Overhaul with Pydantic and format version generic 0.3 / model 0.5

.github/workflows/build.yml

@@ -2,105 +2,109 @@ name: Test and Deploy bioimageio.spec
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ "**" ]
+    branches: ["**"]
 
 jobs:
-  black:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Check files using the black formatter
-        uses: rickstaa/action-black@v1
-        id: action_black
-        with:
-          black_args: "."
-      - name: Annotate diff changes using reviewdog
-        if: steps.action_black.outputs.is_formatted == 'true'
-        uses: reviewdog/action-suggester@v1
-        with:
-          tool_name: blackfmt
-
   test:
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
-
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        include:
+          - python-version: "3.8"
+            test-format: true
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-        cache: 'pip'
-    - name: Install dependencies
-      run: |
-        pip install --upgrade pip
-        pip install -e .[test]
-    - name: Test with pytest
-      run: pytest tests
-    - name: Check passthrough models
-      run: python scripts/generate_passthrough_modules.py check
-# todo: add mypy checks for python 3.10 when we can add KW_ONLY to dataclasses
-#       allowing dataclass inheritance w/o the 'missing' default value
-#    - name: MyPy
-#      if: ${{ matrix.python-version == '3.10' }}
-#      run: |
-#        mkdir -p .mypy-cache
-#        mypy . --install-types --non-interactive --cache-dir .mypy-cache --explicit-package-bases --check-untyped-defs
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[dev]
+      - name: Get Date
+        id: get-date
+        run: |
+          echo "week=$(/bin/date -u "+%Y-%U")" >> $GITHUB_OUTPUT
+        shell: bash
+      - uses: actions/cache@v3
+        with:
+          path: tests/cache
+          key: ${{ runner.os }}-${{ matrix.python-version }}-${{ steps.get-date.outputs.week }}-${{ hashFiles('**/lockfiles') }}
+      - name: Check autogenerated imports
+        run: python scripts/generate_version_submodule_imports.py check
+      - run: black .
+        if: matrix.test-format
+      - run: ruff check **/*.py # ignore notebooks for now
+        if: matrix.test-format
+      - run: pyright --version
+      - run: pyright -p pyproject.toml
+      - run: pytest
 
-  conda-build:
+  deploy:
     runs-on: ubuntu-latest
-    needs: test
     steps:
-    - name: checkout
-      uses: actions/checkout@v3
-      with:
-        fetch-depth: 0
-    - name: Install Conda environment with Micromamba
-      uses: mamba-org/provision-with-micromamba@main
-      with:
-        environment-file: false
-        environment-name: build-env
-        channels: conda-forge
-        extra-specs: |
-          boa
-    - name: linux conda build
-      shell: bash -l {0}
-      run: |
-        conda mambabuild -c conda-forge conda-recipe
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install -e .[dev]
+      - name: Generate spec docs
+        run: python scripts/generate_spec_documentation.py --dist dist/user_docs
+      - name: Generate JSON schemas
+        run: python scripts/generate_json_schemas.py
+      - name: Generate developer docs
+        run: pdoc -o ./dist bioimageio.spec
+      - name: Get branch name to deploy to
+        id: get_branch
+        shell: bash
+        run: |
+          if [[ -n '${{ github.event.pull_request.head.ref }}' ]]; then branch=gh-pages-${{ github.event.pull_request.head.ref }}; else branch=gh-pages; fi
+          echo "::set-output name=branch::$branch"
+      - name: Deploy to ${{ steps.get_branch.outputs.branch }} 🚀
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: ${{ steps.get_branch.outputs.branch }}
+          folder: dist
 
-  deploy:
+  mamba-build:
     runs-on: ubuntu-latest
     needs: test
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.9
-    - name: Install dependencies
-      run: |
-        pip install .
-    - name: Generate Docs
-      run: python scripts/generate_rdf_docs.py
-    - name: Generate pre-/postprocessing docs
-      run: python scripts/generate_processing_docs.py
-    - name: Generate weight formats docs
-      run: python scripts/generate_weight_formats_docs.py
-    - name: Generate JSON Schema
-      run: python scripts/generate_json_specs.py
-    - name: Generate weight formats overview
-      run: python scripts/generate_weight_formats_overview.py generate
-    - name: Get branch name to deploy to
-      id: get_branch
-      shell: bash
-      run: |
-        if [[ -n '${{ github.event.pull_request.head.ref }}' ]]; then branch=gh-pages-${{ github.event.pull_request.head.ref }}; else branch=gh-pages; fi
-        echo "::set-output name=branch::$branch"
-    - name: Deploy to ${{ steps.get_branch.outputs.branch }} 🚀
-      uses: JamesIves/github-pages-deploy-action@v4
-      with:
-        branch: ${{ steps.get_branch.outputs.branch }}
-        folder: dist
+      - name: checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Install Conda environment with Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          cache-downloads: true
+          cache-environment: true
+          environment-name: build-env
+          condarc: |
+            channels:
+            - conda-forge
+          create-args: >-
+            boa
+      - name: linux conda build
+        run: |
+          conda mambabuild -c conda-forge conda-recipe
+        shell: bash -l {0}
+
+#  rattler-build:
+#    name: Build package
+#    runs-on: ubuntu-latest
+#    steps:
+#    - uses: actions/checkout@v4
+#    - name: Build conda package
+#      uses: prefix-dev/[email protected]
+#      with:
+#        recipe-path: conda-recipe/recipe.yaml

