dayhoff-tools 1.4.18__tar.gz → 1.4.19__tar.gz

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  1. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/cli/engine_commands.py +12 -7
  3. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/pyproject.toml +1 -1
  4. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/README.md +0 -0
  5. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/__init__.py +0 -0
  6. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/chemistry/standardizer.py +0 -0
  7. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/chemistry/utils.py +0 -0
  8. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/cli/__init__.py +0 -0
  9. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/cli/cloud_commands.py +0 -0
  10. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/cli/main.py +0 -0
  11. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/cli/swarm_commands.py +0 -0
  12. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/cli/utility_commands.py +0 -0
  13. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/deployment/base.py +0 -0
  14. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  15. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  16. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  17. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/deployment/job_runner.py +0 -0
  18. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/deployment/processors.py +0 -0
  19. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/deployment/swarm.py +0 -0
  20. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/embedders.py +0 -0
  21. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/fasta.py +0 -0
  22. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/file_ops.py +0 -0
  23. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/h5.py +0 -0
  24. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/intake/gcp.py +0 -0
  25. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/intake/gtdb.py +0 -0
  26. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/intake/kegg.py +0 -0
  27. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/intake/mmseqs.py +0 -0
  28. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/intake/structure.py +0 -0
  29. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/intake/uniprot.py +0 -0
  30. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/logs.py +0 -0
  31. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/sqlite.py +0 -0
  32. {dayhoff_tools-1.4.18 → dayhoff_tools-1.4.19}/dayhoff_tools/warehouse.py +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: dayhoff-tools
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- Version: 1.4.18
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+ Version: 1.4.19
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  Summary: Common tools for all the repos at Dayhoff Labs
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  Author: Daniel Martin-Alarcon
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  Author-email: dma@dayhofflabs.com
@@ -686,9 +686,8 @@ def engine_status(
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  status_lines.append("")
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  status_lines.append("[bold]Attached Studios:[/bold]")
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  for studio in attached_studios:
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- attach_time = studio.get("attach_time", "Unknown")
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  status_lines.append(
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- f" • {studio['user']} ({studio['studio_id']}) - attached {attach_time}"
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+ f" • {studio['user']} ({studio['studio_id']})"
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  )
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  console.print(Panel("\n".join(status_lines), title="Engine Status", border_style="blue"))
@@ -1273,13 +1272,14 @@ def create_ami(
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  console.print("Cleaning up instance for AMI creation...")
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  ssm = boto3.client("ssm", region_name="us-east-1")
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- # Stop SSM, wipe registration, remove sentinel, and clear logs/history
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+ # Clean up instance state, stopping SSM agent last to allow proper status reporting
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  cleanup_commands = [
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- "sudo systemctl stop amazon-ssm-agent",
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- "sudo rm -rf /var/lib/amazon/ssm/* /etc/amazon/ssm/*",
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  "sudo rm -f /opt/dayhoff/first_boot_complete.sentinel",
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  "history -c",
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  "sudo rm -rf /tmp/* /var/log/messages /var/log/cloud-init.log",
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+ "sudo rm -rf /var/lib/amazon/ssm/* /etc/amazon/ssm/*",
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+ # Stop SSM agent last with a delay to allow status reporting
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+ "sleep 2 && sudo systemctl stop amazon-ssm-agent &",
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  ]
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  cleanup_response = ssm.send_command(
@@ -1302,9 +1302,14 @@ def create_ami(
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  if result["Status"] in ["Success", "Failed"]:
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  break
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- if result["Status"] != "Success":
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+ # Note: InProgress status is expected when SSM agent stops itself
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+ if result["Status"] not in ["Success", "InProgress"]:
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+ console.print(
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+ f"[yellow]⚠️ Warning: Cleanup command status: {result['Status']}[/yellow]"
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+ )
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+ elif result["Status"] == "InProgress":
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  console.print(
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- "[yellow]⚠️ Warning: Cleanup command may have failed[/yellow]"
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+ "[dim]ℹ️ Cleanup command still in progress (expected when SSM agent stops itself)[/dim]"
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  )
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  # Get instance details to find volumes to exclude
@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
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  [project]
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  name = "dayhoff-tools"
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- version = "1.4.18"
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+ version = "1.4.19"
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  description = "Common tools for all the repos at Dayhoff Labs"
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  authors = [
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  {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}
File without changes