From ecd9fafadd832ec0a78a35ada8af1a1a22ff3e99 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 14 Sep 2026 09:32:20 +0000 Subject: [PATCH 1/4] Bump astral-sh/setup-uv from 10.0.1 to 10.1.0 Bumps [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 10.0.1 to 10.1.0. - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/v10.0.1...v10.1.0) --- updated-dependencies: - dependency-name: astral-sh/setup-uv dependency-version: 10.1.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- .github/workflows/code_checks.yml | 2 +- .github/workflows/integration_tests.yml | 2 +- .github/workflows/unit_tests.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) 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" From 1549150d8d31bc77fac5130f7e8ff28cb2db62dd 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 09:32:35 +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 838bbdbbb411815f2afcff6b58c76eb5ee10e5c5 Mon Sep 17 00:00:00 2001 From: "aieng-bot[bot]" Date: Mon, 14 Sep 2026 22:48:05 +0000 Subject: [PATCH 3/4] Exclude verbatim cohort-check scripts from mypy and typos pre-commit hooks The cohort_check_mimic.py and cohort_check_eicu.py scripts are verbatim snapshots of the VM run that define the published cohort groups. The mypy pyproject.toml exclude pattern is bypassed when pre-commit passes files explicitly; the typos hook was missing the exclude entirely. Extend both hook excludes to match what pyproject.toml and _typos.toml already intend. Co-authored-by: aieng-bot --- .pre-commit-config.yaml | 4 ++-- _typos.toml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ef7b5d02..c7a831fd 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"] From 739825dd3d5c9849a68803164040a827b3f54adc Mon Sep 17 00:00:00 2001 From: "aieng-bot[bot]" Date: Mon, 14 Sep 2026 22:49:55 +0000 Subject: [PATCH 4/4] Fix YAML escape in mypy pre-commit hook exclude pattern Double-quoted YAML strings don't allow \. as an escape sequence. Switch to single quotes so the regex backslash is literal. Co-authored-by: aieng-bot --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c7a831fd..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|scripts/cohort/cohort_check_(mimic|eicu)\.py)" + exclude: '(tests|scripts/cohort/cohort_check_(mimic|eicu)\.py)' - repo: https://github.com/crate-ci/typos rev: v1