.github/workflows/release.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.9"
           cache: 'pip'
       - name: Install dependencies
         run: |

.gitignore

@@ -1,5 +1,12 @@
 __pycache__/
-.vscode
-tmp
+.env
+.vscode/launch.json
 *.egg-info/
-dist
+build/
+dist/
+docs/
+user_docs/
+tests/cache
+tests/generated_json_schemas
+tmp/
+output/

.markdownlint.json

@@ -0,0 +1,6 @@
+{
+    "default": true,
+    "MD013": false,
+    "MD033": false,
+    "MD041": false
+}

.pre-commit-config.yaml

@@ -1,59 +1,37 @@
 repos:
   - repo: https://github.com/ambv/black
-    rev: 22.6.0
+    rev: 24.2.0
     hooks:
-    - id: black
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.991
+      - id: black
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.2.1
     hooks:
-      - id: mypy
-        additional_dependencies: [types-requests]
-        args: [--install-types, --non-interactive, --explicit-package-bases, --check-untyped-defs]
+      - id: ruff
+        args: [--fix]
   - repo: local
     hooks:
-    - id: generate rdf docs
-      name: generate rdf docs
-      entry: python scripts/generate_rdf_docs.py
-      language: system
-      always_run: true
-      pass_filenames: false
-  - repo: local
-    hooks:
-    - id: generate processing docs
-      name: generate processing docs
-      entry: python scripts/generate_processing_docs.py
-      language: system
-      always_run: true
-      pass_filenames: false
-  - repo: local
-    hooks:
-    - id: generate weight formats docs
-      name: generate weight formats docs
-      entry: python scripts/generate_weight_formats_docs.py
-      language: system
-      always_run: true
-      pass_filenames: false
-  - repo: local
-    hooks:
-    - id: generate json schemas
-      name: generate json schemas
-      entry: python scripts/generate_json_specs.py
-      language: system
-      always_run: true
-      pass_filenames: false
-  - repo: local
-    hooks:
-    - id: generate passthrough modules
-      name: generate passthrough modules
-      entry: python scripts/generate_passthrough_modules.py generate
-      language: system
-      always_run: true
-      pass_filenames: false
-  - repo: local
-    hooks:
-    - id: generate weight formats overview
-      name: generate weight formats overview
-      entry: python scripts/generate_weight_formats_overview.py generate
-      language: system
-      always_run: true
-      pass_filenames: false
+      - id: pyright
+        name: pyright
+        entry: pyright
+        language: system
+        always_run: true
+        pass_filenames: true
+        files: ^.*\.py$
+      - id: generate passthrough modules
+        name: generate passthrough modules
+        entry: python scripts/generate_version_submodule_imports.py generate
+        language: system
+        always_run: true
+        pass_filenames: false
+      - id: generate json schemas
+        name: generate json modules
+        entry: python scripts/generate_json_schemas.py
+        language: system
+        always_run: true
+        pass_filenames: false
+      - id: generate spec md docs
+        name: generate spec md docs
+        entry: python scripts/generate_spec_documentation.py
+        language: system
+        always_run: true
+        pass_filenames: false

.vscode/settings.json

@@ -0,0 +1,19 @@
+{
+    "window.title": "bioimageio.spec",
+    "python.testing.unittestArgs": [
+        "-v",
+        "-s",
+        "./tests",
+        "-p",
+        "test_*.py"
+    ],
+    "python.testing.pytestEnabled": true,
+    "python.testing.unittestEnabled": false,
+    "yaml.schemas": {
+        "dist/bioimageio_schema_latest.json": [
+            "rdf.yaml",
+            "bioimageio.yaml",
+            "*.bioimageio.yaml"
+        ],
+    }
+}

CONTRIBUTING.md

@@ -0,0 +1,6 @@
+Thank you for considering to contribute to bioimageio.spec!
+
+Find good first issues [here](https://github.com/bioimage-io/spec-bioimage-io/issues?q=is%3Aopen+is%3Aissue+label%3A%22good+first+issue%22).
+Open or join a discussion [here](https://github.com/bioimage-io/spec-bioimage-io/discussions).
+
+More refined instructions on how to contribute will follow.

MANIFEST.in

@@ -1,4 +1,5 @@
 include bioimageio/spec/VERSION
 include README.md
 include LICENSE
-include bioimageio/spec/static/licenses.json
+include bioimageio/spec/static/spdx_licenses.json
+include bioimageio/spec/static/tag_categories.json