rembi-mifa

Pydantic-based python models for REMBI and MIFA metadata for FAIR bioimaging data.

Usage

See examples/ directory.

Notes

The original specs lack some documentation and have a few other quirks. The implementation here may differ from the intended structure in these cases.

• The REMBI specification refers to but does not define the AnnotationType type; here we use the MIFA AnnotationType enum.
• the REMBI specification refers to the License type but it is empty; there is no MIFA type of the same name (although LicenseType is close). We just accept a string, and recommend using an SPDX identifier.

This implementation is opinionated on certain serialisation/deserialisation features:

• Optional list fields are omitted if empty; optional list fields which are omitted are deserialised to empty lists.
• Date and datetime values are deserialised from RFC 3339 strings or stringified seconds (or milliseconds, depending on the value) since the unix epoch, and serialised to RFC 3339 strings (see the pydantic docs for more details)
• ORCiD IDs may be parsed as only the identifier, but are normalised to URLs; the checksum is also validated
• in a few cases, the specification requires a list but does not state that the list must be non-empty, so this is not validated
• the keywords field of rembi.Study is probably supposed to represent a delimited list, but it's not specified, so it's left as a plain string here

Contributing

Use the justfile for most common development tasks.

Releases should be published from CI. just bump minor will

• run various tests
• check that your working tree is clean
• check you are on the main branch
• bump the minor project version
• commit that change
• tag that commit
• push the changes and tag

Then CI will deploy to PyPI.