Implement frictionless GitHub CLI auth, auto-issue tracking, and ROBOT_README.md for AI context

.devcontainer/devcontainer.json

@@ -39,5 +39,6 @@
         "windsurf.authTokenPath": "~/.windsurf/auth.json"
       }
     }
-  }
+  },
+  "updateContentCommand": "pip install -r requirements.txt && python Agent/agent_runner.py --build-embeddings || true"
 }

.github/workflows/robot_readme.yml

@@ -0,0 +1,42 @@
+name: Update Robot README
+
+on:
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - 'ROBOT_README.md'
+
+jobs:
+  update-robot-readme:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Run update_robot_readme.py
+        run: python Agent/tools/update_robot_readme.py
+
+      - name: Check for changes
+        id: check_changes
+        run: |
+          git diff --quiet ROBOT_README.md || echo "changes=true" >> $GITHUB_OUTPUT
+
+      - name: Commit changes if any
+        if: steps.check_changes.outputs.changes == 'true'
+        run: |
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git add ROBOT_README.md
+          git commit -m "Auto-update ROBOT_README.md [skip ci]"
+          git push 

.vscode/settings.json

@@ -0,0 +1,9 @@
+{
+  // Enable GitLens Issues integration and pin the lab repo issues view
+  "gitlens.views.repositories.issues.enabled": true,
+  "gitlens.views.issues.location": "workbench",
+  "gitlens.views.issues.repositories": [
+    "github.com/james-m-jordan/lab-doc-repo"
+  ],
+  "gitlens.views.issues.pinned": true
+} 

Agent/hooks/post_issue.py

@@ -0,0 +1,24 @@
+import sys
+from pathlib import Path
+from datetime import datetime
+
+# Usage: python post_issue.py <issue_number> <issue_title> <issue_url>
+if len(sys.argv) != 4:
+    print("Usage: python post_issue.py <issue_number> <issue_title> <issue_url>")
+    sys.exit(1)
+
+issue_number = sys.argv[1]
+issue_title = sys.argv[2]
+issue_url = sys.argv[3]
+
+entry = f"- [ ] [#{issue_number}]({issue_url}) {issue_title}  _(added {datetime.now().strftime('%Y-%m-%d %H:%M')})_\n"
+
+# Append to TASKS.md
+Path("TASKS.md").write_text(
+    Path("TASKS.md").read_text() + entry if Path("TASKS.md").exists() else entry
+)
+
+# Append to ISSUES_LOG.md
+Path("ISSUES_LOG.md").write_text(
+    Path("ISSUES_LOG.md").read_text() + entry if Path("ISSUES_LOG.md").exists() else entry
+) 

