openbiox · ShixiangWang · Apr 17, 2026 · Apr 17, 2026 · Apr 17, 2026 · Apr 17, 2026
diff --git a/.github/scripts/generate_skills.py b/.github/scripts/generate_skills.py
@@ -294,7 +294,6 @@ def qmd_to_skill_offline(filepath: Path, base_url: str = DEFAULT_BASE_URL) -> Di
         "tutorial_url": tutorial_url,
         "skill": skill_text,
         "source_file": str(filepath),
-        "skill_file": f"skills/{category}/{filepath.stem}_skill.md",
     }
 
 
@@ -641,7 +640,6 @@ def generate_skill(self, filepath: Path,
             "tutorial_url": tutorial_url,
             "skill": skill_text,
             "source_file": str(filepath),
-            "skill_file": f"skills/{category}/{filepath.stem}_skill.md",
         }
 
 
@@ -687,28 +685,18 @@ def main():
         formatter_class=argparse.RawDescriptionHelpFormatter,
     )
     parser.add_argument("--input", default=".", help="Input QMD file or directory")
-    parser.add_argument("--output", default="skills", help="Output directory")
     parser.add_argument("--base-url", default=DEFAULT_BASE_URL)
-    parser.add_argument("--format", choices=["markdown", "json", "both"],
-                        default="both")
     parser.add_argument("--offline", action="store_true",
                         help="Use offline rule-based extraction (no LLM)")
     parser.add_argument("--files", nargs="*",
                         help="Specific QMD files to process")
     parser.add_argument("--changed-files",
-                        help="Space-separated list of changed QMD files")
+                        help="Space-separated list of changed QMD files (ignored; always processes all)")
     parser.add_argument("--verbose", action="store_true")
     args = parser.parse_args()
 
-    output_dir = Path(args.output)
-    output_dir.mkdir(parents=True, exist_ok=True)
-
     # Determine which files to process
-    if args.changed_files:
-        qmd_files = [Path(f.strip()) for f in args.changed_files.split()
-                     if f.strip().endswith(".qmd")
-                     and not f.strip().endswith(".zh.qmd")]
-    elif args.files:
+    if args.files:
         qmd_files = [Path(f) for f in args.files
                      if f.endswith(".qmd") and not f.endswith(".zh.qmd")]
     else:
@@ -755,89 +743,8 @@ def main():
             errors.append((f, exc))
             print(f"  ✗ {f}: {exc}", file=sys.stderr)
 
