logging the exception
   --> docs/generate_results.py:310:5
    |
308 |           if bc:
309 |               return bc
310 | /     except Exception:
311 | |         pass
    | |____________^
312 |       return PROBLEM_BC_DESCRIPTIONS.get(problem, "")
    |

BLE001 Do not catch blind exception: `Exception`
   --> docs/generate_results.py:310:12
    |
308 |         if bc:
309 |             return bc
310 |     except Exception:
    |            ^^^^^^^^^
311 |         pass
312 |     return PROBLEM_BC_DESCRIPTIONS.get(problem, "")
    |

BLE001 Do not catch blind exception: `Exception`
   --> docs/generate_results.py:354:12
    |
352 |     try:
353 |         return json.loads(path.read_text(encoding="utf-8")).get("results", []) or []
354 |     except Exception:
    |            ^^^^^^^^^
355 |         return []
    |

BLE001 Do not catch blind exception: `Exception`
   --> docs/generate_results.py:534:12
    |
532 |     try:
533 |         ranked = ranker(problem)
534 |     except Exception:
    |            ^^^^^^^^^
535 |         return []
536 |     if not ranked:
    |

S110 `try`-`except`-`pass` detected, consider logging the exception
   --> docs/generate_results.py:651:9
    |
649 |                   params = {**params, "sweep": result["sweep"]}
650 |               return params
651 | /         except Exception:
652 | |             pass
    | |________________^
653 |       return None
    |

BLE001 Do not catch blind exception: `Exception`
   --> docs/generate_results.py:651:16
    |
649 |                 params = {**params, "sweep": result["sweep"]}
650 |             return params
651 |         except Exception:
    |                ^^^^^^^^^
652 |             pass
653 |     return None
    |

ISC004 Unparenthesized implicit string concatenation in collection
   --> docs/generate_results.py:789:13
    |
787 |       if illustration and (OUTPUT_DIR / illustration).exists():
788 |           lines += [
789 | /             f"![]({illustration}){{width=100% "
790 | |             'style="max-width:560px; display:block; margin:0 auto 0.5rem;"}',
    | |____________________________________________________________________________^
791 |               "",
792 |           ]
    |
help: Did you forget a comma?
help: Wrap implicitly concatenated strings in parentheses

S110 `try`-`except`-`pass` detected, consider logging the exception
   --> mosaic/benchmarks/cli/_helpers.py:359:5
    |
358 |           cfg = get_config(cfg.name)
359 | /     except Exception:
360 | |         pass
    | |____________^
361 |       if to_run:
362 |           names = to_run
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/cli/_helpers.py:359:12
    |
358 |         cfg = get_config(cfg.name)
359 |     except Exception:
    |            ^^^^^^^^^
360 |         pass
361 |     if to_run:
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/cli/_helpers.py:385:16
    |
383 |         except FileNotFoundError as exc:
384 |             print_skip(f"{name}: results not found ({exc.filename})")
385 |         except Exception as exc:
    |                ^^^^^^^^^
386 |             if verbose_errors:
387 |                 console.print_exception()
    |

