From 275edd908b9b69fcafb76884839e1990a7455abb Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 14 Sep 2026 09:37:04 +0000
Subject: [PATCH 1/4] Bump polars from 1.44.1 to 1.44.2

Bumps [polars](https://github.com/pola-rs/polars) from 1.44.1 to 1.44.2.
- [Release notes](https://github.com/pola-rs/polars/releases)
- [Commits](https://github.com/pola-rs/polars/compare/py-1.44.1...py-1.44.2)

---
updated-dependencies:
- dependency-name: polars
  dependency-version: 1.44.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 pyproject.toml |  4 ++--
 uv.lock        | 34 +++++++++++++++++-----------------
 2 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 98cad28c..809d5bcf 100644
--- a/pyproject.toml
+++ b/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),
diff --git a/uv.lock b/uv.lock
index fc1993fb..ef958888 100644
--- a/uv.lock
+++ b/uv.lock
@@ -2516,8 +2516,8 @@ requires-dist = [
     { name = "mimic-iv-meds" },
     { name = "omegaconf", marker = "extra == 'survivalpfn'", specifier = ">=2.3.0" },
     { name = "pandas", marker = "extra == 'gemini'", specifier = ">=2.2.0" },
-    { name = "polars", specifier = ">=1.44.1" },
-    { name = "polars", marker = "extra == 'gemini'", specifier = ">=1.44.1" },
+    { name = "polars", specifier = ">=1.44.2" },
+    { name = "polars", marker = "extra == 'gemini'", specifier = ">=1.44.2" },
     { name = "protobuf", marker = "extra == 'text'", specifier = ">=7.36.1" },
     { name = "psycopg2-binary", marker = "extra == 'gemini'", specifier = ">=2.9.0" },
     { name = "pyarrow", marker = "extra == 'gemini'", specifier = ">=15.0.0" },
@@ -2846,30 +2846,30 @@ wheels = [
 
 [[package]]
 name = "polars"
-version = "1.44.1"
+version = "1.44.2"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "polars-runtime-32" },
 ]
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+    { url = "https://files.pythonhosted.org/packages/51/6d/3014112c7f717d1253223faa13b6db3ac3a64ed00ab2a3bc1b942bc9cdd4/polars-1.44.2-py3-none-any.whl", hash = "sha256:1bb331f17a40d9d931101533dcd33637b66edc61eb377b07020dac16a0f0377b", size = 865768, upload-time = "2026-09-09T07:40:12.053Z" },
 ]
 
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 [[package]]

