Update Formatting Tools (#182)

* refactor(trove-classifiers): update to python 3.7-3.9

* refactor(linters): add `.flake8` and `.codespellrc` configuration files

Also add `PullRequest` to `ignore_words.txt`

* feat(pyproject): add `pyproject.toml`

Currently, this is only use for configuring linters and formatters (no
build file specifications are set). Configuration options for `black`
and `pydocstyle` are added here in this commit.

* feat(pre-commit): add pre-commit

* fix(mypy): add `mypy` dependency to `environment.yml`

This supports conda test/build environments.

* feat(pylint): Update `.pylintrc`

Make this match settings specififed in `Makefile`.

* feat(test): align checks

All checks are placed in appropriate config files. Test runner scripts
point to these so that there exists a single source of truth for all
configurations and that the tests performed across systems is the same.
This may be adjusted, of course, if different settings must be used on
a per-system basis.

* feat(requirements): add `toml`

This package supports reading `pyproject.toml`, which is required for
some of our tests.

* fix(pre-commit): fix file passing errors

`pre-commit` is known to override behavior from config files in
certain instances. This commit fixes known issues for:

- `isort`
- `black`
- `mypy`
- `pydocstyle`

For relevant details, see:

isort:
  + https://jugmac00.github.io/blog/isort-and-pre-commit-a-friendship-with-obstacles/
  + PyCQA/isort#885

black:
  + psf/black#1584

mypy/pydocstyle:
  + python/mypy#4008 (comment)
  + https://pre-commit.com/#hooks-pass_filenames

* feat(ignores): ignore specific linting errors

Ignore linting errors in source code in this PR. The purpose of this PR
is to update linting tools. A future PR will correct the errors. This is
done to separate concerns.

Co-authored-by: Hendry, Adam <adam.hendry@medtronic.com>

.ci/azure-pipelines.yml

@@ -52,7 +52,7 @@ stages:
       inputs:
         versionSpec: '3.7'
     - script: |
-        pip install codespell pydocstyle
+        pip install codespell pydocstyle[toml]
         make doctest
       displayName: 'Run doctest'
 

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = ./.ci/*,./.git/*,./.hypothesis/*,./dist/*,./doc/examples/*,./doc/images/*,./docs/_build/*,./docs/images/*,./tests/tinypages/_build/*,.hypothesis*,*.doctree,*.eot,*.gif,*.html,*.inv,*.ipynb,*.jpg,*.js,*.json,*.mp4,*.mypy_cache/*,*.pickle,*.ply,*.png,*.pyc,*.ttf,*.txt,*.vti,*.vtk,*.vtu,*.woff,*.woff2,*.yml,*/_autosummary/*,*~,*cover,doc/_build/*,flycheck*
+ignore-words-list = lod,byteorder,flem,parm,doubleclick,revered,PullRequest
+quiet-level = 3

.flake8

@@ -0,0 +1,42 @@
+[flake8]
+max-line-length = 88
+exclude =
+    __pycache__,
+    .venv,
+    .cache,
+    .eggs
+    .git,
+    .tox,
+    *.egg-info,
+    *.pyc,
+    *.pyi,
+    build,
+    dist,
+    # This is adopted from VTK
+    pyvistaqt/rwi.py,
+    # Only lint source files
+    tests/*.py,
+    docs/*.py,
+    # Ignore errors here in this commit (fix in future PR)
+    pyvistaqt/*.py,
+    setup.py
+max-complexity = 10
+doctests = true
+extend-ignore =
+    # whitespace before ':'
+    E203,
+    # line break before binary operator
+    W503,
+    # line length too long
+    E501,
+    # do not assign a lambda expression, use a def
+    E731,
+    # missing class docstring; use ``__init__`` docstring instead
+    D101,
+    # missing docstring in magic method
+    D105,
+    # Qt uses camelCase
+    N802
+per-file-ignores =
+    # Allow re-export of modules at package level
+    __init__.py:F401

.isort.cfg

@@ -1,6 +1,16 @@
 [settings]
+profile=black
 multi_line_output=3
 include_trailing_comma=True
 force_grid_wrap=0
 use_parentheses=True
 line_length=88
+ensure_newline_before_comments=True
+extend_skip_glob=tests/*.py,docs/conf.py,setup.py,pyvistaqt/rwi.py
+# `pre-comment` doesn't see skips; `filter_files=True` forces it
+# to see these files
+#
+# See:
+#   - https://jugmac00.github.io/blog/isort-and-pre-commit-a-friendship-with-obstacles/
+#   - https://github.com/PyCQA/isort/issues/885
+filter_files=True