S112 `try`-`except`-`continue` detected, consider logging the exception
   --> mosaic/benchmarks/cli/_helpers.py:474:9
    |
472 |           try:
473 |               all_names |= set(get_config(problem).solver_names)
474 | /         except Exception:
475 | |             # Skip problems that fail to import — they'll surface as
476 | |             # "build failed" later in the loop and aren't relevant to a
477 | |             # name-typo check.
478 | |             continue
    | |____________________^
479 |       # Match case-insensitively against the canonical names.
480 |       known_lower = {n.lower() for n in all_names}
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/cli/_helpers.py:474:16
    |
472 |         try:
473 |             all_names |= set(get_config(problem).solver_names)
474 |         except Exception:
    |                ^^^^^^^^^
475 |             # Skip problems that fail to import — they'll surface as
476 |             # "build failed" later in the loop and aren't relevant to a
    |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/cli/_status_helpers.py:46:16
   |
44 |         try:
45 |             cfg = get_config(problem)
46 |         except Exception as exc:
   |                ^^^^^^^^^
47 |             print_warn(f"{problem}: {exc}")
48 |             continue
   |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/cli/_status_helpers.py:59:16
   |
57 |             with open(diff_against) as f:
58 |                 old_snapshot = _json.load(f)
59 |         except Exception as exc:
   |                ^^^^^^^^^
60 |             print_warn(f"could not read --diff-against file: {exc}")
61 |             old_snapshot = None
   |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/cli/build.py:65:16
   |
63 |             # effect here (see test_build_unknown_problem_records_failure).
64 |             _cli_pkg.build_all(cfg, max_workers=jobs)
65 |         except Exception as exc:
   |                ^^^^^^^^^
66 |             print_warn(f"{problem}: {exc}")
67 |             failed.append((problem, str(exc)))
   |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/cli/ics.py:53:20
   |
51 |                 fn(cfg)
52 |                 console.print(f"  [green]{name}[/green] ok")
53 |             except Exception as exc:
   |                    ^^^^^^^^^
54 |                 if traceback:
55 |                     console.print_exception()
   |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/cli/ics.py:63:16
   |
61 |             result = exp_fn(cfg, {})
62 |             console.print(f"  [green]{name}[/green] ok  shape={result['shape']}")
63 |         except Exception as exc:
   |                ^^^^^^^^^
64 |             if traceback:
65 |                 console.print_exception()
   |

S110 `try`-`except`-`pass` detected, consider logging the exception
   --> mosaic/benchmarks/cli/reference.py:177:9
    |
175 |               if sweep and "values" in sweep:
176 |                   return len(sweep["values"])
177 | /         except Exception:
178 | |             pass
    | |________________^
179 |
180 |       # Fallback: count consensus_* keys in the NPZ.
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/cli/reference.py:177:16
    |
175 |             if sweep and "values" in sweep:
176 |                 return len(sweep["values"])
177 |         except Exception:
    |                ^^^^^^^^^
178 |             pass
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/cli/reference.py:184:12
    |
182 |         with np.load(str(fields_path), allow_pickle=False) as data:
183 |             return sum(1 for k in data if k.startswith("consensus_"))
184 |     except Exception:
    |            ^^^^^^^^^
185 |         return 0
    |

S110 `try`-`except`-`pass` detected, consider logging the exception
   --> mosaic/benchmarks/cli/reference.py:196:5
    |
194 |               if "sweep_values" in data:
195 |                   return data["sweep_values"].tolist()
196 | /     except Exception:
197 | |         pass
    | |____________^
198 |       return None
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/cli/reference.py:196:12
    |
194 |             if "sweep_values" in data:
195 |                 return data["sweep_values"].tolist()
196 |     except Exception:
    |            ^^^^^^^^^
197 |         pass
198 |     return None
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/cli/reference.py:284:28
    |
282 |                                 f"    [yellow]✗[/] {s.name} @ {sweep_key}={val}: apply failed"
283 |                             )
284 |                     except Exception as e:
    |                            ^^^^^^^^^
285 |                         console.print(
286 |                             f"    [red]✗[/] {s.name} @ {sweep_key}={val}: {e}"
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/cli/run.py:203:16
    |
201 |                 jobs=jobs,
202 |             )
203 |         except Exception as exc:
    |                ^^^^^^^^^
204 |             msg = f"build failed: {exc}"
205 |             console.print(f"  [red]{msg}[/]")
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/cli/run.py:340:16
    |
338 |             else:
339 |                 run_status[(problem, suite)] = ("skip", "no experiments ran")
340 |         except Exception as exc:
    |                ^^^^^^^^^
341 |             if traceback:
342 |                 console.print_exception()
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/cli/status.py:113:16
    |
111 |         try:
112 |             cfg = get_config(problem)
113 |         except Exception as exc:
    |                ^^^^^^^^^
114 |             print_warn(f"{problem}: {exc}")
115 |             continue
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/config.py:875:24
    |
873 |                 try:
874 |                     fn(cfg, **fn_kw)
875 |                 except Exception as exc:
    |                        ^^^^^^^^^
876 |                     print_warn(f"plot {key}#{view_name}: {type(exc).__name__}: {exc}")
    |

