dayhoff-tools 1.11.6__tar.gz → 1.11.7__tar.gz

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Files changed (38) hide show
  1. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/utility_commands.py +52 -8
  3. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/pyproject.toml +1 -1
  4. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/README.md +0 -0
  5. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/__init__.py +0 -0
  6. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/chemistry/standardizer.py +0 -0
  7. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/chemistry/utils.py +0 -0
  8. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/__init__.py +0 -0
  9. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/cloud_commands.py +0 -0
  10. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/__init__.py +0 -0
  11. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/engine_core.py +0 -0
  12. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/engine_lifecycle.py +0 -0
  13. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/engine_maintenance.py +0 -0
  14. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/engine_management.py +0 -0
  15. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/shared.py +0 -0
  16. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/studio_commands.py +0 -0
  17. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/main.py +0 -0
  18. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/swarm_commands.py +0 -0
  19. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/base.py +0 -0
  20. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  21. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  22. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  23. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/job_runner.py +0 -0
  24. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/processors.py +0 -0
  25. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/swarm.py +0 -0
  26. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/embedders.py +0 -0
  27. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/fasta.py +0 -0
  28. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/file_ops.py +0 -0
  29. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/h5.py +0 -0
  30. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/intake/gcp.py +0 -0
  31. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/intake/gtdb.py +0 -0
  32. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/intake/kegg.py +0 -0
  33. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/intake/mmseqs.py +0 -0
  34. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/intake/structure.py +0 -0
  35. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/intake/uniprot.py +0 -0
  36. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/logs.py +0 -0
  37. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/sqlite.py +0 -0
  38. {dayhoff_tools-1.11.6 → dayhoff_tools-1.11.7}/dayhoff_tools/warehouse.py +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: dayhoff-tools
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- Version: 1.11.6
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+ Version: 1.11.7
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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
@@ -570,12 +570,33 @@ def sync_with_toml(
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  ]
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  print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
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  subprocess.run(sync_cmd, check=True, cwd=str(mac_uv_dir))
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+
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  # Install project from repo root (where source code actually is)
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+ # Temporarily create pyproject.toml at repo root for UV
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  print("Installing project with 'full' extras from repo root…")
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- pip_install_cmd = ["uv", "pip", "install", "-e", ".[full]"]
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- print(f"Running command: {BLUE}{' '.join(pip_install_cmd)}{RESET}")
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- subprocess.run(pip_install_cmd, check=True)
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- print("Project installed with 'full' extras successfully.")
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+ temp_pyproject = False
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+ backup_created = False
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+ try:
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+ if not Path("pyproject.toml").exists():
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+ # Create temp pyproject.toml from platform manifest
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+ Path("pyproject.toml").write_text(mac_manifest.read_text())
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+ temp_pyproject = True
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+ elif Path("pyproject.toml").is_symlink():
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+ # Backup existing symlink
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+ Path("pyproject.toml").rename("pyproject.toml.sync.bak")
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+ Path("pyproject.toml").write_text(mac_manifest.read_text())
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+ backup_created = True
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+
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+ pip_install_cmd = ["uv", "pip", "install", "-e", ".[full]"]
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+ print(f"Running command: {BLUE}{' '.join(pip_install_cmd)}{RESET}")
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+ subprocess.run(pip_install_cmd, check=True)
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+ print("Project installed with 'full' extras successfully.")
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+ finally:
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+ # Clean up temp pyproject.toml
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+ if temp_pyproject and Path("pyproject.toml").exists():
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+ Path("pyproject.toml").unlink()
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+ if backup_created and Path("pyproject.toml.sync.bak").exists():
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+ Path("pyproject.toml.sync.bak").rename("pyproject.toml")
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  else:
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  print("Syncing dependencies into ACTIVE env (project not installed)…")
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  sync_cmd = [
@@ -624,12 +645,35 @@ def sync_with_toml(
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  ]
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  print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
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  subprocess.run(sync_cmd, check=True, cwd=str(aws_uv_dir))
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+
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  # Install project from repo root (where source code actually is)
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+ # Temporarily create pyproject.toml at repo root for UV
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  print("Installing project with 'full' extras from repo root…")
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- pip_install_cmd = ["uv", "pip", "install", "-e", ".[full]"]
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- print(f"Running command: {BLUE}{' '.join(pip_install_cmd)}{RESET}")
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- subprocess.run(pip_install_cmd, check=True)
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- print("Project installed with 'full' extras successfully.")
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+ temp_pyproject = False
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+ backup_created = False
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+ try:
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+ if not Path("pyproject.toml").exists():
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+ # Create temp pyproject.toml from platform manifest
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+ Path("pyproject.toml").write_text(aws_manifest.read_text())
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+ temp_pyproject = True
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+ elif Path("pyproject.toml").is_symlink():
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+ # Backup existing symlink
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+ Path("pyproject.toml").rename("pyproject.toml.sync.bak")
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+ Path("pyproject.toml").write_text(aws_manifest.read_text())
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+ backup_created = True
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+
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+ pip_install_cmd = ["uv", "pip", "install", "-e", ".[full]"]
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+ print(
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+ f"Running command: {BLUE}{' '.join(pip_install_cmd)}{RESET}"
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+ )
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+ subprocess.run(pip_install_cmd, check=True)
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+ print("Project installed with 'full' extras successfully.")
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+ finally:
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+ # Clean up temp pyproject.toml
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+ if temp_pyproject and Path("pyproject.toml").exists():
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+ Path("pyproject.toml").unlink()
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+ if backup_created and Path("pyproject.toml.sync.bak").exists():
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+ Path("pyproject.toml.sync.bak").rename("pyproject.toml")
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  else:
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  print(
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  "Syncing dependencies into ACTIVE env (project not installed)…"
@@ -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 = "1.11.6"
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+ version = "1.11.7"
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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