Merge branch 'main' into jwilber/esm2-sae-dashboard-update

Author: jwilber

.gitleaks.toml

@@ -0,0 +1,12 @@
+# Gitleaks configuration
+# https://github.com/gitleaks/gitleaks
+
+title = "BioNeMo Framework Gitleaks Config"
+
+[extend]
+useDefault = true
+
+[allowlist]
+paths = [
+    '''3rdparty/''',
+]

.gitleaksignore

@@ -0,0 +1,5 @@
+# Gitleaks ignore file - fingerprints of known false positives
+# https://github.com/gitleaks/gitleaks#gitleaksignore
+
+# False positive: training hyperparameter string `lr=3e-4` matches generic-api-key rule
+bionemo-recipes/interpretability/sparse_autoencoders/recipes/esm2/README.md:generic-api-key:116

.pre-commit-config.yaml

@@ -40,13 +40,7 @@ repos:
         - mdformat-black
         - mdformat-frontmatter
         - black==25.12.0
-  - repo: https://github.com/Yelp/detect-secrets
-    rev: v1.5.0
+  - repo: https://github.com/gitleaks/gitleaks
+    rev: v8.24.2
     hooks:
-      - id: detect-secrets
-        name: detect-secrets (everything but notebooks)
-        args: ['--baseline', '.secrets.baseline', '--exclude-files', '(.*\.ipynb|.*\.baseline)$', ]
-        exclude: package.lock.json
-      - id: detect-secrets
-        name: detect-secrets (notebooks only)
-        args: ['--baseline', '.secrets-nb.baseline', '--exclude-files', '^.(?!.*\.ipynb)', '--exclude-lines', '"(hash|id|image/\w+)":.*|<.*at 0x[0-9a-f]+>|object at 0x[0-9a-f]+', ]
+      - id: gitleaks