BLE001 Do not catch blind exception: `Exception`
    --> mosaic/benchmarks/core/config.py:1173:16
     |
1171 |             with open(config_path) as f:
1172 |                 doc = yaml.safe_load(f)
1173 |         except Exception as exc:
     |                ^^^^^^^^^
1174 |             warnings.warn(
1175 |                 f"Solver discovery: cannot parse {config_path}: {exc}",
     |

BLE001 Do not catch blind exception: `Exception`
    --> mosaic/benchmarks/core/config.py:1256:12
     |
1254 |         with Tesseract.from_image(tag) as t:
1255 |             return "vector_jacobian_product" in t.available_endpoints
1256 |     except Exception:
     |            ^^^^^^^^^
1257 |         return False
     |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/experiment.py:516:24
    |
514 |                     kernel_fn(t, _ctx(name, _sweep_values[0]))
515 |                     console.print(f"  [{color}]{name}[/] warmup ok")
516 |                 except Exception as wex:
    |                        ^^^^^^^^^
517 |                     console.print(
518 |                         f"  [{color}]{name}[/] warmup skipped ({type(wex).__name__})"
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/experiment.py:564:28
    |
562 |                         out = kernel_fn(t, _ctx(name, val))
563 |                         exc: Exception | None = None
564 |                     except Exception as e:
    |                            ^^^^^^^^^
565 |                         out, exc = None, e
566 |                 mem = poller.summary
    |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/core/hardware.py:33:12
   |
31 |             total_mib = nvml.nvmlDeviceGetMemoryInfo(handle).total / (1024 * 1024)
32 |             out.append(f"{name}, {total_mib:.0f} MiB")
33 |     except Exception:
   |            ^^^^^^^^^
34 |         return []
35 |     return out
   |

S110 `try`-`except`-`pass` detected, consider logging the exception
  --> mosaic/benchmarks/core/hardware.py:57:5
   |
55 |                       info["cpu"] = line.split(":", 1)[1].strip()
56 |                       break
57 | /     except Exception:
58 | |         pass
   | |____________^
59 |
60 |       # Total RAM via psutil
   |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/core/hardware.py:57:12
   |
55 |                     info["cpu"] = line.split(":", 1)[1].strip()
56 |                     break
57 |     except Exception:
   |            ^^^^^^^^^
58 |         pass
   |

S110 `try`-`except`-`pass` detected, consider logging the exception
  --> mosaic/benchmarks/core/hardware.py:65:5
   |
64 |           info["ram_gb"] = round(psutil.virtual_memory().total / 1e9, 1)
65 | /     except Exception:
66 | |         pass
   | |____________^
67 |
68 |       return info
   |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/core/hardware.py:65:12
   |
64 |         info["ram_gb"] = round(psutil.virtual_memory().total / 1e9, 1)
65 |     except Exception:
   |            ^^^^^^^^^
66 |         pass
   |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/core/hardware.py:78:12
   |
76 |     try:
77 |         return nvml.nvmlDeviceGetCount() > 0
78 |     except Exception:
   |            ^^^^^^^^^
79 |         return False
   |

PYI034 `__enter__` methods in classes like `ResourceSampler` usually return `self` at runtime
   --> mosaic/benchmarks/core/hardware.py:119:9
    |
117 |         self._ram_mib: float | None = None
118 |
119 |     def __enter__(self) -> ResourceSampler:
    |         ^^^^^^^^^
120 |         self._baseline_vram_mib = sample_vram_mib(self.gpu_id)
121 |         return self
    |
help: Use `Self` as return type