Agent/tools/create_issues.py

@@ -0,0 +1,142 @@
+#!/usr/bin/env python3
+"""
+Issue Creator for Lab Agent
+
+This script:
+1. Reads morning_push_2025-05-07.md
+2. Extracts issues to create from the table
+3. Checks if issues already exist
+4. Creates issues and assigns them to james-m-jordan
+5. Runs post_issue.py hook to update TASKS.md and ISSUES_LOG.md
+"""
+
+import os
+import re
+import json
+import subprocess
+from pathlib import Path
+
+# Configuration
+PUSH_PLAN = "morning_push_2025-05-07.md"
+ASSIGNEE = "james-m-jordan"
+REPO = "the-jordan-lab/docs"
+
+def read_push_plan():
+    """Read the push plan markdown file."""
+    try:
+        with open(PUSH_PLAN, 'r') as f:
+            return f.read()
+    except FileNotFoundError:
+        print(f"Error: Could not find {PUSH_PLAN}")
+        return None
+
+def extract_issues(content):
+    """Extract issues from the GitHub Issues table in the markdown."""
+    # Find the issues section
+    issues_section_match = re.search(r'## 3\. GitHub Issues to Create.*?\|\s*#\s*\|\s*Title\s*\|\s*Labels\s*\|.*?\|(.*?)(?=\n\n|$)', 
+                                     content, re.DOTALL)
+    
+    if not issues_section_match:
+        print("Error: Could not find GitHub Issues section in push plan")
+        return []
+    
+    issues_content = issues_section_match.group(1)
+    
+    # Extract rows from the table
+    rows = re.findall(r'\|\s*(\d+|\…)\s*\|\s*(.*?)\s*\|\s*(.*?)\s*\|', issues_content)
+    
+    issues = []
+    for row in rows:
+        if row[0] == '…':
+            continue  # Skip placeholder row
+            
+        issues.append({
+            'number': row[0],
+            'title': row[1].strip(),
+            'labels': [label.strip() for label in row[2].split(',')]
+        })
+    
+    return issues
+
+def check_issue_exists(title):
+    """Check if an issue with the given title already exists."""
+    try:
+        result = subprocess.run(
+            ['gh', 'issue', 'list', '--repo', REPO, '--state', 'all', '--json', 'title'],
+            capture_output=True, text=True, check=True
+        )
+        issues = json.loads(result.stdout)
+        return any(issue['title'] == title for issue in issues)
+    except subprocess.CalledProcessError as e:
+        print(f"Error checking for existing issues: {e}")
+        print(f"Command output: {e.stdout}")
+        print(f"Command error: {e.stderr}")
+        return False
+
+def create_issue(title, labels, section_ref):
+    """Create a GitHub issue with the given title and labels."""
+    try:
+        # Create the issue
+        cmd = [
+            'gh', 'issue', 'create',
+            '--repo', REPO,
+            '--title', title,
+            '--body', f"See {PUSH_PLAN}#{section_ref}",
+            '--assignee', ASSIGNEE
+        ]
+        
+        # Add labels
+        for label in labels:
+            cmd.extend(['--label', label])
+        
+        result = subprocess.run(cmd, capture_output=True, text=True, check=True)
+        
+        # Extract issue number and URL from the output
+        # The output typically looks like: "https://github.com/user/repo/issues/123"
+        url = result.stdout.strip()
+        issue_number = url.split('/')[-1]
+        
+        print(f"Created issue #{issue_number}: {title}")
+        return issue_number, url
+    except subprocess.CalledProcessError as e:
+        print(f"Error creating issue '{title}': {e}")
+        print(f"Command output: {e.stdout}")
+        print(f"Command error: {e.stderr}")
+        return None, None
+
+def run_post_issue_hook(issue_number, title, url):
+    """Run the post_issue.py hook to update TASKS.md and ISSUES_LOG.md."""
+    try:
+        subprocess.run(
+            ['python', 'Agent/hooks/post_issue.py', issue_number, title, url],
+            check=True
+        )
+        print(f"Updated TASKS.md and ISSUES_LOG.md with issue #{issue_number}")
+    except subprocess.CalledProcessError as e:
+        print(f"Error running post-issue hook: {e}")
+
+def main():
+    """Main function to create issues from push plan."""
+    print(f"Reading push plan from {PUSH_PLAN}...")
+    content = read_push_plan()
+    if not content:
+        return
+    
+    issues = extract_issues(content)
+    print(f"Found {len(issues)} issues to process")
+    
+    for issue in issues:
+        title = issue['title']
+        if check_issue_exists(title):
+            print(f"Issue already exists: {title}")
+            continue
+        
+        # Determine the section reference from title content
+        section_ref = "1" if any(keyword in title.lower() for keyword in ['container', 'api', 'key', 'readme', 'hook', 'gitlens', 'ci']) else "2"
+        
+        issue_number, url = create_issue(title, issue['labels'], section_ref)
+        if issue_number and url:
+            run_post_issue_hook(issue_number, title, url)
+
+if __name__ == "__main__":
+    main() 

