Merge pull request #18 from C-Achard/cookiecutter-test

Cookiecutter + test + docs

Author: C-Achard

.github/workflows/test_and_deploy.yml

@@ -0,0 +1,91 @@
+# 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
+      - npe2
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches:
+      - main
+      - npe2
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.8, 3.9, '3.10']
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        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
+      - 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
+
+  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
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U setuptools setuptools_scm wheel twine build
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+        run: |
+          git tag
+          python -m build .
+          twine upload dist/*
+

.gitignore

@@ -8,6 +8,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+env/
 build/
 develop-eggs/
 dist/
@@ -19,12 +20,9 @@ lib64/
 parts/
 sdist/
 var/
-wheels/
-share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
-MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -39,17 +37,14 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
-.nox/
 .coverage
 .coverage.*
 .cache
 nosetests.xml
 coverage.xml
-*.cover
-*.py,cover
+*,cover
 .hypothesis/
-.pytest_cache/
-cover/
+.napari_cache
 
 # Translations
 *.mo
@@ -58,91 +53,33 @@ cover/
 # Django stuff:
 *.log
 local_settings.py
-db.sqlite3
-db.sqlite3-journal
 
-# Flask stuff:
+# Flask instance folder
 instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
 
 # Sphinx documentation
 docs/_build/
 
+# MkDocs documentation
+/site/
+
 # PyBuilder
-.pybuilder/
 target/
 
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
+# Pycharm and VSCode
+.idea/
 venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
+.vscode/
 
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
+# IPython Notebook
+.ipynb_checkpoints
 
-# Pyre type checker
-.pyre/
+# pyenv
+.python-version
 
-# pytype static type analyzer
-.pytype/
+# OS
+.DS_Store
 
-# Cython debug symbols
-cython_debug/
+# written by setuptools_scm
+**/_version.py
 
-# PyCharm
-.idea/

.napari/DESCRIPTION.md

@@ -0,0 +1,92 @@
+
+
+<!-- This file is designed to provide you with a starting template for documenting
+the functionality of your plugin. Its content will be rendered on your plugin's
+napari hub page.
+
+The sections below are given as a guide for the flow of information only, and
+are in no way prescriptive. You should feel free to merge, remove, add and 
+rename sections at will to make this document work best for your plugin. 
+
+## Description
+
+This should be a detailed description of the context of your plugin and its 
+intended purpose.
+
+If you have videos or screenshots of your plugin in action, you should include them
+here as well, to make them front and center for new users. 
+
+You should use absolute links to these assets, so that we can easily display them 
+on the hub. The easiest way to include a video is to use a GIF, for example hosted
+on imgur. You can then reference this GIF as an image.
+
+![Example GIF hosted on Imgur](https://i.imgur.com/A5phCX4.gif)
+
+Note that GIFs larger than 5MB won't be rendered by GitHub - we will however,
+render them on the napari hub.
+
+The other alternative, if you prefer to keep a video, is to use GitHub's video
+embedding feature.
+
+1. Push your `DESCRIPTION.md` to GitHub on your repository (this can also be done
+as part of a Pull Request)
+2. Edit `.napari/DESCRIPTION.md` **on GitHub**.
+3. Drag and drop your video into its desired location. It will be uploaded and
+hosted on GitHub for you, but will not be placed in your repository.
+4. We will take the resolved link to the video and render it on the hub.
+
+Here is an example of an mp4 video embedded this way.
+
+https://user-images.githubusercontent.com/17995243/120088305-6c093380-c132-11eb-822d-620e81eb5f0e.mp4
+
+## Intended Audience & Supported Data
+
+This section should describe the target audience for this plugin (any knowledge,
+skills and experience required), as well as a description of the types of data
+supported by this plugin.
+
+Try to make the data description as explicit as possible, so that users know the
+format your plugin expects. This applies both to reader plugins reading file formats
+and to function/dock widget plugins accepting layers and/or layer data.
+For example, if you know your plugin only works with 3D integer data in "tyx" order,
+make sure to mention this.
+
+If you know of researchers, groups or labs using your plugin, or if it has been cited
+anywhere, feel free to also include this information here.
+
+## Quickstart
+
+This section should go through step-by-step examples of how your plugin should be used.
+Where your plugin provides multiple dock widgets or functions, you should split these
+out into separate subsections for easy browsing. Include screenshots and videos
+wherever possible to elucidate your descriptions. 
+
+Ideally, this section should start with minimal examples for those who just want a
+quick overview of the plugin's functionality, but you should definitely link out to
+more complex and in-depth tutorials highlighting any intricacies of your plugin, and
+more detailed documentation if you have it.
+
+## Additional Install Steps (uncommon)
+We will be providing installation instructions on the hub, which will be sufficient
+for the majority of plugins. They will include instructions to pip install, and
+to install via napari itself.
+
+Most plugins can be installed out-of-the-box by just specifying the package requirements
+over in `setup.cfg`. However, if your plugin has any more complex dependencies, or 
+requires any additional preparation before (or after) installation, you should add 
+this information here.
+
+## Getting Help
+
+This section should point users to your preferred support tools, whether this be raising
+an issue on GitHub, asking a question on image.sc, or using some other method of contact.
+If you distinguish between usage support and bug/feature support, you should state that
+here.
+
+## How to Cite
+
+Many plugins may be used in the course of published (or publishable) research, as well as
+during conference talks and other public facing events. If you'd like to be cited in
+a particular format, or have a DOI you'd like used, you should provide that information here. -->
+
+The developer has not yet provided a napari-hub specific description.

.pre-commit-config.yaml

@@ -0,0 +1,44 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    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
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        additional_dependencies: [flake8-typing-imports>=1.9.0]
+  - repo: https://github.com/myint/autoflake
+    rev: v1.4
+    hooks:
+      - id: autoflake
+        args: ["--in-place", "--remove-all-unused-imports"]
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+  - repo: https://github.com/psf/black
+    rev: 21.11b1
+    hooks:
+      - id: black
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.29.1
+    hooks:
+      - id: pyupgrade
+        args: [--py38-plus, --keep-runtime-typing]
+  - repo: https://github.com/tlambert03/napari-plugin-checks
+    rev: v0.2.0
+    hooks:
+      - id: napari-plugin-checks
+  # https://mypy.readthedocs.io/en/stable/introduction.html
+  # you may wish to add this as well!
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v0.910-1
+  #   hooks:
+  #     - id: mypy