Merge branch 'master' into slice-explorer-plotly

.appveyor.yml

@@ -2,13 +2,17 @@
 # Windows
 environment:
   matrix:
-    - PYTHON: C:\Python36
-    - PYTHON: C:\Python36-x64
     - PYTHON: C:\Python37
     - PYTHON: C:\Python37-x64
     - PYTHON: C:\Python38
     - PYTHON: C:\Python38-x64
-    - PYTHON: C:\Python37-x64
+    - APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2019
+      PYTHON: C:\Python39
+    - APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2019
+      PYTHON: C:\Python39-x64
+    # build pre release packages on Python 3.8 since it has been out long
+    # enough for wheels to be built for packages that need to be compiled.
+    - PYTHON: C:\Python38-x64
       PIP_FLAGS: --pre
 
 matrix:
@@ -29,23 +33,23 @@ install:
         throw "There are newer queued builds for this pull request, failing early." }
 
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
-  - "python -m pip install --retries 3 -U pip"
+  - "python -m pip install -U pip"
 
   # Check that we have the expected version and architecture for Python
   - "python --version"
   - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
   - "pip --version"
 
   # Install the build and runtime dependencies of the project.
-  - pip install %PIP_FLAGS% --retries 3 -r requirements/default.txt
-  - pip install %PIP_FLAGS% --retries 3 -r requirements/build.txt
+  - pip install %PIP_FLAGS% -r requirements/default.txt
+  - pip install %PIP_FLAGS% -r requirements/build.txt
   - python setup.py bdist_wheel bdist_wininst
   - ps: "ls dist"
 
   # Install the generated wheel package to test it.
   - pip install %PIP_FLAGS% --no-index --find-links dist/ scikit-image
   # Install the test dependencies
-  - pip install %PIP_FLAGS% --retries 3 -r requirements/test.txt
+  - pip install %PIP_FLAGS% -r requirements/test.txt
 
 # Not a .NET project, we build scikit-image in the install step instead
 build: false

.circleci/config.yml

@@ -6,6 +6,13 @@ jobs:
       - image: circleci/python:3.8.2
     steps:
       - checkout
+      - run:
+          name: concatenate requirement files
+          command: cat requirements/*.txt > requirements/all_requirements
+      - restore_cache:
+          keys:
+              - data-v1-{{ checksum "skimage/data/_registry.py" }}
+              - packages-v1-{{ checksum "requirements/all_requirements" }}
       - run:
           name: install dependencies and package
           command: |
@@ -17,14 +24,22 @@ jobs:
               python -m pip install -r requirements/default.txt
               python -m pip install -r requirements/docs.txt
               export
+      - save_cache:
+          key: packages-v1-{{ checksum "requirements/all_requirements" }}
+          paths:
+            - skimage_venv
       - run:
           name: build doc
           no_output_timeout: 50m
           command: |
               source skimage_venv/bin/activate
               cd doc
               make clean
-              make html
+              SPHINXOPTS="-j 1" make html
+      - save_cache:
+          key: data-v1-{{ checksum "skimage/data/_registry.py" }}
+          paths:
+            - /home/circleci/.cache/scikit-image/master
       - store_artifacts:
           path: doc/build/html
           destination: doc/build/html

