dayhoff-tools 1.1.1__tar.gz → 1.1.2__tar.gz

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Files changed (30) hide show
  1. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/cli/main.py +3 -5
  3. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/cli/utility_commands.py +0 -11
  4. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/pyproject.toml +2 -3
  5. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/README.md +0 -0
  6. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/__init__.py +0 -0
  7. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/chemistry/standardizer.py +0 -0
  8. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/chemistry/utils.py +0 -0
  9. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/cli/__init__.py +0 -0
  10. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/cli/cloud_commands.py +0 -0
  11. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/cli/swarm_commands.py +0 -0
  12. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/deployment/base.py +0 -0
  13. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  14. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  15. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  16. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/deployment/job_runner.py +0 -0
  17. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/deployment/processors.py +0 -0
  18. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/deployment/swarm.py +0 -0
  19. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/embedders.py +0 -0
  20. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/fasta.py +0 -0
  21. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/file_ops.py +0 -0
  22. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/gcp.py +0 -0
  23. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/h5.py +0 -0
  24. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/kegg.py +0 -0
  25. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/logs.py +0 -0
  26. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/mmseqs.py +0 -0
  27. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/sqlite.py +0 -0
  28. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/structure.py +0 -0
  29. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/dayhoff_tools/uniprot.py +0 -0
  30. {dayhoff_tools-1.1.1 → dayhoff_tools-1.1.2}/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: 1.1.1
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+ Version: 1.1.2
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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
@@ -9,7 +9,6 @@ from dayhoff_tools.cli.utility_commands import (
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  get_ancestry,
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  import_from_warehouse_typer,
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  install_dependencies,
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- rebuild_devcontainer_file,
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  test_github_actions_locally,
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  update_dependencies,
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  )
@@ -23,13 +22,12 @@ app.command("clean")(delete_local_branch)
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  app.command(
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  "install", help="Install dependencies based on pyproject.toml and sync environment."
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  )(install_dependencies)
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- app.command(
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- "update", help="Update dependencies (--all or --dayhoff) and sync environment."
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- )(update_dependencies)
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+ app.command("update", help="Update dayhoff-tools (or all deps) and sync environment.")(
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+ update_dependencies
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+ )
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  # Other Utilities
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  app.command("gha")(test_github_actions_locally)
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- app.command("rebuild")(rebuild_devcontainer_file)
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  app.command("wadd")(add_to_warehouse_typer)
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  app.command("wancestry")(get_ancestry)
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  app.command("wimport")(import_from_warehouse_typer)
@@ -23,17 +23,6 @@ def test_github_actions_locally():
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  print(f"Error occurred while running the script: {e}")
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- def rebuild_devcontainer_file():
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- """Run the script prepare_for_build.py."""
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- script_path = ".devcontainer/scripts/prepare_for_build.py"
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-
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- try:
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- subprocess.check_call([sys.executable, script_path])
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- print("Script ran successfully!")
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- except subprocess.CalledProcessError as e:
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- print(f"Error occurred while running the script: {e}")
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-
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-
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  def get_ancestry(filepath: str) -> None:
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  """Take a .dvc file created from import, and generate an ancestry entry
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  that can be manually copied into other .dvc files."""
@@ -1,17 +1,17 @@
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+ # This block is needed because we package DHT for PyPi.
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  [build-system]
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  requires = ["poetry-core>=2.0"]
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  build-backend = "poetry.core.masonry.api"
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  [project]
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  name = "dayhoff-tools"
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- version = "1.1.1"
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+ version = "1.1.2"
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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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  ]
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  readme = "README.md"
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- # Default dependencies now include the formerly "full" set + base set
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  dependencies = [
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  "firebase-admin>=6.5.0",
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  "pyyaml>=6.0",
@@ -39,7 +39,6 @@ lite = [
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  "typer>=0.9.0",
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  ]
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- # Added UV-specific configuration for PyTorch source (for dev/test env)
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  [[tool.uv.index]]
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  name = "torch-cuda"
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  url = "https://download.pytorch.org/whl/cu121"
File without changes