dayhoff-tools 1.4.5__tar.gz → 1.4.7__tar.gz

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Files changed (32) hide show
  1. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/cli/engine_commands.py +2 -4
  3. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/pyproject.toml +1 -1
  4. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/README.md +0 -0
  5. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/__init__.py +0 -0
  6. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/chemistry/standardizer.py +0 -0
  7. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/chemistry/utils.py +0 -0
  8. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/cli/__init__.py +0 -0
  9. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/cli/cloud_commands.py +0 -0
  10. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/cli/main.py +0 -0
  11. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/cli/swarm_commands.py +0 -0
  12. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/cli/utility_commands.py +0 -0
  13. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/deployment/base.py +0 -0
  14. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  15. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  16. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  17. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/deployment/job_runner.py +0 -0
  18. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/deployment/processors.py +0 -0
  19. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/deployment/swarm.py +0 -0
  20. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/embedders.py +0 -0
  21. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/fasta.py +0 -0
  22. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/file_ops.py +0 -0
  23. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/h5.py +0 -0
  24. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/intake/gcp.py +0 -0
  25. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/intake/gtdb.py +0 -0
  26. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/intake/kegg.py +0 -0
  27. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/intake/mmseqs.py +0 -0
  28. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/intake/structure.py +0 -0
  29. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/intake/uniprot.py +0 -0
  30. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/logs.py +0 -0
  31. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/dayhoff_tools/sqlite.py +0 -0
  32. {dayhoff_tools-1.4.5 → dayhoff_tools-1.4.7}/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: 1.4.5
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+ Version: 1.4.7
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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
@@ -382,8 +382,7 @@ def update_ssh_config_entry(engine_name: str, instance_id: str, ssh_user: str):
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  Host {engine_name} {SSH_MANAGED_COMMENT}
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  HostName {instance_id}
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  User {ssh_user}
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- ProxyCommand sh -c "aws ssm start-session --target %h --document-name AWS-StartSSHSession --idle-timeout 600 --parameters 'portNumber=%p'"
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- """
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+ ProxyCommand sh -c \"AWS_SSM_IDLE_TIMEOUT=600 aws ssm start-session --target %h --document-name AWS-StartSSHSession --parameters 'portNumber=%p'\"\n"""
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  # Check if entry already exists
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  host_line = f"Host {engine_name} {SSH_MANAGED_COMMENT}"
@@ -617,7 +616,6 @@ def engine_status(
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  f"[bold]Instance:[/bold] {engine['instance_id']}",
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  f"[bold]Type:[/bold] {engine['engine_type']} ({engine['instance_type']})",
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  f"[bold]Status:[/bold] {format_status(engine['state'], engine.get('ready'))}",
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- f"[bold]Bootstrap:[/bold] {_colour_stage(stage_val)}",
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  f"[bold]User:[/bold] {engine['user']}",
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  f"[bold]IP:[/bold] {engine.get('public_ip', 'N/A')}",
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  f"[bold]Launched:[/bold] {launch_time.strftime('%Y-%m-%d %H:%M:%S')} ({format_duration(uptime)} ago)",
@@ -945,7 +943,7 @@ def config_ssh(
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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 {ssh_user}",
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- f" ProxyCommand sh -c \"aws ssm start-session --target %h --document-name AWS-StartSSHSession --idle-timeout 600 --parameters 'portNumber=%p'\"",
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+ f" ProxyCommand sh -c \"AWS_SSM_IDLE_TIMEOUT=600 aws ssm start-session --target %h --document-name AWS-StartSSHSession --parameters 'portNumber=%p'\"",
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  ]
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  )
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@@ -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 = "1.4.5"
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+ version = "1.4.7"
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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