ulelab · iraiosub · Apr 22, 2026 · Apr 22, 2026 · Apr 22, 2026 · Apr 22, 2026
diff --git a/.agents/skills/protocol-migration/SKILL.md b/.agents/skills/protocol-migration/SKILL.md
@@ -45,11 +45,12 @@ You may normalize formatting only when the meaning is unchanged and unambiguous:
 - Standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O. Similarly for other chemical formulas (e.g. MgCl2 to MgCl<sub>2</sub>).
 - Do not use Unicode subscript characters such as `₂`.
 - Standardize `RNAseq` or `RNA-Seq` to `RNA-seq`. Same for `ChIP-seq`, `ATAC-seq`, etc.
+- Use numbered lists for procedural actions in sequence. For other non-procedural content, bullets are better. Note-like text such as Note, NB, Optional, Recommended, and Warning should use blockquote style such as `> **Note**`.
 - Normalize bullet formatting and markdown table formatting.
 - Normalize heading structure to match the repository template.
 - For reaction mixes and anything tabular, place them inside a table as in template.
 - Normalize markdown headings, bullets, and tables.
-- "Note" or "NOTE" or "Optional" or "Recommended" or "Warning" are normalized to start with `>` (example `> **Note**`) and are placed immediately after the step they refer to, or at the end of the protocol if they clearly refer to the whole protocol.
+- "Note" or "NOTE" or "NB" or "Optional" or "Recommended" or "Warning" are normalized to start with `>` (example `> **Note**`) and are placed immediately after the step they refer to, or at the end of the protocol if they clearly refer to the whole protocol.
 - Remove empty columns from tables.
 - Synchronize `Contents` with actual headings in the protocol.
 
@@ -82,7 +83,7 @@ You may normalize formatting only when the meaning is unchanged and unambiguous:
 - add `# Migration notes` including:
   - imported protocol metadata from `source-metadata.yml` if present
   - imported protocol metadata from `source-metadata.yml` using only the non-blank lines
-  - template metadata from `template-metadata.yml`
+  - template_version from `template-metadata.yml`
   - ambiguous mappings
   - normalized formatting changes
   - content copied verbatim but not confidently placed

diff --git a/...claude/skills/protocol-migration/SKILL.md → .claude/skills/protocol-migration/SKILL.md b/...claude/skills/protocol-migration/SKILL.md → .claude/skills/protocol-migration/SKILL.md
@@ -45,11 +45,12 @@ You may normalize formatting only when the meaning is unchanged and unambiguous:
 - Standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O. Similarly for other chemical formulas (e.g. MgCl2 to MgCl<sub>2</sub>).
 - Do not use Unicode subscript characters such as `₂`.
 - Standardize `RNAseq` or `RNA-Seq` to `RNA-seq`. Same for `ChIP-seq`, `ATAC-seq`, etc.
+- Use numbered lists for procedural actions in sequence. For other non-procedural content, bullets are better. Note-like text such as Note, NB, Optional, Recommended, and Warning should use blockquote style such as `> **Note**`.
 - Normalize bullet formatting and markdown table formatting.
 - Normalize heading structure to match the repository template.
 - For reaction mixes and anything tabular, place them inside a table as in template.
 - Normalize markdown headings, bullets, and tables.
-- "Note" or "NOTE" or "Optional" or "Recommended" or "Warning" are normalized to start with `>` (example `> **Note**`) and are placed immediately after the step they refer to, or at the end of the protocol if they clearly refer to the whole protocol.
+- "Note" or "NOTE" or "NB" or "Optional" or "Recommended" or "Warning" are normalized to start with `>` (example `> **Note**`) and are placed immediately after the step they refer to, or at the end of the protocol if they clearly refer to the whole protocol.
 - Remove empty columns from tables.
 - Synchronize `Contents` with actual headings in the protocol.
 
