aind-metadata-manager 0.0.1__tar.gz

aind_metadata_manager-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2022 Allen Institute for Neural Dynamics
+
+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.

aind_metadata_manager-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: aind-metadata-manager
+Version: 0.0.1
+Summary: Generated from aind-library-template
+Author: Allen Institute for Neural Dynamics
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: aind-data-schema==1.2.0
+Requires-Dist: aind-data-schema-models==0.7.5
+Requires-Dist: aind-metadata-upgrader==0.0.26
+Requires-Dist: pydantic<2.9,>=2.7
+Requires-Dist: pydantic-settings
+Requires-Dist: tzlocal
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: interrogate; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: Sphinx; extra == "dev"
+Requires-Dist: furo; extra == "dev"
+Dynamic: license-file
+
+
+# AIND Metadata Manager
+
+AIND Metadata Manager is a Python package for managing, upgrading, and validating metadata files used in the Allen Institute for Neural Dynamics (AIND) data pipelines. It provides tools to upgrade metadata schemas, process and validate metadata, and support reproducible data workflows.
+
+## Features
+- Upgrade metadata files to the latest schema versions
+- Validate and process metadata for AIND data pipelines
+- Utilities for handling data descriptions, procedures, and processing metadata
+- Command-line and programmatic interfaces
+
+## Installation
+
+1. Clone the repository:
+	```sh
+	git clone https://github.com/AllenNeuralDynamics/aind-metadata-manager.git
+	cd aind-metadata-manager
+	```
+2. Create and activate a virtual environment (recommended):
+	```sh
+	python -m venv venv
+	venv\Scripts\activate  # On Windows
+	# or
+	source venv/bin/activate  # On macOS/Linux
+	```
+3. Install dependencies:
+	```sh
+	pip install -e .
+	pip install aind-data-schema aind-metadata-upgrader
+	```
+
+## Usage
+
+### As a Python package
+```python
+from aind_metadata_manager.metadata_manager import MetadataManager, MetadataSettings
+settings = MetadataSettings(input_dir='path/to/input', output_dir='path/to/output')
+manager = MetadataManager(settings)
+manager.create_processing_metadata()
+```
+
+### Command Line Interface
+A CLI may be available (see `src/aind_metadata_manager/metadata_manager.py` for details):
+```sh
+python -m aind_metadata_manager.metadata_manager --help
+```
+
+## Development & Testing
+- Tests are located in the `tests/` directory.
+- To run tests:
+  ```sh
+  venv\Scripts\python -m unittest discover -s tests -p "test_*.py" -v
+  ```
+
+## Project Structure
+- `src/aind_metadata_manager/` — Main package code
+- `tests/` — Unit tests and test resources
+- `docs/` — Documentation
+
+## Requirements
+- Python 3.10+
+- aind-data-schema
+- aind-metadata-upgrader
+- pydantic, pydantic-settings
+
+## License
+This project is licensed under the terms of the MIT license. See the `LICENSE` file for details.
+
+## Citation
+If you use this package, please cite as described in `CITATION.cff`.
+
+## Contributing
+See `CONTRIBUTING.md` for guidelines.
+
+## Contact
+For questions or support, please open an issue on GitHub or contact the Allen Institute for Neural Dynamics.