-    write_json = args.format in ("json", "both")
-    write_markdown = args.format in ("markdown", "both")
-
-    # Write individual skill Markdown files
-    if write_markdown:
-        for skill in skills:
-            cat_dir = output_dir / skill["category"]
-            cat_dir.mkdir(parents=True, exist_ok=True)
-            stem = Path(skill["source_file"]).stem
-            out_file = cat_dir / f"{stem}_skill.md"
-            out_file.write_text(skill["skill"], encoding="utf-8")
-        print(f"\nWrote {len(skills)} skill file(s) to {output_dir}/")
-
-    # Build or update index
-    # In full mode (no specific files), replace entirely; in incremental mode, merge
-    incremental = bool(args.changed_files or args.files)
-    index_file = output_dir / "index.json"
-
-    if incremental and index_file.exists():
-        # Load existing index and merge with new skills
-        try:
-            existing_index = json.loads(index_file.read_text(encoding="utf-8"))
-        except (json.JSONDecodeError, OSError):
-            existing_index = []
-
-        new_entries = {s["source_file"]: {k: v for k, v in s.items() if k != "skill"}
-                       for s in skills}
-
-        updated_index = []
-        seen = set()
-        for entry in existing_index:
-            src = entry.get("source_file", "")
-            if src in new_entries:
-                updated_index.append(new_entries[src])
-                seen.add(src)
-            else:
-                updated_index.append(entry)
-        for src, entry in new_entries.items():
-            if src not in seen:
-                updated_index.append(entry)
-    else:
-        # Full replacement
-        updated_index = [{k: v for k, v in s.items() if k != "skill"}
-                         for s in skills]
-
-    with open(index_file, "w", encoding="utf-8") as fh:
-        json.dump(updated_index, fh, ensure_ascii=False, indent=2)
-    print(f"Index written to {index_file} ({len(updated_index)} entries)")
-
-    # Write full skills JSON
-    if write_json:
-        full_file = output_dir / "bizard_skills.json"
-
-        if incremental and full_file.exists():
-            # Merge with existing full JSON
-            try:
-                existing_full = json.loads(full_file.read_text(encoding="utf-8"))
-            except (json.JSONDecodeError, OSError):
-                existing_full = []
-
-            new_full = {s["source_file"]: s for s in skills}
-            updated_full = []
-            seen_full = set()
-            for entry in existing_full:
-                src = entry.get("source_file", "")
-                if src in new_full:
-                    updated_full.append(new_full[src])
-                    seen_full.add(src)
-                else:
-                    updated_full.append(entry)
-            for src, entry in new_full.items():
-                if src not in seen_full:
-                    updated_full.append(entry)
-        else:
-            # Full replacement
-            updated_full = list(skills)
-
-        with open(full_file, "w", encoding="utf-8") as fh:
-            json.dump(updated_full, fh, ensure_ascii=False, indent=2)
-        print(f"Full skills JSON written to {full_file} ({len(updated_full)} entries)")
-
-    # Generate unified SKILL.md from the full index
-    generate_unified_skill(index_file, Path("files/gallery_data.csv"),
+    # Generate unified SKILL.md directly from in-memory skills list
+    generate_unified_skill(skills, Path("files/gallery_data.csv"),
                            Path("SKILL.md"))
 
     # Summary
@@ -888,7 +795,7 @@ def main():
 ]
 
 
-def generate_unified_skill(index_path: Path, gallery_csv: Path,
+def generate_unified_skill(all_skills: List[dict], gallery_csv: Path,
                            output_path: Path) -> None:
     """Generate the unified ``SKILL.md`` — an AI skill instruction document.
 
@@ -898,13 +805,8 @@ def generate_unified_skill(index_path: Path, gallery_csv: Path,
     """
     import csv as _csv
 
-    if not index_path.exists():
-        print(f"  ⚠ Skipping unified SKILL.md: {index_path} not found")
-        return
-
-    all_skills = json.loads(index_path.read_text(encoding="utf-8"))
     if not all_skills:
-        print("  ⚠ Skipping unified SKILL.md: index is empty")
+        print("  ⚠ Skipping unified SKILL.md: no skills provided")
         return
 
     # Gallery row count
@@ -984,6 +886,13 @@ def generate_unified_skill(index_path: Path, gallery_csv: Path,
     )
     L.append("    website: https://openbiox.github.io/Bizard/")
     L.append("    repository: https://github.com/openbiox/Bizard")
+    L.append("    citation: >")
+    L.append(
+        "      - Li, K., Zheng, H., Huang, K., Chai, Y., Peng, Y., Wang, C., "
+        "... & Wang, S. (2026). Bizard: A Community\u2010Driven Platform for "
+        "Accelerating and Enhancing Biomedical Data Visualization. iMetaMed, "
+        "e70038. <https://doi.org/10.1002/imm3.70038>"
+    )
     L.append("---")
     L.append("")
     # ── Title & role ────────────────────────────────────────────────

diff --git a/.github/workflows/generate-skills.yml b/.github/workflows/generate-skills.yml
@@ -12,10 +12,6 @@ on:
       - '.github/scripts/generate_skills.py'
   workflow_dispatch:
     inputs:
-      files:
-        description: 'Space-separated list of QMD files to process (empty = all)'
-        required: false
-        default: ''
       pr_number:
         description: 'PR number (for command-triggered runs)'
         required: false
@@ -69,78 +65,47 @@ jobs:
       - name: Install dependencies
         run: pip install openai
 
