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FynnBeFynnBe
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Merge pull request #346 from bioimage-io/spec_v0_5
Update to bioimageio.spec=0.5
2 parents 7f26c9b + b84d33b commit 099d784

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‎.github/workflows/build.yaml

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name: Test and Deploy bioimageio.core
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ "**" ]
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defaults:
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run:
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shell: micromamba-shell {0}
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jobs:
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black:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: psf/black@stable
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with:
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options: "--check --verbose"
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src: "."
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jupyter: true
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version: "24.3"
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test-spec-conda:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
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steps:
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- uses: actions/checkout@v4
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- name: Install Conda environment with Micromamba
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if: matrix.python-version != '3.8'
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uses: mamba-org/setup-micromamba@v1
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with:
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cache-downloads: true
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cache-environment: true
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environment-file: dev/env-wo-python.yaml
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create-args: >-
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python=${{ matrix.python-version }}
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post-cleanup: 'all'
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- name: Install py3.8 environment
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if: matrix.python-version == '3.8'
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uses: mamba-org/setup-micromamba@v1
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with:
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cache-downloads: true
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cache-environment: true
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environment-file: dev/env-py38.yaml
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post-cleanup: 'all'
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- name: additional setup
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run: pip install --no-deps -e .
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- name: pytest-spec-conda
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run: pytest --disable-pytest-warnings
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test-spec-main:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.8', '3.12']
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steps:
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- uses: actions/checkout@v4
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- name: Install Conda environment with Micromamba
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if: matrix.python-version != '3.8'
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uses: mamba-org/setup-micromamba@v1
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with:
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cache-downloads: true
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cache-environment: true
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environment-file: dev/env-wo-python.yaml
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create-args: >-
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python=${{ matrix.python-version }}
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post-cleanup: 'all'
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- name: Install py3.8 environment
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if: matrix.python-version == '3.8'
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uses: mamba-org/setup-micromamba@v1
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with:
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cache-downloads: true
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cache-environment: true
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environment-file: dev/env-py38.yaml
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post-cleanup: 'all'
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- name: additional setup
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run: |
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conda remove --yes --force bioimageio.spec || true # allow failure for cached env
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pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io
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pip install --no-deps -e .
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- name: pytest-spec-main
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run: pytest --disable-pytest-warnings
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test-tf:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.9', '3.11']
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steps:
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- uses: actions/checkout@v4
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- name: Install Conda environment with Micromamba
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uses: mamba-org/setup-micromamba@v1
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with:
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cache-downloads: true
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cache-environment: true
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environment-file: dev/env-tf.yaml
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condarc: |
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channel-priority: flexible
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create-args: >-
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python=${{ matrix.python-version }}
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post-cleanup: 'all'
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- name: additional setup
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run: pip install --no-deps -e .
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- name: pytest-spec-tf
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run: pytest --disable-pytest-warnings
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conda-build:
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runs-on: ubuntu-latest
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needs: test-spec-conda
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steps:
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- name: checkout
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Install Conda environment with Micromamba
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uses: mamba-org/setup-micromamba@v1
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with:
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cache-downloads: true
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cache-environment: true
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environment-name: build-env
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condarc: |
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channels:
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- conda-forge
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create-args: |
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boa
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- name: linux conda build
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run: |
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conda mambabuild -c conda-forge conda-recipe
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docs:
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if: github.ref == 'refs/heads/main'
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: '3.12'
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cache: 'pip'
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- run: pip install -e .[dev]
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- id: get_version
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run: python -c 'import bioimageio.core;print(f"version={bioimageio.core.__version__}")' >> $GITHUB_OUTPUT
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- name: Generate developer docs
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run: |
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pdoc \
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--logo https://bioimage.io/static/img/bioimage-io-logo.svg \
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--logo-link https://bioimage.io/ \
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--favicon https://bioimage.io/static/img/bioimage-io-icon-small.svg \
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--footer-text 'bioimageio.core ${{steps.get_version.outputs.version}}' \
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-o ./dist bioimageio.core
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- run: cp README.md ./dist/README.md
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- name: Deploy to gh-pages 🚀
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uses: JamesIves/github-pages-deploy-action@v4
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with:
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branch: gh-pages
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folder: dist

‎.github/workflows/build.yml

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‎.github/workflows/release.yml

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- name: Check if there is a parent commit
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id: check-parent-commit
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run: |
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echo "::set-output name=sha::$(git rev-parse --verify --quiet HEAD^)"
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echo "sha=$(git rev-parse --verify --quiet HEAD^)" >> $GITHUB_OUTPUT
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- name: Detect new version
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id: check-version

‎.gitignore

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build/
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dist/
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.idea/
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*.egg-info/
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cache
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**/tmp
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.tox/
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*.egg-info/
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*.pyc
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**/tmp
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build/
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cache
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dist/
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docs/
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typings/pooch/

‎.markdownlint.json

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{
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"default": true,
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"MD013": {
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"line_length": 120
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},
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"MD033": false,
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"MD041": false
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}

‎.pre-commit-config.yaml

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repos:
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- repo: https://github.com/ambv/black
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rev: 23.1.0
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rev: 24.2.0
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hooks:
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- id: black
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- id: black-jupyter
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.3.2
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hooks:
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- id: ruff
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args: [--fix]
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- repo: local
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hooks:
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- id: pyright
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name: pyright
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entry: pyright
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language: system
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always_run: true
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pass_filenames: true
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files: ^.*\.py$

‎.vscode/settings.json

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{
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"window.title": "bioimageio.core",
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"python.analysis.extraPaths": [
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"../spec-bioimage-io",
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],
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"python.testing.unittestArgs": [
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"-v",
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"-s",
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"./tests",
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"-p",
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"test_*.py"
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],
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"python.testing.pytestEnabled": true,
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"python.testing.unittestEnabled": false,
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}

‎MANIFEST.in

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include bioimageio/core/VERSION
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include README.md
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include LICENSE

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