@@ -82,7 +83,7 @@ You may normalize formatting only when the meaning is unchanged and unambiguous:
 - add `# Migration notes` including:
   - imported protocol metadata from `source-metadata.yml` if present
   - imported protocol metadata from `source-metadata.yml` using only the non-blank lines
-  - template metadata from `template-metadata.yml`
+  - template_version from `template-metadata.yml`
   - ambiguous mappings
   - normalized formatting changes
   - content copied verbatim but not confidently placed

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
@@ -38,11 +38,12 @@ You may normalize formatting only when the meaning is unchanged and unambiguous:
 - Standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O. Similarly for other chemical formulas (e.g. MgCl2 to MgCl<sub>2</sub>).
 - Do not use Unicode subscript characters such as `₂`.
 - Standardize `RNAseq` or `RNA-Seq` to `RNA-seq`. Same for `ChIP-seq`, `ATAC-seq`, etc.
+- Use numbered lists for procedural actions in sequence. For other non-procedural content, bullets are better. Note-like text such as Note, NB, Optional, Recommended, and Warning should use blockquote style such as `> **Note**`.
 - Normalize bullet formatting and markdown table formatting.
 - Normalize heading structure to match the repository template.
 - For reaction mixes and anything tabular, place them inside a table as in template.
 - Normalize markdown headings, bullets, and tables.
-- "Note" or "NOTE" or "Optional" or "Recommended" or "Warning" are normalized to start with `>` (example `> **Note**`) and are placed immediately after the step they refer to, or at the end of the protocol if they clearly refer to the whole protocol.
+- "Note" or "NOTE" or "NB" or "Optional" or "Recommended" or "Warning" are normalized to start with `>` (example `> **Note**`) and are placed immediately after the step they refer to, or at the end of the protocol if they clearly refer to the whole protocol.
 - Remove empty columns from tables.
 - Synchronize `Contents` with actual headings in the protocol.
 
@@ -73,7 +74,7 @@ When drafting a migrated protocol:
   - content placed in `## Unplaced content`
   - Imported protocol metadata from `source-metadata.yml` (only the non-blank lines).
   - Imported protocol metadata from `source-metadata.yml` if present.
-  - template metadata from `template-metadata.yml`.
+  - template_version from `template-metadata.yml`.
   - ambiguous mappings.
   - normalized formatting changes.
   - content copied verbatim but not confidently placed.

diff --git a/.github/workflows/validate-protocol.yml b/.github/workflows/validate-protocol.yml
@@ -6,19 +6,23 @@ on:
       - main
     paths:
       - README.md
-      - legacy/source.txt
       - scripts/validate_protocol.py
-      - tests/test_validate_protocol.py
-      - .github/workflows/validate_protocol.yml
+      - scripts/validate_protocol_content.py
+      - scripts/validate_protocol_style.py
+      - tests/test_validate_protocol_content.py
+      - tests/test_validate_protocol_style.py
+      - .github/workflows/validate-protocol.yml
   push:
     branches:
       - main
     paths:
       - README.md
-      - legacy/source.txt
       - scripts/validate_protocol.py
-      - tests/test_validate_protocol.py
-      - .github/workflows/validate_protocol.yml
+      - scripts/validate_protocol_content.py
+      - scripts/validate_protocol_style.py
+      - tests/test_validate_protocol_content.py
+      - tests/test_validate_protocol_style.py
+      - .github/workflows/validate-protocol.yml
   workflow_dispatch:
 
 jobs:
@@ -35,7 +39,7 @@ jobs:
         with:
           python-version: "3.11"
 
-      - name: Check whether validation should run
+      - name: Check whether README validation should run
         id: validation_gate
         run: |
           set -euo pipefail
@@ -56,15 +60,15 @@ jobs:
           echo "should_validate=true" >> "$GITHUB_OUTPUT"
 
       - name: Run validator tests
-        if: steps.validation_gate.outputs.should_validate == 'true'
         run: |
           python -m unittest discover -s tests -p 'test_*.py'
 
-      - name: Run protocol validation
+      - name: Run content validation
         if: steps.validation_gate.outputs.should_validate == 'true'
         run: |
-          if [ -f legacy/source.txt ]; then
-            python scripts/validate_protocol.py README.md legacy/source.txt
-          else
-            python scripts/validate_protocol.py README.md
-          fi
+          python scripts/validate_protocol_content.py README.md
+
+      - name: Run style validation
+        if: steps.validation_gate.outputs.should_validate == 'true'
+        run: |
+          python scripts/validate_protocol_style.py README.md
diff --git a/README.md b/README.md
@@ -19,7 +19,7 @@
 4. [Step 4](#4-step-4)
 5. [Step 5](#5-step-5)
 6. [Step 6](#6-step-6)
-7. [Buffers](#buffers)
+7. [Materials](#7-materials)
 8. [Migration notes](#migration-notes)
 
