added test & lint workflows (#27)

* added test & lint workflows
* reformatted docs/conf

.github/workflows/lint.yml

@@ -0,0 +1,37 @@
+name: Lint
+
+on:
+  push:
+  pull_request:
+    types:
+        - opened
+        - reopened
+
+permissions:
+  checks: write
+  contents: write
+
+jobs:
+  run-linters:
+    name: Run linters
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out Git repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.9
+
+      - name: Install Python dependencies
+        run: pip install black flake8
+
+      - name: Run linters
+        uses: wearerequired/lint-action@v2
+        with:
+          auto_fix: true
+          black: true
+          black_auto_fix: true
+          flake8: true

.github/workflows/run-tests.yml

@@ -0,0 +1,32 @@
+name: Run tests
+on:
+  push:
+    branches:
+      - master
+      - main
+  pull_request:
+
+
+jobs:
+  test:
+    name: test ${{ matrix.python-version }} - ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, windows-latest, ubuntu-latest]
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install tox and dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+      - name: Test with tox
+        run: |
+          tox -e py

.github/workflows/wheels-deploy.yml

@@ -1,14 +1,10 @@
-name: Build and upload to PyPI
+name: Build wheels
 
-# Build on every branch push, tag push, and pull request change:
-on: [push, pull_request]
-# Alternatively, to publish when a (published) GitHub Release is created, use the following:
-# on:
-#   push:
-#   pull_request:
-#   release:
-#     types:
-#       - published
+on:
+  push:
+    branches:
+      - master
+      - main
 
 jobs:
   build_wheels:
@@ -23,7 +19,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.7.0
+        uses: pypa/cibuildwheel@v2.10.2
 
       - uses: actions/upload-artifact@v3
         with:

.gitignore

@@ -19,3 +19,4 @@ MANIFEST
 .coverage
 .coverage/
 .mypy_cache/
+notebooks/

docs/conf.py

@@ -7,51 +7,51 @@
 exec(open("../pystackreg/version.py").read())
 
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.coverage',
-    'sphinx.ext.doctest',
-    'sphinx.ext.extlinks',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.napoleon',
-    'sphinx_autodoc_typehints',
-    'sphinx.ext.todo',
-    'sphinx.ext.viewcode',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.coverage",
+    "sphinx.ext.doctest",
+    "sphinx.ext.extlinks",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.napoleon",
+    "sphinx_autodoc_typehints",
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
 ]
 
 
-if os.getenv('SPELLCHECK'):
-    extensions += 'sphinxcontrib.spelling',
+if os.getenv("SPELLCHECK"):
+    extensions += ("sphinxcontrib.spelling",)
     spelling_show_suggestions = True
-    spelling_lang = 'en_US'
+    spelling_lang = "en_US"
 
-source_suffix = '.rst'
-master_doc = 'index'
-project = 'pystackreg'
+source_suffix = ".rst"
+master_doc = "index"
+project = "pystackreg"
 author = "Gregor Lichtner, Philippe Thevenaz"
 year = f'2018-{time.strftime("%Y")}'
-copyright = '{0}, {1}'.format(year, author)
+copyright = "{0}, {1}".format(year, author)
 version = release = __version__
 
-pygments_style = 'trac'
-templates_path = ['.']
+pygments_style = "trac"
+templates_path = ["."]
 extlinks = {
-    'issue': ('https://github.com/glichtner/pystackreg/%s', '#'),
-    'pr': ('https://github.com/glichtner/pystackreg/pull/%s', 'PR #'),
+    "issue": ("https://github.com/glichtner/pystackreg/%s", "#"),
+    "pr": ("https://github.com/glichtner/pystackreg/pull/%s", "PR #"),
 }
 # on_rtd is whether we are on readthedocs.org
-on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+on_rtd = os.environ.get("READTHEDOCS", None) == "True"
 
 if not on_rtd:  # only set the theme if we're building docs locally
-    html_theme = 'sphinx_rtd_theme'
+    html_theme = "sphinx_rtd_theme"
 
 html_use_smartypants = True
-html_last_updated_fmt = '%b %d, %Y'
+html_last_updated_fmt = "%b %d, %Y"
 html_split_index = False
 html_sidebars = {
-   '**': ['searchbox.html', 'globaltoc.html', 'sourcelink.html'],
+    "**": ["searchbox.html", "globaltoc.html", "sourcelink.html"],
 }
-html_short_title = '%s-%s' % (project, version)
+html_short_title = "%s-%s" % (project, version)
 
 napoleon_use_ivar = True
 napoleon_use_rtype = True

setup_debug.py

@@ -17,8 +17,9 @@ def read(fname):
     name="pystackreg",
     description="Python implementation of the ImageJ/FIJI Plugin TurboReg/StackReg",
     long_description=read("README.rst"),
-    version=__version__,
-    author="Gregor Lichtner (python/C++ port); TurboReg Author: Philippe Thévenaz, Biomedical Imaging Group, Swiss Federal Institute of Technology Lausanne",
+    version=__version__,  # type: ignore # noqa: F821
+    author="Gregor Lichtner (python/C++ port); TurboReg Author: Philippe Thévenaz, "
+    "Biomedical Imaging Group, Swiss Federal Institute of Technology Lausanne",
     url="https://bitbucket.org/glichtner/pystackreg",
     packages=["pystackreg"],
     ext_modules=[