aind-data-schema-models 2.2.0__tar.gz → 2.3.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- aind_data_schema_models-2.3.0/PKG-INFO +72 -0
- aind_data_schema_models-2.3.0/README.md +44 -0
- aind_data_schema_models-2.3.0/src/aind_data_schema_models/__init__.py +3 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/templates/mouse_anatomy.txt +6 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/mouse_anatomy.py +7 -0
- aind_data_schema_models-2.3.0/src/aind_data_schema_models.egg-info/PKG-INFO +72 -0
- aind_data_schema_models-2.2.0/PKG-INFO +0 -134
- aind_data_schema_models-2.2.0/README.md +0 -106
- aind_data_schema_models-2.2.0/src/aind_data_schema_models/__init__.py +0 -3
- aind_data_schema_models-2.2.0/src/aind_data_schema_models.egg-info/PKG-INFO +0 -134
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/.flake8 +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/.github/ISSUE_TEMPLATE/bug_report.md +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/.github/ISSUE_TEMPLATE/feature_request.md +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/.github/ISSUE_TEMPLATE/user-story.md +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/.github/workflows/publish_models_dev.yml +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/.github/workflows/publish_models_main.yml +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/.github/workflows/tag_and_publish_main.yml +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/.github/workflows/test_and_lint.yml +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/.gitignore +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/LICENSE +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/doc_template/Makefile +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/doc_template/make.bat +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/doc_template/source/_static/dark-logo.svg +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/doc_template/source/_static/favicon.ico +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/doc_template/source/_static/light-logo.svg +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/doc_template/source/conf.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/doc_template/source/index.rst +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/pyproject.toml +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/run_all.sh +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/scripts/__init__.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/scripts/write_to_docdb.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/setup.cfg +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/setup.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/__init__.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/dev_utils.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/generator.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/models/brain_atlas.csv +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/models/harp_types.csv +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/models/modalities.csv +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/models/mouse_anatomy.csv +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/models/organizations.csv +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/models/process_names.csv +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/models/registries.csv +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/models/species.csv +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/models/specimen_procedure_types.csv +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/templates/brain_atlas.txt +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/templates/harp_types.txt +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/templates/modalities.txt +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/templates/organizations.txt +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/templates/process_names.txt +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/templates/registries.txt +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/templates/species.txt +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/_generators/templates/specimen_procedure_types.txt +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/brain_atlas.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/data_name_patterns.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/harp_types.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/modalities.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/organizations.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/pid_names.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/process_names.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/registries.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/species.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/specimen_procedure_types.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/system_architecture.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/units.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models/utils.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models.egg-info/SOURCES.txt +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models.egg-info/dependency_links.txt +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models.egg-info/requires.txt +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/src/aind_data_schema_models.egg-info/top_level.txt +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/__init__.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/resources/harp_types.csv +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/test_data_name_patterns.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/test_dev_utils.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/test_generator.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/test_modalities.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/test_models.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/test_mouse_anatomy.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/test_organizations.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/test_pid_names.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/test_process_names.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/test_specimen_procedure_types.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/test_system_architecture.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/test_units.py +0 -0
- {aind_data_schema_models-2.2.0 → aind_data_schema_models-2.3.0}/tests/test_utils.py +0 -0
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Metadata-Version: 2.2
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Name: aind-data-schema-models
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Version: 2.3.0
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Summary: Generated from aind-library-template
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Author: Allen Institute for Neural Dynamics
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License: MIT
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Classifier: Programming Language :: Python :: 3
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Requires-Python: >=3.10
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Description-Content-Type: text/markdown
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License-File: LICENSE
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# aind-data-schema-models
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[](LICENSE)
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[](https://github.com/semantic-release/semantic-release)
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## Installation
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To install from pypi, run
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```bash
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pip install aind-data-schema-models
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```
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To install from source, in the root directory, run
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```bash
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pip install -e .
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```
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```bash
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pip install -e .[dev]
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```
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## Contributing
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### How to add a new model class
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#### tl;dr
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Add new classes to the `_generators/models/*.csv` files.
