hca-schema-validator 0.2.0__tar.gz

hca_schema_validator-0.2.0/NOTICE

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+hca-schema-validator
+Copyright (c) 2025 Human Cell Atlas
+
+This software contains vendored code from:
+
+cellxgene-schema
+Copyright (c) 2021 Chan Zuckerberg Initiative
+Licensed under the MIT License
+Source: https://github.com/chanzuckerberg/single-cell-curation
+
+The vendored code has been modified to support HCA-specific validation requirements.
+All modifications are licensed under the same MIT License as the original work.
+
+The full license text for the vendored code can be found at:
+src/hca_schema_validator/_vendored/cellxgene_schema/LICENSE

hca_schema_validator-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: hca-schema-validator
+Version: 0.2.0
+Summary: HCA schema validation for single-cell datasets
+License: MIT
+License-File: NOTICE
+Author: Clever Canary
+Author-email: dave@clevercanary.com
+Requires-Python: >=3.10,<4.0
+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
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Dist: anndata (>=0.11.0,<0.12)
+Requires-Dist: cellxgene-ontology-guide (>=1.9.0,<2.0)
+Requires-Dist: click (<9)
+Requires-Dist: dask[array,dataframe] (>=2024.0.0)
+Requires-Dist: duckdb (>=1.3.0,<1.4)
+Requires-Dist: ibis-framework[duckdb] (>=10.3)
+Requires-Dist: matplotlib (<4)
+Requires-Dist: numpy (<3)
+Requires-Dist: pandas (>2,<3)
+Requires-Dist: pyarrow (>=19)
+Requires-Dist: pysam (>=0.13.0)
+Requires-Dist: pyyaml (<7)
+Requires-Dist: scipy (<1.16)
+Requires-Dist: semver (<4)
+Requires-Dist: sparse (>=0.15.0,<0.16)
+Requires-Dist: xxhash (<4)
+Project-URL: Homepage, https://github.com/clevercanary/hca-validation-tools
+Description-Content-Type: text/markdown
+
+# HCA Schema Validator
+
+HCA-specific extensions for cellxgene schema validation.
+
+## Installation
+
+### From PyPI (Recommended)
+
+```bash
+pip install hca-schema-validator
+```
+
+### From Source (Development)
+
+```bash
+# Clone the repository
+git clone https://github.com/clevercanary/hca-validation-tools.git
+cd hca-validation-tools/packages/hca-schema-validator
+
+# Install Poetry if you haven't already
+curl -sSL https://install.python-poetry.org | python3 -
+
+# Install dependencies and package
+poetry install
+
+# Run tests
+poetry run pytest tests/
+```
+
+## Usage
+
+```python
+from hca_schema_validator import HCAValidator
+
+# Create validator instance
+validator = HCAValidator()
+
+# Validate an h5ad file
+is_valid = validator.validate_adata("path/to/file.h5ad")
+
+# Check results
+if is_valid:
+    print("✅ Validation passed!")
+else:
+    print("❌ Validation failed:")
+    for error in validator.errors:
+        print(f"  - {error}")
+```
+
+## Development Status
+
+**Current Version: 0.1.0** - Minimal passthrough implementation
+
+Currently a passthrough wrapper around cellxgene-schema Validator.
+HCA-specific validation rules will be added incrementally.
+
+## Testing
+
+```bash
+cd hca_schema_validator
+poetry run pytest tests/
+```
+
+## Project Structure
+
+```
+hca_schema_validator/
+├── src/
+│   └── hca_schema_validator/
+│       ├── __init__.py       # Package exports
+│       └── validator.py      # HCAValidator class
+├── tests/
+│   └── test_validator.py # Unit tests
+├── pyproject.toml        # Poetry configuration & dependencies
+└── README.md            # This file
+```
+
+## License
+
+MIT
+

