docs/building_labagent/morning_push_2025-05-07.md

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.

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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.

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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

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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:

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.

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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

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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.

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Authored automatically by Lab Agent on 2025-05-07