 ---
@@ -32,25 +32,25 @@
 
 ## 1.1 Sub-step of Step 1 TODO if Step 1 is complex
 
-- TODO
-- TODO
-- TODO
+1. TODO
+2. TODO
+3. TODO
 
 ## 1.2 Sub-step of Step 1 TODO if Step 1 is complex
 
-- TODO
-- TODO
-- TODO
+1. TODO
+2. TODO
+3. TODO
 
 > **Note:** TODO
 
 ---
 
 # 2. Step 2
 
-- TODO
-- TODO
-- TODO
+1. TODO
+2. TODO
+3. TODO
 
 ## Reagents / mix
 
@@ -66,9 +66,9 @@
 
 # 3. Step 3
 
-- TODO
-- TODO
-- TODO
+1. TODO
+2. TODO
+3. TODO
 
 ## Program / incubation
 
@@ -82,19 +82,19 @@
 
 # 4. Step 4
 
-- TODO
-- TODO
-- TODO
+1. TODO
+2. TODO
+3. TODO
 
 > **Optional:** TODO
 
 ---
 
 # 5. Step 5
 
-- TODO
-- TODO
-- TODO
+1. TODO
+2. TODO
+3. TODO
 
 ## Reaction setup
 
@@ -108,19 +108,22 @@
 
 # 6. Step 6
 
-- TODO
-- TODO
-- TODO
+1. TODO
+2. TODO
+3. TODO
 
 ## Output / QC
 
-- TODO
-- TODO
-- TODO
+1. TODO
+2. TODO
+3. TODO
 
 ---
 
-# 7. Buffers
+# 7. Materials
+
+## 7.1 Buffers
+## 7.2 Reagents
 
 ---
 
@@ -131,4 +134,4 @@
 
 ## Unplaced content
 
-## CHECK items
+## CHECK items
diff --git a/docs/PROMPT.md b/docs/PROMPT.md
@@ -42,9 +42,10 @@ Normalize formatting only when the meaning is unchanged and unambiguous:
 - standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O and MgCl2 to MgCl<sub>2</sub>
 - do not use Unicode subscript characters such as `₂`
 - standardize `RNAseq` or `RNA-Seq` to `RNA-seq`, and similarly for `ChIP-seq`, `ATAC-seq`, and related names
+- Use numbered lists for procedural actions in sequence. For other non-procedural content, bullets are better. Note-like text such as Note, NB, Optional, Recommended, and Warning should use blockquote style such as `> **Note**`.
 - normalize bullets, headings, and markdown tables to match the repository template
 - use tables for reaction mixes and other tabular content
-- normalize note-like text to blockquote style, for example `> **Note**`
+- normalize note-like text such as Note, NB, Optional, Recommended, and Warning to blockquote style, for example `> **Note**`
 - place note-like text immediately after the step it refers to, or at the end of the protocol if it clearly refers to the whole protocol
 - remove empty columns from tables
 - synchronize `Contents` with the actual headings in the protocol
@@ -78,7 +79,7 @@ Normalize formatting only when the meaning is unchanged and unambiguous:
 - Include the following in `# Migration notes`:
   - imported protocol metadata from `source-metadata.yml` if present
   - imported protocol metadata from `source-metadata.yml` using only the non-blank lines
-  - template metadata from `template-metadata.yml`
+  - template_version from `template-metadata.yml`
   - ambiguous mappings
   - normalized formatting changes
   - content copied verbatim but not confidently placed

diff --git a/docs/USING_THIS_TEMPLATE.md b/docs/USING_THIS_TEMPLATE.md
@@ -74,7 +74,7 @@ The main file you must edit for protocol content is `README.md`. Do not rename t
 7. Follow the guidelines in [3. General guidelines for the protocol file (`README.md`)](#3-general-guidelines-for-the-protocol-file-readmemd)
 8. Commit your changes, then push.
 9. Once you are happy with the result, open a pull request from `import-protocol` into `main`.
-10. A validation GitHub Actions workflow will run on that pull request when `README.md` has changed. It checks the required title, status line, status legend, key headings, unresolved placeholders, and placeholder step names. If checks fail, fix them before merging into `main`.
+10. A validation GitHub Actions workflow will run on that pull request when `README.md` has changed. It runs a content check for the required title, status line, status legend, key headings, unresolved placeholders, and placeholder step names, plus a style check for unit formatting. If checks fail, fix them before merging into `main`.
 11. Ask for a reviewer.
 
