Release v3.0.0

.github/workflows/publish_dev.yml

@@ -21,7 +21,7 @@ jobs:
       - name: Pull latest changes
         run: git pull origin dev
       - name: Install uv
-        uses: astral-sh/setup-uv@v9
+        uses: astral-sh/setup-uv@v10.0.1
         with:
           python-version: '3.10'
       - name: Configure aws credentials
@@ -33,5 +33,5 @@ jobs:
       - name: Create and upload schemas
         run: |
           uv sync --locked
-          uv run python -m aind_data_schema.utils.json_writer --output $TEMP_DIR --attach-version
+          uv run python -m biodata_schema.utils.json_writer --output $TEMP_DIR --attach-version
           uvx --from awscli aws s3 sync $TEMP_DIR s3://${AWS_DATA_SCHEMA_BUCKET}/$S3_PREFIX

.github/workflows/run_dev_tests.yml

@@ -13,11 +13,11 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.11' ]
+        python-version: [ '3.12' ]
     steps:
       - uses: actions/checkout@v3
       - name: Install uv
-        uses: astral-sh/setup-uv@v9
+        uses: astral-sh/setup-uv@v10.0.1
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -29,13 +29,14 @@ jobs:
     strategy:
       matrix:
         python-version: [ '3.10', '3.11', '3.12', '3.13' ]
+        resolution: [ 'lowest-direct', 'highest' ]
     steps:
     - uses: actions/checkout@v3
     - name: Install uv
-      uses: astral-sh/setup-uv@v9
+      uses: astral-sh/setup-uv@v10.0.1
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
-      run: uv sync --locked --group dev --group docs
+      run: uv sync --group dev --group docs --resolution ${{ matrix.resolution }}
     - name: Run tests and coverage
-      run: uv run pytest --cov=aind_data_schema --cov=tests --cov-report=term-missing --cov-fail-under=100
+      run: uv run pytest --cov=biodata_schema --cov=tests --cov-report=term-missing --cov-fail-under=100

.github/workflows/run_main_tests.yml

@@ -19,7 +19,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Install uv
-        uses: astral-sh/setup-uv@v9
+        uses: astral-sh/setup-uv@v10.0.1
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -34,13 +34,13 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Install uv
-      uses: astral-sh/setup-uv@v9
+      uses: astral-sh/setup-uv@v10.0.1
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: uv sync --locked --group dev --group docs
     - name: Run tests and coverage
-      run: uv run pytest --cov=aind_data_schema --cov=tests --cov-report=term-missing --cov-fail-under=100
+      run: uv run pytest --cov=biodata_schema --cov=tests --cov-report=term-missing --cov-fail-under=100
   verify_version:
     runs-on: ubuntu-latest
     steps:

.github/workflows/tag_and_publish_main.yml

@@ -25,7 +25,7 @@ jobs:
     - name: Push git tag
       run: git push origin "v${{ env.tag }}"
     - name: Install uv
-      uses: astral-sh/setup-uv@v9
+      uses: astral-sh/setup-uv@v10.0.1
       with:
         python-version: '3.10'
     - name: Install dependencies
@@ -54,7 +54,7 @@ jobs:
       - name: Pull latest changes
         run: git pull origin main
       - name: Install uv
-        uses: astral-sh/setup-uv@v9
+        uses: astral-sh/setup-uv@v10.0.1
         with:
           python-version: '3.10'
       - name: Configure aws credentials
@@ -66,5 +66,5 @@ jobs:
       - name: Create and upload schemas
         run: |
           uv sync --locked
-          uv run python -m aind_data_schema.utils.json_writer --output $TEMP_DIR --attach-version
+          uv run python -m biodata_schema.utils.json_writer --output $TEMP_DIR --attach-version
           uvx --from awscli aws s3 sync $TEMP_DIR s3://${AWS_DATA_SCHEMA_BUCKET}/$S3_PREFIX

.github/workflows/update_dev_docs.yml

@@ -14,16 +14,16 @@ jobs:
           token: ${{ secrets.SERVICE_TOKEN }}
           ref: ${{ github.head_ref }}
       - name: Install uv
-        uses: astral-sh/setup-uv@v9
+        uses: astral-sh/setup-uv@v10.0.1
         with:
           python-version: '3.10'
       - name: Install dependencies
         run: uv sync --locked --group dev --group docs
       - name: Generate docs
         run: |
-          uv run python src/aind_data_schema/utils/docs/model_generator.py
-          uv run python src/aind_data_schema/utils/docs/registries_generator.py
-          uv run python src/aind_data_schema/utils/docs/doc_generator.py
+          uv run python src/biodata_schema/utils/docs/model_generator.py
+          uv run python src/biodata_schema/utils/docs/registries_generator.py
+          uv run python src/biodata_schema/utils/docs/doc_generator.py
           uv run sphinx-build -b html docs/source/ docs/build/html
       - name: Commit changes
         uses: EndBug/add-and-commit@v9