From baaf6f767e77a89e76f0b8c6dac11f45671dad62 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 14 Sep 2026 09:37:39 +0000
Subject: [PATCH 2/4] [pre-commit.ci] Add auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 scripts/gemini/out/evals/gemini_full_14m_v1_eval_forecast.json  | 2 +-
 scripts/gemini/out/evals/gemini_full_DEC_v12_alerts.json        | 2 +-
 .../gemini/out/evals/gemini_full_DEC_v12_allshards_alerts.json  | 2 +-
 scripts/gemini/out/evals/gemini_full_DEC_v12_concept_atlas.json | 2 +-
 scripts/gemini/out/evals/gemini_full_DEC_v12_eval_forecast.json | 2 +-
 scripts/gemini/out/evals/gemini_full_DEC_v12_steering_full.json | 2 +-
 scripts/gemini/out/evals/gemini_full_v10_15c_alerts.json        | 2 +-
 scripts/gemini/out/evals/gemini_full_v10_15c_alerts_cis.json    | 2 +-
 .../gemini/out/evals/gemini_full_v10_15c_counterfactual.json    | 2 +-
 scripts/gemini/out/evals/gemini_full_v10_15c_eval_forecast.json | 2 +-
 .../gemini/out/evals/gemini_full_v10_15c_intervention_cis.json  | 2 +-
 scripts/gemini/out/evals/gemini_smoke_2_eval_forecast.json      | 2 +-
 12 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/scripts/gemini/out/evals/gemini_full_14m_v1_eval_forecast.json b/scripts/gemini/out/evals/gemini_full_14m_v1_eval_forecast.json
index 6a6b2a3d..a6adb1bc 100644
--- a/scripts/gemini/out/evals/gemini_full_14m_v1_eval_forecast.json
+++ b/scripts/gemini/out/evals/gemini_full_14m_v1_eval_forecast.json
@@ -129,4 +129,4 @@
     "n_positive_gaps": 3639349
   },
   "tail_slice": null
-}
\ No newline at end of file
+}
diff --git a/scripts/gemini/out/evals/gemini_full_DEC_v12_alerts.json b/scripts/gemini/out/evals/gemini_full_DEC_v12_alerts.json
index 84211bd8..d110a460 100644
--- a/scripts/gemini/out/evals/gemini_full_DEC_v12_alerts.json
+++ b/scripts/gemini/out/evals/gemini_full_DEC_v12_alerts.json
@@ -1913,4 +1913,4 @@
     },
     "landmark_protocol_version": 4
   }
-]
\ No newline at end of file
+]
diff --git a/scripts/gemini/out/evals/gemini_full_DEC_v12_allshards_alerts.json b/scripts/gemini/out/evals/gemini_full_DEC_v12_allshards_alerts.json
index efcf285e..be67255b 100644
--- a/scripts/gemini/out/evals/gemini_full_DEC_v12_allshards_alerts.json
+++ b/scripts/gemini/out/evals/gemini_full_DEC_v12_allshards_alerts.json
@@ -1913,4 +1913,4 @@
     },
     "landmark_protocol_version": 4
   }
-]
\ No newline at end of file
+]
diff --git a/scripts/gemini/out/evals/gemini_full_DEC_v12_concept_atlas.json b/scripts/gemini/out/evals/gemini_full_DEC_v12_concept_atlas.json
index 66eedf2b..96da3caa 100644
--- a/scripts/gemini/out/evals/gemini_full_DEC_v12_concept_atlas.json
+++ b/scripts/gemini/out/evals/gemini_full_DEC_v12_concept_atlas.json
@@ -13011,4 +13011,4 @@
    "mean_activation": 0.4445817383871991
   }
  ]
-}
\ No newline at end of file
+}
diff --git a/scripts/gemini/out/evals/gemini_full_DEC_v12_eval_forecast.json b/scripts/gemini/out/evals/gemini_full_DEC_v12_eval_forecast.json
index f8b0699c..2a5636d7 100644
--- a/scripts/gemini/out/evals/gemini_full_DEC_v12_eval_forecast.json
+++ b/scripts/gemini/out/evals/gemini_full_DEC_v12_eval_forecast.json
@@ -543,4 +543,4 @@
   },
   "value_metrics": null,
   "tail_slice": null
-}
\ No newline at end of file
+}
diff --git a/scripts/gemini/out/evals/gemini_full_DEC_v12_steering_full.json b/scripts/gemini/out/evals/gemini_full_DEC_v12_steering_full.json
index 41e55272..634f6db7 100644
--- a/scripts/gemini/out/evals/gemini_full_DEC_v12_steering_full.json
+++ b/scripts/gemini/out/evals/gemini_full_DEC_v12_steering_full.json
@@ -14428,4 +14428,4 @@
    "sign_agreement": 1.0
   }
  ]
-}
\ No newline at end of file
+}
diff --git a/scripts/gemini/out/evals/gemini_full_v10_15c_alerts.json b/scripts/gemini/out/evals/gemini_full_v10_15c_alerts.json
index 7b04a88c..4c6dc770 100644
--- a/scripts/gemini/out/evals/gemini_full_v10_15c_alerts.json
+++ b/scripts/gemini/out/evals/gemini_full_v10_15c_alerts.json
@@ -1913,4 +1913,4 @@
     },
     "landmark_protocol_version": 4
   }
-]
\ No newline at end of file
+]
diff --git a/scripts/gemini/out/evals/gemini_full_v10_15c_alerts_cis.json b/scripts/gemini/out/evals/gemini_full_v10_15c_alerts_cis.json
index e559497c..80b3f7df 100644
--- a/scripts/gemini/out/evals/gemini_full_v10_15c_alerts_cis.json
+++ b/scripts/gemini/out/evals/gemini_full_v10_15c_alerts_cis.json
@@ -704,4 +704,4 @@
    }
   }
  }
-}
\ No newline at end of file
+}
diff --git a/scripts/gemini/out/evals/gemini_full_v10_15c_counterfactual.json b/scripts/gemini/out/evals/gemini_full_v10_15c_counterfactual.json
index 39b70901..0d486be5 100644
--- a/scripts/gemini/out/evals/gemini_full_v10_15c_counterfactual.json
+++ b/scripts/gemini/out/evals/gemini_full_v10_15c_counterfactual.json
@@ -219,4 +219,4 @@
       }
     }
   }
-}
\ No newline at end of file
+}
diff --git a/scripts/gemini/out/evals/gemini_full_v10_15c_eval_forecast.json b/scripts/gemini/out/evals/gemini_full_v10_15c_eval_forecast.json
index 2fb9ffb2..caf52962 100644
--- a/scripts/gemini/out/evals/gemini_full_v10_15c_eval_forecast.json
+++ b/scripts/gemini/out/evals/gemini_full_v10_15c_eval_forecast.json
@@ -383,4 +383,4 @@
   },
   "value_metrics": null,
   "tail_slice": null
-}
\ No newline at end of file
+}
diff --git a/scripts/gemini/out/evals/gemini_full_v10_15c_intervention_cis.json b/scripts/gemini/out/evals/gemini_full_v10_15c_intervention_cis.json
index 7debd16e..033ff473 100644
--- a/scripts/gemini/out/evals/gemini_full_v10_15c_intervention_cis.json
+++ b/scripts/gemini/out/evals/gemini_full_v10_15c_intervention_cis.json
@@ -111,4 +111,4 @@
    "n_boot": 2000
   }
  }
-}
\ No newline at end of file
+}
diff --git a/scripts/gemini/out/evals/gemini_smoke_2_eval_forecast.json b/scripts/gemini/out/evals/gemini_smoke_2_eval_forecast.json
index 6eba1956..d9622d0c 100644
--- a/scripts/gemini/out/evals/gemini_smoke_2_eval_forecast.json
+++ b/scripts/gemini/out/evals/gemini_smoke_2_eval_forecast.json
@@ -129,4 +129,4 @@
     "n_positive_gaps": 3639349
   },
   "tail_slice": null
-}
\ No newline at end of file
+}

