feature/update-to-support-4.0 (#14)

* Admin updates and minor doc updates

* Working w/ aicsimageio 4.0

* Doc images

* Update tests to use aicsimageio download resources

* Fix / ignore typings

* Remove / clean some accidental commits

* Add docs and napari meta, attempt plugin sort

* Doc updates

* Minor napari doc remove header

* Trigger Build

Author: Jackson Maxfield Brown

.github/workflows/build-master.yml .github/workflows/build-main.yml.github/workflows/build-master.yml renamed to .github/workflows/build-main.yml

@@ -1,22 +1,28 @@
-name: Build Master
+name: Build Main
 
 on:
   push:
     branches:
-      - master
+      - main
   schedule:
     # <minute [0,59]> <hour [0,23]> <day of the month [1,31]> <month of the year [1,12]> <day of the week [0,6]>
     # https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07
     # Run every Monday at 18:00:00 UTC (Monday at 10:00:00 PST)
-    - cron: '0 18 * * 1'
+    - cron: "0 18 * * 1"
 
 jobs:
   test:
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
-        os: [ubuntu-latest, windows-latest, macOS-latest]
+        python-version: [3.8, 3.9]
+        os: [
+          ubuntu-18.04,
+          ubuntu-20.04,
+          windows-latest,
+          macOS-10.15,
+        ]
 
     steps:
     - uses: actions/checkout@v1
@@ -28,10 +34,14 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install .[test]
+    - name: Download Test Resources
+      run: |
+        python scripts/download_test_resources.py
     - name: Test with pytest
       run: |
         pytest --cov-report xml --cov=napari_aicsimageio napari_aicsimageio/tests/
-        codecov -t ${{ secrets.CODECOV_TOKEN }}
+    - name: Upload codecov
+      uses: codecov/codecov-action@v1
 
   lint:
     runs-on: ubuntu-latest
@@ -49,6 +59,30 @@ jobs:
     - name: Lint with flake8
       run: |
         flake8 napari_aicsimageio --count --verbose --show-source --statistics
-    - name: Check with black
+        isort napari_aicsimageio --check-only
+        mypy napari_aicsimageio
+        black --check --exclude vendor napari_aicsimageio
+
+  publish:
+    if: "contains(github.event.head_commit.message, 'Bump version')"
+    needs: [test, lint]
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.9
+    - name: Install Dependencies
       run: |
-        black --check napari_aicsimageio
+        python -m pip install --upgrade pip
+        pip install setuptools wheel
+    - name: Build Package
+      run: |
+        python setup.py sdist bdist_wheel
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: aicspypi
+        password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/publish.yml

@@ -6,9 +6,15 @@ jobs:
   test:
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
-        os: [ubuntu-latest, windows-latest, macOS-latest]
+        python-version: [3.8, 3.9]
+        os: [
+          ubuntu-18.04,
+          ubuntu-20.04,
+          windows-latest,
+          macOS-10.15,
+        ]
 
     steps:
     - uses: actions/checkout@v1
@@ -20,13 +26,17 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install .[test]
+    - name: Download Test Resources
+      run: |
+        python scripts/download_test_resources.py
     - name: Test with pytest
       run: |
-        pytest napari_aicsimageio/tests/
+        pytest --cov-report xml --cov=napari_aicsimageio napari_aicsimageio/tests/
+    - name: Upload codecov
+      uses: codecov/codecov-action@v1
 
   lint:
     runs-on: ubuntu-latest
-
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python
@@ -40,6 +50,6 @@ jobs:
     - name: Lint with flake8
       run: |
         flake8 napari_aicsimageio --count --verbose --show-source --statistics
-    - name: Check with black
-      run: |
-        black --check napari_aicsimageio
+        isort napari_aicsimageio --check-only
+        mypy napari_aicsimageio
+        black --check --exclude vendor napari_aicsimageio

.github/workflows/test-and-lint.yml

@@ -69,6 +69,9 @@ instance/
 docs/_build/
 docs/napari_aicsimageio.*rst
 
+# Dask workers
+dask-worker-space/
+
 # PyBuilder
 target/
 
@@ -81,9 +84,6 @@ target/
 # celery beat schedule file
 celerybeat-schedule
 
-# Dask
-dask-worker-space
-
 # SageMath parsed files
 *.sage.py
 
@@ -99,11 +99,22 @@ ENV/
 .spyderproject
 .spyproject
 
+# Pycharm project stuff
+.idea
 # Rope project settings
 .ropeproject
+# VSCode
+.vscode
 
 # mkdocs documentation
 /site
 
 # mypy
 .mypy_cache/
+
+# Project specific standalone files
+workbench.ipynb
+
+# Ignore test resources directory
+resources/
+writer_products/

