biodata-models
Installation
biodata-models provides controlled vocabulary and registry models for biodata-schema. You shouldn't generally install this package in isolation.
Contributing
Install the dev dependencies:
pip install -e .[dev]
How to add a new model class
tl;dr
Add new classes to the _generators/models/*.csv files or create new files containing Enum-derived classes directly in the src folder.
Run ./run_all.sh in the top-level folder to rebuild models from their CSV files.
Details
The model class files, brain_atlas.py etc, are auto-generated. You should never need to modify the class files directly.
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.
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.
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.
Documentation
Internal registries need to be enumerated in the aind-data-schema file src/aind_data_schema/utils/docs/registries_generator.py in the variable registries. This list controls what classes will have documentation automatically generated and cross-referenced correctly.
If you add a new external registry, you need to write the documentation manually in the aind-data-schema file docs/source/biodata_models/external.md.
1 maintainer
Metadata
1 maintainer
Release files for biodata-models 2.0.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| biodata_models-2.0.0.tar.gz | 145.7 kB | With provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| biodata_models-2.0.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 258.2 kB
Release files / biodata_models-2.0.0.tar.gz
| Download URL | biodata_models-2.0.0.tar.gz |
|---|---|
| Size | 145.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
ddb7acae3b462c33136f1a15f80aec16127dcd62d0971922d85d85004111c82a
|
|
BLAKE2b-256 checksum How to use checksums |
af007561931702ed94376e24cbffdb774d5cd7e1b1c2986c628ed4b4c3b65cd6
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 1, 2026.
Transparency logRelease files / biodata_models-2.0.0-py3-none-any.whl
| Download URL | biodata_models-2.0.0-py3-none-any.whl |
|---|---|
| Size | 112.5 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
c7419cbb4083707511474e632a6a93daedef2b5a8528d4e72517d48b45542b10
|
|
BLAKE2b-256 checksum How to use checksums |
9f3f4fd474dc9bb984dab52a3a7dc7fe43dc7f1768f269a5fada33a3e2dc4f37
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 1, 2026.
Transparency logSecurity for biodata-models 2.0.0
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
Full provenance
All 2 files in this release have been uploaded with provenance metadata.
Attestation for biodata_models-2.0.0.tar.gz
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 1, 2026.
Transparency logA note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