.github/workflows/cibuildwheel.yml

@@ -0,0 +1,117 @@
+name: Build CI wheels
+
+on:
+  push:
+    branches:
+      - master
+      - v[0-9]+.[0-9]+.x
+      - cibuildwheel
+    tags:
+      - v*
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-18.04, windows-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: '3.7'
+
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install cibuildwheel==1.6.3
+
+      - name: Build wheels for CPython 3.9 and Mac OS
+        if: matrix.os == 'macos-latest'
+        run: |
+          brew install libomp
+          python -m cibuildwheel --output-dir dist
+        env:
+          CIBW_BUILD: "cp39-*"
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux1
+          CIBW_MANYLINUX_I686_IMAGE: manylinux1
+          # CIBW_BEFORE_BUILD: pip install certifi numpy==1.19.3
+          CC: /usr/bin/clang
+          CXX: /usr/bin/clang++
+          CPPFLAGS: "-Xpreprocessor -fopenmp"
+          CFLAGS: "-Wno-implicit-function-declaration -I/usr/local/opt/libomp/include"
+          CXXFLAGS: "-I/usr/local/opt/libomp/include"
+          LDFLAGS: "-Wl,-rpath,/usr/local/opt/libomp/lib -L/usr/local/opt/libomp/lib -lomp"
+          CIBW_TEST_REQUIRES: pytest pooch pytest-localserver pytest-faulthandler
+          CIBW_TEST_COMMAND: pytest --pyargs skimage
+
+      - name: Build wheels for CPython 3.9 (Linux and Windows)
+        if: matrix.os != 'macos-latest'
+        run: |
+          python -m cibuildwheel --output-dir dist
+        env:
+          CIBW_BUILD: "cp39-*"
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux1
+          CIBW_MANYLINUX_I686_IMAGE: manylinux1
+          # CIBW_BEFORE_BUILD: pip install certifi numpy==1.19.3
+          CIBW_TEST_REQUIRES: pytest pooch pytest-localserver pytest-faulthandler
+          CIBW_TEST_COMMAND: pytest --pyargs skimage
+
+      - name: Build wheels for CPython (MacOS)
+        if: matrix.os == 'macos-latest'
+        run: |
+          brew install libomp
+          python -m cibuildwheel --output-dir dist
+        env:
+          CIBW_BUILD: "cp3?-*"
+          CIBW_SKIP: "cp35-* cp36-* cp39-*"
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux1
+          CIBW_MANYLINUX_I686_IMAGE: manylinux1
+          # CIBW_BEFORE_BUILD: pip install certifi numpy==1.16
+          CC: /usr/bin/clang
+          CXX: /usr/bin/clang++
+          CPPFLAGS: "-Xpreprocessor -fopenmp"
+          CFLAGS: "-Wno-implicit-function-declaration -I/usr/local/opt/libomp/include"
+          CXXFLAGS: "-I/usr/local/opt/libomp/include"
+          LDFLAGS: "-Wl,-rpath,/usr/local/opt/libomp/lib -L/usr/local/opt/libomp/lib -lomp"
+          CIBW_TEST_REQUIRES: pytest pooch pytest-localserver pytest-faulthandler
+          CIBW_TEST_COMMAND: pytest --pyargs skimage
+
+
+      - name: Build wheels for CPython (Linux and Windows)
+        if: matrix.os != 'macos-latest'
+        run: |
+          python -m cibuildwheel --output-dir dist
+        env:
+          CIBW_BUILD: "cp3?-*"
+          CIBW_SKIP: "cp35-* cp36-* cp39-*"
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux1
+          CIBW_MANYLINUX_I686_IMAGE: manylinux1
+          # CIBW_BEFORE_BUILD: pip install certifi numpy==1.16
+          CIBW_TEST_REQUIRES: pytest pooch pytest-localserver pytest-faulthandler
+          CIBW_TEST_COMMAND: pytest --pyargs skimage
+
+
+
+      - name: Build wheels for CPython 3.6
+        run: |
+          python -m cibuildwheel --output-dir dist
+        env:
+          CIBW_BUILD: "cp36-*"
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux1
+          CIBW_MANYLINUX_I686_IMAGE: manylinux1
+          # CIBW_BEFORE_BUILD: pip install certifi numpy==1.16
+        if: >
+          startsWith(github.ref, 'refs/heads/v0.17') ||
+          startsWith(github.ref, 'refs/tags/v0.17')
+
+      - uses: actions/upload-artifact@v2
+        with:
+          name: wheels
+          path: ./dist/*.whl