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#### Details
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The model class files, `brain_atlas.py` etc, are auto-generated. **You should never need to modify the class files directly.**
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Instead, take a look at the `jinja2` templates in the folder `_generators/templates`. The filename of the template is used to pull the corresponding `.csv` file and populate the `data` DataFrame. In the template you can pull data from the various columns and use them to populate each of the fields in your class.
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To re-build all the models, run the `run_all.sh` bash script in the root folder, which loops through the template files and runs them through the `generate_code` function.
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# aind-data-schema-models
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[](LICENSE)
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[](https://github.com/semantic-release/semantic-release)
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## Installation
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To install from pypi, run
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```bash
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pip install aind-data-schema-models
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```
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To install from source, in the root directory, run
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```bash
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pip install -e .
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```
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pip install -e .[dev]
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```
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## Contributing
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### How to add a new model class
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#### Details
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The model class files, `brain_atlas.py` etc, are auto-generated. **You should never need to modify the class files directly.**
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Instead, take a look at the `jinja2` templates in the folder `_generators/templates`. The filename of the template is used to pull the corresponding `.csv` file and populate the `data` DataFrame. In the template you can pull data from the various columns and use them to populate each of the fields in your class.
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There are a few special cases, e.g. if data are missing in columns they will show up as `float: nan`. See the `organizations.txt` template for examples of how to handle this.
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Metadata-Version: 2.2
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Name: aind-data-schema-models
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Version: 2.3.0
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Summary: Generated from aind-library-template
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Author: Allen Institute for Neural Dynamics
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License: MIT
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Classifier: Programming Language :: Python :: 3
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Requires-Python: >=3.10
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: pydantic>=2.7
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Requires-Dist: importlib-resources
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Requires-Dist: requests
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Requires-Dist: flake8; extra == "dev"
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Requires-Dist: isort; extra == "dev"
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Requires-Dist: Sphinx; extra == "dev"
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Requires-Dist: furo; extra == "dev"
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Requires-Dist: aind-flake8-extensions==0.5.2; extra == "dev"
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Requires-Dist: jinja2; extra == "dev"
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Requires-Dist: pandas; extra == "dev"
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Provides-Extra: build
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# aind-data-schema-models
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[](LICENSE)
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[](https://github.com/semantic-release/semantic-release)
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## Installation
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To install from pypi, run
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```bash
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pip install aind-data-schema-models
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```
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To install from source, in the root directory, run
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```bash
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pip install -e .
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+
```
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To develop the code, run
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```bash
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pip install -e .[dev]
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+
```
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## Contributing
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### How to add a new model class
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#### tl;dr
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Add new classes to the `_generators/models/*.csv` files.
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Run `./run_all.sh` in the top-level folder.
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#### Details
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The model class files, `brain_atlas.py` etc, are auto-generated. **You should never need to modify the class files directly.**
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+
Instead, take a look at the `jinja2` templates in the folder `_generators/templates`. The filename of the template is used to pull the corresponding `.csv` file and populate the `data` DataFrame. In the template you can pull data from the various columns and use them to populate each of the fields in your class.
|
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+
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To re-build all the models, run the `run_all.sh` bash script in the root folder, which loops through the template files and runs them through the `generate_code` function.
|
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+
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There are a few special cases, e.g. if data are missing in columns they will show up as `float: nan`. See the `organizations.txt` template for examples of how to handle this.
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Name: aind-data-schema-models
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Version: 2.2.0
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Summary: Generated from aind-library-template
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Author: Allen Institute for Neural Dynamics
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License: MIT
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# aind-data-schema-models
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30
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31
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[](LICENSE)
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32
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[](https://github.com/semantic-release/semantic-release)
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-

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## Installation
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To install from pypi, run
|
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```bash
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pip install aind-data-schema-models
|
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42
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-
```
|
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43
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-
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To install from source, in the root directory, run
|
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```bash
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-
pip install -e .
