dayhoff-tools 1.11.0__tar.gz → 1.11.2__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.
Files changed (39) hide show
  1. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/PKG-INFO +3 -3
  2. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/main.py +10 -4
  3. dayhoff_tools-1.11.2/dayhoff_tools/cli/utility_commands.py +1041 -0
  4. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/pyproject.toml +9 -15
  5. dayhoff_tools-1.11.0/dayhoff_tools/cli/utility_commands.py +0 -626
  6. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/README.md +0 -0
  7. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/__init__.py +0 -0
  8. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/chemistry/standardizer.py +0 -0
  9. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/chemistry/utils.py +0 -0
  10. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/__init__.py +0 -0
  11. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/cloud_commands.py +0 -0
  12. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/__init__.py +0 -0
  13. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/engine_core.py +0 -0
  14. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/engine_lifecycle.py +0 -0
  15. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/engine_maintenance.py +0 -0
  16. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/engine_management.py +0 -0
  17. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/shared.py +0 -0
  18. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/studio_commands.py +0 -0
  19. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/swarm_commands.py +0 -0
  20. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/base.py +0 -0
  21. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  22. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  23. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  24. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/job_runner.py +0 -0
  25. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/processors.py +0 -0
  26. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/swarm.py +0 -0
  27. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/embedders.py +0 -0
  28. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/fasta.py +0 -0
  29. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/file_ops.py +0 -0
  30. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/h5.py +0 -0
  31. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/intake/gcp.py +0 -0
  32. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/intake/gtdb.py +0 -0
  33. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/intake/kegg.py +0 -0
  34. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/intake/mmseqs.py +0 -0
  35. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/intake/structure.py +0 -0
  36. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/intake/uniprot.py +0 -0
  37. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/logs.py +0 -0
  38. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/sqlite.py +0 -0
  39. {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/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: 1.11.0
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+ Version: 1.11.2
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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
@@ -23,8 +23,8 @@ Requires-Dist: firebase-admin (>=6.5.0)
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  Requires-Dist: h5py (>=3.11.0) ; extra == "full"
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  Requires-Dist: h5py (>=3.13.0) ; extra == "embedders"
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  Requires-Dist: numpy (>=1.26.4) ; extra == "embedders"
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- Requires-Dist: pandas (>=2.2.3) ; extra == "embedders"
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- Requires-Dist: pandas (>=2.2.3) ; extra == "full"
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+ Requires-Dist: pandas (>=2.2.0,<2.2.3) ; extra == "embedders"
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+ Requires-Dist: pandas (>=2.2.0,<2.2.3) ; extra == "full"
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  Requires-Dist: pyyaml (>=6.0)
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  Requires-Dist: questionary (>=2.0.1)
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  Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "full"
@@ -4,13 +4,14 @@ import sys
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  from importlib.metadata import PackageNotFoundError, version
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  import typer
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-
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  from dayhoff_tools.cli.cloud_commands import aws_app, gcp_app
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  from dayhoff_tools.cli.engine import engine_app, studio_app
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  from dayhoff_tools.cli.utility_commands import (
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+ add_dependency,
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  build_and_upload_wheel,
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  delete_local_branch,
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- install_dependencies,
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+ remove_dependency,
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+ sync_with_toml,
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  test_github_actions_locally,
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  update_dependencies,
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  )
@@ -45,8 +46,13 @@ app.command("clean")(delete_local_branch)
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  # Dependency Management
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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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+ "tomlsync",
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+ help="Sync environment with platform-specific TOML manifest (install/update dependencies).",
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+ )(sync_with_toml)
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+ app.command("add", help="Add a dependency to all platform manifests.")(add_dependency)
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+ app.command("remove", help="Remove a dependency from all platform manifests.")(
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+ remove_dependency
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+ )
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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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  )