-      # Detect changed files for push events
-      - name: Detect changed QMD files
-        if: github.event_name == 'push' && inputs.files == ''
-        id: changed
-        run: |
-          CHANGED=$(git diff --name-only HEAD~1 HEAD -- '*.qmd' | grep -v '\.zh\.qmd$' || true)
-          echo "files<<EOF" >> "$GITHUB_OUTPUT"
-          echo "$CHANGED" >> "$GITHUB_OUTPUT"
-          echo "EOF" >> "$GITHUB_OUTPUT"
-          echo "Changed QMD files: $CHANGED"
-
-      - name: Generate skill documents
+      - name: Generate unified SKILL.md
         env:
           AI_Model_API_KEY: ${{ secrets.AI_Model_API_KEY }}
           AI_Model_BASE_URL: ${{ secrets.AI_Model_BASE_URL }}
           AI_Model_Name: ${{ secrets.AI_Model_Name }}
           OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
         run: |
-          ARGS="--output skills/ --base-url https://openbiox.github.io/Bizard/ --format both --verbose"
+          ARGS="--base-url https://openbiox.github.io/Bizard/ --verbose"
 
           # Check if offline mode is requested
           if [ "${{ inputs.offline }}" = "true" ]; then
             ARGS="${ARGS} --offline"
           fi
 
-          # Determine which files to process
-          if [ -n "${{ inputs.files }}" ]; then
-            # Specific files from workflow dispatch
-            python .github/scripts/generate_skills.py ${ARGS} --changed-files "${{ inputs.files }}"
-          elif [ -n "${{ steps.changed.outputs.files }}" ]; then
-            # Changed files from push event
-            FILES=$(echo "${{ steps.changed.outputs.files }}" | tr '\n' ' ')
-            python .github/scripts/generate_skills.py ${ARGS} --changed-files "${FILES}"
-          else
-            # Process all files (manual dispatch without file list)
-            python .github/scripts/generate_skills.py ${ARGS}
-          fi
+          python .github/scripts/generate_skills.py ${ARGS}
 
       - name: Check for changes
         id: git-check
         run: |
-          if git diff --quiet && [ -z "$(git ls-files --others --exclude-standard skills/)" ]; then
+          if git diff --quiet SKILL.md; then
             echo "committed=false" >> "$GITHUB_OUTPUT"
-            echo "No skill file changes detected."
+            echo "No SKILL.md changes detected."
           else
             echo "committed=true" >> "$GITHUB_OUTPUT"
-            echo "Skill files updated."
-            git status --short
-          fi
-
-      - name: Check for changes (including unified SKILL.md)
-        id: git-check-unified
-        run: |
-          if git diff --quiet SKILL.md && git diff --quiet -- skills/; then
-            echo "No unified skill or skills directory changes."
-          else
-            echo "unified_changed=true" >> "$GITHUB_OUTPUT"
+            echo "SKILL.md updated."
+            git status --short SKILL.md
           fi
 
-      - name: Commit and push skill documents
-        if: steps.git-check.outputs.committed == 'true' || steps.git-check-unified.outputs.unified_changed == 'true'
+      - name: Commit and push SKILL.md
+        if: steps.git-check.outputs.committed == 'true'
         run: |
           git config user.email "github-actions[bot]@users.noreply.github.com"
           git config user.name  "github-actions[bot]"
-          git add skills/ SKILL.md
-          git commit -m "chore: regenerate AI skill documents" \
-            -m "Auto-generated skill documents from QMD tutorials."
+          git add SKILL.md
+          git commit -m "chore: regenerate AI skill document" \
+            -m "Auto-generated SKILL.md from QMD tutorials."
           BRANCH="${PR_BRANCH:-${{ github.ref_name }}}"
           git push origin "${BRANCH}"
 