|
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47
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-
```
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-
|
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49
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To develop the code, run
|
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```bash
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pip install -e .[dev]
|
|
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|
-
```
|
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53
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-
|
|
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|
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## Contributing
|
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55
|
-
|
|
56
|
-
### How to add a new model class
|
|
57
|
-
|
|
58
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-
The model class files, `brain_atlas.py` etc, are auto-generated. **You should never need to modify the class files directly.**
|
|
59
|
-
|
|
60
|
-
Instead, take a look at the `jinja2` templates in the folder `_generators/templates`. The filename of the template is used to pull the corresponding `.csv` file and populate the `data` DataFrame. In the template you can pull data from the various columns and use them to populate each of the fields in your class.
|
|
61
|
-
|
|
62
|
-
To re-build all the models, run the `run_all.sh` bash script in the root folder, which loops through the template files and runs them through the `generate_code` function.
|
|
63
|
-
|
|
64
|
-
There are a few special cases, e.g. if data are missing in columns they will show up as `float: nan`. See the `organizations.txt` template for examples of how to handle this.
|
|
65
|
-
|
|
66
|
-
### Linters and testing
|
|
67
|
-
|
|
68
|
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There are several libraries used to run linters, check documentation, and run tests.
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69
|
-
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- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:
|
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71
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-
|
|
72
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-
```bash
|
|
73
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coverage run -m unittest discover && coverage report
|
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-
```
|
|
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|
-
|
|
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- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
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-
|
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```bash
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interrogate .
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```
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82
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- Use **flake8** to check that code is up to standards (no unused imports, etc.):
|
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-
```bash
|
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flake8 .
|
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-
```
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- Use **black** to automatically format the code into PEP standards:
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```bash
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black .
|
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90
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```
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- Use **isort** to automatically sort import statements:
|
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```bash
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isort .
|
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|
-
```
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### Pull requests
|
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98
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-
|
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99
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For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:
|
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```text
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<type>(<scope>): <short summary>
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```
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where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:
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105
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- **build**: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
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- **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
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- **docs**: Documentation only changes
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- **feat**: A new feature
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- **fix**: A bugfix
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|
111
|
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- **perf**: A code change that improves performance
|
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|
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- **refactor**: A code change that neither fixes a bug nor adds a feature
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|
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- **test**: Adding missing tests or correcting existing tests
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### Semantic Release
|
|
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|
|
117
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The table below, from [semantic release](https://github.com/semantic-release/semantic-release), shows which commit message gets you which release type when `semantic-release` runs (using the default configuration):
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| Commit message | Release type |
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| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
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| `fix(pencil): stop graphite breaking when too much pressure applied` | ~~Patch~~ Fix Release, Default release |
|
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122
|
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| `feat(pencil): add 'graphiteWidth' option` | ~~Minor~~ Feature Release |
|
|
123
|
-
| `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) |
|
|
124
|
-
|
|
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|
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### Documentation
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|
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To generate the rst files source files for documentation, run
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```bash
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|
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|
-
sphinx-apidoc -o doc_template/source/ src
|
|
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|
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```
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130
|
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Then to create the documentation HTML files, run
|
|
131
|
-
```bash
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|
132
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sphinx-build -b html doc_template/source/ doc_template/build/html
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|
133
|
-
```
|
|
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|
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More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).
|
|
@@ -1,106 +0,0 @@
|
|
|
1
|
-
# aind-data-schema-models
|
|
2
|
-
|
|
3
|
-
[](LICENSE)
|
|
4
|
-

|
|
5
|
-
[](https://github.com/semantic-release/semantic-release)
|
|
6
|
-

|
|
7
|
-

|
|
8
|
-

|
|
9
|
-
|
|
10
|
-
## Installation
|
|
11
|
-
To install from pypi, run
|
|
12
|
-
```bash
|
|
13
|
-
pip install aind-data-schema-models
|
|
14
|
-
```
|
|
15
|
-
|
|
16
|
-
To install from source, in the root directory, run
|
|
17
|
-
```bash
|
|
18
|
-
pip install -e .
