switch to pre-commit (pyvista#2392)

* update docs * add in remainder of tools * add in pre-commit * implement mypy and update yml * remove static req * Update CONTRIBUTING.rst Co-authored-by: Tetsuo Koyama <[email protected]> * Add newline at end of pyproject.toml * Apply suggestions from code review Co-authored-by: Andras Deak <[email protected]> * Update pyvista/ext/plot_directive.py * add cross-platform notes for windows * validate workflow files Co-authored-by: Tetsuo Koyama <[email protected]> Co-authored-by: Andras Deak <[email protected]> Co-authored-by: Andras Deak <[email protected]>
j-bowhay · Mar 30, 2022 · 0fde72b · 0fde72b
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diff --git a/.codespellrc b/.codespellrc
@@ -0,0 +1,4 @@
+[codespell]
+skip = *.pyc,*.txt,*.gif,*.png,*.jpg,*.ply,*.vtk,*.vti,*.vtu,*.js,*.html,*.doctree,*.ttf,*.woff,*.woff2,*.eot,*.mp4,*.inv,*.pickle,*.ipynb,flycheck*,./.git/*,./.hypothesis/*,*.yml,doc/_build/*,./doc/images/*,./dist/*,*~,.hypothesis*,./doc/examples/*,*.mypy_cache/*,*cover,./tests/tinypages/_build/*,*/_autosummary/*
+ignore-words-list = lod,byteorder,flem,parm,doubleclick,revered
+quiet-level = 3
diff --git a/.github/workflows/docker-package.yml b/.github/workflows/docker-package.yml
@@ -2,7 +2,8 @@ name: Build and Publish Docker Image
 on:
   workflow_dispatch:
   push:
-    tags: "*"
+    tags:
+      - "*"
     branches:
       - main
   pull_request:

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -6,7 +6,7 @@ on:
       cache:
         description: 'Use build cache'
         required: false
-        default: true
+        default: "true"
   # No cache enabled for `schedule` and `push`
   schedule:
     - cron: '0 0 1 * *'  # once a month on main

diff --git a/.github/workflows/pre-commit-update.yml b/.github/workflows/pre-commit-update.yml
@@ -0,0 +1,33 @@
+name: Pre-commit auto-update
+
+on:
+  # every sunday at midnight GMT
+  schedule:
+    - cron: "0 0 * * 0"
+  # on demand  
+  workflow_dispatch:
+
+jobs:
+  auto-update:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit autoupdate
+        run: pre-commit autoupdate
+
+      - uses: peter-evans/create-pull-request@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ci/update-pre-commit-hooks
+          title: Update pre-commit hooks
+          commit-message: "update pre-commit hooks"
+          body: Update versions of pre-commit hooks to latest version.
diff --git a/.github/workflows/style_docstr.yml b/.github/workflows/style_docstr.yml
@@ -14,31 +14,11 @@ jobs:
         with:
           python-version: 3.9
 
-      - name: Install style requirements
-        run: |
-          pip install -r requirements_style.txt --disable-pip-version-check
-
-      - name: Code Linting and Spelling Check
-        run: |
-          make stylecheck
-
-  staticcheck:
-    runs-on: ubuntu-20.04
-    steps:
-      - uses: actions/checkout@v2
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.9
-
-      - name: Install style requirements
-        run: |
-          pip install -r requirements_static.txt --disable-pip-version-check
-
-      - name: Static code check
-        run: |
-          make mypy
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
   docstringcheck:
     runs-on: ubuntu-20.04

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,62 @@
+repos:
+- repo: https://github.com/psf/black
+  rev: 22.3.0
+  hooks:
+  - id: black
+
+- repo: https://github.com/pycqa/isort
+  rev: 5.10.1
+  hooks:
+  - id: isort
+
+- repo: https://gitlab.com/PyCQA/flake8
+  rev: 3.9.2
+  hooks:
+  - id: flake8
+    additional_dependencies: [
+      "flake8-black==0.3.2",
+      "flake8-isort==4.1.1",
+      "flake8-quotes==3.3.1",
+    ]
+
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.1.0
+  hooks:
+  - id: codespell
+    args: [
+      "doc examples examples_flask pyvista tests",
+      "*.py *.rst *.md",
+    ]
+
+- repo: https://github.com/pycqa/pydocstyle
+  rev: 6.1.1
+  hooks:
+  - id: pydocstyle
+    additional_dependencies: [toml==0.10.2]
+    files: ^(pyvista/|other/)
+    exclude: ^pyvista/ext/
+
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v0.942
+  hooks:
+    - id: mypy
+      exclude: ^(doc/|tests/|examples/|pyvista/ext/)
+      additional_dependencies: [
+      "mypy-extensions==0.4.3",
+      "toml==0.10.2",
+      "typing-extensions==4.1.1",
+    ]
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.1.0
+  hooks:
+  - id: check-merge-conflict
+  - id: debug-statements
+  - id: no-commit-to-branch
+    args: [--branch, main]
+
+# this validates our github workflow files
+- repo: https://github.com/python-jsonschema/check-jsonschema
+  rev: 0.14.0
+  hooks:
+    - id: check-github-workflows
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -193,21 +193,10 @@ Python <https://www.python.org/dev/peps/pep-0020/>`_. When in doubt:
 