.github/workflows/update_docs.yml

@@ -15,19 +15,19 @@ jobs:
         with:
           token: ${{ secrets.SERVICE_TOKEN }}
       - name: Install uv
-        uses: astral-sh/setup-uv@v9
+        uses: astral-sh/setup-uv@v10.0.1
         with:
           python-version: '3.10'
       - name: Install dependencies
         run: uv sync --locked --group dev
       - name: Bump schema versions
         run: |
-          uv run python -m aind_data_schema.utils.schema_version_bump
+          uv run python -m biodata_schema.utils.schema_version_bump
           echo "Finished schema version bump"
       - name: Update schemas
         run: |
           rm -rf $OUTPUT_DIR
-          uv run python -m aind_data_schema.utils.json_writer --output $OUTPUT_DIR
+          uv run python -m biodata_schema.utils.json_writer --output $OUTPUT_DIR
       - name: Create example schemas
         run: |
           cd examples
@@ -53,7 +53,7 @@ jobs:
       - name: Pull latest changes
         run: git pull origin ${{ github.ref_name }}
       - name: Install uv
-        uses: astral-sh/setup-uv@v9
+        uses: astral-sh/setup-uv@v10.0.1
         with:
           python-version: '3.10'
       - name: Install dependencies

.readthedocs.yaml

@@ -1,23 +1,23 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
     python: "3.13"
     nodejs: "20"
   jobs:
-    # Build the interactive React Flow schema diagram bundle into
-    # docs/source/_static/ before Sphinx runs (the bundle is git-ignored and
-    # regenerated here; the JSON it fetches is generated by conf.py).
+    # Build the interactive React Flow schema diagram before Sphinx runs.
     pre_build:
       - npm --prefix diagram-app ci
       - npm --prefix diagram-app run build
-    pre_install:
-      - python -m pip install uv
-      - uv sync --locked --group dev --group docs
 
 python:
-  install: []
+  install:
+    - method: uv
+      command: sync
+      groups:
+        - dev
+        - docs
 
 sphinx:
   # Path to your Sphinx configuration file.

CONTRIBUTING.md

@@ -39,9 +39,9 @@ Documentation is automatically built when you open a PR into the biodata-schema
 To generate the source files for the documentation and model class links, run:
 
 ```bash
-uv run python src/aind_data_schema/utils/docs/model_generator.py
-uv run python src/aind_data_schema/utils/docs/registries_generator.py
-uv run python src/aind_data_schema/utils/docs/doc_generator.py
+uv run python src/biodata_schema/utils/docs/model_generator.py
+uv run python src/biodata_schema/utils/docs/registries_generator.py
+uv run python src/biodata_schema/utils/docs/doc_generator.py
 ```
 
 The front page embeds an interactive React Flow diagram of the `Metadata` schema (`diagram-app/`). Build its JS/CSS bundle once before building the docs (it's git-ignored and only needs rebuilding when `diagram-app/` changes):
@@ -73,7 +73,7 @@ Testing is required to open a PR in this repository to ensure robustness and rel
   - Please test your changes using pytest and coverage:
 
     ```bash
-    uv run pytest --cov=aind_data_schema --cov=tests --cov-report=term-missing
+    uv run pytest --cov=biodata_schema --cov=tests --cov-report=term-missing
     ```
 
     To open the coverage report in a browser, you can run
@@ -110,7 +110,7 @@ Use `uv run ruff format .` to apply Ruff's formatting.
 **NOTE**: Please note that these linters are automatically run in github actions when a PR is opened. These linters must pass for a PR to merge. 
 
 ### Units
-Unit types (i.e. anything from [aind_data_schema_models.units](https://github.com/AllenNeuralDynamics/aind-data-schema-models/blob/main/src/aind_data_schema_models/units.py)) should always be paired with a variable in one of two patterns.
+Unit types (i.e. anything from [biodata_models.units](https://github.com/AllenNeuralDynamics/biodata-models/blob/main/src/biodata_models/units.py)) should always be paired with a variable in one of two patterns.
 
 When you have a single `variable` with a unit, you should add the `_unit` suffix on the name of the unit:
 
@@ -157,7 +157,7 @@ When you are ready to open a pull request, please link any relevant issues and r
 ## Release
 
 - From dev, create a branch called release-vX.Y.Z
-- Manually increment the version number in the aind_data_schema/__init__.py file to match
+- Manually increment the version number in the biodata_schema/__init__.py file to match
 - Manually increment the major/minor/patch versions of the core files as needed
 - Push the branch and open a PR into main
 - After this push, any last minute changes to the release-vX.Y.Z will have to done to via a PR