diff --git a/.github/workflows/code_checks.yml b/.github/workflows/code_checks.yml
index 76522657..5003a6d5 100644
--- a/.github/workflows/code_checks.yml
+++ b/.github/workflows/code_checks.yml
@@ -39,7 +39,7 @@ jobs:
       - uses: actions/checkout@v7.0.1
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.1.0
         with:
           # Install a specific version of uv.
           version: "0.9.11"
diff --git a/.github/workflows/integration_tests.yml b/.github/workflows/integration_tests.yml
index 67b574b4..45a9e27e 100644
--- a/.github/workflows/integration_tests.yml
+++ b/.github/workflows/integration_tests.yml
@@ -47,7 +47,7 @@ jobs:
       - uses: actions/checkout@v7.0.1
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.1.0
         with:
           # Install a specific version of uv.
           version: "0.9.11"
diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
index 93736ab5..08fcae93 100644
--- a/.github/workflows/unit_tests.yml
+++ b/.github/workflows/unit_tests.yml
@@ -47,7 +47,7 @@ jobs:
       - uses: actions/checkout@v7.0.1
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v10.0.1
+        uses: astral-sh/setup-uv@v10.1.0
         with:
           # Install a specific version of uv.
           version: "0.9.11"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ef7b5d02..31aff6ab 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -42,7 +42,7 @@ repos:
       entry: python3 -m mypy --config-file pyproject.toml
       language: system
       types: [python]
-      exclude: "tests"
+      exclude: '(tests|scripts/cohort/cohort_check_(mimic|eicu)\.py)'
 
   - repo: https://github.com/crate-ci/typos
     rev: v1
@@ -56,7 +56,7 @@ repos:
         # etc.), not ours to rename; see _typos.toml for the same exclusion
         # (this one is what actually stops the hook, since pre-commit's own
         # file filtering runs before typos ever sees its own config)
-        exclude: ^(docs/experiments\.md|odyssey/data/resources/.*\.csv|scripts/gemini/out/.*)$
+        exclude: ^(docs/experiments\.md|odyssey/data/resources/.*\.csv|scripts/gemini/out/.*|scripts/cohort/cohort_check_(mimic|eicu)\.py)$
 
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.9.1
diff --git a/_typos.toml b/_typos.toml
index 7aa8f26a..3d8d3581 100644
--- a/_typos.toml
+++ b/_typos.toml
@@ -37,4 +37,4 @@ get_rolling_window_indicies = "get_rolling_window_indicies"
 # ours to rename and will keep showing up as new false positives every time
 # a fresh report is committed, so the whole directory is excluded rather
 # than growing an extend-words entry per column.
-extend-exclude = ["scripts/gemini/out/"]
+extend-exclude = ["scripts/gemini/out/", "scripts/cohort/cohort_check_mimic.py", "scripts/cohort/cohort_check_eicu.py"]
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
+}