Agent/tools/create_labels.py

@@ -0,0 +1,88 @@
+#!/usr/bin/env python3
+"""
+Label Creator for GitHub Issues
+
+This script creates standard labels needed for the Lab Agent issue tracking system.
+It ensures all labels exist before attempting to create issues.
+"""
+
+import subprocess
+import sys
+
+# Repository
+REPO = "the-jordan-lab/docs"
+
+# List of labels to create with their colors and descriptions
+LABELS = [
+    {
+        "name": "infra",
+        "color": "0366d6",
+        "description": "Infrastructure and DevOps improvements"
+    },
+    {
+        "name": "high-priority",
+        "color": "d93f0b",
+        "description": "High priority tasks that need immediate attention"
+    },
+    {
+        "name": "security",
+        "color": "d93f0b",
+        "description": "Security-related issues and improvements"
+    },
+    {
+        "name": "docs",
+        "color": "0075ca",
+        "description": "Documentation updates and additions"
+    },
+    {
+        "name": "tooling",
+        "color": "1d76db",
+        "description": "Tools and automation improvements"
+    },
+    {
+        "name": "ci",
+        "color": "fbca04",
+        "description": "Continuous Integration and GitHub Actions"
+    },
+    {
+        "name": "lab",
+        "color": "0e8a16",
+        "description": "Wet-lab related issues and experiments"
+    }
+]
+
+def create_label(label):
+    """Create a label in the GitHub repository."""
+    try:
+        cmd = [
+            'gh', 'label', 'create',
+            '--repo', REPO,
+            label['name'],
+            '--color', label['color'],
+            '--description', label['description'],
+            '--force'  # Update if already exists
+        ]
+        
+        result = subprocess.run(cmd, capture_output=True, text=True, check=True)
+        print(f"✅ Created/updated label: {label['name']}")
+        return True
+    except subprocess.CalledProcessError as e:
+        print(f"❌ Error creating label '{label['name']}': {e}")
+        print(f"Command output: {e.stdout}")
+        print(f"Command error: {e.stderr}")
+        return False
+
+def main():
+    """Create all required labels."""
+    print(f"Creating labels in repository: {REPO}")
+    
+    success_count = 0
+    for label in LABELS:
+        if create_label(label):
+            success_count += 1
+    
+    print(f"Successfully created/updated {success_count} of {len(LABELS)} labels")
+    return 0 if success_count == len(LABELS) else 1
+
+if __name__ == "__main__":
+    sys.exit(main()) 

