dayhoff-tools 1.3.18__tar.gz → 1.3.20__tar.gz

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Files changed (32) hide show
  1. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/cli/engine_commands.py +5 -5
  3. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/pyproject.toml +1 -1
  4. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/README.md +0 -0
  5. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/__init__.py +0 -0
  6. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/chemistry/standardizer.py +0 -0
  7. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/chemistry/utils.py +0 -0
  8. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/cli/__init__.py +0 -0
  9. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/cli/cloud_commands.py +0 -0
  10. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/cli/main.py +0 -0
  11. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/cli/swarm_commands.py +0 -0
  12. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/cli/utility_commands.py +0 -0
  13. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/deployment/base.py +0 -0
  14. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  15. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  16. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  17. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/deployment/job_runner.py +0 -0
  18. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/deployment/processors.py +0 -0
  19. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/deployment/swarm.py +0 -0
  20. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/embedders.py +0 -0
  21. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/fasta.py +0 -0
  22. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/file_ops.py +0 -0
  23. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/h5.py +0 -0
  24. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/intake/gcp.py +0 -0
  25. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/intake/gtdb.py +0 -0
  26. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/intake/kegg.py +0 -0
  27. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/intake/mmseqs.py +0 -0
  28. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/intake/structure.py +0 -0
  29. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/intake/uniprot.py +0 -0
  30. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/logs.py +0 -0
  31. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/dayhoff_tools/sqlite.py +0 -0
  32. {dayhoff_tools-1.3.18 → dayhoff_tools-1.3.20}/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: 1.3.18
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+ Version: 1.3.20
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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
@@ -381,7 +381,7 @@ def update_ssh_config_entry(engine_name: str, instance_id: str, username: str):
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  new_entry = f"""
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  Host {engine_name} {SSH_MANAGED_COMMENT}
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  HostName {instance_id}
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- User {username}
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+ User ec2-user
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  ProxyCommand sh -c "aws ssm start-session --target %h --document-name AWS-StartSSHSession --parameters 'portNumber=%p'"
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  """
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@@ -632,7 +632,7 @@ def engine_status(
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  res = ssm.send_command(
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  InstanceIds=[engine["instance_id"]],
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  DocumentName="AWS-RunShellScript",
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- Parameters={"commands": ["cat /var/run/engine-health.json || true"], "executionTimeout": ["10"]},
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+ Parameters={"commands": ["cat /opt/dayhoff/state/engine-health.json 2>/dev/null || cat /var/run/engine-health.json 2>/dev/null || true"], "executionTimeout": ["10"]},
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  )
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  cid = res["Command"]["CommandId"]
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  time.sleep(1)
@@ -903,7 +903,7 @@ def config_ssh(
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  "",
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  f"Host {engine['name']} {SSH_MANAGED_COMMENT}",
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  f" HostName {engine['instance_id']}",
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- f" User {username}",
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+ f" User ec2-user",
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  f" ProxyCommand sh -c \"aws ssm start-session --target %h --document-name AWS-StartSSHSession --parameters 'portNumber=%p'\"",
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  ]
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  )
@@ -2090,8 +2090,8 @@ def debug_engine(
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  # Check multiple files and systemd status
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  checks = [
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- ("Stage file", "cat /var/run/engine-init.stage 2>/dev/null || echo 'MISSING'"),
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- ("Health file", "cat /var/run/engine-health.json 2>/dev/null || echo 'MISSING'"),
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+ ("Stage file", "cat /opt/dayhoff/state/engine-init.stage 2>/dev/null || cat /var/run/engine-init.stage 2>/dev/null || echo 'MISSING'"),
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+ ("Health file", "cat /opt/dayhoff/state/engine-health.json 2>/dev/null || cat /var/run/engine-health.json 2>/dev/null || echo 'MISSING'"),
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  ("Sentinel file", "ls -la /opt/dayhoff/first_boot_complete.sentinel 2>/dev/null || echo 'MISSING'"),
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  ("Setup service", "systemctl status setup-aws-vm.service --no-pager || echo 'Service not found'"),
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  ("Bootstrap log tail", "tail -20 /var/log/engine-setup.log 2>/dev/null || echo 'No log'"),
@@ -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 = "1.3.18"
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+ version = "1.3.20"
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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