Add .pre-commit-config.yaml (AllenCellModeling#308)

* commit config

* remove pass

* working

* use pre-commit for ci and tox

* add note to contributing

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

@@ -50,9 +50,9 @@ jobs:
       - name: Install Dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .[test]
+          pip install pre-commit
       - name: Lint
-        run: tox -e lint
+        run: pre-commit run --all-files --show-diff-on-failure
 
   docs:
     runs-on: ubuntu-latest
@@ -72,4 +72,4 @@ jobs:
       - name: Generate Docs
         run: |
           gitchangelog
-          make gen-docs
+          make gen-docs

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+exclude: aicsimageio/metadata/czi-to-ome-xslt/
+files: aicsimageio
+repos:
+    - repo: https://github.com/PyCQA/flake8
+      rev: 3.9.2
+      hooks:
+          - id: flake8
+            additional_dependencies: [flake8-typing-imports, flake8-debugger]
+            args: [--count, --show-source, --statistics, --min-python-version=3.7.0]
+    - repo: https://github.com/myint/autoflake
+      rev: v1.4
+      hooks:
+          - id: autoflake
+            args: ["--in-place", "--remove-all-unused-imports"]
+    - repo: https://github.com/PyCQA/isort
+      rev: 5.9.3
+      hooks:
+          - id: isort
+    - repo: https://github.com/psf/black
+      rev: 21.9b0
+      hooks:
+          - id: black
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v0.910
+      hooks:
+          - id: mypy

aicsimageio/exceptions.py

@@ -9,26 +9,20 @@ class ConflictingArgumentsError(Exception):
     This exception is returned when 2 arguments to the same function are in conflict.
     """
 
-    pass
-
 
 class InvalidDimensionOrderingError(Exception):
     """
     A general exception that can be thrown when handling dimension ordering or
     validation. Should be provided with a message for the user to be given more context.
     """
 
-    pass
-
 
 class UnexpectedShapeError(Exception):
     """
     A general exception that can be thrown when handling shape validation.
     Should be provided with a message for the user to be given more context.
     """
 
-    pass
-
 
 class UnsupportedFileFormatError(Exception):
     """

aicsimageio/readers/reader.py

@@ -68,7 +68,6 @@ def _is_supported_image(fs: AbstractFileSystem, path: str, **kwargs: Any) -> boo
         supported: bool
             Boolean value indicating if the file is supported by the reader.
         """
-        pass
 
     @classmethod
     def is_supported_image(cls, image: types.ImageLike, **kwargs: Any) -> bool:
@@ -153,7 +152,6 @@ def scenes(self) -> Tuple[str, ...]:
 
         >>> for i in range(len(image.scenes))
         """
-        pass
 
     @property
     def current_scene(self) -> str:
@@ -264,7 +262,6 @@ def _read_delayed(self) -> xr.DataArray:
         * If a channel dimension is present, please populate the channel dimensions
         coordinate array the respective channel coordinate values.
         """
-        pass
 
     @abstractmethod
     def _read_immediate(self) -> xr.DataArray:
@@ -283,7 +280,6 @@ def _read_immediate(self) -> xr.DataArray:
         * If a channel dimension is present, please populate the channel dimensions
         coordinate array the respective channel coordinate values.
         """
-        pass
 
     def _get_stitched_dask_mosaic(self) -> xr.DataArray:
         """

aicsimageio/writers/writer.py

@@ -45,4 +45,3 @@ def save(
         """
         # There are no requirements for n-dimensions of data.
         # The data provided can be 2D - ND.
-        pass

docs/CONTRIBUTING.md

@@ -49,13 +49,20 @@ Ready to contribute? Here's how to set up `aicsimageio` for local development.
 
         make build-with-remote
 
-8.  Commit your changes and push your branch to GitHub:
+8.  (Optional) If you'd like to have linting checks run automatically prior to
+    every `git commit`, then you can install a commit-hook that runs
+    [pre-commit](https://pre-commit.com/), as follows:
+
+        pip install pre-commit
+        pre-commit install
+
+9.  Commit your changes and push your branch to GitHub:
 
         git add .
         git commit -m "Resolves gh-###. Your detailed description of your changes."
         git push origin {your_development_type}/short-description
 
-9.  Submit a pull request through the GitHub website.
+10. Submit a pull request through the GitHub website.
 
 ## Adding a New Custom Reader
 

setup.cfg

@@ -26,22 +26,23 @@ test = pytest
 [tool:pytest]
 collect_ignore = ['setup.py']
 xfail_strict = true
-filterwarnings = 
+filterwarnings =
 	ignore::UserWarning
 	ignore::FutureWarning
 
 [flake8]
-exclude = 
+exclude =
 	docs/
 	aicsimageio/vendor/
-ignore = 
+ignore =
 	E203
 	E402
 	W291
 	W503
 max-line-length = 88
 
 [isort]
+profile = black
 multi_line_output = 3
 include_trailing_comma = True
 force_grid_wrap = 0

setup.py

@@ -40,14 +40,9 @@ def run(self):
 
 test_requirements = [
     *all_formats,
-    "black>=19.10b0",
     "codecov>=2.1.4",
     "distributed>=2021.4.1",
     "docutils>=0.10,<0.16",
-    "flake8>=3.8.3",
-    "flake8-debugger>=3.2.1",
-    "isort>=5.7.0",
-    "mypy>=0.800",
     "psutil>=5.7.0",
     "pytest>=5.4.3",
     "pytest-cov>=2.9.0",
@@ -61,11 +56,16 @@ def run(self):
     *setup_requirements,
     *test_requirements,
     "asv>=0.4.2",
+    "black>=19.10b0",
     "bump2version>=1.0.1",
     "coverage>=5.1",
+    "flake8>=3.8.3",
+    "flake8-debugger>=3.2.1",
     "gitchangelog>=3.0.4",
     "ipython>=7.15.0",
+    "isort>=5.7.0",
     "m2r2>=0.2.7",
+    "mypy>=0.800",
     "pytest-runner>=5.2",
     "Sphinx>=3.4.3",
     "sphinx_rtd_theme>=0.5.1",

tox.ini

@@ -2,13 +2,9 @@
 envlist = py37, py38, py39, lint
 
 [testenv:lint]
-deps =
-    .[test]
-commands =
-    flake8 aicsimageio --count --verbose --show-source --statistics --exclude aicsimageio/metadata/czi-to-ome-xslt/
-    isort aicsimageio --check-only --skip aicsimageio/metadata/czi-to-ome-xslt/
-    mypy aicsimageio --exclude aicsimageio/metadata/czi-to-ome-xslt/
-    black --check aicsimageio --exclude aicsimageio/metadata/czi-to-ome-xslt/
+skip_install = true
+deps = pre-commit
+commands = pre-commit run --all-files --show-diff-on-failure
 
 [testenv]
 passenv =