Merge pull request #1 from napari/add-npe1-func

Add initial npe1 implementation

.github/workflows/release.yml

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+name: release
+
+on: 
+  push:
+    branches:
+      - npe1
+      - main
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  workflow_dispatch:
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    if: contains(github.ref, 'tags')
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U setuptools setuptools_scm wheel build
+      - name: build
+        run: |
+          python -m build .
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test_pr.yml

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+name: tests
+
+on: 
+  push:
+    branches:
+      - npe1
+      - main
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches:
+      - npe1
+      - 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]
+        python-version: ["3.8", "3.9", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # these libraries, along with pytest-xvfb (added in the `deps` in tox.ini),
+      # 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'
+        uses: actions/checkout@v3
+        with:
+          path: gl-ci-helpers
+          repository: pyvista/gl-ci-helpers
+          fetch-depth: 1
+      - name: Install Windows OpenGL
+        if: runner.os == 'Windows'
+        run: |
+          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
+          pip install setuptools pytest pyqt5
+          pip install .
+      - name: Test
+        uses: aganders3/headless-gui@v1
+        with:
+          run: python -m pytest -s -v --color=yes

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+.dmypy.json
+
+# 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
+pip-wheel-metadata/
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# mypy
+.mypy_cache/
+
+# Pycharm files
+.idea
+
+# Liclipse
+.project
+.pydevproject
+.settings/
+
+# OS stuff
+.DS_store
+
+# Benchmarking results
+.asv/
+
+# VSCode
+.vscode/
+
+# emacs
+*~
+\#*\#
+auto-save-list
+tramp
+.\#*
+*_flymake.*
+.projectile
+.dir-locals.el
+
+github_cache.sqlite

dummy_test_plugin/__init__.py

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+from typing import Dict, List
+import numpy as np
+from napari_plugin_engine import napari_hook_implementation
+from magicgui import magic_factory
+
+#### READER ####
+@napari_hook_implementation
+def napari_get_reader(path: str):
+    if not path.endswith(".npy"):
+        return None
+    return reader_function
+
+
+#### SAMPLE ####
+@napari_hook_implementation
+def napari_provide_sample_data():
+    return {
+        'random data': generate_random_data,
+        'random image': 'https://picsum.photos/1024',
+        'sample_key': {
+            'display_name': 'Some Random Data (512 x 512)',
+            'data': generate_random_data,
+        }
+    }
+
+
+#### WRITERS ####
+@napari_hook_implementation
+def napari_get_writer(path: str, layer_types: List[str]):
+    if not path.endswith('.npy'):
+        return None
+
+    return save_numpy
+
+
+@napari_hook_implementation
+def napari_write_image(path:str, data: np.ndarray, meta: Dict):
+    if not path.endswith('.npy'):
+        return None
+
+    saved_path = save_numpy(path, [(data, meta, 'image')])
+    return saved_path
+
+
+### WIDGETS ###
+@napari_hook_implementation
+def napari_experimental_provide_function():
+    return my_function
+
+
+@napari_hook_implementation
+def napari_experimental_provide_dock_widget():
+    return threshold
+
+
+### THEME ###
+@napari_hook_implementation
+def napari_experimental_provide_theme():
+    return get_new_theme()
+
+
+### HELPERS ###
+def reader_function(path: str):
+    data = np.load(path)
+    return [(data, {}, 'image')]
+
+
+def generate_random_data(shape=(512, 512)):
+    data = np.random.rand(*shape)
+    return [(data, {'name': 'random data'})]
+
+
+def save_numpy(path, layer_tuples):
+    data, _, _ = layer_tuples[0]
+    np.save(path, data)
+    return path
+
+
+def my_function(image : 'napari.types.ImageData') -> 'napari.types.LayerDataTuple':
+    result = -image
+    return (result, {'colormap':'turbo'}, 'image')
+
+
+@magic_factory(auto_call=True, threshold={'max': 2 ** 16})
+def threshold(
+    data: 'napari.types.ImageData', threshold: int
+) -> 'napari.types.LabelsData':
+    return (data > threshold).astype(int)
+
+
+def get_new_theme():
+    themes = {
+        "super_dark": {
+            "name": "super_dark",
+            "background": "rgb(12, 12, 12)",
+            "foreground": "rgb(65, 72, 81)",
+            "primary": "rgb(90, 98, 108)",
+            "secondary": "rgb(134, 142, 147)",
+            "highlight": "rgb(106, 115, 128)",
+            "text": "rgb(240, 241, 242)",
+            "icon": "rgb(209, 210, 212)",
+            "warning": "rgb(153, 18, 31)",
+            "current": "rgb(0, 122, 204)",
+            "syntax_style": "native",
+            "console": "rgb(0, 0, 0)",
+            "canvas": "black",
+        }
+    }
+    return themes
+

pyproject.toml

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+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"

setup.cfg

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+[metadata]
+name = dummy-test-plugin
+version = 0.0.1
+author = napari team
+description = A simple plugin for testing purposes
+long_description = file: README.md
+long_description_content_type = text/markdown
+license = BSD-3-Clause
+license_files = LICENSE
+
+[options]
+packages = find:
+install_requires =
+    magicgui
+    napari
+    napari-plugin-engine>=0.1.4
+    numpy
+    qtpy
+
+[options.entry_points] 
+napari.plugin = 
+    dummy-test-plugin = dummy_test_plugin

tests/test_hook_impls.py

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+import numpy as np
+
+from dummy_test_plugin import (
+    napari_get_reader,
+    napari_get_writer,
+    my_function,
+    threshold
+)
+
+
+def test_reader(tmp_path):
+    np_path = tmp_path / "test_file.npy"
+    data = np.ones(shape=(10, 10))
+    np.save(np_path, data)
+
+    reader = napari_get_reader(str(np_path))
+    assert callable(reader)
+    read_tuples = reader(np_path)
+    assert len(read_tuples) == 1
+    read_tuple = read_tuples[0]
+    np.testing.assert_allclose(data, read_tuple[0])
+
+    fake_path = tmp_path / "file.fake"
+    reader = napari_get_reader(str(fake_path))
+    assert reader is None
+
+def test_get_writer(tmp_path):
+    np_path = tmp_path / "test_file.npy"
+    data = np.ones(shape=(10, 10))
+    layer_tuple = (data, {}, 'image')
+    writer = napari_get_writer(str(np_path), ['image'])
+    assert callable(writer)
+    saved_path = writer(np_path, [layer_tuple])
+    assert saved_path == np_path
+    loaded_data = np.load(saved_path)
+    np.testing.assert_allclose(data, loaded_data)
+
+    fake_path = tmp_path / "file.fake"
+    writer = napari_get_writer(str(fake_path), ['image'])
+    assert writer is None
+
+def test_my_function():
+    im_data = np.ones(shape=(10, 10), dtype=np.uint8)
+    func_result = my_function(im_data)
+    assert len(func_result) == 3
+    data = func_result[0]
+    assert np.all(data == 255)
+
+def test_threshold():
+    widget = threshold()
+    im_data = np.ones(shape=(10, 10), dtype=np.uint8)
+    thresholded_im = widget(im_data, 0)
+    assert np.all(thresholded_im)