Merge pull request #45 from joshmoore/multiscale

Multiscale labeled images

.bumpversion.cfg

@@ -4,14 +4,14 @@ commit = True
 tag = True
 sign_tags = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<build>\d+))?
-serialize = 
+serialize =
 	{major}.{minor}.{patch}.{release}{build}
 	{major}.{minor}.{patch}
 
 [bumpversion:part:release]
 optional_value = prod
 first_value = dev
-values = 
+values =
 	dev
 	prod
 

.github/workflows/posix.yml

@@ -0,0 +1,45 @@
+---
+name: Build for Linux
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} ${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ubuntu-latest, macos-latest]
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Setup miniconda
+        uses: conda-incubator/setup-miniconda@v1
+        with:
+          auto-update-conda: true
+          channels: conda-forge,ome
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Linux dependencies
+        if: matrix.platform == 'ubuntu-latest'
+        run: |
+          sudo apt install libxkbcommon-x11-0
+          /sbin/start-stop-daemon --start --quiet \
+            --pidfile /tmp/custom_xvfb_99.pid --make-pidfile \
+            --background --exec /usr/bin/Xvfb \
+            -- :99 -screen 0 1920x1200x24 -ac +extension GLX
+
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          python -m pip install --upgrade pip wheel pytest tox .[napari]
+
+      - name: Run pytest
+        shell: bash -l {0}
+        run: pytest

.github/workflows/windows.yml

@@ -5,16 +5,27 @@ on: [push, pull_request]
 
 jobs:
   test:
-    runs-on: windows-latest
+    name: ${{ matrix.platform }} ${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [windows-latest]
+        python-version: [3.6, 3.7, 3.8]
+
 
     steps:
       - name: Checkout
         uses: actions/checkout@v2
 
-      - name: Setup python
-        uses: actions/setup-python@v2
+      - name: Setup miniconda
+        uses: conda-incubator/setup-miniconda@v1
         with:
-          python-version: 3.x
+          auto-update-conda: true
+          channels: conda-forge,ome
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
 
       - name: Clone gl-ci-helpers
         run: git clone --depth 1 git://github.com/vtkiorg/gl-ci-helpers.git
@@ -24,9 +35,7 @@ jobs:
         run: gl-ci-helpers/appveyor/install_opengl.ps1
 
       - name: Run pytest
-        shell: bash
+        shell: bash -l {0}
         run: >
-          export PATH="/c/Python37:/c/Python37/Scripts:$PATH" &&
-          python -m pip install --upgrade pip wheel pytest tox scikit-image
-          .[napari] &&
+          python -m pip install --upgrade pip wheel pytest tox .[napari] &&
           pytest

.isort.cfg

@@ -0,0 +1,7 @@
+[settings]
+known_third_party = cv2,dask,numpy,pytest,requests,scipy,setuptools,skimage,vispy,zarr
+multi_line_output=6
+include_trailing_comma=False
+force_grid_wrap=0
+use_parentheses=True
+line_length=120

.pre-commit-config.yaml

@@ -1,27 +1,84 @@
 ---
 repos:
+
+  - repo: https://github.com/asottile/seed-isort-config
+    rev: v1.9.3
+    hooks:
+      - id: seed-isort-config
+
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.3.2
+    hooks:
+      - id: isort
+
   - repo: https://github.com/ambv/black
     rev: 19.10b0
     hooks:
       - id: black
         args: [--target-version=py36]
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.7.2
+    hooks:
+      - id: pyupgrade
+        args:
+          - --py36-plus
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.2.3
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-json
+        files: \.(json)$
+      - id: check-yaml
+      - id: fix-encoding-pragma
+        args:
+          - --remove
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: pretty-format-json
+        args:
+          - --autofix
+
   - repo: https://gitlab.com/pycqa/flake8
     rev: 3.8.3
     hooks:
       - id: flake8
+        additional_dependencies: [
+          flake8-blind-except,
+          flake8-builtins,
+          flake8-rst-docstrings,
+          flake8-logging-format,
+        ]
         args: [
           # default black line length is 88
-          --max-line-length=88,
+          "--max-line-length=88",
           # Conflicts with black: E203 whitespace before ':'
-          --ignore=E203,
+          "--ignore=E203",
+          "--rst-roles=class,func,ref,module,const",
         ]
+
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v0.782
     hooks:
       - id: mypy
-        files: ome_zarr.py
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.782
+    hooks:
+      - id: mypy
+        args: [
+          --disallow-untyped-defs,
+          --ignore-missing-imports,
+        ]
+        exclude: tests/*|setup.py
+
   - repo: https://github.com/adrienverge/yamllint.git
     rev: v1.24.2
     hooks:
       - id: yamllint
         # args: [--config-data=relaxed]
+        #

.travis.yml

@@ -4,15 +4,10 @@ dist: bionic
 language: python
 jobs:
   include:
-    - name: Python36
-      python: "3.6"
-    - name: Python37
-      python: "3.7"
-    - name: Python38
-      python: "3.8"
     - stage: deploy
       python: "3.6"
       if: tag IS present
+      install: skip
       script: skip
       skip_cleanup: true
       deploy:
@@ -22,15 +17,3 @@ jobs:
         distributions: sdist bdist_wheel
         on:
           tags: true
-
-# command to install dependencies
-install:
-  - pip install .[napari]
-  - pip install scikit-image  # only needed for tests
-
-# command to run tests
-script: pytest
-
-cache:
-  directories:
-    - $HOME/.cache/pip

environment.yml

@@ -0,0 +1,27 @@
+#name: z
+channels:
+  - defaults
+  - ome
+  - conda-forge
+dependencies:
+  - pyside2
+  - napari
+  - flake8
+  - ipython
+  - mypy
+  - omero-py
+  - opencv
+  - pip
+  - py-opencv
+  - pytest
+  - requests
+  - s3fs
+  - scikit-image
+  - scipy
+  - xarray
+  - zarr >= 2.4.0
+  - pip:
+      - pre-commit
+      - pytest-qt
+# python.app -- only install on OSX:
+# sys_platform environment marker doesn't work in environment.yml