|
|
19
|
-
```
|
|
20
|
-
|
|
21
|
-
To develop the code, run
|
|
22
|
-
```bash
|
|
23
|
-
pip install -e .[dev]
|
|
24
|
-
```
|
|
25
|
-
|
|
26
|
-
## Contributing
|
|
27
|
-
|
|
28
|
-
### How to add a new model class
|
|
29
|
-
|
|
30
|
-
The model class files, `brain_atlas.py` etc, are auto-generated. **You should never need to modify the class files directly.**
|
|
31
|
-
|
|
32
|
-
Instead, take a look at the `jinja2` templates in the folder `_generators/templates`. The filename of the template is used to pull the corresponding `.csv` file and populate the `data` DataFrame. In the template you can pull data from the various columns and use them to populate each of the fields in your class.
|
|
33
|
-
|
|
34
|
-
To re-build all the models, run the `run_all.sh` bash script in the root folder, which loops through the template files and runs them through the `generate_code` function.
|
|
35
|
-
|
|
36
|
-
There are a few special cases, e.g. if data are missing in columns they will show up as `float: nan`. See the `organizations.txt` template for examples of how to handle this.
|
|
37
|
-
|
|
38
|
-
### Linters and testing
|
|
39
|
-
|
|
40
|
-
There are several libraries used to run linters, check documentation, and run tests.
|
|
41
|
-
|
|
42
|
-
- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:
|
|
43
|
-
|
|
44
|
-
```bash
|
|
45
|
-
coverage run -m unittest discover && coverage report
|
|
46
|
-
```
|
|
47
|
-
|
|
48
|
-
- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
|
|
49
|
-
|
|
50
|
-
```bash
|
|
51
|
-
interrogate .
|
|
52
|
-
```
|
|
53
|
-
|
|
54
|
-
- Use **flake8** to check that code is up to standards (no unused imports, etc.):
|
|
55
|
-
```bash
|
|
56
|
-
flake8 .
|
|
57
|
-
```
|
|
58
|
-
|
|
59
|
-
- Use **black** to automatically format the code into PEP standards:
|
|
60
|
-
```bash
|
|
61
|
-
black .
|
|
62
|
-
```
|
|
63
|
-
|
|
64
|
-
- Use **isort** to automatically sort import statements:
|
|
65
|
-
```bash
|
|
66
|
-
isort .
|
|
67
|
-
```
|
|
68
|
-
|
|
69
|
-
### Pull requests
|
|
70
|
-
|
|
71
|
-
For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:
|
|
72
|
-
```text
|
|
73
|
-
<type>(<scope>): <short summary>
|
|
74
|
-
```
|
|
75
|
-
|
|
76
|
-
where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:
|
|
77
|
-
|
|
78
|
-
- **build**: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
|
|
79
|
-
- **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
|
|
80
|
-
- **docs**: Documentation only changes
|
|
81
|
-
- **feat**: A new feature
|
|
82
|
-
- **fix**: A bugfix
|
|
83
|
-
- **perf**: A code change that improves performance
|
|
84
|
-
- **refactor**: A code change that neither fixes a bug nor adds a feature
|
|
85
|
-
- **test**: Adding missing tests or correcting existing tests
|
|
86
|
-
|
|
87
|
-
### Semantic Release
|
|
88
|
-
|
|
89
|
-
The table below, from [semantic release](https://github.com/semantic-release/semantic-release), shows which commit message gets you which release type when `semantic-release` runs (using the default configuration):
|
|
90
|
-
|
|
91
|
-
| Commit message | Release type |
|
|
92
|
-
| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
|
|
93
|
-
| `fix(pencil): stop graphite breaking when too much pressure applied` | ~~Patch~~ Fix Release, Default release |
|
|
94
|
-
| `feat(pencil): add 'graphiteWidth' option` | ~~Minor~~ Feature Release |
|
|
95
|
-
| `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) |
|
|
96
|
-
|
|
97
|
-
### Documentation
|
|
98
|
-
To generate the rst files source files for documentation, run
|
|
99
|
-
```bash
|
|
100
|
-
sphinx-apidoc -o doc_template/source/ src
|
|
101
|
-
```
|
|
102
|
-
Then to create the documentation HTML files, run
|
|
103
|
-
```bash
|
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104
|
-
sphinx-build -b html doc_template/source/ doc_template/build/html
|
|
105
|
-
```
|
|
106
|
-
More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).
