dayhoff-tools 1.13.11__tar.gz → 1.13.13__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 (53) hide show
  1. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/main.py +2 -0
  3. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/deployment/base.py +8 -2
  4. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/pyproject.toml +1 -1
  5. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/README.md +0 -0
  6. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/__init__.py +0 -0
  7. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/chemistry/standardizer.py +0 -0
  8. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/chemistry/utils.py +0 -0
  9. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/__init__.py +0 -0
  10. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/cloud_commands.py +0 -0
  11. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engine1/__init__.py +0 -0
  12. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engine1/engine_core.py +0 -0
  13. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engine1/engine_lifecycle.py +0 -0
  14. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engine1/engine_maintenance.py +0 -0
  15. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engine1/engine_management.py +0 -0
  16. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engine1/shared.py +0 -0
  17. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engine1/studio_commands.py +0 -0
  18. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/__init__.py +0 -0
  19. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/api_client.py +0 -0
  20. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/auth.py +0 -0
  21. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/engine-studio-cli.md +0 -0
  22. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/engine_commands.py +0 -0
  23. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/progress.py +0 -0
  24. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/simulators/cli-simulators.md +0 -0
  25. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/simulators/demo.sh +0 -0
  26. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/simulators/engine_list_simulator.py +0 -0
  27. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/simulators/engine_status_simulator.py +0 -0
  28. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/simulators/idle_status_simulator.py +0 -0
  29. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/simulators/simulator_utils.py +0 -0
  30. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/simulators/studio_list_simulator.py +0 -0
  31. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/simulators/studio_status_simulator.py +0 -0
  32. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/engines_studios/studio_commands.py +0 -0
  33. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/swarm_commands.py +0 -0
  34. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/cli/utility_commands.py +0 -0
  35. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  36. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  37. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  38. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/deployment/job_runner.py +0 -0
  39. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/deployment/processors.py +0 -0
  40. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/deployment/swarm.py +0 -0
  41. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/embedders.py +0 -0
  42. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/fasta.py +0 -0
  43. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/file_ops.py +0 -0
  44. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/h5.py +0 -0
  45. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/intake/gcp.py +0 -0
  46. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/intake/gtdb.py +0 -0
  47. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/intake/kegg.py +0 -0
  48. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/intake/mmseqs.py +0 -0
  49. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/intake/structure.py +0 -0
  50. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/intake/uniprot.py +0 -0
  51. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/logs.py +0 -0
  52. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/sqlite.py +0 -0
  53. {dayhoff_tools-1.13.11 → dayhoff_tools-1.13.13}/dayhoff_tools/warehouse.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: dayhoff-tools
3
- Version: 1.13.11
3
+ Version: 1.13.13
4
4
  Summary: Common tools for all the repos at Dayhoff Labs
5
5
  Author: Daniel Martin-Alarcon
6
6
  Author-email: dma@dayhofflabs.com
@@ -78,6 +78,7 @@ app.add_typer(studio_app, name="studio", help="Manage persistent development stu
78
78
  @app.command(
79
79
  "engine2",
80
80
  context_settings={"allow_extra_args": True, "ignore_unknown_options": True},
81
+ add_help_option=False,
81
82
  )
82
83
  def engine2_cmd(ctx: typer.Context):
83
84
  """Manage engines (new implementation with progress tracking)."""
@@ -90,6 +91,7 @@ def engine2_cmd(ctx: typer.Context):
90
91
  @app.command(
91
92
  "studio2",
92
93
  context_settings={"allow_extra_args": True, "ignore_unknown_options": True},
94
+ add_help_option=False,
93
95
  )
94
96
  def studio2_cmd(ctx: typer.Context):
95
97
  """Manage studios (new implementation with progress tracking)."""
@@ -177,8 +177,14 @@ def build_job_image(config: dict) -> str:
177
177
  platform = docker_config.get("platform", "linux/amd64")
178
178
  build_image_command.extend(["--platform", platform])
179
179
 
180
- # Add build context
181
- build_image_command.append(".") # Use the root of the repo as image context
180
+ # Add build args if provided (for parameterized Dockerfiles)
181
+ build_args = docker_config.get("build_args", {})
182
+ for arg_name, arg_value in build_args.items():
183
+ build_image_command.extend(["--build-arg", f"{arg_name}={arg_value}"])
184
+
185
+ # Add build context (defaults to "." for backward compatibility)
186
+ build_context = docker_config.get("build_context", ".")
187
+ build_image_command.append(build_context)
182
188
  subprocess.run(build_image_command, check=True)
183
189
 
184
190
  # Get and print image size
@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
5
5
 
6
6
  [project]
7
7
  name = "dayhoff-tools"
8
- version = "1.13.11"
8
+ version = "1.13.13"
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"}