S110 `try`-`except`-`pass` detected, consider logging the exception
   --> mosaic/benchmarks/core/hardware.py:129:9
    |
128 |               self._ram_mib = psutil.Process().memory_info().rss / 1e6
129 | /         except Exception:
130 | |             pass
    | |________________^
131 |
132 |       @property
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/hardware.py:129:16
    |
128 |             self._ram_mib = psutil.Process().memory_info().rss / 1e6
129 |         except Exception:
    |                ^^^^^^^^^
130 |             pass
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/harness.py:184:12
    |
182 |                     wall_limit_hit = True
183 |                     break
184 |     except Exception as exc:
    |            ^^^^^^^^^
185 |         failure = {
186 |             "failure_type": classify_failure(type(exc).__name__, str(exc)),
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/io.py:303:12
    |
301 |     try:
302 |         return load_json(p)
303 |     except Exception:
    |            ^^^^^^^^^
304 |         return None
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/io.py:321:12
    |
319 |         with np.load(p, allow_pickle=False) as f:
320 |             return {k: np.asarray(f[k]) for k in f.files}
321 |     except Exception:
    |            ^^^^^^^^^
322 |         return {}
    |

LOG015 `warning()` call on root logger
   --> mosaic/benchmarks/core/io.py:908:9
    |
906 |       _flock_dt = time.monotonic() - _flock_t0
907 |       if _flock_dt > 60:
908 | /         logging.warning(
909 | |             "save_experiment flock held for %.1fs at %s (solvers=%s)",
910 | |             _flock_dt,
911 | |             result_path,
912 | |             sorted(new_tesseract_hashes.keys()),
913 | |         )
    | |_________^
    |
help: Use own logger instead

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/core/memory.py:57:16
   |
55 |             pynvml.nvmlInit()
56 |             _NVML_OK = True
57 |         except Exception:
   |                ^^^^^^^^^
58 |             _NVML_OK = False
59 |             return None
   |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/core/memory.py:73:12
   |
72 |         return docker.from_env()
73 |     except Exception:
   |            ^^^^^^^^^
74 |         return None
   |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/core/memory.py:92:12
   |
90 |         handle = nvml.nvmlDeviceGetHandleByIndex(int(gpu_id))
91 |         return nvml.nvmlDeviceGetMemoryInfo(handle).used / (1024 * 1024)
92 |     except Exception:
   |            ^^^^^^^^^
93 |         return None
   |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/memory.py:110:12
    |
108 |         usage = stats.get("memory_stats", {}).get("usage")
109 |         return float(usage) / (1024 * 1024) if usage is not None else None
110 |     except Exception:
    |            ^^^^^^^^^
111 |         return None
    |

PYI034 `__enter__` methods in classes like `MemoryPoller` usually return `self` at runtime
   --> mosaic/benchmarks/core/memory.py:170:9
    |
168 |         self._thread: threading.Thread | None = None
169 |
170 |     def __enter__(self) -> MemoryPoller:
    |         ^^^^^^^^^
171 |         self._thread = threading.Thread(target=self._loop, daemon=True)
172 |         self._thread.start()
    |
help: Use `Self` as return type

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/core/resources.py:32:12
   |
31 |         total_bytes = psutil.virtual_memory().total
32 |     except Exception:
   |            ^^^^^^^^^
33 |         return []
   |

PLW1510 `subprocess.run` without explicit `check` argument
   --> mosaic/benchmarks/core/runner.py:129:13
    |
127 |     for name in names:
128 |         try:
129 |             subprocess.run(
    |             ^^^^^^^^^^^^^^
130 |                 ["docker", "rm", "-f", name],
131 |                 capture_output=True,
    |
help: Add explicit `check=False`

S110 `try`-`except`-`pass` detected, consider logging the exception
   --> mosaic/benchmarks/core/runner.py:134:9
    |
132 |                   timeout=10,
133 |               )
134 | /         except Exception:
135 | |             pass
    | |________________^
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/runner.py:134:16
    |
132 |                 timeout=10,
133 |             )
134 |         except Exception:
    |                ^^^^^^^^^
135 |             pass
    |

PLW1510 `subprocess.run` without explicit `check` argument
   --> mosaic/benchmarks/core/runner.py:237:13
    |
235 |         tesseract_path = cfg.tesseract_dir / spec.dir
236 |         t0 = time.monotonic()
237 |         r = subprocess.run(
    |             ^^^^^^^^^^^^^^
238 |             ["tesseract", "build", "--tag", tag, str(tesseract_path)],
239 |             capture_output=True,
    |
help: Add explicit `check=False`

