submission-schema

The NMDC submission schema.

Note that the while this repo is named submission-schema, the generated artifacts are named nmdc_submission_schema for disambiguation purposes when publishing to PyPI.

Website

https://microbiomedata.github.io/submission-schema

Repository Structure

examples/ - example data
project/ - project files (do not edit these)
src/ - source files (edit these)
- nmdc_submission_schema
  - schema -- LinkML schema (edit this)
datamodel -- Generated python datamodel
tests - python tests

Developer Documentation

Updating the submission schema

The version of nmdc-schema used as a basis when building the submission schema is controlled by a dependency in the dev group, specified in pyproject.toml. You can update the version used by running:

uv add --group dev "nmdc-schema==X.Y.Z"  # replace X.Y.Z with the desired version

[!NOTE]
It is important to use the == version constraint to ensure the exact version is installed.

Building the submission schema

Here's how you can generate the submission schema release artifacts:

Container-based process

Prerequisites

Docker is installed on your computer
You are in the root directory of the repository

Procedure

Build the container image you will later use to build the submission schema:
```
docker build -t submission-schema-builder -f builder.Dockerfile .
```
If you haven't already done so (see the "Updating the submission schema" section above), use that container image to update the nmdc-schema dependency of the submission schema:
```
docker run --rm -it -v ${PWD}:/submission-schema submission-schema-builder \
    uv add --group dev "nmdc-schema==X.Y.Z"  # replace X.Y.Z
```
Then, rebuild the container image (so it has that new version of nmdc-schema installed):
```
docker build -t submission-schema-builder -f builder.Dockerfile .
```

Use the container image to build the submission schema:

docker run --rm -it -v ${PWD}:/submission-schema submission-schema-builder

Commit the changes, using the new nmdc-schema version number as the commit message; like this:
```
git add .
git commit -m "X.Y.Z"  # replace X.Y.Z with the nmdc-schema version
```

(Optional) Delete the container image:

docker image rm submission-schema-builder

Direct process

Procedure

Install Python dependencies:
```
uv sync
```
Generate the release artifacts:
```
make clean all
```
Commit the changes, using the new nmdc-schema version number as the commit message; like this:
```
git add .
git commit -m "X.Y.Z"  # replace X.Y.Z with the nmdc-schema version
```

Credits

this project was made with linkml-project-cookiecutter

Release files for nmdc-submission-schema 11.23.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for nmdc-submission-schema 11.23.0
File	Size	Uploaded
nmdc_submission_schema-11.23.0.tar.gz	741.0 kB	Aug 14, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for nmdc-submission-schema 11.23.0
File	Interpreter	ABI	Platform	Reset
nmdc_submission_schema-11.23.0-py3-none-any.whl 757.5 kB Aug 14, 2026	Python 3	none	any	Details

Total release size: 1.5 MB

Release files / nmdc_submission_schema-11.23.0.tar.gz

Download URL	nmdc_submission_schema-11.23.0.tar.gz
Size	741.0 kB
Tags	Source
SHA-256 checksum How to use checksums	`d94d84054a39fd65724a5d406a0597b11954951dc9649edb206e962fa3c46796`
BLAKE2b-256 checksum How to use checksums	`c8c69a940b3a4b28c92fa9978106b9db1ab7677b80c3203571ad153511652590`
Upload date	Aug 14, 2026
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.

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/microbiomedata/submission-schema
Publishing commit: github.com/microbiomedata/submission-schema/tree/a18e87c0ff257e660ddb057183c28100ac2b2ee5

Workflow

Publishing configuration: github.com/microbiomedata/submission-schema/blob/a18e87c0ff257e660ddb057183c28100ac2b2ee5/.github/workflows/pypi-publish.yaml
Publishing logs: github.com/microbiomedata/submission-schema/actions/runs/31757382266/attempts/1

Artifact

Subject: nmdc_submission_schema-11.23.0.tar.gz
SHA-256 checksum: d94d84054a39fd65724a5d406a0597b11954951dc9649edb206e962fa3c46796 Verifying attestations

Release files / nmdc_submission_schema-11.23.0-py3-none-any.whl

Download URL	nmdc_submission_schema-11.23.0-py3-none-any.whl
Size	757.5 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`dad12cfa03206dc3ee958b24830092491f57c1027f389344395f2426f70b3b9d`
BLAKE2b-256 checksum How to use checksums	`6afdbc55d47612de88ae6ebf5fd58ab32d3120f8471a9c4365c99101667932b1`
Upload date	Aug 14, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/microbiomedata/submission-schema
Publishing commit: github.com/microbiomedata/submission-schema/tree/a18e87c0ff257e660ddb057183c28100ac2b2ee5

Workflow

Publishing configuration: github.com/microbiomedata/submission-schema/blob/a18e87c0ff257e660ddb057183c28100ac2b2ee5/.github/workflows/pypi-publish.yaml
Publishing logs: github.com/microbiomedata/submission-schema/actions/runs/31757382266/attempts/1

Artifact

Subject: nmdc_submission_schema-11.23.0-py3-none-any.whl
SHA-256 checksum: dad12cfa03206dc3ee958b24830092491f57c1027f389344395f2426f70b3b9d Verifying attestations