ci(github): Run pre-commit in github actions

- Configure github actions to run pre-commit on the repo to check
style, etc.
- Update to stable/new versions of hooks to avoid spurious failures from
upstream updates.
- Flag a few imports in tests and examples with NOQA.  This is to avoid
bugs in isort.  In particular, isort is environment dependent.

    PyCQA/isort#1147
    PyCQA/isort#952
    PyCQA/isort#1007

- Disable one flake8 lint: 501, line too long

.github/workflows/pre-commit.yml

@@ -0,0 +1,22 @@
+# https://github.com/pre-commit/action
+# Run all pre-commit lints
+
+name: pre-commit
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - uses: actions/setup-python@v1
+    - name: set PY
+      run: echo "::set-env name=PY::$(python --version --version | sha256sum | cut -d' ' -f1)"
+    - uses: actions/cache@v1
+      with:
+        path: ~/.cache/pre-commit
+        key: pre-commit|${{ env.PY }}|${{ hashFiles('.pre-commit-config.yaml') }}
+    - uses: pre-commit/action@v1.0.1

.pre-commit-config.yaml

@@ -2,23 +2,22 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.4.0
+    rev: v2.5.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
 
 -   repo: https://github.com/psf/black
-    rev: stable
+    rev: 19.10b0
     hooks:
       - id: black
 
 -   repo: https://github.com/timothycrosley/isort
-    rev: 4.3.21-2
+    rev: 4.3.21
     hooks:
       - id: isort
-        types: ['python']
 
 -   repo: https://gitlab.com/pycqa/flake8
     rev: '3.7.9'  # pick a git hash / tag to point to

examples/example_basic.py

@@ -5,7 +5,8 @@
 import matplotlib.pyplot as plt  # type: ignore
 import numpy as np  # type: ignore
 
-from learn_as_you_go.emulator import emulator
+# TODO: remove NOQA when isort is fixed
+from learn_as_you_go.emulator import emulator  # NOQA
 
 
 def main():

examples/example_emcee.py

@@ -4,7 +4,8 @@
 
 import numpy as np  # type: ignore
 
-from learn_as_you_go.emulator import emulator
+# TODO: remove NOQA when isort is fixed
+from learn_as_you_go.emulator import emulator  # NOQA
 
 
 def main():

setup.cfg

@@ -1,3 +1,11 @@
 [tool:pytest]
 python_files = test_*.py *_test.py testing/*/*.py example_*.py
 python_functions = test_* example_*
+
+[flake8]
+ignore =
+    # line too long
+    E501,
+
+[tool:isort]
+known_first_party=learn_as_you_go

tests/test_check_good.py

@@ -10,7 +10,8 @@
 import numpy as np  # type: ignore
 import pytest  # type: ignore
 
-from learn_as_you_go.emulator import check_good
+# TODO: remove NOQA when isort is fixed
+from learn_as_you_go.emulator import check_good  # NOQA
 
 
 @pytest.mark.parametrize("test_input", [0, 1, 1.0, np.array(1.0)])

tests/test_emulator_accuracy.py

@@ -1,7 +1,8 @@
 import numpy as np  # type: ignore
 import pytest  # type: ignore
 
-from learn_as_you_go.emulator import emulator
+# TODO: remove NOQA when isort is fixed
+from learn_as_you_go.emulator import emulator  # NOQA
 
 DEFAULT_ABS_ERR = 0.05
 DEFAULT_REL_ERR = 1.0

tests/test_train_threshold.py

@@ -1,7 +1,8 @@
 import numpy as np  # type: ignore
 import pytest  # type: ignore
 
-from learn_as_you_go.emulator import emulator
+# TODO: remove NOQA when isort is fixed
+from learn_as_you_go.emulator import emulator  # NOQA
 
 
 @pytest.mark.xfail