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/runner.py:284:24
    |
282 |                     name, img_tag = future.result()
283 |                     images[name] = img_tag
284 |                 except Exception as exc:
    |                        ^^^^^^^^^
285 |                     failed.append(solver_name)
286 |                     print_warn(f"BUILD FAILED: {solver_name} — {exc}")
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/runner.py:418:16
    |
416 |         except NotImplementedError as exc:
417 |             print_skip(str(exc))
418 |         except Exception as exc:
    |                ^^^^^^^^^
419 |             if verbose_errors:
420 |                 console.print_exception()
    |

S110 `try`-`except`-`pass` detected, consider logging the exception
   --> mosaic/benchmarks/core/runner.py:431:13
    |
430 |                   jax.clear_caches()
431 | /             except Exception:
432 | |                 pass
    | |____________________^
433 |
434 |       if plots and plot_fns:
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/runner.py:431:20
    |
430 |                 jax.clear_caches()
431 |             except Exception:
    |                    ^^^^^^^^^
432 |                 pass
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/runner.py:442:16
    |
441 |             _plot_cfg = _get_cfg(cfg.name)
442 |         except Exception:
    |                ^^^^^^^^^
443 |             _plot_cfg = cfg
444 |         # Regular per-experiment plots: only fire when the matching experiment ran.
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/runner.py:449:24
    |
447 |                 try:
448 |                     plot_fns[name](_plot_cfg, suffix=suffix)
449 |                 except Exception as exc:
    |                        ^^^^^^^^^
450 |                     if verbose_errors:
451 |                         console.print_exception()
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/runner.py:460:20
    |
458 |             try:
459 |                 fn(_plot_cfg)
460 |             except Exception as exc:
    |                    ^^^^^^^^^
461 |                 if verbose_errors:
462 |                     console.print_exception()
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/runner.py:684:20
    |
682 |                 with _tracked_tesseract(tags[name], _gpus, _NO_HC) as t:
683 |                     fn(name, t)
684 |             except Exception as exc:
    |                    ^^^^^^^^^
685 |                 print_warn(f"{name} failed: {exc}")
686 |                 if on_error is not None:
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/runner.py:703:16
    |
701 |             with _tracked_tesseract(tags[name], [gid], _NO_HC) as t:
702 |                 fn(name, t)
703 |         except Exception as exc:
    |                ^^^^^^^^^
704 |             print_warn(f"{name} failed: {exc}")
705 |             if on_error is not None:
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/runner.py:804:12
    |
802 |         }
803 |         return arr, extras, state
804 |     except Exception as exc:
    |            ^^^^^^^^^
805 |         _exc_name = type(exc).__name__
806 |         if isinstance(exc, TimeoutError):
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/status.py:220:12
    |
218 |     try:
219 |         return isinstance(x, float) and math.isnan(x)
220 |     except Exception:
    |            ^^^^^^^^^
221 |         return False
    |

PERF102 When using only the values of a dict use the `values()` method
   --> mosaic/benchmarks/core/status.py:347:25
    |
345 |         best_cos = None
346 |         best_rel = None
347 |         for _eps, st in sweep.items():
    |                         ^^^^^^^^^^^
348 |             if not isinstance(st, dict):
349 |                 continue
    |
help: Replace `.items()` with `.values()`

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/status.py:676:12
    |
674 |         target = getattr(mod, attr_path)
675 |         h = harness_fn_hash(target) or None
676 |     except Exception:
    |            ^^^^^^^^^
677 |         h = None
678 |     cache[qualname] = h
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/core/status.py:900:12
    |
898 |     try:
899 |         data = load_json(result_path)
900 |     except Exception as exc:
    |            ^^^^^^^^^
901 |         row.cells = {s: Cell(FAILED, f"unreadable result.json: {exc}") for s in solvers}
902 |         # Even when the file is corrupted, exclusions still take precedence —
    |

ISC004 Unparenthesized implicit string concatenation in collection
   --> mosaic/benchmarks/core/status_checks.py:109:13
    |
107 |           return (
108 |               "anomaly",
109 | /             f"error {worst[1]:.3g} at sweep={worst[0]} is {ratio:.1f}× peer median ({worst[2]:.3g}); "
110 | |             f"threshold k={k}",
    | |______________________________^
111 |           )
    |
help: Did you forget a comma?
help: Wrap implicitly concatenated strings in parentheses