       - name: Post PR comment
-        if: (steps.git-check.outputs.committed == 'true' || steps.git-check-unified.outputs.unified_changed == 'true') && inputs.pr_number != ''
+        if: steps.git-check.outputs.committed == 'true' && inputs.pr_number != ''
         uses: actions/github-script@v7
         with:
           script: |
@@ -150,5 +115,5 @@ jobs:
               owner: context.repo.owner,
               repo: context.repo.repo,
               issue_number: prNumber,
-              body: `✅ **Skill documents regenerated** and pushed to the PR branch.\n\nSee the [workflow run](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}) for details.`
+              body: `✅ **SKILL.md regenerated** and pushed to the PR branch.\n\nSee the [workflow run](${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}) for details.`
             });
diff --git a/.github/workflows/quarto-publish.yml b/.github/workflows/quarto-publish.yml
@@ -24,7 +24,6 @@ on:
     paths-ignore:
       - '*.md'
       - 'LICENSE'
-      - 'skills/**'
       - 'scripts/**'
       - '.github/scripts/**'
       - '.github/workflows/auto-translate.yml'

diff --git a/.github/workflows/skill-command.yml b/.github/workflows/skill-command.yml
@@ -8,9 +8,7 @@ name: Handle /skill PR Comment Command
 #   3. Dispatches generate-skills.yml (workflow_dispatch) with the PR context
 #
 # Usage in a PR comment:
-#   /skill                          → regenerate skills for all changed QMD files
-#   /skill Omics/VolcanoPlot.qmd    → regenerate skill for one specific file
-#   /skill File1.qmd File2.qmd      → regenerate skills for multiple files
+#   /skill                          → regenerate SKILL.md from all QMD tutorials
 #   /skill --offline                → use offline mode (no LLM API)
 # ──────────────────────────────────────────────────────────────────────────────
 on:
@@ -79,9 +77,6 @@ jobs:
             // ── Parse arguments ───────────────────────────────────────────────
             const parts = context.payload.comment.body.trim().split(/\s+/).slice(1);
             const offline = parts.includes('--offline') ? 'true' : 'false';
-            const files = parts
-              .filter(p => (p.endsWith('.qmd') || p.endsWith('.Qmd')) && !p.endsWith('.zh.qmd'))
-              .join(' ');
 
             // ── Dispatch the skill generation workflow ────────────────────────
             const defaultBranch = context.payload.repository.default_branch;
@@ -92,20 +87,16 @@ jobs:
               ref:         defaultBranch,
               inputs: {
                 pr_number: String(context.issue.number),
-                files:     files || '',
                 offline:   offline,
               },
             });
 
             // ── Post acknowledgement comment ──────────────────────────────────
             const runsUrl = `https://github.com/${context.repo.owner}/${context.repo.repo}/actions/workflows/generate-skills.yml`;
-            const filesMsg = files
-              ? `\n\n**Target files:** \`${files.replace(/ /g, '`, `')}\``
-              : '';
             const modeMsg = offline === 'true' ? ' (offline mode)' : '';
             await github.rest.issues.createComment({
               owner:        context.repo.owner,
               repo:         context.repo.repo,
               issue_number: context.issue.number,
-              body:         `🤖 Skill generation workflow dispatched by @${commenter}${modeMsg}.${filesMsg}\n\n[View recent workflow runs](${runsUrl})`,
+              body:         `🤖 Skill generation workflow dispatched by @${commenter}${modeMsg}.\n\n[View recent workflow runs](${runsUrl})`,
             });
diff --git a/.gitignore b/.gitignore
@@ -20,3 +20,9 @@ __pycache__
 
 # Julia generated files
 Julia/Manifest.toml
+
+# Individual per-tutorial skill markdown files (unified into SKILL.md)
+skills/**/*_skill.md
+
+# Entire skills/ directory (superseded by SKILL.md)
+skills/
diff --git a/SKILL.md b/SKILL.md
@@ -19,6 +19,8 @@ metadata:
     skill-author: Bizard Collaboration Group, Luo Lab, and Wang Lab
     website: https://openbiox.github.io/Bizard/
     repository: https://github.com/openbiox/Bizard
+    citation: >
+      - Li, K., Zheng, H., Huang, K., Chai, Y., Peng, Y., Wang, C., ... & Wang, S. (2026). Bizard: A Community‐Driven Platform for Accelerating and Enhancing Biomedical Data Visualization. iMetaMed, e70038. <https://doi.org/10.1002/imm3.70038>
 ---
 
 # Bizard — Biomedical Visualization Atlas AI Skill