 > **Note:** Always check accuracy and make sure required sections, such as protocol status and the status legend, are present.
@@ -121,7 +121,7 @@ This route can save time. It helps keep the template structure consistent, norma
 14. Follow the guidelines in [3. General guidelines for the protocol file (`README.md`)](#3-general-guidelines-for-the-protocol-file-readmemd)
 15. Commit your changes, then push.
 16. Once you are happy with the result, open a pull request from `import-protocol` into `main`.
-17. A validation GitHub Actions workflow will run on that pull request when `README.md` has changed. It checks the required title, status line, status legend, key headings, unresolved placeholders, and placeholder step names. If `legacy/source.txt` is present, it also checks that key quantities from the source appear in `README.md`. If checks fail, fix them before merging into `main`.
+17. A validation GitHub Actions workflow will run on that pull request when `README.md` has changed. It runs a content check for the required title, status line, status legend, key headings, unresolved placeholders, and placeholder step names, plus a style check for unit formatting. If checks fail, fix them before merging into `main`.
 18. Ask for a reviewer.
 
 ---
@@ -141,6 +141,7 @@ Mandatory items for validation:
 - a status legend row containing `[OK]`, `[?]`, and `[X]`
 - a short description (`# About`)
 - contents (`## Contents`)
+- a materials section (`# ... Materials`)
 
 Recommended content:
 

diff --git a/docs/template-metadata.yml b/docs/template-metadata.yml
@@ -6,4 +6,4 @@ template_authors:
   - name: Ira A. Iosub
 template_doi:
 template_version: 1.0.0dev
-template_release_date: 2026-04-10
+template_release_date: 
diff --git a/protocol-template.pdf b/protocol-template.pdf
diff --git a/scripts/validate_protocol.py b/scripts/validate_protocol.py
@@ -1,43 +1,15 @@
-"""Validate a protocol README against template requirements and optional source text."""
+"""Backward-compatible entrypoint for protocol README validation."""
 
 from pathlib import Path
-import re
 import sys
 from typing import Dict, List, Optional, Tuple
 
-HEADING_RE = re.compile(r"^(#{1,6})\s+(.+?)\s*$", re.MULTILINE)
-STATUS_LINE_RE = re.compile(
-    r"^### Status:\s+.*`\[(?:OK|\?|X)\]`.*$",
-    re.MULTILINE,
-)
-STATUS_LEGEND_RE = re.compile(
-    r"^\| \*\*\*Status legend\*\*\*:.*`\[OK\]`.*`\[\?\]`.*`\[X\]`.*\|$",
-    re.MULTILINE,
-)
-PLACEHOLDER_STEP_HEADING_RE = re.compile(
-    r"^#{1,6}\s+\d+(?:\.\d+)*(?:\.)?\s+(?:Step|Sub-step)\b.*$",
-    re.MULTILINE,
-)
-PLACEHOLDER_CONTENTS_RE = re.compile(
-    r"^\d+\.\s+\[Step\s+\d+\]\(#.*$",
-    re.MULTILINE,
-)
-
-REQUIRED_HEADINGS = [
-    (1, "About"),
-    (2, "Contents"),
-]
-
-BAD_PLACEHOLDERS = {
-    "TODO": re.compile(r"\bTODO\b"),
-    "TBD": re.compile(r"\bTBD\b"),
-    "XXX": re.compile(r"\bXXX\b"),
-    "CHECK:": re.compile(r"CHECK:"),
-}
-
-DISALLOWED_TEMPLATE_TEXT = [
-    "> Template repository: Click `Use this template` to create a new protocol repo. Template docs are in [docs/USING_THIS_TEMPLATE.md](https://github.com/ulelab/protocol-template/blob/main/docs/USING_THIS_TEMPLATE.md)",
-]
+try:
+    from scripts.validate_protocol_content import validate_readme as validate_content
+    from scripts.validate_protocol_style import validate_readme_style
+except ModuleNotFoundError:
+    from validate_protocol_content import validate_readme as validate_content
+    from validate_protocol_style import validate_readme_style
 
 
 def extract_headings(text: str) -> List[Tuple[int, str]]:
@@ -213,9 +185,7 @@ def main() -> None:
         sys.exit(1)
 
     readme = Path(sys.argv[1]).read_text(encoding="utf-8")
-    source = Path(sys.argv[2]).read_text(encoding="utf-8") if len(sys.argv) == 3 else None
-
-    failures = validate_readme(readme, source)
+    failures = validate_readme(readme)
 
     if failures:
         print("VALIDATION FAILED")