LLMs-Universal-Life-Science-and-Clinical-Skills- gh-fix-ci

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install
source · Clone the upstream repo
git clone https://github.com/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- "$T" && mkdir -p ~/.claude/skills && cp -r "$T/Skills/External_Collections/Babu_OpenAI_skills-main (2)/skills/.curated/gh-fix-ci" ~/.claude/skills/mdbabumiamssm-llms-universal-life-science-and-clinical-skills-gh-fix-ci && rm -rf "$T"
manifest: Skills/External_Collections/Babu_OpenAI_skills-main (2)/skills/.curated/gh-fix-ci/SKILL.md
source content
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---name: gh-fix-ci description: Inspect GitHub PR checks with gh, pull failing GitHub Actions logs, summarize failure context, then create a fix plan and implement after user approval. Use when a user asks to debug or fix failing PR CI/CD checks on GitHub Actions and wants a plan + code changes; for external checks (e.g., Buildkite), only report the details URL and mark them out of scope. metadata: short-description: Fix failing Github CI actions

keywords:

  • gh-fix-ci
  • automation
  • biomedical measurable_outcome: execute task with >95% success rate. allowed-tools:
  • read_file
  • run_shell_command ---"

Gh Pr Checks Plan Fix

Overview

Use gh to locate failing PR checks, fetch GitHub Actions logs for actionable failures, summarize the failure snippet, then propose a fix plan and implement after explicit approval.

  • Depends on the
    plan
    skill for drafting and approving the fix plan.

Prereq: ensure

gh
is authenticated (for example, run
gh auth login
once), then run
gh auth status
with escalated permissions (include workflow/repo scopes) so
gh
commands succeed. If sandboxing blocks
gh auth status
, rerun it with
sandbox_permissions=require_escalated
.

Inputs

  • repo
    : path inside the repo (default
    .
    )
  • pr
    : PR number or URL (optional; defaults to current branch PR)
  • gh
    authentication for the repo host

Quick start

  • python "<path-to-skill>/scripts/inspect_pr_checks.py" --repo "." --pr "<number-or-url>"
  • Add
    --json
    if you want machine-friendly output for summarization.

Workflow

  1. Verify gh authentication.
    • Run
      gh auth status
      in the repo with escalated scopes (workflow/repo) after running
      gh auth login
      .
    • If sandboxed auth status fails, rerun the command with
      sandbox_permissions=require_escalated
      to allow network/keyring access.
    • If unauthenticated, ask the user to log in before proceeding.
  2. Resolve the PR.
    • Prefer the current branch PR:
      gh pr view --json number,url
      .
    • If the user provides a PR number or URL, use that directly.
  3. Inspect failing checks (GitHub Actions only).
    • Preferred: run the bundled script (handles gh field drift and job-log fallbacks):
      • python "<path-to-skill>/scripts/inspect_pr_checks.py" --repo "." --pr "<number-or-url>"
      • Add
        --json
        for machine-friendly output.
    • Manual fallback:
      • gh pr checks <pr> --json name,state,bucket,link,startedAt,completedAt,workflow
        • If a field is rejected, rerun with the available fields reported by
          gh
          .
      • For each failing check, extract the run id from
        detailsUrl
        and run:
        • gh run view <run_id> --json name,workflowName,conclusion,status,url,event,headBranch,headSha
        • gh run view <run_id> --log
      • If the run log says it is still in progress, fetch job logs directly:
        • gh api "/repos/<owner>/<repo>/actions/jobs/<job_id>/logs" > "<path>"
  4. Scope non-GitHub Actions checks.
    • If
      detailsUrl
      is not a GitHub Actions run, label it as external and only report the URL.
    • Do not attempt Buildkite or other providers; keep the workflow lean.
  5. Summarize failures for the user.
    • Provide the failing check name, run URL (if any), and a concise log snippet.
    • Call out missing logs explicitly.
  6. Create a plan.
    • Use the
      plan
      skill to draft a concise plan and request approval.
  7. Implement after approval.
    • Apply the approved plan, summarize diffs/tests, and ask about opening a PR.
  8. Recheck status.
    • After changes, suggest re-running the relevant tests and
      gh pr checks
      to confirm.

Bundled Resources

scripts/inspect_pr_checks.py

Fetch failing PR checks, pull GitHub Actions logs, and extract a failure snippet. Exits non-zero when failures remain so it can be used in automation.

Usage examples:

  • python "<path-to-skill>/scripts/inspect_pr_checks.py" --repo "." --pr "123"
  • python "<path-to-skill>/scripts/inspect_pr_checks.py" --repo "." --pr "https://github.com/org/repo/pull/123" --json
  • python "<path-to-skill>/scripts/inspect_pr_checks.py" --repo "." --max-lines 200 --context 40
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