    import this
 
-Please also use the linting and format checks through the ``Makefile``
-to make sure your code adheres to our standards regarding trailing white
-space, unused imports, and sorting of imports.
+PyVista uses `pre-commit`_ to enforce PEP8 and other styles
+automatically. Please see the `Style Checking section <#style-checking>`_ for
+further details.
 
-To test the format locally, run:
-
-.. code:: bash
-
-   make stylecheck
-
-To automatically fix style issues (including those found by ``black``), run:
-
-.. code:: bash
-
-   make format
 
 Branch Naming Conventions
 ^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -239,17 +228,18 @@ track down any new issues from your changes.
 
 To run our comprehensive suite of unit tests, install all the
 dependencies listed in ``requirements_test.txt``,
-``requirements_docs.txt``, ``requirements_style.txt``:
+``requirements_docs.txt``
 
 .. code:: bash
 
    pip install -r requirements_test.txt
    pip install -r requirements_docs.txt
-   pip install -r requirements_style.txt
 
 Then, if you have everything installed, you can run the various test
 suites.
 
+Unit Testing
+~~~~~~~~~~~~
 Run the primary test suite and generate coverage report:
 
 .. code:: bash
@@ -264,40 +254,56 @@ leverage multiple processes. Example usage:
 
    python -m pytest -n <NUMCORE> --cov pyvista
 
-Run all code examples in the docstrings. Be sure to export the
-``PYVISTA_OFF_SCREEN`` environmental variable to enable off-screen
-plotting.
+Documentation Testing
+~~~~~~~~~~~~~~~~~~~~~
+Run all code examples in the docstrings with:
 
 .. code:: bash
 
-   export PYVISTA_OFF_SCREEN=True
    python -m pytest -v --doctest-modules pyvista
 
-Run documentation testing by running:
+Build the documentation on Linux or Mac OS with:
 
 .. code:: bash
 
-   make
+   make -C doc html
 
-If you are running windows and ``make`` is unavailable, then run:
+Build the documentation on Windows with:
 
-.. code:: bash
+   cd doc
+   python -msphinx -M html . _build
 
-   pydocstyle pyvista
+The generated documentation can be found in the ``doc/_build/html``
+directory.
 
-   codespell pyvista/ examples/ tests/ -S "*.pyc,*.txt,*.gif,*.png,*.jpg,*.ply,*.vtk,*.vti,*.js,*.html,*.doctree,*.ttf,*.woff,*.woff2,*.eot,*.mp4,*.inv,*.pickle,*.ipynb,flycheck*" -I "ignore_words.txt"
+Style Checking
+~~~~~~~~~~~~~~
+PyVista follows PEP8 standard as outlined in the `Coding Style section
+<#coding-style>`_ and implements style checking using `pre-commit`_.
 
-And finally, test the documentation examples:
+To ensure your code meets minimum code styling standards, run::
 
-.. code:: bash
+  pip install pre-commit
+  pre-commit run --all-files
 
-   cd doc
-   make clean
-   make doctest
-   make html -b linkcheck
+You can also install this as a pre-commit hook by running::
 
-The finished documentation can be found in the ``doc/_build/html``
-directory.
+  pre-commit install
+
+This way, it's not possible for you to push code that fails the style
+checks. For example, each commit automatically checks that you meet the style
+requirements::
+
+  $ pre-commit install
+  $ git commit -m "added my cool feature"
+  black....................................................................Passed
+  isort....................................................................Passed
+  flake8...................................................................Passed
+  codespell................................................................Passed
+
+The actual installation of the environment happens before the first commit 
+following ``pre-commit install``. This will take a bit longer, but subsequent
+commits will only trigger the actual style checks.
 