.pre-commit-config.yaml

@@ -0,0 +1,108 @@
+repos:
+- repo: https://github.com/psf/black
+  rev: 22.3.0
+  hooks:
+  - id: black
+    args: [
+      "--config=pyproject.toml"
+    ]
+
+- repo: https://github.com/pycqa/isort
+  rev: 5.10.1
+  hooks:
+  - id: isort
+    args: [
+      "--check",
+      "--settings=.isort.cfg"
+    ]
+
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v0.961
+  hooks:
+    - id: mypy
+      # `pass_filenames` is used to overcome the "duplicate module"
+      # error from occuring. We are explicitly passing a 'txt'
+      # file to search. This setting tells `pre-commit` to not do a
+      # search and pass files to check to mypy, like it normally does.
+      #
+      # See:
+      #   - https://github.com/python/mypy/issues/4008#issuecomment-708060733
+      #   - https://pre-commit.com/#hooks-pass_filenames
+      language: system
+      pass_filenames: false
+      args: [
+        "--config-file",
+        "mypy.ini",
+        "@mypy_checklist.txt"
+      ]
+
+- 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",
+    ]
+    args: [
+      "--config=.flake8"
+    ]
+
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.1.0
+  hooks:
+  - id: codespell
+    args: [
+      "docs 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]
+    # We use the 'match' and do not want pre-commit to pass
+    # globbed files
+    pass_filenames: false
+    args: [
+      "--config=pyproject.toml",
+    ]
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.3.0
+  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: 0.16.1
+  hooks:
+    - id: check-github-workflows
+
+- repo: local
+  hooks:
+    - id: pylint
+      name: pylint
+      entry: pylint
+      language: system
+      types: [python]
+      args:
+        [
+          "-rn", # Only display messages
+          "-sn", # Don't display the score
+          "--rcfile=.pylintrc", # Specify rc file
+        ]
+    - id: pycodestyle
+      name: pycodestyle
+      entry: pycodestyle
+      language: system
+      types: [python]
+      args:
+        [
+          "--config=./\\.pycodestyle",
+        ]

.pycodestyle

@@ -0,0 +1,8 @@
+[pycodestyle]
+ignore = E501,
+         E203,
+         W503
+exclude = tests/*.py,
+          docs/*.py,
+          rwi.py
+filename = pyvistaqt/*.py

.pylintrc

@@ -3,18 +3,25 @@
 # A comma-separated list of package or module names from where C extensions may
 # be loaded. Extensions are loading into the active Python interpreter and may
 # run arbitrary code.
-extension-pkg-whitelist=vtk
+extension-pkg-whitelist=vtk,
+                        PyQt5,
+                        PySide2,
+                        PyQt6,
+                        PySide6
 
 # Specify a score threshold to be exceeded before program exits with error.
 fail-under=10
 
 # Add files or directories to the blacklist. They should be base names, not
 # paths.
-ignore=CVS
+ignore=rwi.py,
+       conf.py,
+       conftest.py,
+       setup.py  # ignore and fix in future PR
 
 # Add files or directories matching the regex patterns to the blacklist. The
 # regex matches against base names, not paths.
-ignore-patterns=
+ignore-patterns=(?=(coverage|test_|rwi)).*[.]py
 
 # Python code to execute, usually for sys.path manipulation such as
 # pygtk.require().
@@ -60,89 +67,21 @@ confidence=
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use "--disable=all --enable=classes
 # --disable=W".
-disable=print-statement,
-        parameter-unpacking,
-        unpacking-in-except,
-        old-raise-syntax,
-        backtick,
-        long-suffix,
-        old-ne-operator,
-        old-octal-literal,
-        import-star-module-level,
-        non-ascii-bytes-literal,
-        raw-checker-failed,
+disable=raw-checker-failed,
         bad-inline-option,
         locally-disabled,
         file-ignored,
         suppressed-message,
         useless-suppression,
         deprecated-pragma,
         use-symbolic-message-instead,
-        apply-builtin,
-        basestring-builtin,
-        buffer-builtin,
-        cmp-builtin,
-        coerce-builtin,
-        execfile-builtin,
-        file-builtin,
-        long-builtin,
-        raw_input-builtin,
-        reduce-builtin,
-        standarderror-builtin,
-        unicode-builtin,
-        xrange-builtin,
-        coerce-method,
-        delslice-method,
-        getslice-method,
-        setslice-method,
-        no-absolute-import,
-        old-division,
-        dict-iter-method,
-        dict-view-method,
-        next-method-called,
-        metaclass-assignment,
-        indexing-exception,
-        raising-string,
-        reload-builtin,
-        oct-method,
-        hex-method,
-        nonzero-method,
-        cmp-method,
-        input-builtin,
-        round-builtin,
-        intern-builtin,
-        unichr-builtin,
-        map-builtin-not-iterating,
-        zip-builtin-not-iterating,
-        range-builtin-not-iterating,
-        filter-builtin-not-iterating,
-        using-cmp-argument,
-        eq-without-hash,
-        div-method,
-        idiv-method,
-        rdiv-method,
-        exception-message-attribute,
-        invalid-str-codec,
-        sys-max-int,
-        bad-python3-import,
-        deprecated-string-function,
-        deprecated-str-translate-call,
-        deprecated-itertools-function,
-        deprecated-types-field,
-        next-method-defined,
-        dict-items-not-iterating,
-        dict-keys-not-iterating,
-        dict-values-not-iterating,
-        deprecated-operator-function,
-        deprecated-urllib-function,
-        xreadlines-attribute,
-        deprecated-sys-function,
-        exception-escape,
-        comprehension-escape,
-        bad-continuation,
         arguments-differ,
         no-name-in-module,
-        no-member
+        no-member,
+        # Redundant alias imports required for type hinting by PEP 484
+        useless-import-alias,
+        # Qt uses PascalCase
+        invalid-name,
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option