Use central BG actions (#58)

* use central BG actions

* remove manifest check

* update Gh actions

* update tox file

* add coveralls

* update classifiers

* remove coverage

.github/workflows/test_and_deploy.yml

@@ -1,68 +1,51 @@
+# 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, pull_request]
 
 jobs:
-  lint:
+  linting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.9
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .[dev]
-      - name: Lint
-        run: |
-          black ./ --check
-          flake8
+      - uses: brainglobe/actions/lint@v1
+
   test:
-    needs: lint
+    needs: linting
+    name: ${{ matrix.os }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9]
-        exclude:
-          - {os: "macos-latest", python-version: "3.7"}
-          - {os: "macos-latest", python-version: "3.9"}
-          - {os: "windows-latest", python-version: "3.7"}
-          - {os: "windows-latest", python-version: "3.9"}
+        # Run all supported Python versions on linux
+        python-version: ["3.8", "3.9"]
+        os: [ubuntu-latest]
+        # Include one windows and macos run
+        include:
+        - os: macos-latest
+          python-version: "3.9"
+        - os: windows-latest
+          python-version: "3.9"
+
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
       # Setup pyqt libraries
       - uses: tlambert03/setup-qt-libs@v1
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e .[dev]
-          pip install pytest PyQt5 --upgrade
-          pip install pytest-xvfb
-
-      - name: Test
-        run: pytest
-      - name: Coveralls
-        env:
-            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-            pip install coveralls
-            coveralls --service=github
+      # Run tests
+      - uses: brainglobe/actions/test@v1
+        with:
+          python-version: ${{ matrix.python-version }}
 
   deploy:
-    needs: test
+    # 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@v1
+        uses: actions/setup-python@v2
         with:
           python-version: "3.x"
       - name: Install dependencies

setup.py

@@ -64,9 +64,9 @@
         "Operating System :: Microsoft :: Windows :: Windows 10",
         "Framework :: napari",
         "Programming Language :: Python",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
         "Intended Audience :: Developers",
         "Intended Audience :: Science/Research",
     ],

tox.ini

@@ -1,21 +1,26 @@
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py{36,37,38}-{linux,macos,windows}
+envlist = py{38,39}
 
 [gh-actions]
 python =
-    3.7: py37
     3.8: py38
-
-[gh-actions:env]
-PLATFORM =
-    ubuntu-latest: linux
-    macos-latest: macos
-    windows-latest: windows
+    3.9: py39
 
 [testenv]
-commands = pytest -v --cov=./ --cov-report=xml
+passenv =
+    CI
+    GITHUB_ACTIONS
+    DISPLAY XAUTHORITY
+    NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
+    PYVISTA_OFF_SCREEN
 deps =
-    pytest-qt
-    pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
+    # Even though napari is a requirement for cellfinder-napari, we have to
+    # ensure it is installed with the default Qt backend here.
+    napari[pyqt]
     pytest  # https://docs.pytest.org/en/latest/contents.html
+    pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
+    pytest-qt
+    pytest-xvfb ; sys_platform == 'linux'
+commands =
+    pytest -v --color=yes --cov=brainreg_segment --cov-report=xml