From 3dccbe1ac25544d1b877ce3c29854d2c8d6e8d67 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 16 Mar 2026 19:35:41 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
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Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/uv-pre-commit: 0.8.22 → 0.10.10](https://github.com/astral-sh/uv-pre-commit/compare/0.8.22...0.10.10)
- [github.com/astral-sh/ruff-pre-commit: v0.12.12 → v0.15.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.12...v0.15.6)
- [github.com/pre-commit/mirrors-mypy: v1.17.1 → v1.19.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.17.1...v1.19.1)
- [github.com/crate-ci/typos: v1.37.1 → v1](https://github.com/crate-ci/typos/compare/v1.37.1...v1)
---
 .pre-commit-config.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9f5e40b..de9b14a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -20,12 +20,12 @@ repos:
     - id: check-toml
 
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.8.22
+    rev: 0.10.10
     hooks:
       - id: uv-lock
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.12.12'
+    rev: 'v0.15.6'
     hooks:
     - id: ruff-check
       args: [--fix, --unsafe-fixes, --exit-non-zero-on-fix]
@@ -34,7 +34,7 @@ repos:
       types_or: [python, jupyter]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.17.1
+    rev: v1.19.1
     hooks:
     - id: mypy
       entry: python3 -m mypy --config-file pyproject.toml
@@ -43,7 +43,7 @@ repos:
       exclude: "data"
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.37.1
+    rev: v1
     hooks:
       - id: typos
         exclude: ^data/

From 55ef9c547953ac5819ea2981ea2a51683d8b845f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 16 Mar 2026 19:37:23 +0000
Subject: [PATCH 2/2] [pre-commit.ci] Add auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/biothink/self_reflection/data_process/process_data.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/biothink/self_reflection/data_process/process_data.py b/src/biothink/self_reflection/data_process/process_data.py
index 804cc6d..d7eca50 100644
--- a/src/biothink/self_reflection/data_process/process_data.py
+++ b/src/biothink/self_reflection/data_process/process_data.py
@@ -201,9 +201,11 @@ def process_dataset(dataset, remove_original_output=False):
     # First, filter out rows with unwanted tokens to avoid multiprocessing issues
     print("Filtering dataset to remove unwanted tokens...")
     filtered = dataset.filter(
-        lambda x: "[No Retrieval]" not in x.get("output", "")
-        and "[Continue to Use Evidence]" not in x.get("output", "")
-        and x.get("output", "").startswith("[Retrieval]"),
+        lambda x: (
+            "[No Retrieval]" not in x.get("output", "")
+            and "[Continue to Use Evidence]" not in x.get("output", "")
+            and x.get("output", "").startswith("[Retrieval]")
+        ),
         num_proc=4,
     )