csrlite 0.1.0__tar.gz

csrlite-0.1.0/MANIFEST.in

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+# Include important files
+include README.md
+include pyproject.toml
+
+# Include source code
+recursive-include src *.py *.yaml *.yml
+
+# Exclude everything else
+global-exclude *.pyc
+global-exclude *.pyo
+global-exclude *.pyd
+global-exclude __pycache__
+global-exclude .DS_Store
+
+# Exclude development, testing, and documentation files
+prune tests
+prune docs
+prune data
+prune studies
+prune .github
+exclude .gitignore
+exclude .pyre_configuration
+exclude _quarto.yml
+exclude custom.scss
+exclude index.qmd
+exclude agents.md
+exclude CLAUDE.md
+exclude requirements.txt
+exclude uv.lock

csrlite-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: csrlite
+Version: 0.1.0
+Summary: A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials
+Author-email: Clinical Biostatistics Team <biostat@example.com>
+License: MIT
+Project-URL: Homepage, https://github.com/elong0527/csrlite
+Project-URL: Documentation, https://elong0527.github.io/csrlite
+Project-URL: Repository, https://github.com/elong0527/csrlite.git
+Project-URL: Bug Tracker, https://github.com/elong0527/csrlite/issues
+Keywords: clinical-trials,biostatistics,yaml,tlf,tables,listings,figures
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: polars>=0.20.0
+Requires-Dist: rtflite>=2.1.1
+Provides-Extra: rtf
+Requires-Dist: rtflite; extra == "rtf"
+Provides-Extra: plotting
+Requires-Dist: matplotlib>=3.5.0; extra == "plotting"
+Requires-Dist: plotly>=5.0.0; extra == "plotting"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: black>=22.0.0; extra == "dev"
+Requires-Dist: isort>=5.0.0; extra == "dev"
+Requires-Dist: mypy>=1.0.0; extra == "dev"
+Requires-Dist: pytest>=9.0.1; extra == "dev"
+Requires-Dist: jupyter>=1.1.1; extra == "dev"
+Requires-Dist: jupyter-cache>=1.0.1; extra == "dev"
+Requires-Dist: nbformat>=5.10.4; extra == "dev"
+Requires-Dist: ruff>=0.1.0; extra == "dev"
+Requires-Dist: pyre-check>=0.9.18; extra == "dev"
+Provides-Extra: all
+Requires-Dist: rtflite; extra == "all"
+Requires-Dist: matplotlib>=3.5.0; extra == "all"
+Requires-Dist: plotly>=5.0.0; extra == "all"
+
+# csrlite
+
+[![CI](https://github.com/elong0527/csrlite/actions/workflows/ci.yml/badge.svg)](https://github.com/elong0527/csrlite/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/elong0527/csrlite/branch/main/graph/badge.svg)](https://codecov.io/gh/elong0527/csrlite)
+[![PyPI version](https://badge.fury.io/py/csrlite.svg)](https://badge.fury.io/py/csrlite)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+
+A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials.
+
+## Installation
+
+```bash
+pip install csrlite
+```
+
+## Documentation
+
+Visit [https://elong0527.github.io/csrlite](https://elong0527.github.io/csrlite) for full documentation.
+
+## License
+
+MIT License - see [LICENSE](LICENSE) file for details.

csrlite-0.1.0/README.md

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+# csrlite
+
+[![CI](https://github.com/elong0527/csrlite/actions/workflows/ci.yml/badge.svg)](https://github.com/elong0527/csrlite/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/elong0527/csrlite/branch/main/graph/badge.svg)](https://codecov.io/gh/elong0527/csrlite)
+[![PyPI version](https://badge.fury.io/py/csrlite.svg)](https://badge.fury.io/py/csrlite)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+
+A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials.
+
+## Installation
+
+```bash
+pip install csrlite
+```
+
+## Documentation
+
+Visit [https://elong0527.github.io/csrlite](https://elong0527.github.io/csrlite) for full documentation.
+
+## License
+
+MIT License - see [LICENSE](LICENSE) file for details.

