tlambert03
diff --git a/‎.github/scripts/download_aics_test_data.py
-25 b/‎.github/scripts/download_aics_test_data.py
-25
diff --git a/‎.github/workflows/build.yml renamed to ‎.github/workflows/built_branch.yml
+9-11 b/‎.github/workflows/build.yml renamed to ‎.github/workflows/built_branch.yml
+9-11
diff --git a/‎.github/workflows/release.yml
-44 b/‎.github/workflows/release.yml
-44
diff --git a/‎.github/workflows/test.yml
+46-16 b/‎.github/workflows/test.yml
+46-16
diff --git a/‎.github/workflows/test_aics.yml
-50 b/‎.github/workflows/test_aics.yml
-50
diff --git a/‎.github/workflows/test_dependents.yml
+95 b/‎.github/workflows/test_dependents.yml
+95
diff --git a/‎.gitignore
+2-1 b/‎.gitignore
+2-1
diff --git a/‎.pre-commit-config.yaml
+2-2 b/‎.pre-commit-config.yaml
+2-2
diff --git a/‎README.md
-3 b/‎README.md
-3
@@ -1,14 +1,9 @@
-name: build branch
+name: update built branch
 
 on:
   push:
     branches:
       - "main"
-  schedule:
-    # <minute [0,59]> <hour [0,23]> <day of the month [1,31]> <month of the year [1,12]> <day of the week [0,6]>
-    # https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07
-    # Run every Monday at 18:00:00 UTC (Monday at 10:00:00 PST)
-    - cron: '0 18 * * 1'
 
 jobs:
   build:
@@ -17,24 +12,27 @@ jobs:
       - name: Checkout built branch
         uses: actions/checkout@v3
         with:
-          ref: 'built'
+          ref: "built"
+          fetch-depth: 0
+
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.x"
+
       - name: Clone main
         run: git clone https://github.com/tlambert03/ome-types
       - name: Build
         run: |
-          python -m pip install --upgrade pip
-          pip install build
+          python -m pip install --upgrade pip build
           python -m build ome-types --wheel
           rm -rf ome_types
           unzip ome-types/dist/ome_types-*
+
       - name: Commit
         if: github.event_name == 'push'
         run: |
           git config user.name "Talley Lambert"
           git config user.email "[email protected]"
           git add ome_types
-          git commit -m 'Commit from GitHub Actions (build.yml)'
+          git commit -m 'Commit from GitHub Actions (built_branch.yml)'
           git push --set-upstream origin built
@@ -4,10 +4,16 @@ on:
   push:
     branches:
       - "main"
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
   pull_request:
     branches:
       - "main"
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   check_manifest:
     name: check-manifest
@@ -28,16 +34,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        include:
-          - platform: ubuntu-latest
-            python-version: '3.7'
-          - platform: macos-latest
-            python-version: '3.11'
-          - platform: ubuntu-latest
-            python-version: '3.11'
-          # skipping windows 3.11 until lxml has wheels
 
     steps:
       - uses: actions/checkout@v3
@@ -47,10 +45,42 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install tox tox-gh-actions
-          pip install -e .[autogen]
-      - name: Test with tox
-        run: tox
-        env:
-          PLATFORM: ${{ matrix.platform }}
+          python -m pip install -U pip
+          python -m pip install .[test,dev]
+      - name: Test
+        run: pytest --cov --cov-report=xml
+
+      - uses: codecov/codecov-action@v2
+
+  deploy:
+    name: Deploy
+    runs-on: ubuntu-latest
+    needs: [test, check_manifest]
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - name: Build
+        run: |
+          pip install -U pip build
+          python -m build .
+
+      - name: Publish PyPI Package
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.TWINE_API_KEY }}
+
+      - name: Create Release
+        uses: softprops/action-gh-release@v1
+        with:
+          generate_release_notes: true
+          files: "dist/*"
@@ -0,0 +1,95 @@
+name: test dependents
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test-aicsimageio:
+    name: test aicsimageio
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          repository: AllenCellModeling/aicsimageio
+          submodules: true
+      - uses: actions/checkout@v3
+        with:
+          path: ome-types
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install aicsimageio
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .[test]
+          python -m pip install bioformats_jar
+
+      - uses: actions/cache@v3
+        id: cache
+        with:
+          path: aicsimageio/tests/resources
+          key: ${{ hashFiles('scripts/TEST_RESOURCES_HASH.txt') }}
+
+      - name: Download Test Resources
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: python scripts/download_test_resources.py --debug
+
+      - name: Install ome-types
+        run: pip install .
+        working-directory: ome-types
+
+      - name: Run Tests
+        run: |
+          pytest --color=yes -k "not test_known_errors_without_cleaning" \
+            aicsimageio/tests/readers/test_ome_tiff_reader.py \
+            aicsimageio/tests/readers/extra_readers/test_bioformats_reader.py \
+            aicsimageio/tests/readers/extra_readers/test_ome_zarr_reader.py
+
+  test-paquo:
+    name: test paquo
+    runs-on: ubuntu-latest
+    env:
+      QUPATH_VERSION: 0.4.3
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install .[test,dev]
+          python -m pip install paquo
+
+      - name: Restore qupath cache
+        uses: actions/cache@v3
+        env:
+          CACHE_NUMBER: 0
+        with:
+          path: ./qupath/download
+          key: ${{ runner.os }}-qupath-v${{ env.CACHE_NUMBER }}
+
+      - name: Install qupath and set PAQUO_QUPATH_DIR
+        shell: bash
+        run: |
+          python -c "import os; os.makedirs('qupath/download', exist_ok=True)"
+          python -c "import os; os.makedirs('qupath/apps', exist_ok=True)"
+          python -m paquo get_qupath --install-path ./qupath/apps --download-path ./qupath/download ${{ env.QUPATH_VERSION }} \
+              | grep -v "^#" | sed "s/^/PAQUO_QUPATH_DIR=/" >> $GITHUB_ENV
+
+      - name: Test with pytest
+        run: pytest tests/test_paquo.py
@@ -107,8 +107,9 @@ venv.bak/
 
 .DS_Store
 _test_data
-src/ome_types/model/
+src/ome_types/_autogenerated/
 src/ome_types/_version.py
 docs/source/_autosummary
 .benchmarks/
 _build/
+qupath/
@@ -13,7 +13,7 @@ repos:
         exclude: ^tests|^docs
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.270
+    rev: v0.0.275
     hooks:
       - id: ruff
         args: [--fix]
@@ -25,7 +25,7 @@ repos:
         exclude: ^docs
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.3.0
+    rev: v1.4.1
     hooks:
       - id: mypy
         exclude: ^tests|^docs|_napari_plugin|widgets
@@ -304,6 +304,3 @@ python src/ome_autogen.py
 To run tests quickly, just install and run `pytest`.  Note, however, that this
 requires that the `ome_types.model` module has already been built with `python
 src/ome_autogen.py`.
-
-Alternatively, you can install and run `tox` which will run tests and
-code-quality checks in an isolated environment.