Cherry-pick commits into branch (stopped)

[Copilot]

Task was to cherry-pick two commits from the refassem branch:

• 2ec46f6dfb445b1651ed8aeab16b533940cc1a43 - draft marlin subworkflow, modules, and config
• 64a70a53aff72198f76cede4828869b31a3ba5e7 - finish draft marlin subworkflow, clean refassem branch

Status

Work stopped per user request. No changes were successfully applied.

Blockers Encountered

• Repository in shallow clone state with limited fetch configuration
• Git authentication failed when attempting to fetch refassem branch
• GitHub API returned 403 Forbidden for file content access
• Unable to retrieve commit contents through raw.githubusercontent.com (404 errors)

Attempted Approaches

• Modified git fetch refspecs to include refassem branch
• Attempted direct file downloads via GitHub raw content API
• Tried GitHub REST API for file contents at specific commit SHA
• All methods blocked by authentication or access restrictions

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• https://api.github.com/repos/treangenlab/Somatem/commits/2ec46f6dfb445b1651ed8aeab16b533940cc1a43
  • Triggering command: /usr/bin/curl curl -H Authorization: token REDACTED (http block)
• https://api.github.com/repos/treangenlab/Somatem/contents/bin/build_contigs.py
  • Triggering command: /usr/bin/python3 python3 /tmp/cherrypick/fetch_via_api.py (http block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

Can you cherrypick these commits into this branch please?
2ec46f6
64a70a5

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