Standard pre commit and isort, flake8 settings

.flake8

[flake8]
max-line-length = 88
max-complexity = 12
select = C,E,F,W,B,B950
ignore = E203, E501, W503

.isort.cfg

[settings]
multi_line_output=3
include_trailing_comma=True
force_grid_wrap=0
use_parentheses=True
line_length=80
known_third_party=
known_first_party=

.pre-commit-config.yaml

---
repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v2.4.0
    hooks:
      - id: end-of-file-fixer
        language_version: python3.5
        stages: [commit, push]

      - id: trailing-whitespace
        language_version: python3.5
        args: [--markdown-linebreak-ext=md]
        stages: [commit, push]

  - repo: https://github.com/asottile/seed-isort-config
    rev: v1.9.3
    hooks:
      - id: seed-isort-config

  - repo: https://github.com/pre-commit/mirrors-isort
    rev: v4.3.21
    hooks:
      - id: isort
        language_version: python3.5
        stages: [commit, push]

  - repo: https://github.com/python/black
    rev: 19.10b0
    hooks:
      - id: black
        language_version: python3.6
        args: [--line-length=80]
        stages: [commit, push]

  # Lint Python and Pass/Fail
  # - repo: https://github.com/PyCQA/pydocstyle
  #   rev: 4.0.1
  #   hooks:
  #     - id: pydocstyle
  #       language_version: python3.5
  #       stages: [commit, push]

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v2.4.0
    hooks:
      - id: check-byte-order-marker
        language_version: python3.5
        stages: [commit, push]

  - repo: https://gitlab.com/pycqa/flake8
    rev: 3.7.9
    hooks:
      - id: flake8
        language_version: python3.5
        args: [--max-line-length=88]
        stages: [commit, push]

  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v0.740
    hooks:
      - id: mypy
        language_version: python3.5
        stages: [commit, push]

  # Other Linters
  - repo: https://github.com/adrienverge/yamllint.git
    rev: v1.18.0
    hooks:
      - id: yamllint
        args: ["-d {extends: relaxed, rules: {line-length: {max: 120}}}"]
        stages: [commit, push]

  - repo: https://github.com/pryorda/dockerfilelint-precommit-hooks
    rev: v0.1.0
    hooks:
      - id: dockerfilelint
        stages: [commit, push]

  - repo: local
    hooks:
      - id: rtestthat
        name: rtestthat
        entry: /usr/bin/make test
        language: script
        pass_filenames: false
        # alternatively you could `types: [r]` so it only runs when r files change
        # though tests might be invalidated if you were to say change a data file
        always_run: true
...

Makefile

test:
	Rscript -e 'source("tests/testthat.R")'