ISC004 Unparenthesized implicit string concatenation in collection
   --> mosaic/benchmarks/core/status_checks.py:143:13
    |
141 |           return (
142 |               "anomaly",
143 | /             f"median time {s.solver_median_time:.1f}s is {ratio:.0f}× peer median "
144 | |             f"({s.peer_median_time:.2f}s); threshold k={k}",
    | |___________________________________________________________^
145 |           )
    |
help: Did you forget a comma?
help: Wrap implicitly concatenated strings in parentheses

ISC004 Unparenthesized implicit string concatenation in collection
   --> mosaic/benchmarks/core/status_checks.py:188:13
    |
186 |           return (
187 |               "anomaly",
188 | /             f"best-ε rel_err {s.best_rel_err:.2e} is {ratio:.1f}× peer median "
189 | |             f"({s.peer_rel_err_median:.2e}); threshold k={k}",
    | |_____________________________________________________________^
190 |           )
    |
help: Did you forget a comma?
help: Wrap implicitly concatenated strings in parentheses

PERF402 Use `list` or `list.copy` to create a copy of a list
   --> mosaic/benchmarks/core/utils.py:165:13
    |
163 |     if experiment:
164 |         for p in experiment.split("/"):
165 |             parts.append(p)
    |             ^^^^^^^^^^^^^^^
166 |     if sub:
167 |         for p in sub.split("/"):
    |

PERF402 Use `list` or `list.copy` to create a copy of a list
   --> mosaic/benchmarks/core/utils.py:168:13
    |
166 |     if sub:
167 |         for p in sub.split("/"):
168 |             parts.append(p)
    |             ^^^^^^^^^^^^^^^
169 |     # Try longest prefix first.
170 |     for n in range(len(parts), 0, -1):
    |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/problems/__init__.py:58:16
   |
56 |         try:
57 |             mod = importlib.import_module(module_name)
58 |         except Exception as exc:
   |                ^^^^^^^^^
59 |             log.warning("skipping %s: %s", module_name, exc)
60 |             continue
   |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/problems/navier_stokes_3d_grid/optimization.py:270:16
    |
268 |             )
269 |             tgt = apply_tesseract(t, inp_true)[output_key]
270 |         except Exception as exc:
    |                ^^^^^^^^^
271 |             from mosaic.benchmarks.core.console import print_warn
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/problems/navier_stokes_3d_grid/optimization.py:434:12
    |
432 |             grad_proj_fn=grad_proj_fn,
433 |         )
434 |     except Exception as exc:
    |            ^^^^^^^^^
435 |         from mosaic.benchmarks.core.console import print_warn
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/problems/navier_stokes_3d_grid/optimization.py:489:12
    |
487 |         )
488 |         target = apply_tesseract(t, inputs_true_fixed)[output_key]
489 |     except Exception as exc:
    |            ^^^^^^^^^
490 |         from mosaic.benchmarks.core.console import print_warn
    |

BLE001 Do not catch blind exception: `Exception`
    --> mosaic/benchmarks/problems/navier_stokes_3d_grid/optimization.py:1040:12
     |
1038 |         inp_rec = make_inputs(name, ic_opt, domain_extent=domain_extent, **fphys)
1039 |         snaps["final_rec"] = np.asarray(apply_tesseract(t, inp_rec)[output_key])
1040 |     except Exception:
     |            ^^^^^^^^^
1041 |         snaps["final_rec"] = np.zeros_like(np.asarray(ic_opt))
     |

BLE001 Do not catch blind exception: `Exception`
    --> mosaic/benchmarks/problems/navier_stokes_3d_grid/optimization.py:1056:16
     |
1054 |             )
1055 |             snaps["final_perturbed"] = np.asarray(apply_tesseract(t, inp_p)[output_key])
1056 |         except Exception:
     |                ^^^^^^^^^
1057 |             snaps["final_perturbed"] = np.zeros_like(np.asarray(ic_true))
     |

