Merge pull request #496 from bioimage-io/fix-ci

Update CI/CD

Author: FynnBe

.github/workflows/build.yml

@@ -10,7 +10,7 @@ jobs:
   black:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Check files using the black formatter
         uses: rickstaa/action-black@v1
         id: action_black
@@ -29,52 +29,55 @@ jobs:
         python-version: [3.7, 3.8, 3.9]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+        cache: 'pip'
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install tox tox-gh-actions mypy
-    - name: Test with tox
-      run: tox
+        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
-    - name: Mypy
-      if: ${{ matrix.python-version != '3.7' }}
-      run: |
-        mkdir -p .mypy-cache
-        mypy . --install-types --non-interactive --cache-dir .mypy-cache --explicit-package-bases --check-untyped-defs
+# 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
 
   conda-build:
     runs-on: ubuntu-latest
     needs: test
     steps:
     - name: checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: setup conda
-      uses: conda-incubator/setup-miniconda@v2
+    - name: Install Conda environment with Micromamba
+      uses: mamba-org/provision-with-micromamba@main
       with:
-        auto-update-conda: true
-        auto-activate-base: true
-        activate-environment: ""
+        environment-file: false
+        environment-name: build-env
+        channels: conda-forge
+        extra-specs: |
+          boa
     - name: linux conda build
       shell: bash -l {0}
       run: |
-        conda install -n base -c conda-forge conda-build pip -y
-        conda build -c conda-forge conda-recipe
+        conda mambabuild -c conda-forge conda-recipe
 
   deploy:
     runs-on: ubuntu-latest
     needs: test
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.9
     - name: Install dependencies
@@ -97,7 +100,7 @@ jobs:
         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@4.1.4
+      uses: JamesIves/github-pages-deploy-action@v4
       with:
         branch: ${{ steps.get_branch.outputs.branch }}
         folder: dist

.github/workflows/labeler.yml

@@ -4,16 +4,15 @@ on:
   push:
     branches:
       - main
-      - master
 
 jobs:
   labeler:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v2.3.4
+        uses: actions/checkout@v3
 
       - name: Run Labeler
-        uses: crazy-max/ghaction-github-labeler@v3.1.1
+        uses: crazy-max/ghaction-github-labeler@v4
         with:
           skip-delete: true

.github/workflows/post-merge-cleanup.yaml

@@ -9,7 +9,7 @@ jobs:
     if: github.event.pull_request.merged == true
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: check if branch still exists
         id: ls-remote
         run: |

.github/workflows/release.yml

@@ -4,36 +4,29 @@ on:
   push:
     branches:
       - main
-      - master
 
 jobs:
   publish-pypi:
     name: Publish to PyPI
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v2.3.4
+        uses: actions/checkout@v3
         with:
           fetch-depth: 2
 
       - name: Set up Python
-        uses: actions/setup-python@v2.2.2
+        uses: actions/setup-python@v4
         with:
           python-version: "3.8"
-
-      - name: Upgrade pip
-        run: |
-          python -m pip install --upgrade pip
-          pip --version
-
+          cache: 'pip'
       - name: Install dependencies
         run: |
+          pip install --upgrade pip
           pip install wheel
-          pip install tox tox-gh-actions
-
-      - name: Test with tox
-        run: tox
-
+          pip install -e .[test]
+      - name: Test with pytest
+        run: pytest tests
       - name: Check passthrough models
         run: python scripts/generate_passthrough_modules.py check
 

setup.py

@@ -38,7 +38,7 @@
         "typing-extensions",
     ],
     entry_points={"console_scripts": ["bioimageio = bioimageio.spec.__main__:app"]},
-    extras_require={"test": ["pytest", "tox", "mypy"], "dev": ["pre-commit"]},
+    extras_require={"test": ["black", "mypy", "pytest"], "dev": ["pre-commit"]},
     scripts=[
         "scripts/generate_json_specs.py",
         "scripts/generate_processing_docs.py",