Agent/tools/update_robot_readme.py

@@ -0,0 +1,155 @@
+#!/usr/bin/env python3
+"""
+Robot README Updater
+
+This script automatically updates ROBOT_README.md based on the repository structure.
+It scans for top-level markdown files and directories, generating a structured table
+of contents for AI assistants to understand the repository organization.
+
+Usage:
+  python update_robot_readme.py
+
+This can be run manually or as a pre-commit hook to ensure the robot table of
+contents stays in sync with the repository.
+"""
+
+import os
+import re
+from collections import defaultdict
+from pathlib import Path
+
+# Configuration
+ROBOT_README = "ROBOT_README.md"
+REPO_ROOT = "."  # Current directory
+EXCLUDE_DIRS = [".git", ".github", ".vscode", "__pycache__", "node_modules"]
+EXCLUDE_FILES = [ROBOT_README]  # Don't include self in the listing
+
+# Descriptions for known files and directories
+FILE_DESCRIPTIONS = {
+    "README.md": "Main repository README with quick-start instructions and overview.",
+    "ENVIRONMENT_SETUP.md": "Guide for setting up the development environment, including GitHub CLI and OpenAI API key configuration.",
+    "LAB_AGENT_GUIDE.md": "Detailed guide on how to use the Lab Agent, including examples and troubleshooting.",
+    "TASKS.md": "Tracks ongoing lab and development tasks, automatically updated by the Lab Agent.",
+    "ISSUES_LOG.md": "Logs all GitHub issues created, automatically updated by the Lab Agent.",
+    "morning_push_2025-05-06.md": "Checklist for May 6, 2025 morning push tasks.",
+    "morning_push_2025-05-07.md": "Checklist for May 7, 2025 morning push tasks.",
+}
+
+DIR_DESCRIPTIONS = {
+    "Protocols": "Contains standard operating procedures and experimental protocols.",
+    "Projects": "Groups related experiments under broad project titles.",
+    "Experiments": "Records of individual experiments or lab sessions.",
+    "Data": "Storage for data outputs or references to data.",
+    "Templates": "Contains starter templates for various YAML structures.",
+    "Agent": "Contains the code for the AI agent integration, including the task-runner and hooks.",
+}
+
+def scan_repository():
+    """Scan the repository for top-level markdown files and directories."""
+    md_files = []
+    directories = []
+    
+    for item in os.listdir(REPO_ROOT):
+        path = Path(os.path.join(REPO_ROOT, item))
+        
+        # Skip excluded items
+        if item in EXCLUDE_DIRS or item in EXCLUDE_FILES:
+            continue
+        
+        # Skip hidden files and directories
+        if item.startswith('.'):
+            continue
+            
+        if path.is_file() and item.endswith('.md'):
+            md_files.append(item)
+        elif path.is_dir() and not item.startswith('.'):
+            directories.append(item)
+    
+    return sorted(md_files), sorted(directories)
+
+def extract_existing_descriptions():
+    """Extract existing descriptions from ROBOT_README.md if it exists."""
+    descriptions = defaultdict(str)
+    
+    if not os.path.exists(ROBOT_README):
+        return descriptions
+        
+    with open(ROBOT_README, 'r') as f:
+        content = f.read()
+        
+    # Extract existing descriptions using regex
+    file_matches = re.findall(r'\*\*([^*]+\.md)\*\*:\s*([^\n]+)', content)
+    dir_matches = re.findall(r'\*\*([^*]+)/\*\*:\s*([^\n]+)', content)
+    
+    for name, desc in file_matches + dir_matches:
+        descriptions[name] = desc.strip()
+    
+    return descriptions
+
+def get_description(item, is_dir, existing_descriptions):
+    """Get description for an item, using existing description if available."""
+    if item in (FILE_DESCRIPTIONS if not is_dir else DIR_DESCRIPTIONS):
+        return FILE_DESCRIPTIONS[item] if not is_dir else DIR_DESCRIPTIONS[item]
+    elif item in existing_descriptions:
+        return existing_descriptions[item]
+    else:
+        return "No description available." if not is_dir else "Directory containing repository files."
+
+def generate_robot_readme(md_files, directories, existing_descriptions):
+    """Generate the content for ROBOT_README.md."""
+    content = [
+        "# Robot Table of Contents",
+        "",
+        "This file serves as a robot table of contents for the repository. It lists the structure of the repository and points to relevant .md files for context.",
+        "",
+        "## Repository Structure",
+        ""
+    ]
+    
+    # Add markdown files
+    if md_files:
+        for file in md_files:
+            description = get_description(file, False, existing_descriptions)
+            content.append(f"- **{file}**: {description}")
+        content.append("")
+    
+    # Add directories section
+    if directories:
+        content.append("## Additional Directories")
+        content.append("")
+        for directory in directories:
+            description = get_description(directory, True, existing_descriptions)
+            content.append(f"- **{directory}/**: {description}")
+        content.append("")
+    
+    # Add footer
+    content.append("---")
+    content.append("")
+    content.append("_This file will be updated whenever the repository structure changes to ensure the robot has the latest context._")
+    
+    return "\n".join(content)
+
+def update_robot_readme():
+    """Update ROBOT_README.md if the content has changed."""
+    existing_descriptions = extract_existing_descriptions()
+    md_files, directories = scan_repository()
+    new_content = generate_robot_readme(md_files, directories, existing_descriptions)
+    
+    # Check if the file exists and if content has changed
+    if os.path.exists(ROBOT_README):
+        with open(ROBOT_README, 'r') as f:
+            current_content = f.read()
+            
+        if current_content.strip() == new_content.strip():
+            print(f"No changes needed for {ROBOT_README}")
+            return False
+    
+    # Write the updated content
+    with open(ROBOT_README, 'w') as f:
+        f.write(new_content)
+    
+    print(f"Updated {ROBOT_README} with latest repository structure")
+    return True
+
+if __name__ == "__main__":
+    update_robot_readme() 