hca_schema_validator-0.2.0/README.md

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+# HCA Schema Validator
+
+HCA-specific extensions for cellxgene schema validation.
+
+## Installation
+
+### From PyPI (Recommended)
+
+```bash
+pip install hca-schema-validator
+```
+
+### From Source (Development)
+
+```bash
+# Clone the repository
+git clone https://github.com/clevercanary/hca-validation-tools.git
+cd hca-validation-tools/packages/hca-schema-validator
+
+# Install Poetry if you haven't already
+curl -sSL https://install.python-poetry.org | python3 -
+
+# Install dependencies and package
+poetry install
+
+# Run tests
+poetry run pytest tests/
+```
+
+## Usage
+
+```python
+from hca_schema_validator import HCAValidator
+
+# Create validator instance
+validator = HCAValidator()
+
+# Validate an h5ad file
+is_valid = validator.validate_adata("path/to/file.h5ad")
+
+# Check results
+if is_valid:
+    print("✅ Validation passed!")
+else:
+    print("❌ Validation failed:")
+    for error in validator.errors:
+        print(f"  - {error}")
+```
+
+## Development Status
+
+**Current Version: 0.1.0** - Minimal passthrough implementation
+
+Currently a passthrough wrapper around cellxgene-schema Validator.
+HCA-specific validation rules will be added incrementally.
+
+## Testing
+
+```bash
+cd hca_schema_validator
+poetry run pytest tests/
+```
+
+## Project Structure
+
+```
+hca_schema_validator/
+├── src/
+│   └── hca_schema_validator/
+│       ├── __init__.py       # Package exports
+│       └── validator.py      # HCAValidator class
+├── tests/
+│   └── test_validator.py # Unit tests
+├── pyproject.toml        # Poetry configuration & dependencies
+└── README.md            # This file
+```
+
+## License
+
+MIT

hca_schema_validator-0.2.0/pyproject.toml

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+[tool.poetry]
+name = "hca-schema-validator"
+version = "0.2.0"
+description = "HCA schema validation for single-cell datasets"
+authors = ["Clever Canary <dave@clevercanary.com>"]
+license = "MIT"
+readme = "README.md"
+homepage = "https://github.com/clevercanary/hca-validation-tools"
+packages = [{include = "hca_schema_validator", from = "src"}]
+
+[tool.poetry.dependencies]
+python = "^3.10"
+# Dependencies for vendored cellxgene_schema code
+anndata = ">=0.11.0,<0.12"
+cellxgene-ontology-guide = ">=1.9.0,<2.0"
+click = "<9"
+dask = {extras = ["array", "dataframe"], version = ">=2024.0.0"}
+duckdb = ">=1.3.0,<1.4"  # Pinned for ibis compatibility
+ibis-framework = {extras = ["duckdb"], version = ">=10.3"}
+numpy = "<3"
+pandas = ">2,<3"
+pyarrow = ">=19"
+pyyaml = "<7"
+scipy = "<1.16"
+sparse = ">=0.15.0,<0.16"
+semver = "<4"
+xxhash = "<4"
+matplotlib = "<4"
+pysam = ">=0.13.0"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.0"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

hca_schema_validator-0.2.0/src/hca_schema_validator/__init__.py

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+"""HCA Schema Validator - HCA-specific extensions for cellxgene schema validation."""
+
+# Define constants first (before importing validator to avoid circular import)
+__version__ = "0.2.0"
+__schema_version__ = "1.0.0"  # HCA schema version (independent from CELLxGENE)
+__schema_reference_url__ = "https://data.humancellatlas.org/metadata"  # Static URL, no version in path
+
+# Import after constants are defined
+from .validator import HCAValidator
+
+__all__ = ["HCAValidator"]

hca_schema_validator-0.2.0/src/hca_schema_validator/_vendored/__init__.py

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+"""
+Vendored dependencies for hca-schema-validator.
+
+This directory contains vendored copies of third-party code that has been
+modified for HCA-specific use.
+
+Vendored packages:
+- cellxgene_schema: Modified version of cellxgene-schema
+  Original: https://github.com/chanzuckerberg/single-cell-curation
+  Copyright (c) 2020-Present Chan Zuckerberg Initiative
+  License: MIT (see cellxgene_schema/LICENSE)
+  
+  This code has been vendored and modified to support HCA-specific validation
+  requirements. All modifications are also licensed under MIT.
+
+The vendored code is maintained as part of this package and does not require
+external updates.
+"""

hca_schema_validator-0.2.0/src/hca_schema_validator/_vendored/cellxgene_schema/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2020-Present Chan Zuckerberg Initiative
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

hca_schema_validator-0.2.0/src/hca_schema_validator/_vendored/cellxgene_schema/__init__.py

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+__schema_version__ = "7.0.0"