aind_metadata_manager-0.0.1/README.md

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+
+# AIND Metadata Manager
+
+AIND Metadata Manager is a Python package for managing, upgrading, and validating metadata files used in the Allen Institute for Neural Dynamics (AIND) data pipelines. It provides tools to upgrade metadata schemas, process and validate metadata, and support reproducible data workflows.
+
+## Features
+- Upgrade metadata files to the latest schema versions
+- Validate and process metadata for AIND data pipelines
+- Utilities for handling data descriptions, procedures, and processing metadata
+- Command-line and programmatic interfaces
+
+## Installation
+
+1. Clone the repository:
+	```sh
+	git clone https://github.com/AllenNeuralDynamics/aind-metadata-manager.git
+	cd aind-metadata-manager
+	```
+2. Create and activate a virtual environment (recommended):
+	```sh
+	python -m venv venv
+	venv\Scripts\activate  # On Windows
+	# or
+	source venv/bin/activate  # On macOS/Linux
+	```
+3. Install dependencies:
+	```sh
+	pip install -e .
+	pip install aind-data-schema aind-metadata-upgrader
+	```
+
+## Usage
+
+### As a Python package
+```python
+from aind_metadata_manager.metadata_manager import MetadataManager, MetadataSettings
+settings = MetadataSettings(input_dir='path/to/input', output_dir='path/to/output')
+manager = MetadataManager(settings)
+manager.create_processing_metadata()
+```
+
+### Command Line Interface
+A CLI may be available (see `src/aind_metadata_manager/metadata_manager.py` for details):
+```sh
+python -m aind_metadata_manager.metadata_manager --help
+```
+
+## Development & Testing
+- Tests are located in the `tests/` directory.
+- To run tests:
+  ```sh
+  venv\Scripts\python -m unittest discover -s tests -p "test_*.py" -v
+  ```
+
+## Project Structure
+- `src/aind_metadata_manager/` — Main package code
+- `tests/` — Unit tests and test resources
+- `docs/` — Documentation
+
+## Requirements
+- Python 3.10+
+- aind-data-schema
+- aind-metadata-upgrader
+- pydantic, pydantic-settings
+
+## License
+This project is licensed under the terms of the MIT license. See the `LICENSE` file for details.
+
+## Citation
+If you use this package, please cite as described in `CITATION.cff`.
+
+## Contributing
+See `CONTRIBUTING.md` for guidelines.
+
+## Contact
+For questions or support, please open an issue on GitHub or contact the Allen Institute for Neural Dynamics.

aind_metadata_manager-0.0.1/pyproject.toml

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+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "aind-metadata-manager"
+description = "Generated from aind-library-template"
+license = {text = "MIT"}
+requires-python = ">=3.10"
+authors = [
+    {name = "Allen Institute for Neural Dynamics"}
+]
+classifiers = [
+    "Programming Language :: Python :: 3"
+]
+readme = "README.md"
+dynamic = ["version"]
+
+dependencies = [
+    'aind-data-schema==1.2.0',
+    'aind-data-schema-models==0.7.5',
+    'aind-metadata-upgrader==0.0.26',
+    'pydantic>=2.7,<2.9',
+    'pydantic-settings',
+    'tzlocal'
+]
+
+[project.optional-dependencies]
+dev = [
+    'black',
+    'coverage',
+    'flake8',
+    'interrogate',
+    'isort',
+    'Sphinx',
+    'furo'
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.dynamic]
+version = {attr = "aind_metadata_manager.__version__"}
+
+[tool.black]
+line-length = 79
+target_version = ['py310']
+exclude = '''
+
+(
+  /(
+      \.eggs         # exclude a few common directories in the
+    | \.git          # root of the project
+    | \.hg
+    | \.mypy_cache
+    | \.tox
+    | \.venv
+    | _build
+    | build
+    | dist
+    | .conda
+  )/
+  | .gitignore
+)
+'''
+
+[tool.coverage.run]
+omit = ["*__init__*"]
+source = ["aind_metadata_manager", "tests"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "if __name__ == .__main__.:",
+    "^from .* import .*",
+    "^import .*",
+    "pragma: no cover"
+]
+fail_under = 90
+
+[tool.isort]
+line_length = 79
+profile = "black"
+skip = [".conda"]
+
+[tool.interrogate]
+exclude = ["setup.py", "docs", "build", ".conda"]
+fail-under = 100

aind_metadata_manager-0.0.1/setup.cfg

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

aind_metadata_manager-0.0.1/setup.py

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+from setuptools import setup
+
+if __name__ == "__main__":
+    setup()

aind_metadata_manager-0.0.1/src/aind_metadata_manager/__init__.py

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+"""Init package"""
+
+__version__ = "0.0.1"