Merge pull request #718 from bioimage-io/dev

include bioimageio_schema.json in python package

Author: FynnBe

.github/workflows/build.yml

@@ -13,10 +13,10 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.9", "3.10", "3.11","3.12", "3.13"]
-        pydantic-version: ["2.10.3", "2.11.0"]
+        pydantic-version: ["2.10.6", "2.11.9"]
         include:
-          - python-version: "3.12"
-            pydantic-version: "2.11.0"
+          - python-version: "3.10"
+            pydantic-version: "2.11.9"
             is-dev-version: true
             run-expensive-tests: true
     steps:
@@ -50,11 +50,11 @@ jobs:
         run: |
           pyright --version
           pyright -p pyproject.toml --pythonversion ${{ matrix.python-version }}
-      - run: pytest --cov bioimageio --cov-report xml --cov-append --capture no
+      - run: pytest --cov bioimageio --cov-append --capture no
         env:
           BIOIMAGEIO_CACHE_PATH: bioimageio_cache
           RUN_EXPENSIVE_TESTS: ${{ matrix.run-expensive-tests && 'true' || 'false' }}
-      - run: pytest --cov bioimageio --cov-report xml --cov-append --capture no scripts  # also test docstrings in scripts for dev-version
+      - run: pytest --cov bioimageio --cov-append --capture no scripts  # also test docstrings in scripts for dev-version
         if: ${{matrix.is-dev-version}}
         env:
           BIOIMAGEIO_CACHE_PATH: bioimageio_cache
@@ -64,35 +64,57 @@ jobs:
         with:
           path: bioimageio_cache
           key: "py${{ matrix.python-version }}-${{ steps.get-date.outputs.date }}"
-      - if: matrix.is-dev-version && github.event_name == 'pull_request'
-        uses: orgoro/[email protected]
+
+      - run: cp .coverage .coverage.${{ matrix.python-version }}-${{ matrix.pydantic-version }}
+      - uses: actions/upload-artifact@v4
+        with:
+          name: .coverage.${{ matrix.python-version }}-${{ matrix.pydantic-version }}
+          retention-days: 1
+          path: .coverage.${{ matrix.python-version }}-${{ matrix.pydantic-version }}
+          include-hidden-files: true
+  coverage:
+    needs: [test]
+    if: github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v6
+      - run: |
+          pip install coverage
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: .coverage.*
+      - run: |
+          ls -l
+          coverage combine
+          coverage xml -o coverage.xml
+      - uses: orgoro/[email protected]
         with:
           coverageFile: coverage.xml
           token: ${{ secrets.GITHUB_TOKEN }}
           thresholdAll: 0.7
           thresholdNew: 0.9
           thresholdModified: 0.6
-      - if: matrix.is-dev-version
+      - name: generate coverage badge and html report
         run: |
           pip install genbadge[coverage]
           genbadge coverage --input-file coverage.xml --output-file ./dist/coverage/coverage-badge.svg
           coverage html -d dist/coverage
-      - if: matrix.is-dev-version
-        uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v4
         with:
-          name: coverage
+          name: coverage-summary
           retention-days: 1
           path: dist
 
 
   deploy:
-    needs: [test]
+    needs: [test,coverage]
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: actions/download-artifact@v4
         with:
-          name: coverage
+          name: coverage-summary
           path: dist
       - uses: actions/setup-python@v6
         with:
@@ -108,8 +130,6 @@ jobs:
         env:
           PYTHONPATH: "./scripts"
         run: python -m interactive_docs
-      - name: Generate JSON schemas
-        run: python scripts/generate_json_schemas.py
       - name: Generate JSON schema documentation
         run: python scripts/generate_json_schema_documentation.py
       - name: Generate developer docs
@@ -155,7 +175,7 @@ jobs:
         shell: bash -l {0}
         run: |
           mkdir -p ./pkgs/noarch
-          conda-build -c conda-forge conda-recipe --no-test --output-folder ./pkgs
+          conda-build -c conda-forge conda-recipe --output-folder ./pkgs
 
 #  rattler-build:
 #    name: Build package
@@ -199,8 +219,7 @@ jobs:
         with:
           create-tag: false
           version-command: |
-            python -c "from pathlib import Path;p = p_src if (p_src:=Path('src/bioimageio/spec/__init__.py')).exists() else Path('bioimageio/spec/__init__.py');print(p.read_text().split('__version__ = \"')[1].split('\"')[0])"
-
+            python -c "from pathlib import Path;print(p_version.read_text().split('VERSION = \"')[1].split('\"')[0] if (p_version:=Path('src/bioimageio/spec/_version.py')).exists() else Path('src/bioimageio/spec/__init__.py').read_text().split('__version__ = \"')[1].split('\"')[0])"
       - name: Push tag
         id: tag-version
         if: github.ref == 'refs/heads/main' && steps.check-version.outputs.previous-version != steps.check-version.outputs.current-version