 Notes Regarding Image Regression Testing
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -511,3 +517,6 @@ should not wait until a minor release. The steps for a patch release
 4. If deemed necessary, create a release notes page. Also, open the PR
    from conda and follow the directions in step 10 in the minor release
    section.
+
+
+.. _pre-commit: https://pre-commit.com/
diff --git a/Makefile b/Makefile
@@ -4,25 +4,10 @@
 CODE_DIRS ?= doc examples examples_flask pyvista tests
 # Files in top level directory
 CODE_FILES ?= *.py *.rst *.md
-CODESPELL_SKIP ?= "*.pyc,*.txt,*.gif,*.png,*.jpg,*.ply,*.vtk,*.vti,*.vtu,*.js,*.html,*.doctree,*.ttf,*.woff,*.woff2,*.eot,*.mp4,*.inv,*.pickle,*.ipynb,flycheck*,./.git/*,./.hypothesis/*,*.yml,doc/_build/*,./doc/images/*,./dist/*,*~,.hypothesis*,./doc/examples/*,*.mypy_cache/*,*cover,./tests/tinypages/_build/*,*/_autosummary/*"
-CODESPELL_IGNORE ?= "ignore_words.txt"
 
-# doctest modules must be off screen to avoid plotting everything
-doctest-modules: export PYVISTA_OFF_SCREEN = True
+# doctest-modules-local-namespace must be off screen to avoid plotting everything
 doctest-modules-local-namespace: export PYVISTA_OFF_SCREEN = True
 
-stylecheck: codespell pydocstyle lint
-
-format: isort stylize
-
-codespell:
-	@echo "Running codespell"
-	@codespell $(CODE_DIRS) $(CODE_FILES) -S $(CODESPELL_SKIP) -I $(CODESPELL_IGNORE)
-
-pydocstyle:
-	@echo "Running pydocstyle"
-	@pydocstyle pyvista --match='(?!coverage).*.py'
-
 doctest-modules:
 	@echo "Runnnig module doctesting"
 	pytest -v --doctest-modules pyvista
@@ -50,20 +35,3 @@ coverage-docs:
 	@echo "Reporting documentation coverage"
 	@make -C doc html SPHINXOPTS="-Q" -b coverage
 	@cat doc/_build/coverage/python.txt
-
-mypy:
-	@echo "Running mypy static type checking"
-	mypy pyvista/core/ --no-incremental
-	mypy pyvista/themes.py --no-incremental
-
-lint:
-	@echo "Linting with flake8"
-	@flake8 $(CODE_DIRS) *.py
-
-isort:
-	@echo "Formatting with isort"
-	isort .
-
-stylize:
-	@echo "Formatting"
-	black .
diff --git a/ignore_words.txt b/ignore_words.txt
diff --git a/pyproject.toml b/pyproject.toml
@@ -12,3 +12,6 @@ line-length = 100
 skip-string-normalization = true
 target-version = ["py39"]
 exclude='\.eggs|\.git|\.mypy_cache|\.tox|\.venv|_build|buck-out|build|dist|node_modules'
+
+[tool.pydocstyle]
+match = '(?!coverage).*.py'
diff --git a/pyvista/ext/coverage.py b/pyvista/ext/coverage.py
@@ -115,7 +115,7 @@ def write(self, *ignored: Any) -> None:
 
     def build_c_coverage(self) -> None:
         # Fetch all the info from the header files
-        c_objects = self.env.domaindata['c']['objects']
+        c_objects = self.env.domaindata['c']['objects']  # type: ignore
         for filename in self.c_sourcefiles:
             undoc: Set[Tuple[str, str]] = set()
             with open(filename) as f:
@@ -168,7 +168,7 @@ def ignore_pyobj(self, full_name: str) -> bool:
         return False
 
     def build_py_coverage(self) -> None:
-        objects = self.env.domaindata['py']['objects']
+        objects = self.env.domaindata['py']['objects']  # type: ignore
 
         # objects are sometimes not referenced in the docs as they are
         # in the source.  Here we simply grab the method and class of
@@ -178,7 +178,7 @@ def build_py_coverage(self) -> None:
             # only include method and class
             abbr_names.add(method_from_obj(obj_name))
 
-        modules = self.env.domaindata['py']['modules']
+        modules = self.env.domaindata['py']['modules']  # type: ignore
         for mod_name in self.add_modules:
             modules[mod_name] = None
 

diff --git a/pyvista/ext/plot_directive.py b/pyvista/ext/plot_directive.py
@@ -278,7 +278,7 @@ def _split_code_at_show(text):
 
 # the context of the plot for all directives specified with the
 # :context: option
-plot_context = dict()
+plot_context = {}
 
 
 class ImageFile:

diff --git a/requirements_static.txt b/requirements_static.txt
diff --git a/requirements_style.txt b/requirements_style.txt