diff --git a/.github/workflows/validate-pr.yml b/.github/workflows/validate-pr.yml
index cb842c4..89ef4cc 100644
--- a/.github/workflows/validate-pr.yml
+++ b/.github/workflows/validate-pr.yml
@@ -85,7 +85,7 @@ jobs:
           if [ -z "$changed" ]; then
             echo "✅ No added/modified plugins to validate." >> "$GITHUB_STEP_SUMMARY"
             echo "toml_valid=true" >> "$GITHUB_OUTPUT"
-          elif python head/scripts/generate_index.py -t "$GH_TOKEN" --strict -p $changed; then
+          elif python head/scripts/generate_index.py head/repositories.toml -t "$GH_TOKEN" --strict -p $changed; then
             echo "✅ All changed plugins validated successfully." >> "$GITHUB_STEP_SUMMARY"
             echo "toml_valid=true" >> "$GITHUB_OUTPUT"
           else
@@ -142,7 +142,9 @@ jobs:
 
           See the [workflow summary](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}) for details."
 
-          gh pr comment ${{ github.event.pull_request.number }} --body "$comment"
+          gh pr comment ${{ github.event.pull_request.number }} \
+            --repo "${{ github.repository }}" \
+            --body "$comment"
 
       # ── Final: fail the job if any check failed ──
       - name: Fail on validation errors
diff --git a/repositories.toml b/repositories.toml
index d4372fa..b9fe69d 100644
--- a/repositories.toml
+++ b/repositories.toml
@@ -129,3 +129,7 @@ git.commit = "d1cd86cf9dd5154fe3066a64d5e500dc9ac9fe8e"
 git.repo = "https://github.com/matterhorn103/avogadro-crest"
 git.commit = "4ac0a3135fc62e6e5c3d04a56a6b828a0050936e"
 release-tag = "0.1.1"
+
+[pypept]
+git.repo = "https://github.com/ghutchis/avogadro-pypept"
+git.commit = "e933ae40dbe1d5d5e3a76cac36eed69b6d430766"
\ No newline at end of file