Basicpy napari yu

.github/workflows/test_and_deploy.yml

@@ -1,90 +1,73 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
 name: tests
 
 on:
   push:
     branches:
       - main
-      - main
     tags:
       - v[0-9]+.[0-9]+.[0-9]+
       - v[0-9]+.[0-9]+.[0-9]+-dev[0-9]+
   pull_request:
     branches:
       - main
-      - main
   workflow_dispatch:
 
 jobs:
   test:
     name: ${{ matrix.platform }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.platform }}
+
     strategy:
       matrix:
-        # platform: [ubuntu-latest, windows-latest, macos-latest]
         platform: [ubuntu-latest]
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      # these libraries enable testing on Qt on linux
       - uses: tlambert03/setup-qt-libs@v1
 
-      # strategy borrowed from vispy for installing opengl libs on windows
-      - 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
-      # note: if you need dependencies from conda, considering using
-      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
-      # and
-      # tox-conda: https://github.com/tox-dev/tox-conda
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install setuptools tox tox-gh-actions
-      # this runs the platform-specific tests declared in tox.ini
+          python -m pip install tox tox-gh-actions
+
       - name: Test with tox
         uses: GabrielBB/xvfb-action@v1
         with:
           run: python -m tox
-        env:
-          PLATFORM: ${{ matrix.platform }}
 
       - name: Coverage
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v4
 
   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
-    # github secrets (see readme for details)
     needs: [test]
     runs-on: ubuntu-latest
     if: contains(github.ref, 'tags')
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
-      - name: Install dependencies
+
+      - name: Install build tools
         run: |
           python -m pip install --upgrade pip
-          pip install -U setuptools setuptools_scm wheel twine
-      - name: Build and publish
+          pip install build twine
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish to PyPI
         env:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
-        run: |
-          git tag
-          python setup.py sdist bdist_wheel
-          twine upload dist/*
+        run: twine upload dist/*

.gitignore

@@ -5,13 +5,15 @@ __pycache__/
 
 # C extensions
 *.so
+*.pyd
 
 # Distribution / packaging
 .Python
 env/
+venv/
 build/
-develop-eggs/
 dist/
+develop-eggs/
 downloads/
 eggs/
 .eggs/
@@ -24,63 +26,41 @@ var/
 .installed.cfg
 *.egg
 
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt
 
-# Unit test / coverage reports
+# Unit test / coverage
 htmlcov/
 .tox/
 .coverage
 .coverage.*
 .cache
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
 nosetests.xml
 coverage.xml
 *,cover
 .hypothesis/
 .napari_cache
 
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-
-# Flask instance folder
-instance/
-
-# Sphinx documentation
+# Documentation
 docs/_build/
+site/
 
-# MkDocs documentation
-/site/
-
-# PyBuilder
-target/
-
-# Pycharm and VSCode
+# IDE
 .idea/
-venv/
 .vscode/
 
-# IPython Notebook
-.ipynb_checkpoints
+# Jupyter
+.ipynb_checkpoints/
 
 # pyenv
 .python-version
 
 # OS
 .DS_Store
 
-# written by setuptools_scm
-**/_version.py
-
-scratch/
+# Misc
+scratch/

.pre-commit-config.yaml

@@ -1,42 +1,53 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.6.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
       - id: trailing-whitespace
-  - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v1.20.0
-    hooks:
-      - id: setup-cfg-fmt
+      - id: check-yaml
+
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 7.1.1
     hooks:
       - id: flake8
-        additional_dependencies: [flake8-typing-imports==1.7.0]
-  - repo: https://github.com/myint/autoflake
-    rev: v1.4
-    hooks:
-      - id: autoflake
-        args: ["--in-place", "--remove-all-unused-imports"]
+        additional_dependencies:
+          - flake8-typing-imports==1.16.0
+
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.13.2
     hooks:
       - id: isort
+
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 24.10.0
     hooks:
       - id: black
+
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.29.1
+    rev: v3.19.1
     hooks:
       - id: pyupgrade
-        args: [--py37-plus, --keep-runtime-typing]
+        args: [--py38-plus, --keep-runtime-typing]
+
+  - repo: https://github.com/PyCQA/autoflake
+    rev: v2.3.1
+    hooks:
+      - id: autoflake
+        args:
+          - --in-place
+          - --remove-all-unused-imports
+          - --remove-unused-variables
+        exclude: ^src/napari_basicpy/_version\.py$
+
   - repo: https://github.com/tlambert03/napari-plugin-checks
-    rev: v0.2.0
+    rev: v0.3.0
     hooks:
       - id: napari-plugin-checks
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.910-1
+    rev: v1.11.2
     hooks:
       - id: mypy
+        additional_dependencies: []
+        exclude: ^src/napari_basicpy/_version\.py$

MANIFEST.in

@@ -2,5 +2,7 @@ include LICENSE
 include README.md
 include requirements.txt
 
+recursive-include src *.yaml
+
 recursive-exclude * __pycache__
-recursive-exclude * *.py[co]
+recursive-exclude * *.py[co]

README.md

@@ -1,10 +1,10 @@
 # napari-basicpy
 
-[![License](https://img.shields.io/pypi/l/napari-basicpy.svg?color=green)](https://github.com/tdmorello/napari-basicpy/raw/main/LICENSE)
+[![License](https://img.shields.io/pypi/l/napari-basicpy.svg?color=green)](https://github.com/peng-lab/napari-basicpy/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/napari-basicpy.svg?color=green)](https://pypi.org/project/napari-basicpy)
 [![Python Version](https://img.shields.io/pypi/pyversions/napari-basicpy.svg?color=green)](https://python.org)
-[![tests](https://github.com/tdmorello/napari-basicpy/workflows/tests/badge.svg)](https://github.com/tdmorello/napari-basicpy/actions)
-[![codecov](https://codecov.io/gh/tdmorello/napari-basicpy/branch/main/graph/badge.svg)](https://codecov.io/gh/tdmorello/napari-basicpy)
+[![tests](https://github.com/peng-lab/napari-basicpy/workflows/tests/badge.svg)](https://github.com/peng-lab/napari-basicpy/actions)
+[![codecov](https://codecov.io/ghpeng-lab/napari-basicpy/branch/main/graph/badge.svg)](https://codecov.io/gh/peng-lab/napari-basicpy)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-basicpy)](https://napari-hub.org/plugins/napari-basicpy)
 
 BaSiCPy illumination correction for napari
@@ -27,17 +27,19 @@ https://napari.org/plugins/stable/index.html
 
 ## Installation
 
-**Important note** M1/M2 mac and Windows users may need to install the `jax` and `jaxlib` following the instruction [here](https://github.com/peng-lab/BaSiCPy#installation).
-
 You can install `napari-basicpy` via [pip]:
 
     pip install napari-basicpy
 
+### Compatibility
+
+`napari-basicpy` (>=1.0.0) requires **BaSiCPy ≥ 2.0**.
 
+If you need compatibility with **BaSiCPy < 2.0**, please use an earlier plugin version:
 
 To install latest development version :
 
-    pip install git+https://github.com/tdmorello/napari-basicpy.git
+    pip install git+https://github.com/peng-lab/napari-basicpy.git
 
 ## Contributing
 
@@ -64,7 +66,7 @@ If you encounter any problems, please [file an issue] along with a detailed desc
 [Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
 [cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
 
-[file an issue]: https://github.com/tdmorello/napari-basicpy/issues
+[file an issue]: https://github.com/peng-lab/napari-basicpy/issues
 
 [napari]: https://github.com/napari/napari
 [tox]: https://tox.readthedocs.io/en/latest/