S110 `try`-`except`-`pass` detected, consider logging the exception
  --> mosaic/benchmarks/problems/navier_stokes_grid/optimization.py:61:5
   |
59 |           if vel is not None:
60 |               return np.array(vel)
61 | /     except Exception:
62 | |         pass
   | |____________^
63 |       return None
   |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/problems/navier_stokes_grid/optimization.py:61:12
   |
59 |         if vel is not None:
60 |             return np.array(vel)
61 |     except Exception:
   |            ^^^^^^^^^
62 |         pass
63 |     return None
   |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/problems/navier_stokes_grid/optimization.py:124:12
    |
122 |         vel = out_f.get("result")
123 |         return final_drag, (np.array(vel) if vel is not None else None)
124 |     except Exception:
    |            ^^^^^^^^^
125 |         return (losses[-1] if losses else float("nan")), None
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/problems/shared/optimization.py:191:16
    |
189 |         try:
190 |             live = len(jax.live_arrays())
191 |         except Exception:
    |                ^^^^^^^^^
192 |             live = -1
193 |         print(
    |

BLE001 Do not catch blind exception: `Exception`
  --> mosaic/benchmarks/problems/shared/plots/ics.py:94:12
   |
92 |         candidate = np.asarray(to_2d(ic), dtype=np.float32)
93 |         arr2d = candidate if candidate.ndim == 2 else None
94 |     except Exception:
   |            ^^^^^^^^^
95 |         arr2d = None
96 |     if arr2d is None:
   |

S112 `try`-`except`-`continue` detected, consider logging the exception
   --> mosaic/benchmarks/problems/shared/plots/ics.py:175:13
    |
173 |               try:
174 |                   arr = spec(**plot_params)
175 | /             except Exception:
176 | |                 continue
    | |________________________^
177 |           projected = _ic_to_2d(
178 |               arr,
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/problems/shared/plots/ics.py:175:20
    |
173 |             try:
174 |                 arr = spec(**plot_params)
175 |             except Exception:
    |                    ^^^^^^^^^
176 |                 continue
177 |         projected = _ic_to_2d(
    |

BLE001 Do not catch blind exception: `Exception`
   --> mosaic/benchmarks/problems/thermal_mesh/physics.py:206:12
    |
204 |     try:
205 |         T_nodal = spla.spsolve(K.tocsc(), f)
206 |     except Exception:
    |            ^^^^^^^^^
207 |         T_nodal = np.zeros(n_nodes, dtype=np.float64)
208 |     return T_nodal.astype(np.float32)
    |

TRY004 Prefer `TypeError` exception for invalid type
  --> mosaic/templates/scaffold.py:79:9
   |
77 |         doc = yaml.safe_load(f)
78 |     if not isinstance(doc, dict):
79 |         raise ValueError(f"{path}: expected a YAML mapping, got {type(doc).__name__}")
   |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
80 |     for key in ("name", "schema_module", "output_key"):
81 |         if key not in doc:
   |

PLW1510 `subprocess.run` without explicit `check` argument
  --> mosaic/tesseracts/navier-stokes-grid/openfoam/tesseract_api.py:51:14
   |
49 | def _run_of(cmd: str, cwd: Path) -> None:
50 |     """Run an OpenFOAM command by sourcing the OF environment first."""
51 |     result = subprocess.run(
   |              ^^^^^^^^^^^^^^
52 |         ["bash", "-c", f". {_OF_BASHRC} && {cmd}"],
53 |         cwd=str(cwd),
   |
help: Add explicit `check=False`

PLR0124 Name compared with itself, consider replacing `v != v`
  --> mosaic/tesseracts/navier-stokes-grid/warp-ns/tesseract_api.py:41:8
   |
39 |     """
40 |     # NaN check: v != v is true only for NaN
41 |     if v != v:
   |        ^
42 |         v = wp.float32(0.0)
43 |     if v > wp.float32(1.0e30):
   |

