dayhoff-tools 1.13.18__tar.gz → 1.14.1__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 (54) hide show
  1. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engine1/shared.py +7 -3
  3. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/main.py +37 -10
  4. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/pyproject.toml +1 -1
  5. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/README.md +0 -0
  6. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/__init__.py +0 -0
  7. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/chemistry/standardizer.py +0 -0
  8. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/chemistry/utils.py +0 -0
  9. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/__init__.py +0 -0
  10. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/cloud_commands.py +0 -0
  11. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engine1/__init__.py +0 -0
  12. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engine1/engine_core.py +0 -0
  13. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engine1/engine_lifecycle.py +0 -0
  14. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engine1/engine_maintenance.py +0 -0
  15. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engine1/engine_management.py +0 -0
  16. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engine1/studio_commands.py +0 -0
  17. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/__init__.py +0 -0
  18. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/api_client.py +0 -0
  19. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/auth.py +0 -0
  20. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/engine-studio-cli.md +0 -0
  21. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/engine_commands.py +0 -0
  22. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/progress.py +0 -0
  23. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/simulators/cli-simulators.md +0 -0
  24. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/simulators/demo.sh +0 -0
  25. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/simulators/engine_list_simulator.py +0 -0
  26. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/simulators/engine_status_simulator.py +0 -0
  27. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/simulators/idle_status_simulator.py +0 -0
  28. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/simulators/simulator_utils.py +0 -0
  29. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/simulators/studio_list_simulator.py +0 -0
  30. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/simulators/studio_status_simulator.py +0 -0
  31. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/engines_studios/studio_commands.py +0 -0
  32. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/github_commands.py +0 -0
  33. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/swarm_commands.py +0 -0
  34. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/cli/utility_commands.py +0 -0
  35. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/deployment/base.py +0 -0
  36. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  37. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  38. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  39. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/deployment/job_runner.py +0 -0
  40. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/deployment/processors.py +0 -0
  41. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/deployment/swarm.py +0 -0
  42. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/embedders.py +0 -0
  43. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/fasta.py +0 -0
  44. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/file_ops.py +0 -0
  45. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/h5.py +0 -0
  46. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/intake/gcp.py +0 -0
  47. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/intake/gtdb.py +0 -0
  48. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/intake/kegg.py +0 -0
  49. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/intake/mmseqs.py +0 -0
  50. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/intake/structure.py +0 -0
  51. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/intake/uniprot.py +0 -0
  52. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/logs.py +0 -0
  53. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/sqlite.py +0 -0
  54. {dayhoff_tools-1.13.18 → dayhoff_tools-1.14.1}/dayhoff_tools/warehouse.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
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  Name: dayhoff-tools
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- Version: 1.13.18
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+ Version: 1.14.1
4
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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
@@ -143,13 +143,17 @@ def make_api_request(
143
143
  api_url = get_api_url()
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  url = f"{api_url}{endpoint}"
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+ # Mark this as intentional v1 API usage (via engine1/studio1 commands)
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+ # This prevents the deprecation error for users who explicitly choose v1
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+ headers = {"X-DH-V1-Explicit": "true"}
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+
146
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  try:
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  if method == "GET":
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- response = requests.get(url, params=params)
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+ response = requests.get(url, params=params, headers=headers)
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  elif method == "POST":
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- response = requests.post(url, json=json_data)
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+ response = requests.post(url, json=json_data, headers=headers)
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  elif method == "DELETE":
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- response = requests.delete(url)
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+ response = requests.delete(url, headers=headers)
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  else:
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  raise ValueError(f"Unsupported HTTP method: {method}")
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@@ -6,7 +6,7 @@ from importlib.metadata import PackageNotFoundError, version
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  import typer
7
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  from dayhoff_tools.cli.cloud_commands import aws_app, gcp_app
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  from dayhoff_tools.cli.github_commands import gh_app
9
- from dayhoff_tools.cli.engine1 import engine_app, studio_app
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+ from dayhoff_tools.cli.engine1 import engine_app as engine1_app, studio_app as studio1_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,
@@ -70,23 +70,50 @@ app.add_typer(gcp_app, name="gcp", help="Manage GCP authentication and impersona
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  app.add_typer(aws_app, name="aws", help="Manage AWS SSO authentication.")
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  app.add_typer(gh_app, name="gh", help="Manage GitHub authentication.")
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72
 
