Bump polars from 1.44.1 to 1.44.2

_typos.toml

@@ -1,4 +1,9 @@
 [default.extend-words]
+# evn = short for "event name" (loop variable) in the verbatim cohort check
+# scripts (scripts/cohort/cohort_check_mimic.py and cohort_check_eicu.py),
+# not a typo for "even". These files cannot be edited without redefining the
+# published cohort groups; see the header comment in each file.
+evn = "evn"
 # ND = MIMIC-IV prescription route abbreviation (nasal, with NU/NS/NAS) in
 # odyssey/data/concepts.py's ANTIBIOTIC_ROUTE_EXCLUDE, not a typo for "AND".
 ND = "ND"

pyproject.toml

@@ -12,7 +12,7 @@ dependencies = [
     # MIMIC-IV -> MEDS extraction (hosp + icu modules; ED not yet covered upstream)
     "MIMIC_IV_MEDS",
     # Used directly (not just transitively via MIMIC_IV_MEDS) for concept labeling.
-    "polars>=1.44.1",
+    "polars>=1.44.2",
     # Model dev. Mac (local, CPU/MPS) installs plain torch, floating freely.
     # On the GCP A100 host, torch is pinned to an exact cu124 build and
     # mamba-ssm (below) to an exact version -- discovered the hard way that
@@ -106,7 +106,7 @@ gemini = [
     # dependencies above) since run.sh's minimal extract-node install is
     # `--no-deps` + this extra only, and skips the base dependency list
     # entirely.
-    "polars>=1.44.1",
+    "polars>=1.44.2",
 ]
 
 # TabICLv2 in-context-learning baseline (odyssey/inference/tabicl_baseline.py),
@@ -222,7 +222,7 @@ explicit = true
 # Same reason as the ruff exclude above: these two ran on the VMs and
 # are committed verbatim, so they cannot be annotated without editing
 # the code that produced the published table.
-exclude = "^scripts/cohort/cohort_check_(mimic|eicu)\\.py$"
+exclude = "cohort_check_(mimic|eicu)\\.py$"
 ignore_missing_imports = true
 install_types = true
 pretty = true
@@ -244,6 +244,21 @@ implicit_reexport = false
 strict_equality = true
 extra_checks = true
 
+# The cohort check scripts are committed verbatim as they ran on the VM.
+# They cannot be annotated without redefining the published cohort groups.
+# polars 1.44.2 tightened quantile()'s return type to float | None, which
+# triggers new mypy errors in these files. The exclude above handles file
+# discovery; this override silences errors when pre-commit passes the files
+# explicitly on the command line (mypy ignores exclude for explicit args).
+[[tool.mypy.overrides]]
+module = [
+    "cohort_check_mimic",
+    "cohort_check_eicu",
+    "scripts.cohort.cohort_check_mimic",
+    "scripts.cohort.cohort_check_eicu",
+]
+ignore_errors = true
+
 [tool.ruff]
 include = ["*.py", "pyproject.toml", "*.ipynb"]
 exclude = [

scripts/gemini/out/evals/gemini_full_14m_v1_eval_forecast.json

@@ -129,4 +129,4 @@
     "n_positive_gaps": 3639349
   },
   "tail_slice": null
-}
+}

scripts/gemini/out/evals/gemini_full_DEC_v12_alerts.json

@@ -1913,4 +1913,4 @@
     },
     "landmark_protocol_version": 4
   }
-]
+]

scripts/gemini/out/evals/gemini_full_DEC_v12_allshards_alerts.json

@@ -1913,4 +1913,4 @@
     },
     "landmark_protocol_version": 4
   }
-]
+]

scripts/gemini/out/evals/gemini_full_DEC_v12_concept_atlas.json

@@ -13011,4 +13011,4 @@
    "mean_activation": 0.4445817383871991
   }
  ]
-}
+}

scripts/gemini/out/evals/gemini_full_DEC_v12_eval_forecast.json

@@ -543,4 +543,4 @@
   },
   "value_metrics": null,
   "tail_slice": null
-}
+}

scripts/gemini/out/evals/gemini_full_DEC_v12_steering_full.json

@@ -14428,4 +14428,4 @@
    "sign_agreement": 1.0
   }
  ]
-}
+}

scripts/gemini/out/evals/gemini_full_v10_15c_alerts.json

@@ -1913,4 +1913,4 @@
     },
     "landmark_protocol_version": 4
   }
-]
+]

scripts/gemini/out/evals/gemini_full_v10_15c_alerts_cis.json

@@ -704,4 +704,4 @@
    }
   }
  }
-}
+}

scripts/gemini/out/evals/gemini_full_v10_15c_counterfactual.json

@@ -219,4 +219,4 @@
       }
     }
   }
-}
+}

scripts/gemini/out/evals/gemini_full_v10_15c_eval_forecast.json

@@ -383,4 +383,4 @@
   },
   "value_metrics": null,
   "tail_slice": null
-}
+}

scripts/gemini/out/evals/gemini_full_v10_15c_intervention_cis.json

@@ -111,4 +111,4 @@
    "n_boot": 2000
   }
  }
-}
+}

scripts/gemini/out/evals/gemini_smoke_2_eval_forecast.json

@@ -129,4 +129,4 @@
     "n_positive_gaps": 3639349
   },
   "tail_slice": null
-}
+}