dayhoff-tools 1.2.5__tar.gz → 1.3.0__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 (31) hide show
  1. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/PKG-INFO +6 -4
  2. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/pyproject.toml +6 -6
  3. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/README.md +0 -0
  4. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/__init__.py +0 -0
  5. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/chemistry/standardizer.py +0 -0
  6. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/chemistry/utils.py +0 -0
  7. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/cli/__init__.py +0 -0
  8. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/cli/cloud_commands.py +0 -0
  9. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/cli/main.py +0 -0
  10. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/cli/swarm_commands.py +0 -0
  11. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/cli/utility_commands.py +0 -0
  12. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/deployment/base.py +0 -0
  13. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  14. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  15. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  16. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/deployment/job_runner.py +0 -0
  17. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/deployment/processors.py +0 -0
  18. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/deployment/swarm.py +0 -0
  19. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/embedders.py +0 -0
  20. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/fasta.py +0 -0
  21. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/file_ops.py +0 -0
  22. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/h5.py +0 -0
  23. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/intake/gcp.py +0 -0
  24. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/intake/gtdb.py +0 -0
  25. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/intake/kegg.py +0 -0
  26. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/intake/mmseqs.py +0 -0
  27. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/intake/structure.py +0 -0
  28. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/intake/uniprot.py +0 -0
  29. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/logs.py +0 -0
  30. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/sqlite.py +0 -0
  31. {dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/dayhoff_tools/warehouse.py +0 -0
{dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/PKG-INFO RENAMED
@@ -1,11 +1,13 @@
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  Metadata-Version: 2.3
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  Name: dayhoff-tools
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- Version: 1.2.5
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+ Version: 1.3.0
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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
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- Requires-Python: >=3.12,<4.0
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+ Requires-Python: >=3.10,<4.0
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  Classifier: Programming Language :: Python :: 3
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+ Classifier: Programming Language :: Python :: 3.10
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+ Classifier: Programming Language :: Python :: 3.11
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  Classifier: Programming Language :: Python :: 3.12
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  Classifier: Programming Language :: Python :: 3.13
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  Provides-Extra: embedders
@@ -24,13 +26,13 @@ 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: pyyaml (>=6.0)
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  Requires-Dist: questionary (>=2.0.1)
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- Requires-Dist: rdkit (>=2025.3.2) ; extra == "full"
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+ Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "full"
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  Requires-Dist: requests (>=2.31.0)
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  Requires-Dist: sentencepiece (>=0.2.0) ; extra == "embedders"
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  Requires-Dist: sentencepiece (>=0.2.0) ; extra == "full"
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  Requires-Dist: sqlalchemy (>=2.0.40,<3.0.0) ; extra == "full"
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  Requires-Dist: toml (>=0.10)
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- Requires-Dist: torch (>=2.5.0) ; extra == "embedders"
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+ Requires-Dist: torch (>=2.4.0) ; extra == "embedders"
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  Requires-Dist: tqdm (>=4.67.1) ; extra == "embedders"
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  Requires-Dist: tqdm (>=4.67.1) ; extra == "full"
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  Requires-Dist: transformers (==4.36.2) ; extra == "full"
{dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/pyproject.toml RENAMED
@@ -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 = "1.2.5"
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+ version = "1.3.0"
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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"}
@@ -21,7 +21,7 @@ dependencies = [
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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 = ">=3.12,<4.0"
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+ requires-python = ">=3.10,<4.0"
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  [project.optional-dependencies]
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  full = [
@@ -31,7 +31,7 @@ full = [
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  "fair-esm>=2.0.0",
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  "h5py>=3.11.0",
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  "pandas>=2.2.3",
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- "rdkit>=2025.3.2",
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+ "rdkit-pypi>=2022.9.5",
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  "sqlalchemy (>=2.0.40,<3.0.0)",
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  "transformers==4.36.2",
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  "sentencepiece>=0.2.0",
@@ -44,7 +44,7 @@ embedders = [
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  "numpy>=1.26.4",
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  "pandas>=2.2.3",
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  "sentencepiece>=0.2.0",
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- "torch>=2.5.0",
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+ "torch>=2.4.0",
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  "tqdm>=4.67.1",
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  "transformers>=4.36.2",
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  ]
@@ -79,8 +79,8 @@ dev-dependencies = [
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  "pytest>=8.0.2,<9",
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  "pytest-cov>=4.1.0,<5",
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  "pytest-mock>=3.12.0,<4",
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- "torch>=2.5.0",
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- "torchvision>=0.20.0",
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+ "torch==2.4.0+cu121",
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+ "torchvision==0.19.0+cu121",
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  ]
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  [project.scripts]
{dayhoff_tools-1.2.5 → dayhoff_tools-1.3.0}/README.md RENAMED
File without changes