dayhoff-tools 1.1.30__tar.gz → 1.1.33__tar.gz

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Files changed (31) hide show
  1. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/PKG-INFO +2 -1
  2. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/deployment/deploy_gcp.py +23 -1
  3. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/deployment/job_runner.py +2 -4
  4. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/pyproject.toml +2 -1
  5. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/README.md +0 -0
  6. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/__init__.py +0 -0
  7. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/chemistry/standardizer.py +0 -0
  8. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/chemistry/utils.py +0 -0
  9. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/cli/__init__.py +0 -0
  10. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/cli/cloud_commands.py +0 -0
  11. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/cli/main.py +0 -0
  12. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/cli/swarm_commands.py +0 -0
  13. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/cli/utility_commands.py +0 -0
  14. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/deployment/base.py +0 -0
  15. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  16. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  17. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/deployment/processors.py +0 -0
  18. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/deployment/swarm.py +0 -0
  19. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/embedders.py +0 -0
  20. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/fasta.py +0 -0
  21. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/file_ops.py +0 -0
  22. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/h5.py +0 -0
  23. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/intake/gcp.py +0 -0
  24. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/intake/gtdb.py +0 -0
  25. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/intake/kegg.py +0 -0
  26. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/intake/mmseqs.py +0 -0
  27. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/intake/structure.py +0 -0
  28. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/intake/uniprot.py +0 -0
  29. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/logs.py +0 -0
  30. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/dayhoff_tools/sqlite.py +0 -0
  31. {dayhoff_tools-1.1.30 → dayhoff_tools-1.1.33}/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: 1.1.30
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+ Version: 1.1.33
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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
@@ -38,6 +38,7 @@ Requires-Dist: tqdm (>=4.67.1) ; extra == "full"
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  Requires-Dist: transformers (==4.36.2) ; extra == "full"
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  Requires-Dist: transformers (>=4.36.2) ; extra == "embedders"
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  Requires-Dist: typer (>=0.9.0)
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+ Requires-Dist: tzdata (>=2025.2)
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  Description-Content-Type: text/markdown
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  # dayhoff-tools
@@ -75,9 +75,20 @@ def create_batch_job_config(config: dict, image_uri: str) -> dict:
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  "commands": ["-c", " ".join(entrypoint_command)],
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  }
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+ # Handle container options - both shared memory and any custom options
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+ docker_options = []
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+
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  # Add shared memory option if specified
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  if "shared_memory" in config.get("docker", {}):
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- container_config["options"] = f"--shm-size={config['docker']['shared_memory']}"
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+ docker_options.append(f"--shm-size={config['docker']['shared_memory']}")
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+
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+ # Add any custom Docker options if specified
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+ if "options" in config.get("docker", {}):
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+ docker_options.append(config["docker"]["options"])
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+
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+ # Set the options field if any options were collected
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+ if docker_options:
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+ container_config["options"] = " ".join(docker_options)
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  # Build the task group configuration
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  task_group = {
@@ -123,6 +134,17 @@ def create_batch_job_config(config: dict, image_uri: str) -> dict:
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  print("Machine Type:", policy.get("machineType", "Not specified"))
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  print("Accelerators:", policy.get("accelerators", "Not specified"))
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  print("Environment Variables:", list(env_vars.keys()))
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+ if (
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+ "runnables" in task_group["taskSpec"]
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+ and task_group["taskSpec"]["runnables"]
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+ ):
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+ print(
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+ "Container Options:",
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+ task_group["taskSpec"]["runnables"][0]
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+ .get("container", {})
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+ .get("options", "Not specified"),
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+ )
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+
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  except KeyError as e:
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  print(f"Warning: Could not find {e} in configuration")
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@@ -94,9 +94,9 @@ def run_command() -> None:
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  stderr=None, # Use parent's stderr
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  )
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- logger.info("Command completed successfully")
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+ logger.info("Job command completed successfully")
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  except subprocess.CalledProcessError as e:
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- logger.error(f"Command failed with return code: {e.returncode}")
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+ logger.error(f"Job command failed with return code: {e.returncode}")
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  raise
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  except Exception as e:
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  logger.error(f"Error executing command: {str(e)}")
@@ -153,8 +153,6 @@ def run_job(
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  if mode in ["execute", "setup_and_execute"]:
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  run_command()
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- logger.info("Job completed successfully")
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-
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  except Exception as e:
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  logger.error(f"Job failed with error: {str(e)}", exc_info=True)
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  sys.exit(1)
@@ -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 = "1.1.30"
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+ version = "1.1.33"
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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"}
@@ -19,6 +19,7 @@ dependencies = [
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  "typer>=0.9.0",
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  "toml>=0.10",
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  "questionary>=2.0.1",
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+ "tzdata>=2025.2",
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  ]
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  requires-python = ">=3.10,<4.0"
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