73
- # Engine and Studio commands (original implementation)
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- app.add_typer(engine_app, name="engine", help="Manage compute engines for development.")
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- app.add_typer(studio_app, name="studio", help="Manage persistent development studios.")
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+ # Engine and Studio commands (v2 - new default with progress tracking)
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+ # These use Click instead of Typer, so we need a passthrough wrapper
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+ @app.command(
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+ "engine",
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+ context_settings={"allow_extra_args": True, "ignore_unknown_options": True},
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+ add_help_option=False,
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+ )
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+ def engine_cmd(ctx: typer.Context):
81
+ """Manage compute engines for development."""
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+ from dayhoff_tools.cli.engines_studios import engine_cli
76
83
 
84
+ # Pass arguments directly to Click CLI
85
+ engine_cli(ctx.args, standalone_mode=False)
77
86
 
78
- # Engine and Studio commands (new implementation with progress tracking)
79
- # These use Click instead of Typer, so we need a passthrough wrapper
87
+
88
+ @app.command(
89
+ "studio",
90
+ context_settings={"allow_extra_args": True, "ignore_unknown_options": True},
91
+ add_help_option=False,
92
+ )
93
+ def studio_cmd(ctx: typer.Context):
94
+ """Manage persistent development studios."""
95
+ from dayhoff_tools.cli.engines_studios import studio_cli
96
+
97
+ # Pass arguments directly to Click CLI
98
+ studio_cli(ctx.args, standalone_mode=False)
99
+
100
+
101
+ # Engine and Studio commands (v1 - legacy, uses old infrastructure)
102
+ app.add_typer(engine1_app, name="engine1", help="[Legacy v1] Manage engines.")
103
+ app.add_typer(studio1_app, name="studio1", help="[Legacy v1] Manage studios.")
104
+
105
+
106
+ # Backward compatibility aliases for v2 commands (engine2/studio2 -> engine/studio)
80
107
  @app.command(
81
108
  "engine2",
82
109
  context_settings={"allow_extra_args": True, "ignore_unknown_options": True},
83
110
  add_help_option=False,
111
+ hidden=True, # Hide from help, but still works
84
112
  )
85
113
  def engine2_cmd(ctx: typer.Context):
86
- """Manage engines (new implementation with progress tracking)."""
114
+ """[Alias] Use 'dh engine' instead."""
87
115
  from dayhoff_tools.cli.engines_studios import engine_cli
88
116
 
89
- # Pass arguments directly to Click CLI
90
117
  engine_cli(ctx.args, standalone_mode=False)
91
118
 
92
119
 
@@ -94,12 +121,12 @@ def engine2_cmd(ctx: typer.Context):
94
121
  "studio2",
95
122
  context_settings={"allow_extra_args": True, "ignore_unknown_options": True},
96
123
  add_help_option=False,
124
+ hidden=True, # Hide from help, but still works
97
125
  )
98
126
  def studio2_cmd(ctx: typer.Context):
99
- """Manage studios (new implementation with progress tracking)."""
127
+ """[Alias] Use 'dh studio' instead."""
100
128
  from dayhoff_tools.cli.engines_studios import studio_cli
101
129
 
102
- # Pass arguments directly to Click CLI
103
130
  studio_cli(ctx.args, standalone_mode=False)
104
131
 
105
132
 
@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
5
5
 
6
6
  [project]
7
7
  name = "dayhoff-tools"
8
- version = "1.13.18"
8
+ version = "1.14.1"
9
9
  description = "Common tools for all the repos at Dayhoff Labs"
10
10
  authors = [
11
11
  {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}