ISSUES_LOG.md

@@ -0,0 +1,12 @@
+# Issues Log
+
+This file is automatically updated with every new GitHub issue created (via the post_issue.py hook or manually). Each entry includes the issue number, title, and link.
+
+--- - [ ] [#9](https://github.com/the-jordan-lab/docs/issues/9) Pre-build Dev Container for instant Agent boot  _(added 2025-05-07 10:37)_
+- [ ] [#10](https://github.com/the-jordan-lab/docs/issues/10) Add repo-level OPENAI_API_KEY secret & document  _(added 2025-05-07 10:37)_
+- [ ] [#11](https://github.com/the-jordan-lab/docs/issues/11) Rewrite README Quick-Start for students  _(added 2025-05-07 10:37)_
+- [ ] [#12](https://github.com/the-jordan-lab/docs/issues/12) Implement automated ISSUE → TASKS.md hook  _(added 2025-05-07 10:37)_
+- [ ] [#13](https://github.com/the-jordan-lab/docs/issues/13) Add GitLens default issue view configuration  _(added 2025-05-07 10:37)_
+- [ ] [#14](https://github.com/the-jordan-lab/docs/issues/14) CI: Codespace headless smoke test  _(added 2025-05-07 10:37)_
+- [ ] [#15](https://github.com/the-jordan-lab/docs/issues/15) [Wet-Lab] Complete HEK293T thaw & viability check  _(added 2025-05-07 10:37)_
+- [ ] [#16](https://github.com/the-jordan-lab/docs/issues/16) [Wet-Lab] Prepare Ybx1 & control siRNA mixes  _(added 2025-05-07 10:37)_

LAB_AGENT_GUIDE.md

@@ -137,4 +137,15 @@ You can always skim these files (or GitHub commit history) to catch up after a b
 
 ---
 
+## 10. Automated Issue Logging (NEW)
+Whenever you create a GitHub issue (e.g., with `gh issue create`), you can call the hook script:
+
+```bash
+python Agent/hooks/post_issue.py <issue_number> <issue_title> <issue_url>
+```
+
+This will append the issue to both `TASKS.md` and `ISSUES_LOG.md` for easy tracking inside the repo. (You can automate this in your workflow or call it manually after each issue is created.)
+
+---
+
 Made with ☕ and 🤖.  Enjoy streamlined, reproducible record-keeping! 

README.md

@@ -2,6 +2,51 @@
 
 ---
 
+# Lab Workspace Quick-Start
+
+Welcome to the Lab Codespace! This environment is pre-configured for you. Just follow these steps:
+
+## 🚀 1. Open the Codespace
+- Click "Code" > "Codespaces" > "Create codespace on main" (or your assigned branch).
+
+## ⏳ 2. Wait for Setup
+- The environment will build automatically. This takes ~1-2 minutes the first time.
+- All dependencies, the Lab Agent, and required secrets (like the OpenAI API key) are pre-loaded.
+
+## 💬 3. Start Chatting
+- Open the **Cursor** or **Copilot Chat** tab in VS Code.
+- Type your request (e.g., "Create a new experiment using the cell staining protocol tomorrow at 10 AM").
+- The Lab Agent will handle the rest!
+
+---
+
+### FAQ
+- **Do I need to set up any API keys or secrets?**
+  - _No!_ All required secrets are injected automatically. You cannot see them, but the Agent can use them.
+- **What if I see a warning about missing tools?**
+  - Try rebuilding the container (F1 > "Rebuild Container"). If issues persist, contact @james-m-jordan.
+- **Where do my files and issues go?**
+  - Protocols, experiments, and projects are saved in their respective folders. Issues you create are logged and visible in the repo (see below).
+
+---
+
+### For Maintainers
+- **OpenAI API Key**: Add it as a Codespaces secret at the repo level (`OPENAI_API_KEY`).
+- **GitHub CLI Authentication**: The CLI is pre-installed, but requires one-time auth per user:
+  ```bash
+  gh auth login
+  # Choose GitHub.com → HTTPS → Paste a token with 'repo' scope
+  ```
+- **Auto-Issue Tracking**: Issues are automatically added to `TASKS.md` and `ISSUES_LOG.md` via hooks.
+- **Robot Context**: `ROBOT_README.md` contains repository structure information for AI assistants.
+- For more advanced setup or troubleshooting, see `ENVIRONMENT_SETUP.md` and `LAB_AGENT_GUIDE.md`.
+
+---
+
+Enjoy your streamlined lab experience!
+
+---
+
 ## 🚀 Quick Start (for Researchers)
 
 1. **Open in GitHub Codespaces** (or locally with Dev Containers)

