dayhoff-tools 1.0.19__tar.gz → 1.0.20__tar.gz

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Files changed (30) hide show
  1. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/cli/utility_commands.py +11 -5
  3. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/pyproject.toml +1 -1
  4. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/README.md +0 -0
  5. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/__init__.py +0 -0
  6. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/chemistry/standardizer.py +0 -0
  7. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/chemistry/utils.py +0 -0
  8. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/cli/__init__.py +0 -0
  9. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/cli/cloud_commands.py +0 -0
  10. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/cli/main.py +0 -0
  11. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/cli/swarm_commands.py +0 -0
  12. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/deployment/base.py +0 -0
  13. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  14. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  15. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  16. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/deployment/job_runner.py +0 -0
  17. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/deployment/processors.py +0 -0
  18. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/deployment/swarm.py +0 -0
  19. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/embedders.py +0 -0
  20. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/fasta.py +0 -0
  21. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/file_ops.py +0 -0
  22. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/gcp.py +0 -0
  23. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/h5.py +0 -0
  24. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/kegg.py +0 -0
  25. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/logs.py +0 -0
  26. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/mmseqs.py +0 -0
  27. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/sqlite.py +0 -0
  28. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/structure.py +0 -0
  29. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/dayhoff_tools/uniprot.py +0 -0
  30. {dayhoff_tools-1.0.19 → dayhoff_tools-1.0.20}/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: 1.0.19
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+ Version: 1.0.20
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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
@@ -419,15 +419,20 @@ def update_dayhoff_tools():
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  print(f"Updating {pyproject_path} version constraint...")
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  try:
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  content = pyproject_path.read_text()
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- # Regex to find the dayhoff-tools dependency line, capturing name+extra
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- # Matches 'dayhoff-tools' or \"dayhoff-tools\", optional [extra], >= constraints etc.
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+ # Adjusted Regex: Capture quoted package name (group 1),
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+ # match operators, then match non-quote/comma chars for version.
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  pattern = re.compile(
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- r"(^[\'\"](dayhoff-tools(?:\[[^\\\]]+\\])?)[\'\"]\s*)[\\>\\<\\=\\~\\^\\(\\)\\s,0-9\\.\\*\'\"]+",
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+ # Capture group 1: Start, whitespace, quote, pkg name + optional extra, quote, whitespace
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+ r"(^\\s*[\'\"](dayhoff-tools(?:\\\[[^\\\]]+\\])?)[\'\"]\\s*)" +
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+ # Match version specifiers: operators followed by non-quote/comma chars
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+ r"[><=~^]*[^\'\",]*",
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  re.MULTILINE,
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  )
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  new_constraint = f">= {locked_version}"
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  new_content, num_replacements = pattern.subn(
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- rf"\1{new_constraint}", content
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+ # Replace the whole match with group 1 + new constraint
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+ rf"\\1{new_constraint}",
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+ content,
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  )
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  if num_replacements > 0:
@@ -451,7 +456,8 @@ def update_dayhoff_tools():
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  # Step 4: Sync environment based on updated lock file
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  print("Syncing environment...")
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- sync_cmd = ["uv", "sync", "--no-install-project"]
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+ # Adding --all-groups to ensure dev dependencies are synced too
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+ sync_cmd = ["uv", "sync", "--all-groups", "--no-install-project"]
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  print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
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  subprocess.run(sync_cmd, check=True)
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@@ -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 = "1.0.19"
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+ version = "1.0.20"
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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"}
File without changes