fix: include all optional extras in dependency refresh workflow

[stranske]

Source: Issue #123

Automated Status Summary

Scope

After merging PR #103 (multi-agent routing infrastructure), we need to:

1. Validate the CLI agent pipeline works end-to-end with the new task-focused prompts
2. Add GITHUB_STEP_SUMMARY output so iteration results are visible in the Actions UI
3. Streamline the Automated Status Summary to reduce clutter when using CLI agents
4. Clean up comment patterns to avoid a mix of old UI-agent and new CLI-agent comments

Context for Agent

Design Decisions & Constraints

• 4. Clean up comment patterns to avoid a mix of old UI-agent and new CLI-agent comments
• The keepalive loop now:
• | <!-- keepalive-loop-summary --> | github-actions[bot] | NEW: CLI agent iteration tracking | ✅ Keep for CLI agents |
• | <!-- keepalive-state:v1 --> | agents-workflows-bot[bot] | State tracking | ⚠️ Multiple copies accumulate |
• | <!-- keepalive-round: N --> | stranske | OLD: Instruction comment | ❌ CLI agents dont need this |
• The goal: For CLI agents (agent:* label), we should have exactly one updating comment (<!-- keepalive-loop-summary -->) instead of accumulating 10+ comments per PR.
• Requires PR #103 to be merged first
• This round you MUST:
• Review the Scope/Tasks/Acceptance below, identify the next incomplete task that requires code, implement it, then post a reply comment with the completed items using their exact original text.

Related Issues/PRs

• #103
• #89
• #123

References

• https://github.com/stranske/Workflows/compare/main...codex/issue-123?expand=1

Blockers & Dependencies

• After merging PR #103 (multi-agent routing infrastructure), we need to:
• 3. Mark a task checkbox complete ONLY after verifying the implementation works.

Tasks

Pipeline Validation

• After PR chore(codex): bootstrap PR for issue #101 #103 merges, create a test PR with agent:codex label
• Verify task appendix appears in Codex prompt (check workflow logs)
• Verify Codex works on actual tasks (not random infrastructure work)
• Verify keepalive comment updates with iteration progress

GITHUB_STEP_SUMMARY

• Add step summary output to agents-keepalive-loop.yml after agent run
• Include: iteration number, tasks completed, files changed, outcome
• Ensure summary is visible in workflow run UI

Conditional Status Summary

• Modify buildStatusBlock() in agents_pr_meta_update_body.js to accept agentType parameter
• When agentType is set (CLI agent): hide workflow table, hide head SHA/required checks
• Keep Scope/Tasks/Acceptance checkboxes for all cases
• Pass agent type from workflow to the update_body job

Comment Pattern Cleanup

• For CLI agents (agent:* label):
• Suppress <!-- gate-summary: --> comment posting (use step summary instead)
• Suppress <!-- keepalive-round: N --> instruction comments (task appendix replaces this)
• Update <!-- keepalive-loop-summary --> to be the single source of truth
• Ensure state marker is embedded in the summary comment (not separate)
• For UI Codex (no agent:* label):
• Keep existing comment patterns (instruction comments, connector bot reports)
• Keep <!-- gate-summary: --> comment
• Add agent_type output to detect job so downstream workflows know the mode
• Update agents-pr-meta.yml to conditionally skip gate summary for CLI agent PRs

Acceptance criteria

• CLI agent receives explicit tasks in prompt and works on them
• Iteration results visible in Actions workflow run summary
• PR body shows checkboxes but not workflow clutter when using CLI agents
• UI Codex path (no agent label) continues to show full status summary
• CLI agent PRs have ≤3 bot comments total (summary, one per iteration update) instead of 10+
• State tracking is consolidated in the summary comment, not scattered

Head SHA: 465a5d0
Latest Runs: ✅ success — Gate
Required: gate: ✅ success

Workflow / Job	Result	Logs
Agents PR meta manager	❔ in progress	View run
CI Autofix Loop	✅ success	View run
Gate	✅ success	View run
Health 40 Sweep	✅ success	View run
Health 44 Gate Branch Protection	✅ success	View run
Health 45 Agents Guard	✅ success	View run
Health 50 Security Scan	✅ success	View run
Health 67 Integration Sync Check	✅ success	View run
Maint 52 Validate Workflows	✅ success	View run
PR 11 - Minimal invariant CI	✅ success	View run
Selftest CI	✅ success	View run
Validate Sync Manifest	✅ success	View run

[github-actions]

Automated Status Summary

Head SHA: fde6a8f
Latest Runs: ⏳ pending — Gate
Required contexts: Gate / gate, Health 45 Agents Guard / Enforce agents workflow protections
Required: core tests (3.11): ⏳ pending, core tests (3.12): ⏳ pending, docker smoke: ⏳ pending, gate: ⏳ pending

Workflow / Job	Result	Logs
(no jobs reported)	⏳ pending	—

Coverage Overview

• Coverage history entries: 1

Coverage Trend

Metric	Value
Current	92.21%
Baseline	85.00%
Delta	+7.21%
Minimum	70.00%
Status	✅ Pass

Top Coverage Hotspots (lowest coverage)

File	Coverage	Missing
scripts/workflow_health_check.py	62.6%	28
scripts/classify_test_failures.py	62.9%	37
scripts/ledger_validate.py	65.3%	63
scripts/mypy_return_autofix.py	82.6%	11
scripts/ledger_migrate_base.py	85.5%	13
scripts/fix_cosmetic_aggregate.py	92.3%	1
scripts/coverage_history_append.py	92.8%	2
scripts/workflow_validator.py	93.3%	4
scripts/update_autofix_expectations.py	93.9%	1
scripts/pr_metrics_tracker.py	95.7%	3
scripts/generate_residual_trend.py	96.6%	1
scripts/build_autofix_pr_comment.py	97.0%	2
scripts/aggregate_agent_metrics.py	97.2%	0
scripts/fix_numpy_asserts.py	98.1%	0
scripts/sync_test_dependencies.py	98.3%	1

Updated automatically; will refresh on subsequent CI/Docker completions.

