Merge pull request #721 from bioimage-io/dev

update subprocess calls and avoid shell=True

Author: FynnBe

.github/workflows/build.yml

@@ -4,27 +4,27 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: ["**"]
+    branches: ['**']
 
 jobs:
   test:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11","3.12", "3.13"]
-        pydantic-version: ["2.10.6", "2.11.9"]
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+        pydantic-version: ['2.10.6', '2.11.9']
         include:
-          - python-version: "3.10"
-            pydantic-version: "2.11.9"
+          - python-version: '3.10'
+            pydantic-version: '2.11.9'
             is-dev-version: true
             run-expensive-tests: true
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-          cache: "pip"
+          cache: 'pip'
       - name: Install dependencies
         run: |
           pip install --upgrade pip
@@ -38,7 +38,7 @@ jobs:
       - uses: actions/cache/restore@v4
         with:
           path: bioimageio_cache
-          key: "py${{ matrix.python-version }}-${{ steps.get-date.outputs.date }}"
+          key: 'py${{ matrix.python-version }}-${{ steps.get-date.outputs.date }}'
       - name: Check autogenerated imports
         run: python scripts/generate_version_submodule_imports.py check
       - run: ruff check
@@ -50,11 +50,11 @@ jobs:
         run: |
           pyright --version
           pyright -p pyproject.toml --pythonversion ${{ matrix.python-version }}
-      - run: pytest --cov bioimageio --cov-append --capture no
+      - run: pytest -v --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-append --capture no scripts  # also test docstrings in scripts for dev-version
+      - run: pytest -v --cov bioimageio --cov-append --capture no scripts # also test docstrings in scripts for dev-version
         if: ${{matrix.is-dev-version}}
         env:
           BIOIMAGEIO_CACHE_PATH: bioimageio_cache
@@ -63,7 +63,7 @@ jobs:
         # explicit restore/save instead of cache action to cache even if coverage fails
         with:
           path: bioimageio_cache
-          key: "py${{ matrix.python-version }}-${{ steps.get-date.outputs.date }}"
+          key: 'py${{ matrix.python-version }}-${{ steps.get-date.outputs.date }}'
 
       - run: cp .coverage .coverage.${{ matrix.python-version }}-${{ matrix.pydantic-version }}
       - uses: actions/upload-artifact@v4
@@ -84,8 +84,9 @@ jobs:
       - uses: actions/download-artifact@v4
         with:
           pattern: .coverage.*
+          merge-multiple: true
       - run: |
-          ls -l
+          ls -la .coverage*
           coverage combine
           coverage xml -o coverage.xml
       - uses: orgoro/[email protected]
@@ -106,9 +107,8 @@ jobs:
           retention-days: 1
           path: dist
 
-
   deploy:
-    needs: [test,coverage]
+    needs: [test, coverage]
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -118,8 +118,8 @@ jobs:
           path: dist
       - uses: actions/setup-python@v6
         with:
-          python-version: "3.12"
-          cache: "pip"
+          python-version: '3.12'
+          cache: 'pip'
       - name: Install dependencies
         run: |
           pip install --upgrade pip
@@ -128,13 +128,13 @@ jobs:
         run: python scripts/generate_spec_documentation.py --dist dist/user_docs
       - name: Generate interactive documentation
         env:
-          PYTHONPATH: "./scripts"
+          PYTHONPATH: './scripts'
         run: python -m interactive_docs
       - name: Generate JSON schema documentation
         run: python scripts/generate_json_schema_documentation.py
       - name: Generate developer docs
         run: ./scripts/pdoc/run.sh
-      - name: copy legacy file until BioImage.IO-packager is updated  # TODO: remove if packager does not depend on it anymore
+      - name: copy legacy file until BioImage.IO-packager is updated # TODO: remove if packager does not depend on it anymore
         run: cp weight_formats_spec.json ./dist/weight_formats_spec.json
       - name: Get branch name to deploy to
         id: get_branch
@@ -159,7 +159,7 @@ jobs:
         with:
           auto-update-conda: true
           auto-activate-base: true
-          activate-environment: ""
+          activate-environment: ''
           channel-priority: strict
           miniforge-version: latest
           conda-solver: libmamba
@@ -177,15 +177,15 @@ jobs:
           mkdir -p ./pkgs/noarch
           conda-build -c conda-forge conda-recipe --output-folder ./pkgs
 
-#  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
+  #  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
 
   pip-build:
     name: Build and publish to PyPI
@@ -237,14 +237,14 @@ jobs:
         uses: pypa/gh-action-pypi-publish@release/v1.12
         with:
           user: __token__
-          password: "${{ secrets.PYPI_TOKEN }}"
+          password: '${{ secrets.PYPI_TOKEN }}'
           packages-dir: dist/
 
       - name: Publish the release notes
         if: github.ref == 'refs/heads/main'
         uses: release-drafter/[email protected]
         with:
           publish: "${{ steps.tag-version.outputs.new_tag != '' }}"
-          tag: "${{ steps.tag-version.outputs.new_tag }}"
+          tag: '${{ steps.tag-version.outputs.new_tag }}'
         env:
-          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'

.gitignore

@@ -16,3 +16,5 @@ user_docs/
 scripts/pdoc/original.py
 scripts/pdoc/patched.py
 bioimageio_cache/
+example/my_bioimageio_dataset.zip
+example/my_model.zip

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 0.5.5.5
+
+- use OS specific conda command to fix conda subprocess issues
+- keep track of original source name for prettier validation summary display
+
 #### bioimageio.spec 0.5.5.4
 
 - include bioimageio_schema.json in python package