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
         pass_filenames: false
       - id: generate json schemas
         name: generate json schemas
-        entry: python scripts/generate_json_schemas.py
+        entry: python scripts/write_json_schema.py
         language: system
         always_run: true
         pass_filenames: false

MANIFEST.in

@@ -2,3 +2,4 @@ include README.md
 include LICENSE
 include src/bioimageio/spec/static/spdx_licenses.json
 include src/bioimageio/spec/static/tag_categories.json
+include src/bioimageio/spec/static/bioimageio_schema.json

changelog.md

@@ -10,6 +10,11 @@ In this file we log both:
 
 This changelog includes implementation details and my reference the [changes to the Resource Description Format](#changes-to-the-resource-description-format), e.g. in entry [bioimageio.spec 0.5.2](#bioimageiospec-052).
 
+#### bioimageio.spec 0.5.5.4
+
+- include bioimageio_schema.json in python package
+- fix issues with setuptools and importlib.metadata.version (by avoiding use of `importlib.metadata.version`)
+
 #### bioimageio.spec 0.5.5.3
 
 - Fix MANIFEST.in

conda-recipe/meta.yaml

@@ -1,7 +1,7 @@
 {% set pyproject = load_file_data('pyproject.toml') %}
 {% set version_match = load_file_regex(
-  load_file="src/bioimageio/spec/__init__.py",
-  regex_pattern='__version__ = "(.+)"') %}
+  load_file="src/bioimageio/spec/_version.py",
+  regex_pattern='VERSION = "(.+)"') %}
 {% set version = version_match[1] %}
 
 package:

pyproject.toml

@@ -16,6 +16,7 @@ dependencies = [
     "numpy>=1.21",
     "packaging>=17.0",
     "platformdirs",
+    "pydantic-core",
     "pydantic-settings>=2.5,<3",
     "pydantic>=2.10.3,<2.12",
     "python-dateutil",
@@ -64,7 +65,7 @@ build-backend = "setuptools.build_meta"
 where = ["src/"]
 
 [tool.setuptools.dynamic]
-version = { attr = "bioimageio.spec.__version__" }
+version = { attr = "bioimageio.spec._version.VERSION" }
 
 [tool.pyright]
 exclude = [

scripts/generate_json_schemas.py

@@ -1,13 +1,15 @@
 import sys
 from pathlib import Path
 
-from typing_extensions import assert_never
+from typing_extensions import Final, assert_never
 
-from bioimageio.spec import SpecificResourceDescr
-from scripts.generate_json_schemas import MAJOR_MINOR_VERSION
+from bioimageio.spec import SpecificResourceDescr, __version__
 
 from . import generate_docs
 
+MAJOR_MINOR_VERSION: Final[str] = "v" + "-".join(__version__.split(".")[0:2])
+
+
 html_result: "str | Exception" = generate_docs(
     raw_type=SpecificResourceDescr, root_path=["Delivery"]
 )

scripts/interactive_docs/__main__.py

@@ -0,0 +1,20 @@
+import json
+import sys
+from pathlib import Path
+
+from bioimageio.spec._internal.json_schema import generate_json_schema
+
+
+def write_schema():
+    schema = generate_json_schema()
+    path = (
+        Path(__file__).parent / "../src/bioimageio/spec/static/bioimageio_schema.json"
+    )
+    with path.open("w") as f:
+        json.dump(schema, f, indent=2)
+
+    print(f"written `{path}")
+
+
+if __name__ == "__main__":
+    sys.exit(write_schema())

scripts/write_json_schema.py

@@ -1,9 +1,8 @@
 """
 .. include:: ../../README.md
 """
-# ruff: noqa: E402
 
-__version__ = "0.5.5.3"
+# ruff: noqa: E402
 from loguru import logger
 
 logger.disable("bioimageio.spec")
@@ -47,6 +46,7 @@
     save_bioimageio_package_to_stream,
 )
 from ._upload import upload
+from ._version import VERSION as __version__
 from .application import AnyApplicationDescr, ApplicationDescr
 from .dataset import AnyDatasetDescr, DatasetDescr
 from .generic import AnyGenericDescr, GenericDescr