omicslab 1.0.0__tar.gz

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Files changed (37) hide show
  1. omicslab-1.0.0/.gitignore +41 -0
  2. omicslab-1.0.0/PKG-INFO +59 -0
  3. omicslab-1.0.0/README.md +36 -0
  4. omicslab-1.0.0/pixi.lock +705 -0
  5. omicslab-1.0.0/pixi.toml +19 -0
  6. omicslab-1.0.0/pyproject.toml +42 -0
  7. omicslab-1.0.0/src/omicslab/__init__.py +21 -0
  8. omicslab-1.0.0/src/omicslab/_version.py +1 -0
  9. omicslab-1.0.0/src/omicslab/cli/__init__.py +0 -0
  10. omicslab-1.0.0/src/omicslab/cli/analysis_commands.py +141 -0
  11. omicslab-1.0.0/src/omicslab/cli/auth_commands.py +45 -0
  12. omicslab-1.0.0/src/omicslab/cli/context_commands.py +137 -0
  13. omicslab-1.0.0/src/omicslab/cli/job_commands.py +168 -0
  14. omicslab-1.0.0/src/omicslab/cli/main.py +316 -0
  15. omicslab-1.0.0/src/omicslab/cli/org_commands.py +131 -0
  16. omicslab-1.0.0/src/omicslab/cli/storage_commands.py +95 -0
  17. omicslab-1.0.0/src/omicslab/cli/studio_commands.py +149 -0
  18. omicslab-1.0.0/src/omicslab/cli/token_commands.py +99 -0
  19. omicslab-1.0.0/src/omicslab/cli/utils.py +357 -0
  20. omicslab-1.0.0/src/omicslab/cli/workspace_commands.py +155 -0
  21. omicslab-1.0.0/src/omicslab/client.py +128 -0
  22. omicslab-1.0.0/src/omicslab/config.py +136 -0
  23. omicslab-1.0.0/src/omicslab/exceptions.py +42 -0
  24. omicslab-1.0.0/src/omicslab/resources/__init__.py +0 -0
  25. omicslab-1.0.0/src/omicslab/resources/analysis.py +50 -0
  26. omicslab-1.0.0/src/omicslab/resources/base.py +9 -0
  27. omicslab-1.0.0/src/omicslab/resources/credentials.py +83 -0
  28. omicslab-1.0.0/src/omicslab/resources/jobs.py +82 -0
  29. omicslab-1.0.0/src/omicslab/resources/orgs.py +58 -0
  30. omicslab-1.0.0/src/omicslab/resources/storage.py +51 -0
  31. omicslab-1.0.0/src/omicslab/resources/studio.py +53 -0
  32. omicslab-1.0.0/src/omicslab/resources/tokens.py +31 -0
  33. omicslab-1.0.0/src/omicslab/resources/workspaces.py +89 -0
  34. omicslab-1.0.0/tests/__init__.py +0 -0
  35. omicslab-1.0.0/tests/conftest.py +28 -0
  36. omicslab-1.0.0/tests/test_cli.py +410 -0
  37. omicslab-1.0.0/tests/test_client.py +224 -0
omicslab-1.0.0/.gitignore ADDED
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+ # Build and Release Folders
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+ bin-debug/
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+ bin-release/
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+ [Oo]bj/
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+ [Bb]in/
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+
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+ # Other files and folders
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+ .settings/
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+
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+ # Executables
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+ *.swf
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+ *.air
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+ *.ipa
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+ *.apk
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+
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+ # db
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+ db.sqlite3
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+ # env
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+ .env.all
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+ .env.dev
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+ .env.prod
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+ .env.stg
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+ # python
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+ venv
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+ .coverage
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+ __pycache__
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+ .pytest_cache
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+ # volume
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+ volume
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+ env
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+ .env
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+ data
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+ # pixi environments
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+ .pixi/*
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+ !.pixi/config.toml
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+
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+ # agent-browser browser automation tests
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+ frontend/agent-browser/
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+
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+ # temp scratch files
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+ temp/
omicslab-1.0.0/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: omicslab
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+ Version: 1.0.0
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+ Summary: Python SDK and CLI for the RIVER (OmicsLab) Platform
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+ Project-URL: Homepage, https://platform.riverxdata.com
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+ Project-URL: Repository, https://github.com/gianglabs/omicslab-platform
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+ Author: RIVER Platform Team
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+ License-Expression: GPL-3.0
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+ Keywords: bioinformatics,cli,hpc,omics
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+ Classifier: Development Status :: 3 - Alpha
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+ Classifier: Intended Audience :: Developers
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
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+ Classifier: Programming Language :: Python :: 3.12
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+ Requires-Python: >=3.12
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+ Requires-Dist: httpx>=0.27
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+ Requires-Dist: pydantic>=2
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+ Requires-Dist: python-dotenv>=1
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+ Requires-Dist: questionary>=2.1
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+ Requires-Dist: rich>=13
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+ Requires-Dist: typer>=0.15
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+ Description-Content-Type: text/markdown
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+
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+ # OmicsLab SDK
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+
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+ Python SDK and CLI for the RIVER (OmicsLab) Platform.
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+
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+ ## Installation
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+
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+ ```bash
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+ pip install -e .
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+ ```
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+
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+ ## Quick Start
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+
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+ ```python
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+ from omicslab import Client
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+
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+ client = Client(token="omx_...")
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+
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+ # List workspaces
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+ workspaces = client.workspaces.list()
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+
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+ # Launch a job
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+ job = client.jobs.launch_analysis(
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+ workspace_id="...",
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+ analysis_id="...",
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+ compute_id="...",
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+ params={"threads": 8},
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+ )
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+ ```
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+
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+ ## CLI Usage
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+
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+ ```bash
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+ omicslab auth login --token omx_...
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+ omicslab ws list
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+ omicslab jobs launch -w <workspace_id> -a <analysis_id> -c <compute_id>
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+ ```
omicslab-1.0.0/README.md ADDED
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+ # OmicsLab SDK
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+
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+ Python SDK and CLI for the RIVER (OmicsLab) Platform.
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+
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+ ## Installation
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+
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+ ```bash
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+ pip install -e .
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+ ```
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+
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+ ## Quick Start
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+
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+ ```python
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+ from omicslab import Client
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+
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+ client = Client(token="omx_...")
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+
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+ # List workspaces
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+ workspaces = client.workspaces.list()
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+
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+ # Launch a job
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+ job = client.jobs.launch_analysis(
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+ workspace_id="...",
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+ analysis_id="...",
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+ compute_id="...",
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+ params={"threads": 8},
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+ )
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+ ```
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+
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+ ## CLI Usage
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+
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+ ```bash
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+ omicslab auth login --token omx_...
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+ omicslab ws list
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+ omicslab jobs launch -w <workspace_id> -a <analysis_id> -c <compute_id>
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+ ```