PLW1510 `subprocess.run` without explicit `check` argument
   --> mosaic/tesseracts/structural-mesh/dealii-structural/tesseract_api.py:164:14
    |
162 |     """Invoke the deal.II struct_solver binary."""
163 |     cmd = [_DEALII_SOLVER, str(wd / "input.json")]
164 |     result = subprocess.run(cmd, cwd=str(wd), capture_output=True, text=True)
    |              ^^^^^^^^^^^^^^
165 |     if result.returncode != 0:
166 |         raise RuntimeError(
    |
help: Add explicit `check=False`

PLW1510 `subprocess.run` without explicit `check` argument
   --> mosaic/tesseracts/thermal-mesh/dealii-heat/tesseract_api.py:152:14
    |
150 |     """Invoke the deal.II heat_solver binary."""
151 |     cmd = [_DEALII_SOLVER, str(wd / "input.json")]
152 |     result = subprocess.run(cmd, cwd=str(wd), capture_output=True, text=True)
    |              ^^^^^^^^^^^^^^
153 |     if result.returncode != 0:
154 |         raise RuntimeError(
    |
help: Add explicit `check=False`

BLE001 Do not catch blind exception: `Exception`
  --> tests/core/test_npz_merge.py:78:20
   |
76 |                 barrier.wait(timeout=5)
77 |                 save_npz_merged(path, {key: np.array([value])})
78 |             except Exception as exc:
   |                    ^^^^^^^^^
79 |                 errors.append(exc)
   |

PERF102 When using only the values of a dict use the `values()` method
   --> tests/core/test_status.py:307:24
    |
306 |     def test_every_score_weight_maps_to_a_colour(self) -> None:
307 |         for _key, w in SCORE_WEIGHTS.items():
    |                        ^^^^^^^^^^^^^^^^^^^
308 |             color = weight_color(w)
309 |             self.assertTrue(
    |
help: Replace `.items()` with `.values()`

PLW1510 `subprocess.run` without explicit `check` argument
  --> tests/test_cli_smoke.py:23:12
   |
22 | def _run_help(args: list[str]) -> subprocess.CompletedProcess:
23 |     return subprocess.run(
   |            ^^^^^^^^^^^^^^
24 |         [*MOSAIC, *args, "--help"],
25 |         capture_output=True,
   |
help: Add explicit `check=False`

BLE001 Do not catch blind exception: `Exception`
   --> tests/test_dummy_integration.py:396:24
    |
394 |                 try:
395 |                     cfg.experiments[exp_key].fn(cfg, tags)
396 |                 except Exception as exc:
    |                        ^^^^^^^^^
397 |                     errors[(problem, exp_key)] = exc
398 |         yield {"results_root": results_root, "errors": errors}
    |

PLW1510 `subprocess.run` without explicit `check` argument
  --> tests/test_integration.py:28:13
   |
26 |     try:
27 |         return (
28 |             subprocess.run(
   |             ^^^^^^^^^^^^^^
29 |                 ["docker", "info"],
30 |                 capture_output=True,
   |
help: Add explicit `check=False`

PLW1510 `subprocess.run` without explicit `check` argument
  --> tests/test_integration.py:51:14
   |
49 | def built_solver():
50 |     """Build the Exponax tesseract once for all tests in this module."""
51 |     result = subprocess.run(
   |              ^^^^^^^^^^^^^^
52 |         ["tesseract", "build", _SOLVER_DIR],
53 |         capture_output=True,
   |
help: Add explicit `check=False`

PLW1510 `subprocess.run` without explicit `check` argument
  --> tests/test_plots_only.py:40:14
   |
38 | def test_plots_only_gradient():
39 |     """Mosaic run --plots-only must succeed with existing gradient results."""
40 |     result = subprocess.run(
   |              ^^^^^^^^^^^^^^
41 |         [*MOSAIC, "run", "--plots-only", "-p", "ns-grid", "--suites", "gradient"],
42 |         capture_output=True,
   |
help: Add explicit `check=False`

Found 130 errors.
No fixes available (8 hidden fixes can be enabled with the `--unsafe-fixes` option).

ruff format..............................................................Passed
update-uv-env............................................................Passed
update-requirements......................................................Passed
prettier.................................................................Passed