From d759793c7222d223833d9d888f9f356302e5046c Mon Sep 17 00:00:00 2001
From: "aieng-bot[bot]" <aieng-bot@vectorinstitute.ai>
Date: Mon, 14 Sep 2026 22:49:43 +0000
Subject: [PATCH 3/4] Fix lint/mypy CI failures from polars 1.44.2 type-stub
 changes

- Broaden mypy exclude pattern in pyproject.toml to match the cohort
  check scripts regardless of whether mypy receives an absolute or
  relative path (remove leading ^ anchor). These verbatim scripts
  cannot be annotated; polars 1.44.2 tightened quantile()'s return
  type to float | None, causing new mypy errors.
- Whitelist `evn` (event-name loop variable) in _typos.toml so the
  typos hook does not flag it as a misspelling of "even" in the
  verbatim cohort check scripts.

Co-authored-by: aieng-bot <aieng-bot@vectorinstitute.ai>
---
 _typos.toml    | 5 +++++
 pyproject.toml | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/_typos.toml b/_typos.toml
index 7aa8f26a..e4beec75 100644
--- a/_typos.toml
+++ b/_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"
diff --git a/pyproject.toml b/pyproject.toml
index 809d5bcf..b72385f6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -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

From c9a637e9427de71944adf232d5a0887fd11cbf3c Mon Sep 17 00:00:00 2001
From: "aieng-bot[bot]" <aieng-bot@vectorinstitute.ai>
Date: Mon, 14 Sep 2026 22:58:35 +0000
Subject: [PATCH 4/4] Add mypy.overrides to silence verbatim cohort-check
 script errors

The cohort check scripts (cohort_check_mimic.py, cohort_check_eicu.py)
cannot be annotated without redefining the published cohort groups.
The existing `exclude` pattern in [tool.mypy] suppresses discovery-based
checking, but mypy ignores that option when files are passed explicitly
on the command line (which is how pre-commit invokes it). polars 1.44.2
tightened quantile()'s return type to float | None, surfacing 8 new
mypy errors in these two files. Adding [[tool.mypy.overrides]] with
ignore_errors = true is the correct way to suppress errors for
explicitly-passed files.

Co-authored-by: aieng-bot <aieng-bot@vectorinstitute.ai>
---
 pyproject.toml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index b72385f6..f7e34054 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -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 = [