|
|
@@ -1,134 +0,0 @@
|
|
|
1
|
-
Metadata-Version: 2.2
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2
|
-
Name: aind-data-schema-models
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|
3
|
-
Version: 2.2.0
|
|
4
|
-
Summary: Generated from aind-library-template
|
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5
|
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Author: Allen Institute for Neural Dynamics
|
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6
|
-
License: MIT
|
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Classifier: Programming Language :: Python :: 3
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Requires-Python: >=3.10
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: pydantic>=2.7
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Requires-Dist: importlib-resources
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Requires-Dist: requests
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Provides-Extra: dev
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Requires-Dist: codespell; extra == "dev"
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Requires-Dist: black; extra == "dev"
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Requires-Dist: coverage; extra == "dev"
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Requires-Dist: flake8; extra == "dev"
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|
-
Requires-Dist: interrogate; extra == "dev"
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Requires-Dist: isort; extra == "dev"
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Requires-Dist: Sphinx; extra == "dev"
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Requires-Dist: furo; extra == "dev"
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Requires-Dist: aind-flake8-extensions==0.5.2; extra == "dev"
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Requires-Dist: jinja2; extra == "dev"
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# aind-data-schema-models
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-
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[](LICENSE)
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-

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[](https://github.com/semantic-release/semantic-release)
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## Installation
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To install from pypi, run
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```bash
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pip install aind-data-schema-models
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```
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To install from source, in the root directory, run
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```bash
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pip install -e .
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```
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To develop the code, run
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```bash
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pip install -e .[dev]
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```
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## Contributing
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### How to add a new model class
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The model class files, `brain_atlas.py` etc, are auto-generated. **You should never need to modify the class files directly.**
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Instead, take a look at the `jinja2` templates in the folder `_generators/templates`. The filename of the template is used to pull the corresponding `.csv` file and populate the `data` DataFrame. In the template you can pull data from the various columns and use them to populate each of the fields in your class.
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To re-build all the models, run the `run_all.sh` bash script in the root folder, which loops through the template files and runs them through the `generate_code` function.
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There are a few special cases, e.g. if data are missing in columns they will show up as `float: nan`. See the `organizations.txt` template for examples of how to handle this.
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### Linters and testing
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There are several libraries used to run linters, check documentation, and run tests.
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- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:
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```bash
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coverage run -m unittest discover && coverage report
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```
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- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
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```bash
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interrogate .
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```
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- Use **flake8** to check that code is up to standards (no unused imports, etc.):
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```bash
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flake8 .
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```
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- Use **black** to automatically format the code into PEP standards:
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```bash
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black .
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```
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- Use **isort** to automatically sort import statements:
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```bash
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isort .
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```
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### Pull requests
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For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:
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```text
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<type>(<scope>): <short summary>
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```
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where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:
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- **build**: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
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- **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
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- **docs**: Documentation only changes
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- **feat**: A new feature
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- **fix**: A bugfix
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- **perf**: A code change that improves performance
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- **refactor**: A code change that neither fixes a bug nor adds a feature
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- **test**: Adding missing tests or correcting existing tests
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### Semantic Release
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The table below, from [semantic release](https://github.com/semantic-release/semantic-release), shows which commit message gets you which release type when `semantic-release` runs (using the default configuration):
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| Commit message | Release type |
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| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
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| `fix(pencil): stop graphite breaking when too much pressure applied` | ~~Patch~~ Fix Release, Default release |
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| `feat(pencil): add 'graphiteWidth' option` | ~~Minor~~ Feature Release |
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| `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) |
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### Documentation
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To generate the rst files source files for documentation, run
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```bash
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sphinx-apidoc -o doc_template/source/ src
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```
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Then to create the documentation HTML files, run
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```bash
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sphinx-build -b html doc_template/source/ doc_template/build/html
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```
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More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).
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