---

Keepalive checklist

Scope

After merging PR #103 (multi-agent routing infrastructure), we need to:

1. Validate the CLI agent pipeline works end-to-end with the new task-focused prompts
2. Add GITHUB_STEP_SUMMARY output so iteration results are visible in the Actions UI
3. Streamline the Automated Status Summary to reduce clutter when using CLI agents
4. Clean up comment patterns to avoid a mix of old UI-agent and new CLI-agent comments

Context for Agent

Design Decisions & Constraints

• 4. Clean up comment patterns to avoid a mix of old UI-agent and new CLI-agent comments
• The keepalive loop now:
• | <!-- keepalive-loop-summary --> | github-actions[bot] | NEW: CLI agent iteration tracking | ✅ Keep for CLI agents |
• | <!-- keepalive-state:v1 --> | agents-workflows-bot[bot] | State tracking | ⚠️ Multiple copies accumulate |
• | <!-- keepalive-round: N --> | stranske | OLD: Instruction comment | ❌ CLI agents dont need this |
• The goal: For CLI agents (agent:* label), we should have exactly one updating comment (<!-- keepalive-loop-summary -->) instead of accumulating 10+ comments per PR.
• Requires PR #103 to be merged first
• This round you MUST:
• Review the Scope/Tasks/Acceptance below, identify the next incomplete task that requires code, implement it, then post a reply comment with the completed items using their exact original text.

Related Issues/PRs

• #103
• #89
• #123

References

• https://github.com/stranske/Workflows/compare/main...codex/issue-123?expand=1

Blockers & Dependencies

• After merging PR #103 (multi-agent routing infrastructure), we need to:
• 3. Mark a task checkbox complete ONLY after verifying the implementation works.

Tasks

Pipeline Validation

• After PR chore(codex): bootstrap PR for issue #101 #103 merges, create a test PR with agent:codex label
• Verify task appendix appears in Codex prompt (check workflow logs)
• Verify Codex works on actual tasks (not random infrastructure work)
• Verify keepalive comment updates with iteration progress

GITHUB_STEP_SUMMARY

• Add step summary output to agents-keepalive-loop.yml after agent run
• Include: iteration number, tasks completed, files changed, outcome
• Ensure summary is visible in workflow run UI

Conditional Status Summary

• Modify buildStatusBlock() in agents_pr_meta_update_body.js to accept agentType parameter
• When agentType is set (CLI agent): hide workflow table, hide head SHA/required checks
• Keep Scope/Tasks/Acceptance checkboxes for all cases
• Pass agent type from workflow to the update_body job

Comment Pattern Cleanup

• For CLI agents (agent:* label):
• Suppress <!-- gate-summary: --> comment posting (use step summary instead)
• Suppress <!-- keepalive-round: N --> instruction comments (task appendix replaces this)
• Update <!-- keepalive-loop-summary --> to be the single source of truth
• Ensure state marker is embedded in the summary comment (not separate)
• For UI Codex (no agent:* label):
• Keep existing comment patterns (instruction comments, connector bot reports)
• Keep <!-- gate-summary: --> comment
• Add agent_type output to detect job so downstream workflows know the mode
• Update agents-pr-meta.yml to conditionally skip gate summary for CLI agent PRs

Acceptance criteria

• CLI agent receives explicit tasks in prompt and works on them
• Iteration results visible in Actions workflow run summary
• PR body shows checkboxes but not workflow clutter when using CLI agents
• UI Codex path (no agent label) continues to show full status summary
• CLI agent PRs have ≤3 bot comments total (summary, one per iteration update) instead of 10+
• State tracking is consolidated in the summary comment, not scattered

[github-actions]

🤖 Keepalive Loop Status

PR #885 | Agent: Codex | Iteration 0/5

Current State

Metric	Value
Iteration progress	[----------] 0/5
Action	wait (missing-agent-label)
Disposition	skipped (transient)
Gate	success
Tasks	0/10 complete
Timeout	45 min (default)
Timeout usage	2m elapsed (5%, 43m remaining)
Keepalive	❌ disabled
Autofix	❌ disabled

🔍 Failure Classification

| Error type | infrastructure |
| Error category | resource |
| Suggested recovery | Confirm the referenced resource exists (repo, PR, branch, workflow, or file). |

[Copilot]

Pull request overview

This PR fixes a sustainability issue in the dependency refresh workflow that was only compiling the lock file with the dev extra, missing the langchain optional dependencies. This caused test failures and required manual intervention.

Changes:

• Updated the dependency refresh workflow to include both --extra dev and --extra langchain flags
• Corrected documentation to reflect the actual extras in this repo (dev, langchain) instead of incorrect examples from another repo
• Regenerated requirements.lock with all extras included

Reviewed changes

Copilot reviewed 3 out of 4 changed files in this pull request and generated no comments.

File	Description
.github/workflows/maint-51-dependency-refresh.yml	Added --extra langchain to the compile command and verification step to ensure all optional dependencies are included
templates/dependency-refresh.yml	Updated template for consumer repos to include the langchain extra
DEPENDENCY_TESTING.md	Corrected documentation examples to reflect actual extras in this repo instead of outdated examples from a different repo
requirements.lock	Regenerated lock file with updated dependencies and corrected header comment showing the proper compile command

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.