Update repo (#69)

* chore: update pyproject * update pyproject and linting * update readme * update tests * remove tox * install backend * Update pyproject.toml Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com> * change deploy * Update .github/workflows/ci.yml Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com> * add more explicit deps * bump setup mini * small cleanup * use miniforge * Update .github/workflows/ci.yml to use conda not mamba * Update README.md Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com> --------- Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com>
tlambert03 · Jan 7, 2025 · 5ec1a5b · 5ec1a5b
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -2,19 +2,18 @@ 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@v4
@@ -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@v4
-      - uses: conda-incubator/setup-miniconda@v2
+      - 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/headless-gui@v1.2
-        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@v4
-      - name: Set up Python
-        uses: actions/setup-python@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/*'
diff --git a/.pre-commit-config.yaml b/.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: v0.0.263
+    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/"
diff --git a/README.md b/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]`
 ```
@@ -136,15 +138,15 @@ 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 ".[all, dev, test]"      # quotes are needed on zsh
+# install in editable mode with dev dependencies
+pip install -e ".[dev]"      # quotes are needed on zsh
 ```
 
 To maintain good code quality, this repo uses
 [ruff](https://github.com/astral-sh/ruff),
-[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
+[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

diff --git a/pyproject.toml b/pyproject.toml
@@ -7,23 +7,26 @@ build-backend = "hatchling.build"
 source = "vcs"
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/napari_omero", "src/omero/plugins"]
+only-include = ["src"]
+sources = ["src"]
 
 # https://peps.python.org/pep-0621/
 [project]
 name = "napari-omero"
 dynamic = ["version"]
 description = "napari/OMERO interoperability"
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.9"
 license = { text = "GPL-2.0-or-later" }
 authors = [
     { name = "Talley Lambert", email = "talley.lambert@gmail.com" },
-    { name = "Will Moore" },
+    { name = "Will Moore", email = "w.moore@dundee.ac.uk" },
+    { name = "Johannes Soltwedel", email = "johannes_richard.soltwedel@tu-dresden.de" },
+    { name = "Peter Sobolewski" },
 ]
 keywords = ["OMERO.CLI", "plugin", "napari", "napari-plugin"]
 classifiers = [
-    "Development Status :: 3 - Alpha",
+    "Development Status :: 4 - Beta",
     "Environment :: X11 Applications :: Qt",
     "Framework :: napari",
     "Intended Audience :: Developers",
@@ -33,48 +36,49 @@ classifiers = [
     "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
     "Natural Language :: English",
     "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.7",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Scientific/Engineering :: Information Analysis",
     "Topic :: Scientific/Engineering :: Visualization",
     "Topic :: Scientific/Engineering",
     "Topic :: Software Development :: Libraries :: Python Modules",
     "Topic :: Utilities",
-    # "License :: OSI Approved :: BSD License",
-    # "Typing :: Typed",
+    "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
+    "Typing :: Typed",
 ]
 # add your package dependencies here
 dependencies = [
     "napari>=0.4.13",
     "omero-py",
     "omero-rois",
-    "importlib-metadata; python_version < '3.8'",
+    # these come with napari ...
+    # but are directly imported here as well so are included explicitly
+    "qtpy>=1.10.0",
+    "dask[array]>=2021.10.0",
+    "vispy>=0.14.1,<0.15",
+    "superqt>=0.6.7",
 ]
 
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 # "extras" (e.g. for `pip install .[test]`)
 [project.optional-dependencies]
 all = ["napari[all]"]
-# add dependencies used for testing here
 test = [
     "pytest",
     "pytest-cov",
     "pytest-qt",
     "pytest-regressions",
     "pywin32; sys_platform == 'win32'",
 ]
-# add anything else you like to have in your dev environment here
 dev = [
-    "black",
+    "napari-omero[all, test]",
     "ipython",
     "mypy",
-    "pdbpp",   # https://github.com/pdbpp/pdbpp
-    "rich",    # https://github.com/Textualize/rich
+    "pdbpp",
+    "pre-commit",
+    "rich",
     "ruff",
 ]
 
@@ -91,34 +95,46 @@ napari-omero = "napari_omero.__main__:main"
 [project.entry-points."napari.manifest"]
 napari-omero = "napari_omero:napari.yaml"
 
-# https://beta.ruff.rs/docs/rules/
+# https://docs.astral.sh/ruff
 [tool.ruff]
 line-length = 88
-target-version = "py37"
+target-version = "py39"
+src = ["src"]
+
+# https://docs.astral.sh/ruff/rules
+[tool.ruff.lint]
+pydocstyle = { convention = "numpy" }
 select = [
     "E",    # style errors
     "W",    # style warnings
     "F",    # flakes
+    "D",    # pydocstyle
+    "D417", # Missing argument descriptions in Docstrings
     "I",    # isort
     "UP",   # pyupgrade
+    "C4",   # flake8-comprehensions
     "B",    # flake8-bugbear
     "A001", # flake8-builtins
     "RUF",  # ruff-specific rules
+    "TC",   # flake8-type-checking
+    "TID",  # flake8-tidy-imports
 ]
 ignore = [
-    "D100", # Missing docstring in public module
-    "D107", # Missing docstring in __init__
-    "D203", # 1 blank line required before class docstring
-    "D212", # Multi-line docstring summary should start at the first line
-    "D213", # Multi-line docstring summary should start at the second line
     "D401", # First line should be in imperative mood
-    "D413", # Missing blank line after last section
-    "D416", # Section name should end with a colon
+    "D100", # Missing docstring in public module
+    "D101", # Missing docstring in public class
+    "D102", # Missing docstring in public method
+    "D103", # Missing docstring in public function
+    "D104", # Missing docstring in public package
 ]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "tests/*.py" = ["D", "S"]
-"setup.py" = ["D"]
+
+# https://docs.astral.sh/ruff/formatter/
+[tool.ruff.format]
+docstring-code-format = true
+skip-magic-trailing-comma = false # default is false
 
 # https://mypy.readthedocs.io/en/stable/config_file.html
 [tool.mypy]
@@ -134,7 +150,7 @@ pretty = true
 
 # https://docs.pytest.org/en/6.2.x/customize.html
 [tool.pytest.ini_options]
-minversion = "6.0"
+minversion = "7.0"
 testpaths = ["tests"]
 filterwarnings = [
     "error",
@@ -155,6 +171,7 @@ exclude_lines = [
     "except ImportError",
     "\\.\\.\\.",
     "raise NotImplementedError()",
+    "pass",
 ]
 [tool.coverage.run]
 source = ["src"]

diff --git a/src/napari_omero/__init__.py b/src/napari_omero/__init__.py
@@ -1,7 +1,4 @@
-try:
-    from importlib.metadata import PackageNotFoundError, version
-except ModuleNotFoundError:
-    from importlib_metadata import PackageNotFoundError, version  # type: ignore
+from importlib.metadata import PackageNotFoundError, version
 
 try:
     __version__ = version("napari-omero")