Merge remote-tracking branch 'origin/main' into claude/issue-35-20251222-1949

Author: caufieldjh

.github/workflows/claude-code-review.yml

@@ -27,7 +27,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 1
 

.github/workflows/claude-issue-summarize.yml

@@ -14,7 +14,7 @@ jobs:
       issues: write
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           ref: ${{ github.ref }}
 

.github/workflows/claude-issue-triage.yml

@@ -14,7 +14,7 @@ jobs:
       issues: write
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           ref: ${{ github.ref }}
 

.github/workflows/claude-ontology-review.yml

@@ -29,7 +29,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 1
 

.github/workflows/claude.yml

@@ -26,7 +26,7 @@ jobs:
       actions: read # Required for Claude to read CI results on PRs
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 1
 

.github/workflows/deploy-docs.yaml

@@ -20,7 +20,7 @@ jobs:
     steps:
       # https://github.com/actions/checkout
       - name: Checkout
-        uses: actions/checkout@v4.2.2
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0  # otherwise, you will fail to push refs to dest repo
 

.github/workflows/dragon-ai.yml

@@ -21,7 +21,7 @@ jobs:
       result: ${{ steps.check.outputs.result }}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         # this seems to be necessary to ensure actions uses the latest; see
         # https://github.com/actions/checkout/issues/439
         with:
@@ -101,7 +101,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           ref: ${{ github.ref }}
           token: ${{ secrets.PAT_FOR_PR }}  # Use PAT for checkout to allow committing later

.github/workflows/main.yaml

@@ -26,7 +26,7 @@ jobs:
 
       # https://github.com/actions/checkout
       - name: Check out repository
-        uses: actions/checkout@v4.2.2
+        uses: actions/checkout@v6
         with:
           persist-credentials: false
 

.github/workflows/pypi-publish.yaml

@@ -28,7 +28,7 @@ jobs:
     steps:
       # https://github.com/actions/checkout
       - name: Check out repository
-        uses: actions/checkout@v4.2.2
+        uses: actions/checkout@v6
         with:
           persist-credentials: false
 

cache/enums/diseaseterm_cb9fbc86f8a3.csv

@@ -62,3 +62,5 @@ MONDO:0007444
 MONDO:0008491
 MONDO:0007606
 MONDO:0700294
+MONDO:0017276
+MONDO:0007488