ROBOT_README.md

@@ -0,0 +1,32 @@
+# Robot Table of Contents
+
+This file serves as a robot table of contents for the repository. It lists the structure of the repository and points to relevant .md files for context.
+
+## Repository Structure
+
+- **CHANGELOG.md**: No description available.
+- **ENVIRONMENT_SETUP.md**: Guide for setting up the development environment, including GitHub CLI and OpenAI API key configuration.
+- **ISSUES_LOG.md**: Logs all GitHub issues created, automatically updated by the Lab Agent.
+- **LAB_AGENT_GUIDE.md**: Detailed guide on how to use the Lab Agent, including examples and troubleshooting.
+- **README.md**: Main repository README with quick-start instructions and overview.
+- **TASKS.md**: Tracks ongoing lab and development tasks, automatically updated by the Lab Agent.
+- **branching_explainer.md**: No description available.
+- **morning_push_2025-05-06.md**: Checklist for May 6, 2025 morning push tasks.
+- **morning_push_2025-05-07.md**: Checklist for May 7, 2025 morning push tasks.
+- **proof.md**: No description available.
+
+## Additional Directories
+
+- **Agent/**: Contains the code for the AI agent integration, including the task-runner and hooks.
+- **Aims/**: Directory containing repository files.
+- **Analysis/**: Directory containing repository files.
+- **Cell-prep-forms/**: Directory containing repository files.
+- **Data/**: Storage for data outputs or references to data.
+- **Templates/**: Contains starter templates for various YAML structures.
+- **agent-case-studies/**: Directory containing repository files.
+- **cursor_env/**: Directory containing repository files.
+- **protocols/**: Directory containing repository files.
+
+---
+
+_This file will be updated whenever the repository structure changes to ensure the robot has the latest context._

TASKS.md

@@ -1,3 +1,9 @@
+# Lab Task List
+
+This file tracks all ongoing lab and dev tasks. Issues created via GitHub and the Lab Agent are appended automatically below.
+
+---
+
 # TASKS
 
 _Note: This file is now automatically updated by the agent/task-runner. Tasks are marked done when experiments are completed, and new tasks may be added as needed._
@@ -29,4 +35,11 @@ _Note: This file is now automatically updated by the agent/task-runner. Tasks ar
 - [ ] Update documentation to reflect new naming conventions
 - [ ] Evaluate need for TASKS.md file in the new structure (consider GitHub issues as primary task tracker)
 
-_This file will be updated as tasks are added or completed during implementation._ 
+_This file will be updated as tasks are added or completed during implementation._ - [ ] [#9](https://github.com/the-jordan-lab/docs/issues/9) Pre-build Dev Container for instant Agent boot  _(added 2025-05-07 10:37)_
+- [ ] [#10](https://github.com/the-jordan-lab/docs/issues/10) Add repo-level OPENAI_API_KEY secret & document  _(added 2025-05-07 10:37)_
+- [ ] [#11](https://github.com/the-jordan-lab/docs/issues/11) Rewrite README Quick-Start for students  _(added 2025-05-07 10:37)_
+- [ ] [#12](https://github.com/the-jordan-lab/docs/issues/12) Implement automated ISSUE → TASKS.md hook  _(added 2025-05-07 10:37)_
+- [ ] [#13](https://github.com/the-jordan-lab/docs/issues/13) Add GitLens default issue view configuration  _(added 2025-05-07 10:37)_
+- [ ] [#14](https://github.com/the-jordan-lab/docs/issues/14) CI: Codespace headless smoke test  _(added 2025-05-07 10:37)_
+- [ ] [#15](https://github.com/the-jordan-lab/docs/issues/15) [Wet-Lab] Complete HEK293T thaw & viability check  _(added 2025-05-07 10:37)_
+- [ ] [#16](https://github.com/the-jordan-lab/docs/issues/16) [Wet-Lab] Prepare Ybx1 & control siRNA mixes  _(added 2025-05-07 10:37)_