csrlite-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=45", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "csrlite"
+version = "0.1.0"
+description = "A hierarchical YAML-based framework for generating Tables, Listings, and Figures in clinical trials"
+authors = [{name = "Clinical Biostatistics Team", email = "biostat@example.com"}]
+license = {text = "MIT"}
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+keywords = ["clinical-trials", "biostatistics", "yaml", "tlf", "tables", "listings", "figures"]
+
+dependencies = [
+    "pydantic>=2.0.0",
+    "pyyaml>=6.0",
+    "polars>=0.20.0",
+    "rtflite>=2.1.1",
+]
+
+[project.optional-dependencies]
+rtf = ["rtflite"]
+plotting = ["matplotlib>=3.5.0", "plotly>=5.0.0"]
+dev = [
+    "pytest>=7.0.0",
+    "pytest-cov>=4.0.0",
+    "black>=22.0.0",
+    "isort>=5.0.0",
+    "mypy>=1.0.0",
+    "pytest>=9.0.1",
+    "jupyter>=1.1.1",
+    "jupyter-cache>=1.0.1",
+    "nbformat>=5.10.4",
+    "ruff>=0.1.0",
+    "pyre-check>=0.9.18",
+]
+all = ["rtflite", "matplotlib>=3.5.0", "plotly>=5.0.0"]
+
+[project.urls]
+Homepage = "https://github.com/elong0527/csrlite"
+Documentation = "https://elong0527.github.io/csrlite"
+Repository = "https://github.com/elong0527/csrlite.git"
+"Bug Tracker" = "https://github.com/elong0527/csrlite/issues"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+csrlite = ["*.yaml", "*.yml"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "--strict-markers",
+    "--strict-config",
+    "--verbose",
+]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+    "integration: marks tests as integration tests",
+]
+
+[tool.coverage.run]
+source = ["src/csrlite"]
+branch = true
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "raise AssertionError",
+    "raise NotImplementedError",
+]
+
+[tool.black]
+line-length = 100
+target-version = ['py38']
+include = '\.pyi?$'
+extend-exclude = '''
+/(
+  # directories
+  \.eggs
+  | \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | build
+  | dist
+)/
+'''
+
+[tool.isort]
+profile = "black"
+line_length = 100
+known_first_party = ["csrlite"]
+
+[tool.mypy]
+python_version = "3.10"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+check_untyped_defs = true
+disallow_untyped_decorators = true
+no_implicit_optional = true
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_no_return = true
+warn_unreachable = true
+strict_equality = true
+exclude = ["build/", "tests/"]
+
+[[tool.mypy.overrides]]
+module = [
+    "polars.*",
+    "yaml.*",
+    "rtflite.*",
+    "matplotlib.*",
+    "plotly.*",
+]
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = ["tests.*"]
+ignore_errors = true
+
+[tool.ruff]
+line-length = 100
+target-version = "py310"
+
+[tool.ruff.lint]
+select = ["E", "F", "I"]
+ignore = []
+
+[dependency-groups]
+dev = [
+    "jupyter>=1.1.1",
+    "jupyter-cache>=1.0.1",
+    "nbclient>=0.10.2",
+    "notebook>=7.5.0",
+]

csrlite-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

csrlite-0.1.0/src/csrlite/__init__.py

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+from .ae.ae_listing import (
+    # AE listing functions
+    ae_listing,
+    study_plan_to_ae_listing,
+)
+from .ae.ae_specific import (
+    # AE specific functions
+    ae_specific,
+    study_plan_to_ae_specific,
+)
+from .ae.ae_summary import (
+    # AE summary functions
+    ae_summary,
+    study_plan_to_ae_summary,
+)
+from .common.count import (
+    count_subject,
+    count_subject_with_observation,
+)
+from .common.parse import (
+    StudyPlanParser,
+    parse_filter_to_sql,
+)
+from .common.plan import (
+    # Core classes
+    load_plan,
+)
+from .disposition.disposition import study_plan_to_disposition_summary
+
+# Main exports for common usage
+__all__ = [
+    # Primary user interface
+    "load_plan",
+    # AE analysis (direct pipeline wrappers)
+    "ae_summary",
+    "ae_specific",
+    "ae_listing",
+    # AE analysis (StudyPlan integration)
+    "study_plan_to_ae_summary",
+    "study_plan_to_ae_specific",
+    "study_plan_to_ae_listing",
+    # Disposition analysis
+    "study_plan_to_disposition_summary",
+    # Count functions
+    "count_subject",
+    "count_subject_with_observation",
+    # Parse utilities
+    "StudyPlanParser",
+    "parse_filter_to_sql",
+]

csrlite-0.1.0/src/csrlite/ae/__init__.py

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+# pyre-strict