intelliseq-iflow 0.2.7__tar.gz

intelliseq_iflow-0.2.7/.gitignore

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intelliseq_iflow-0.2.7/PKG-INFO

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+Metadata-Version: 2.4
+Name: intelliseq-iflow
+Version: 0.2.7
+Summary: CLI tool for iFlow - genomic data management and workflow execution
+Project-URL: Homepage, https://intelliseq.com
+Project-URL: Documentation, https://docs.iflow.intelliseq.com
+Author-email: IntelliSeq <contact@intelliseq.com>
+License: MIT
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10
+Requires-Dist: click>=8.0.0
+Requires-Dist: httpx>=0.27.0
+Requires-Dist: keyring>=25.0.0
+Requires-Dist: keyrings-alt>=5.0.0
+Requires-Dist: pydantic-settings>=2.0.0
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: rich>=13.0.0
+Provides-Extra: dev
+Requires-Dist: pytest-asyncio>=0.23.0; extra == 'dev'
+Requires-Dist: pytest>=8.0.0; extra == 'dev'
+Requires-Dist: ruff>=0.3.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# intelliseq-iflow
+
+CLI tool for iFlow - genomic data management and workflow execution.
+
+## Installation
+
+```bash
+pip install intelliseq-iflow
+```
+
+## Usage
+
+### Authentication
+
+Login using OAuth Device Flow:
+
+```bash
+iflow login
+```
+
+This will open a browser for authentication. Your credentials are stored securely in your system keyring.
+
+Check login status:
+
+```bash
+iflow status
+```
+
+Logout:
+
+```bash
+iflow logout
+```
+
+### File Operations
+
+List files in a project:
+
+```bash
+iflow files ls --project PROJECT_ID
+iflow files ls --project PROJECT_ID --path data/raw/
+```
+
+Download a file:
+
+```bash
+iflow files download --project PROJECT_ID --path data/file.txt
+iflow files download --project PROJECT_ID --path data/file.txt -o local_file.txt
+```
+
+Upload a file:
+
+```bash
+iflow files upload --project PROJECT_ID local_file.txt data/uploaded.txt
+```
+
+### Running Pipelines
+
+Submit a pipeline run:
+
+```bash
+iflow runs submit --pipeline hereditary-mock \
+  -P case_id=patient-001 \
+  -P child_fastq=data/R1.fastq.gz \
+  --watch
+```
+
+With LIS callback:
+
+```bash
+iflow runs submit --pipeline hereditary-panel \
+  -P vcf_file=data/sample.vcf.gz \
+  --callback-url https://lis.example.com/api/callback
+```
+
+## Configuration
+
+Configure environment:
+
+```bash
+iflow config env dev    # Development
+iflow config env stg    # Staging
+iflow config env prod   # Production
+```
+
+Select default project:
+
+```bash
+iflow config select-project
+```
+
+View current configuration:
+
+```bash
+iflow config show
+```
+
+## Development
+
+```bash
+# Install in development mode
+pip install -e ".[dev]"
+
+# Run tests
+pytest
+
+# Format code
+ruff format .
+ruff check --fix .
+```

intelliseq_iflow-0.2.7/README.md

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+# intelliseq-iflow
+
+CLI tool for iFlow - genomic data management and workflow execution.
+
+## Installation
+
+```bash
+pip install intelliseq-iflow
+```
+
+## Usage
+
+### Authentication
+
+Login using OAuth Device Flow:
+
+```bash
+iflow login
+```
+
+This will open a browser for authentication. Your credentials are stored securely in your system keyring.
+
+Check login status:
+
+```bash
+iflow status
+```
+
+Logout:
+
+```bash
+iflow logout
+```
+
+### File Operations
+
+List files in a project:
+
+```bash
+iflow files ls --project PROJECT_ID
+iflow files ls --project PROJECT_ID --path data/raw/
+```
+
+Download a file:
+
+```bash
+iflow files download --project PROJECT_ID --path data/file.txt
+iflow files download --project PROJECT_ID --path data/file.txt -o local_file.txt
+```
+
+Upload a file:
+
+```bash
+iflow files upload --project PROJECT_ID local_file.txt data/uploaded.txt
+```
+
+### Running Pipelines
+
+Submit a pipeline run:
+
+```bash
+iflow runs submit --pipeline hereditary-mock \
+  -P case_id=patient-001 \
+  -P child_fastq=data/R1.fastq.gz \
+  --watch
+```
+
+With LIS callback:
+
+```bash
+iflow runs submit --pipeline hereditary-panel \
+  -P vcf_file=data/sample.vcf.gz \
+  --callback-url https://lis.example.com/api/callback
+```
+
+## Configuration
+
+Configure environment:
+
+```bash
+iflow config env dev    # Development
+iflow config env stg    # Staging
+iflow config env prod   # Production
+```
+
+Select default project:
+
+```bash
+iflow config select-project
+```
+
+View current configuration:
+
+```bash
+iflow config show
+```
+
+## Development
+
+```bash
+# Install in development mode
+pip install -e ".[dev]"
+
+# Run tests
+pytest
+
+# Format code
+ruff format .
+ruff check --fix .
+```

intelliseq_iflow-0.2.7/pyproject.toml

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+[project]
+name = "intelliseq-iflow"
+version = "0.2.7"
+description = "CLI tool for iFlow - genomic data management and workflow execution"
+readme = "README.md"
+requires-python = ">=3.10"
+license = {text = "MIT"}
+authors = [
+    {name = "IntelliSeq", email = "contact@intelliseq.com"},
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "click>=8.0.0",
+    "httpx>=0.27.0",
+    "rich>=13.0.0",
+    "keyring>=25.0.0",
+    "keyrings.alt>=5.0.0",  # Fallback for environments without system keyring
+    "pydantic>=2.0.0",
+    "pydantic-settings>=2.0.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=8.0.0",
+    "pytest-asyncio>=0.23.0",
+    "ruff>=0.3.0",
+]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+asyncio_mode = "auto"
+
+[project.scripts]
+iflow = "iflow.cli:main"
+
+[project.urls]
+Homepage = "https://intelliseq.com"
+Documentation = "https://docs.iflow.intelliseq.com"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/iflow"]
+
+[tool.ruff]
+line-length = 100
+target-version = "py310"
+
+[tool.ruff.lint]
+select = ["E", "F", "I", "UP"]

intelliseq_iflow-0.2.7/src/iflow/__init__.py

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+"""iseq-flow - CLI tool for IntelliSeq Flow cloud file management."""
+
+__version__ = "0.2.7"