dayhoff-tools 1.4.2__tar.gz → 1.4.4__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/PKG-INFO +1 -1
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/cli/engine_commands.py +5 -12
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/pyproject.toml +1 -1
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/README.md +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/__init__.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/chemistry/standardizer.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/chemistry/utils.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/cli/__init__.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/cli/cloud_commands.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/cli/main.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/cli/swarm_commands.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/cli/utility_commands.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/deployment/base.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/deployment/deploy_aws.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/deployment/deploy_utils.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/deployment/job_runner.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/deployment/processors.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/deployment/swarm.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/embedders.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/fasta.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/file_ops.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/h5.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/intake/gcp.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/intake/gtdb.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/intake/kegg.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/intake/mmseqs.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/intake/structure.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/intake/uniprot.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/logs.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/sqlite.py +0 -0
- {dayhoff_tools-1.4.2 → dayhoff_tools-1.4.4}/dayhoff_tools/warehouse.py +0 -0
@@ -382,7 +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 --parameters 'portNumber=%p'"
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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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# Check if entry already exists
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@@ -945,7 +945,7 @@ 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 --parameters 'portNumber=%p'\"",
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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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]
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)
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@@ -1253,7 +1253,7 @@ def create_ami(
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console.print(f"AMI Name: [cyan]{ami_name}[/cyan]")
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console.print(f"Description: {ami_description}")
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console.print(
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"\n[yellow]⚠️ Important: This will reboot the engine to ensure a clean snapshot.[/yellow]"
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"\n[yellow]⚠️ Important: This will detach all studios and reboot the engine to ensure a clean snapshot.[/yellow]"
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)
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if not Confirm.ask("\nContinue with AMI creation?"):
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@@ -1322,15 +1322,10 @@ def create_ami(
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attached_studios = attached_resp.json().get("studios", []) if attached_resp.status_code == 200 else []
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if attached_studios:
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console.print(f"
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console.print(f"Detaching {len(attached_studios)} studio(s) from this engine…")
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for s in attached_studios:
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console.print(f" • {s['user']} ({s['studio_id']})")
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if not Confirm.ask("Detach all studios before AMI creation?"):
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console.print("AMI creation cancelled.")
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return
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console.print("Detaching studios…")
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for s in attached_studios:
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resp = make_api_request("POST", f"/studios/{s['studio_id']}/detach")
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if resp.status_code != 200:
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@@ -1354,9 +1349,7 @@ def create_ami(
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TextColumn("[progress.description]{task.description}"),
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transient=True,
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) as progress:
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progress.add_task(
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"Creating AMI (this will take several minutes)...", total=None
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)
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progress.add_task("Creating AMI (this will take several minutes)...", total=None)
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create_params = {
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"InstanceId": engine["instance_id"],
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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.
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version = "1.4.4"
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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"}
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