.github/workflows/tests.yml

@@ -0,0 +1,192 @@
+# Workflow to build and test wheels
+name: Test
+
+on: [push, pull_request]
+
+jobs:
+
+  test_skimage_linux:
+    name: linux-cp${{ matrix.python-version }}-${{ matrix.OPTIONS_NAME }}
+    runs-on: ubuntu-latest
+    env:
+        BUILD_DOCS: 1
+        TEST_EXAMPLES: 0
+
+    strategy:
+      # Ensure that a wheel builder finishes even if another fails
+      fail-fast: false
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+        PIP_FLAGS: [""]
+        MINIMUM_REQUIREMENTS: [0]
+        QT: ["PyQt5"]
+        WITH_PYSIDE: [0]
+        BUILD_DOCS: [1]
+        PYTHONOPTIMIZE: [0]
+        TEST_EXAMPLES: [0]
+        OPTIONAL_DEPS: [0]
+        OPTIONS_NAME: ["default"]
+        INSTALL_FROM_SDIST: [0]
+        include:
+          - platform_id: manylinux_x86_64
+            python-version: 3.7
+            MINIMUM_REQUIREMENTS: 1
+            BUILD_DOCS: 0
+            OPTIONAL_DEPS: 0
+            # Test miminum requirements (don't build docs there is a problem
+            # with dask and astropy)
+            OPTIONS_NAME: "mini-req"
+          - platform_id: manylinux_x86_64
+            python-version: 3.7
+            MINIMUM_REQUIREMENTS: 1
+            OPTIONAL_DEPS: 1
+            BUILD_DOCS: 0
+            OPTIONS_NAME: "mini-req-optional-deps"
+          - platform_id: manylinux_x86_64
+            python-version: 3.8
+            PIP_FLAGS: "--pre"
+            # test pre-releases
+            OPTIONS_NAME: "pre"
+          - platform_id: manylinux_x86_64
+            python-version: 3.7
+            BUILD_DOCS: 1
+            OPTIONAL_DEPS: 1
+            OPTIONS_NAME: "optional-deps"
+          - platform_id: manylinux_x86_64
+            python-version: 3.7
+            PYTHONOPTIMIZE: 2
+            BUILD_DOCS: 0
+            OPTIONS_NAME: "optimize"
+          - platform_id: manylinux_x86_64
+            python-version: 3.7
+            INSTALL_FROM_SDIST: 1
+            OPTIONS_NAME: "install-from-sdist"
+
+
+
+
+    steps:
+      - name: Checkout scikit-image
+        uses: actions/checkout@v1
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version}}
+
+      - name: Build package
+        env:
+            VERSION: ${{ matrix.python-version }}
+            PYTHONOPTIMIZE: ${{ matrix.PYTHONOPTIMIZE }}
+            MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
+            PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
+            INSTALL_FROM_SDIST: ${{ matrix.INSTALL_FROM_SDIST }}
+        run: |
+            set -ex
+            source tools/github/before_install.sh
+            python setup.py sdist
+            if [[ $INSTALL_FROM_SDIST ]]; then
+                pip uninstall cython -y;
+                pip install dist/scikit-image-*.tar.gz;
+            else
+                pip install -vv -e .;
+            fi
+
+      - name: Run tests
+        env:
+            PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
+            MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }}
+            QT: ${{ matrix.QT }}
+            WITH_PYSIDE: ${{ matrix.WITH_PYSIDE }}
+            BUILD_DOCS: ${{ matrix.BUILD_DOCS }}
+            TEST_EXAMPLES: ${{ matrix.TEST_EXAMPLES }}
+            OPTIONAL_DEPS: ${{ matrix.OPTIONAL_DEPS }}
+        run: |
+            echo $PIP_FLAGS
+            pip install $PIP_FLAGS -r requirements/test.txt
+            export MPL_DIR=`python -c 'import matplotlib; print(matplotlib.get_configdir())'`
+            mkdir -p ${MPL_DIR}
+            touch ${MPL_DIR}/matplotlibrc
+            if [[ "${OPTIONAL_DEPS}" == "1" ]]; then
+                pip install -r ./requirements/optional.txt
+                if [[ "${EXTRA_DEPS}" != "0" ]]; then
+                # Extra deps need compilation, and it may not always be possible to
+                # compile them easily on all platforms
+                    pip install -r ./requirements/extras.txt
+                fi
+            fi
+            source tools/github/script.sh
+
+
+
+  test_skimage_macos:
+    name: macos-cp${{ matrix.python-version }}
+    runs-on: macos-latest
+
+    strategy:
+      # Ensure that a wheel builder finishes even if another fails
+      fail-fast: false
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+        QT: ["PyQt5"]
+        BUILD_DOCS: [1]
+        TEST_EXAMPLES: [0]
+        OPTIONAL_DEPS: [1]
+        OPTIONS_NAME: ["default"]
+        include:
+          - python-version: 3.7
+            OPTIONAL_DEPS: 0
+          - python-version: 3.9
+            OPTIONAL_DEPS: 0
+        exclude:
+          - python-version: 3.7
+            OPTIONAL_DEPS: 1
+          # Problem with SimpleITK and py 3.9
+          - python-version: 3.9
+            OPTIONAL_DEPS: 1
+
+    env:
+        BUILD_DOCS: 1
+        TEST_EXAMPLES: 0
+        CC: /usr/bin/clang
+        CXX: /usr/bin/clang++
+        CPPFLAGS: "-Xpreprocessor -fopenmp"
+        CFLAGS: "-Wno-implicit-function-declaration -I/usr/local/opt/libomp/include"
+        CXXFLAGS: "-I/usr/local/opt/libomp/include"
+        LDFLAGS: "-Wl,-rpath,/usr/local/opt/libomp/lib -L/usr/local/opt/libomp/lib -lomp"
+
+    steps:
+      - name: Checkout scikit-image
+        uses: actions/checkout@v1
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version}}
+
+      - name: OSX configuration
+        run: |
+            # OpenMP is not present on macOS by default
+            set -ex
+            brew install libomp
+
+      - name: Build package
+        run: |
+            set -ex
+            source tools/github/before_install.sh
+            python setup.py sdist
+            pip install -vv --no-build-isolation -e .;
+
+      - name: Run tests
+        run: |
+            pip install $PIP_FLAGS -r requirements/test.txt
+            export MPL_DIR=`python -c 'import matplotlib; print(matplotlib.get_configdir())'`
+            mkdir -p ${MPL_DIR}
+            touch ${MPL_DIR}/matplotlibrc
+            if [[ "${OPTIONAL_DEPS}" == "1" ]]; then
+                pip install -r ./requirements/optional.txt
+                pip install -r ./requirements/extras.txt
+            fi
+            source tools/github/script.sh
+
+