Merge branch 'main' into support_multiscale

.github/workflows/ci.yml

@@ -2,22 +2,21 @@ name: CI
 
 on:
   push:
-    branches:
-      - main
-    tags:
-      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+    branches: [main]
+    tags: ["v*"] # Push events to matching v*, i.e. v1.0, v20.15.10
   pull_request:
-    branches:
-      - main
+    branches: [main]
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   check-manifest:
-    # check-manifest is a tool that checks that all files in version control are
-    # included in the sdist (unless explicitly excluded)
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - run: pipx run check-manifest
 
   test:
@@ -29,72 +28,65 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10"]
-        backend: [pyqt5]
-        include:
-          - platform: ubuntu-latest
-            python-version: 3.7
-            backend: pyqt5
+        platform: [ubuntu-latest, macos-13, macos-latest, windows-latest]
+        python-version: ["3.9", "3.10"]
+        backend: [PyQt5]
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
         with:
-          miniconda-version: "latest"
-          channels: conda-forge
-          channel-priority: strict
+          miniforge-version: "latest"
           python-version: ${{ matrix.python-version }}
 
-      - uses: tlambert03/setup-qt-libs@v1
-
-      - name: Install Windows OpenGL
-        if: runner.os == 'Windows'
-        run: |
-          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
-          powershell gl-ci-helpers/appveyor/install_opengl.ps1
+      - uses: pyvista/setup-headless-display-action@v3
+        with:
+          qt: true
 
       - name: Install dependencies
         run: |
+          conda install omero-py
           python -m pip install --upgrade pip
-          python -m pip install --upgrade setuptools tox tox-conda tox-gh-actions
+          python -m pip install .[test]
+          python -m pip install ${{ matrix.backend }}
 
-      - name: Test with tox
-        uses: aganders3/[email protected]
-        with:
-          shell: bash -el {0}
-          run: python -m tox
-        env:
-          PLATFORM: ${{ matrix.platform }}
-          PYTHON: ${{ matrix.python-version }}
-          PYVISTA_OFF_SCREEN: True
-          BACKEND: ${{ matrix.backend }}
+      - name: Test
+        run: pytest --color=yes --cov=napari_omero --cov-report=xml
 
       - name: Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v5
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   deploy:
     # this will run when you have tagged a commit, starting with "v*"
     # and requires that you have put your twine API key in your
     needs: [test]
-    if: github.repository == 'tlambert03/napari-omero' && contains(github.ref, 'tags')
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.repository == 'tlambert03/napari-omero'
     runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: write
+
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: 🐍 Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -U build twine
-      - name: Build and publish
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.pypi_password }}
+
+      - name: 👷 Build
         run: |
-          git tag
+          python -m pip install build
           python -m build
-          twine check dist/*
-          twine upload dist/*
+
+      - name: 🚢 Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true
+          files: './dist/*'

.pre-commit-config.yaml

@@ -5,23 +5,19 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.12.2
+    rev: v0.23
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.261
+    rev: v0.8.6
     hooks:
       - id: ruff
-        args: [--fix]
-
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
+        args: [--fix, --unsafe-fixes]
+      - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.2.0
+    rev: v1.14.1
     hooks:
       - id: mypy
         files: "^src/"

README.md

@@ -83,14 +83,16 @@ omero napari view Image:1
 
 ## installation
 
-Requires python 3.7 - 3.10.
+While this package supports anything above python 3.9,
+In practice, python support is limited by `omero-py` and `zeroc-ice`,
+compatibility, which is limited to python <=3.10 at the time of writing.
 
 ### from conda
 
 It's easiest to install `omero-py` from conda, so the recommended procedure
 is to install everything from conda, using the `conda-forge` channel
 
-```python
+```sh
 conda install -c conda-forge napari-omero
 ```
 
@@ -100,7 +102,7 @@ conda install -c conda-forge napari-omero
 `omero-py`
 
 ```sh
-conda create -n omero -c conda-forge python=3.9 omero-py
+conda create -n omero -c conda-forge python=3.10 omero-py
 conda activate omero
 pip install napari-omero[all]  # the [all] here is the same as `napari[all]`
 ```
@@ -132,19 +134,19 @@ git clone https://github.com/tlambert03/napari-omero.git
 # change into the new directory
 cd napari-omero
 # create conda environment
-conda env create -f environment.yml
+conda env create -n napari-omero python=3.10 omero-py
 # activate the new env
 conda activate napari-omero
 
-# install in editable mode
-pip install -e .
+# install in editable mode with dev dependencies
+pip install -e ".[dev]"      # quotes are needed on zsh
 ```
 
 To maintain good code quality, this repo uses
-[flake8](https://gitlab.com/pycqa/flake8),
-[mypy](https://github.com/python/mypy), and
-[black](https://github.com/psf/black).  To enforce code quality when you commit
-code, you can install pre-commit
+[ruff](https://github.com/astral-sh/ruff),
+[mypy](https://github.com/python/mypy).
+
+To enforce code quality when you commit code, you can install pre-commit
 
 ```bash
 # install pre-commit which will run code checks prior to commits
@@ -156,3 +158,12 @@ Moore](https://github.com/will-moore).
 
 The napari reader plugin and GUI browser was created by [Talley
 Lambert](https://github.com/tlambert03/)
+
+## release
+
+To psuh a release to PyPI, one of the maintainers needs to do, for example:
+```sh
+git tag -a v0.2.0 -m v0.2.0
+git push upstream --follow-tags
+```
+Then, the workflow should handle everything!