morning_push_2025-05-07.md

@@ -0,0 +1,82 @@
+# Morning Push Checklist – 2025-05-07
+
+## Objective
+Deliver a **zero-friction boot experience** for students: open Codespace ➜ talk to Lab Agent immediately, with no extra setup.  All necessary secrets, tools, and docs must already be in place.
+
+---
+
+## 1. Infrastructure / Dev-Ops Tasks (NEW)
+- [ ] **Pre-build Dev Container**
+  - Configure `devcontainer.json` → `features` & `updateContentCommand` so that Python deps, GitHub CLI, and Agent embeddings are built during Codespaces prebuilds.
+  - Verify a fresh Codespace reaches "Agent ready" in <2 min.
+- [ ] **Centralise `OPENAI_API_KEY` secret**
+  - Add repo-level Codespaces secret `OPENAI_API_KEY` (owner only).  Students inherit runtime access, cannot view value.
+  - Document in README > _Secrets are pre-loaded; no action required_.
+- [ ] **README Quick-Start for Students**
+  - Replace multi-step environment instructions with a 3-step "Open ➜ Wait ➜ Chat" section.
+  - Include GIF / screenshot.
+- [ ] **Automated Issue Logging**
+  - Implement small Python hook (`Agent/hooks/post_issue.py`) to append newly created GitHub issues to `TASKS.md` and `ISSUES_LOG.md`.
+  - Add instructions in `Lab Agent Guide`.
+- [ ] **GitLens Integration**
+  - Add `.vscode/settings.json` to enable GitLens "Worktree Issues" view and pin lab-repo issues by default.
+- [ ] **CI Smoke Test** (optional)
+  - GitHub Action that boots Codespace headless and runs `Agent/agent_runner.py --healthcheck`.
+
+---
+
+## 2. Carried-Over Wet-Lab Tasks (from 2025-05-06)
+These remain **open** and must be tracked alongside dev tasks.
+- [ ] Thaw HEK293T cells and check viability
+- [ ] Prepare transfection master mixes
+  - [ ] siRNA targeting Ybx1
+  - [ ] Control siRNA
+- [ ] Set up reverse transfection in 24-well plates
+  - [ ] Label all plates and wells
+  - [ ] Prepare Lipofectamine RNAiMAX and Opti-MEM mixtures
+  - [ ] Add siRNA to appropriate wells
+  - [ ] Add cells to all wells
+- [ ] Place plates in 37 °C incubator with 5 % CO₂
+- [ ] Update experiment status in repository
+- [ ] Upcoming Day 3 tasks (May 8) – verify knockdown & start actinomycin D time course
+- [ ] Materials check: Actinomycin D, RNA extraction kits, qPCR primers
+
+---
+
+## 3. GitHub Issues to Create (assign to @james-m-jordan)
+| # | Title | Labels |
+|---|-------|--------|
+| 1 | Pre-build Dev Container for instant Agent boot | infra, high-priority |
+| 2 | Add repo-level OPENAI_API_KEY secret & document | infra, security |
+| 3 | Rewrite README Quick-Start for students | docs |
+| 4 | Implement automated ISSUE → TASKS.md hook | tooling |
+| 5 | Add GitLens default issue view configuration | tooling |
+| 6 | CI: Codespace headless smoke test | ci |
+| 7 | [Wet-Lab] Complete HEK293T thaw & viability check | lab |
+| 8 | [Wet-Lab] Prepare Ybx1 & control siRNA mixes | lab |
+| … | _Continue one issue per checklist bullet above_ | |
+
+> **How to batch-create:**
+> ```bash
+> gh issue create -t "Pre-build Dev Container for instant Agent boot" -b "See morning_push_2025-05-07.md#1" -a james-m-jordan -l infra,high-priority
+> # Repeat for each row or use gh api to script.
+> ```
+
+---
+
+## 4. Deliverables for May 7 End-of-Day
+- Updated **README.md** (student quick-start)
+- Merged PR implementing dev-ops tasks 1–2
+- All GitHub issues above created and assigned
+- `ISSUES_LOG.md` scaffold committed
+
+---
+
+## 5. Review & Next Steps
+1. Mid-day stand-up: confirm secret injection works in fresh Codespace.
+2. Evening: demo 60-second "clone → chat" workflow with new student account.
+3. Plan May 8 push: continue lab experiment tracking + smoke test results.
+
+---
+
+_Authored automatically by Lab Agent on 2025-05-07_