dayhoff-tools 1.0.16__tar.gz → 1.0.17__tar.gz

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Files changed (30) hide show
  1. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/cli/utility_commands.py +12 -13
  3. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/pyproject.toml +2 -2
  4. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/README.md +0 -0
  5. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/__init__.py +0 -0
  6. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/chemistry/standardizer.py +0 -0
  7. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/chemistry/utils.py +0 -0
  8. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/cli/__init__.py +0 -0
  9. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/cli/cloud_commands.py +0 -0
  10. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/cli/main.py +0 -0
  11. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/cli/swarm_commands.py +0 -0
  12. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/deployment/base.py +0 -0
  13. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  14. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  15. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  16. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/deployment/job_runner.py +0 -0
  17. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/deployment/processors.py +0 -0
  18. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/deployment/swarm.py +0 -0
  19. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/embedders.py +0 -0
  20. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/fasta.py +0 -0
  21. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/file_ops.py +0 -0
  22. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/gcp.py +0 -0
  23. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/h5.py +0 -0
  24. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/kegg.py +0 -0
  25. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/logs.py +0 -0
  26. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/mmseqs.py +0 -0
  27. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/sqlite.py +0 -0
  28. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/structure.py +0 -0
  29. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/dayhoff_tools/uniprot.py +0 -0
  30. {dayhoff_tools-1.0.16 → dayhoff_tools-1.0.17}/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: 1.0.16
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+ Version: 1.0.17
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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
@@ -357,22 +357,21 @@ def build_and_upload_wheel(bump_part: str = "patch"):
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  def update_dayhoff_tools():
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  """Update the dayhoff-tools package to the latest version using uv.
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- Runs `uv add dayhoff-tools@latest --group common` which attempts to update
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- dayhoff-tools within the 'common' dependency group.
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+ Runs `uv add dayhoff-tools@latest`. Note: This command might not correctly
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+ update dayhoff-tools if it's only listed in a top-level [dependency-groups]
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+ table in the target project's pyproject.toml. It works best for dependencies
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+ in [project.dependencies] or [project.optional-dependencies].
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  """
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  try:
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- print(
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- "Updating dayhoff-tools to the latest version in 'common' group using uv..."
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- )
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- # Use uv add with --group common to explicitly target the dependency
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- subprocess.run(
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- ["uv", "add", "dayhoff-tools@latest", "--group", "common"], check=True
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- )
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- print(
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- "Update complete! Run 'uv sync --group common' or relevant sync command if needed."
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- )
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+ print("Attempting to update dayhoff-tools to the latest version using uv...")
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+ # Reverted to simple uv add, acknowledging limitations with top-level groups
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+ subprocess.run(["uv", "add", "dayhoff-tools@latest"], check=True)
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+ print("Update attempt complete! Check pyproject.toml and run sync if needed.")
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  except subprocess.CalledProcessError as e:
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- print(f"Error occurred while updating: {e}")
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+ print(f"Error occurred while attempting update: {e}")
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+ except FileNotFoundError:
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+ print("Error: 'uv' command not found. Is uv installed and in PATH?")
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+ sys.exit(1)
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  def sync_dependencies():
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
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  [project]
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  name = "dayhoff-tools"
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- version = "1.0.16"
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+ version = "1.0.17"
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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"}
@@ -36,7 +36,7 @@ full = [
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  "torchvision>=0.16.0",
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  ]
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- [tool.uv.dependency-groups]
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+ [dependency-groups]
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  common = [
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  "black>=25.1.0,<26",
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  "boto3>=1.36.8",
File without changes