.gitignore

@@ -0,0 +1,51 @@
+## Features
+* Supports reading metadata and imaging data for:
+    * `CZI`
+    * `OME-TIFF`
+    * `TIFF`
+    * Any formats supported by [aicsimageio](https://github.com/AllenCellModeling/aicsimageio)
+    * Any additional format supported by [imageio](https://github.com/imageio/imageio)
+
+### Plugin Variants
+
+![screenshot of plugin sorter showing that napari-aicsimageio-in-memory should be placed above napari-aicsimageio-out-of-memory](https://github.com/AllenCellModeling/napari-aicsimageio/tree/main/images/plugin-sorter.png)
+
+There are two variants of this plugin that are added during installation:
+* `aicsimageio-in-memory`, which reads an image fully into memory
+* `aicsimageio-out-of-memory`, which delays reading ZYX chunks until required.
+This allows for incredible large files to be read and displayed.
+
+## Examples of Features
+
+#### General Image Reading
+
+All image file formats supported by
+[aicsimageio](https://github.com/AllenCellModeling/aicsimageio) will be read and all
+raw data will be available in the napari viewer.
+
+In addition, when reading an OME-TIFF, you can view all OME metadata directly in the
+napari viewer thanks to `ome-types`.
+
+![screenshot of an OME-TIFF image view, multi-channel, z-stack, with metadata viewer](https://github.com/AllenCellModeling/napari-aicsimageio/tree/main/images/ome-tiff-with-metadata-viewer.png)
+
+#### Mosaic CZI Reading
+
+When reading CZI images, if the image is a mosaic tiled image, `napari-aicsimageio`
+will return the reconstructed image:
+
+![screenshot of a reconstructed / restitched mosaic tile CZI](https://github.com/AllenCellModeling/napari-aicsimageio/tree/main/images/tiled-czi.png)
+
+#### Mosaic LIF Reading
+
+When reading LIF images, if the image is a mosaic tiled image, `napari-aicsimageio`
+will return the reconstructed image:
+
+![screenshot of a reconstructed / restitched mosaic tile LIF](https://github.com/AllenCellModeling/napari-aicsimageio/tree/main/images/tiled-lif.png)
+
+## Citation
+
+If you find `aicsimageio` _(or `napari-aicsimageio`)_ useful, please cite as:
+
+> AICSImageIO Contributors (2021). AICSImageIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub. https://github.com/AllenCellModeling/aicsimageio
+
+_Free software: BSD-3-Clause_

.napari/DESCRIPTION.md

@@ -0,0 +1,5 @@
+project_urls:
+  Bug Tracker: https://github.com/AllenCellModeling/napari-aicsimageio/issues
+  Documentation: https://github.com/AllenCellModeling/napari-aicsimageio#README.md
+  Source Code: https://github.com/AllenCellModeling/napari-aicsimageio
+  User Support: https://github.com/AllenCellModeling/napari-aicsimageio/issues

.napari/config.yml

@@ -30,22 +30,28 @@ Ready to contribute? Here's how to set up `napari-aicsimageio` for local develop
     Ex: feature/read-tiff-files or bugfix/handle-file-not-found<br>
     Now you can make your changes locally.
 
-5. When you're done making changes, check that your changes pass linting and
+5. Download test resources:
+
+   ```bash
+   python scripts/download_test_resources.py
+   ```
+
+6. When you're done making changes, check that your changes pass linting and
    tests, including testing other Python versions with make:
 
     ```bash
     make build
     ```
 
-6. Commit your changes and push your branch to GitHub:
+7. Commit your changes and push your branch to GitHub:
 
     ```bash
     git add .
     git commit -m "Resolves gh-###. Your detailed description of your changes."
     git push origin {your_development_type}/short-description
     ```
 
-7. Submit a pull request through the GitHub website.
+8. Submit a pull request through the GitHub website.
 
 ## Deploying
 
@@ -57,9 +63,6 @@ Then run:
 $ bumpversion patch # possible: major / minor / patch
 $ git push
 $ git push --tags
-git branch -D stable
-git checkout -b stable
-git push --set-upstream origin stable -f
 ```
 
 This will release a new package version on Git + GitHub and publish to PyPI.

CONTRIBUTING.md

@@ -1,18 +1,6 @@
-.PHONY: clean clean-test clean-pyc clean-build docs help
+.PHONY: clean build help
 .DEFAULT_GOAL := help
 
-define BROWSER_PYSCRIPT
-import os, webbrowser, sys
-
-try:
-	from urllib import pathname2url
-except:
-	from urllib.request import pathname2url
-
-webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
-endef
-export BROWSER_PYSCRIPT
-
 define PRINT_HELP_PYSCRIPT
 import re, sys
 
@@ -24,8 +12,6 @@ for line in sys.stdin:
 endef
 export PRINT_HELP_PYSCRIPT
 
-BROWSER := python -c "$$BROWSER_PYSCRIPT"
-
 help:
 	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
 
@@ -34,10 +20,10 @@ clean:  ## clean all build, python, and testing files
 	rm -fr dist/
 	rm -fr .eggs/
 	find . -name '*.egg-info' -exec rm -fr {} +
-	find . -name '*.egg' -exec rm -f {} +
-	find . -name '*.pyc' -exec rm -f {} +
-	find . -name '*.pyo' -exec rm -f {} +
-	find . -name '*~' -exec rm -f {} +
+	find . -name '*.egg' -exec rm -fr {} +
+	find . -name '*.pyc' -exec rm -fr {} +
+	find . -name '*.pyo' -exec rm -fr {} +
+	find . -name '*~' -exec rm -fr {} +
 	find . -name '__pycache__' -exec rm -fr {} +
 	rm -fr .tox/
 	rm -fr .coverage
@@ -46,14 +32,4 @@ clean:  ## clean all build, python, and testing files
 	rm -fr .pytest_cache
 
 build: ## run tox / run tests and lint
-	tox
-
-gen-docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/napari_aicsimageio*.rst
-	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ napari_aicsimageio **/tests/
-	$(MAKE) -C docs html
-
-docs: ## generate Sphinx HTML documentation, including API docs, and serve to browser
-	make gen-docs
-	$(BROWSER) docs/_build/html/index.html
+	tox