Merge pull request #53 from newgene/add-pre-commit-hooks

Setup pre-commit hooks
newgene · Aug 2, 2022 · 2e2a7c6 · 2e2a7c6
2 parents 4d45c3f + 0bfc9a2
commit 2e2a7c6
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,15 @@
+fail_fast: false
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: 11cdc8d8201091a19ff1c28f7b7c75c3691954ad
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: debug-statements
+      - id: no-commit-to-branch
+      - id: check-merge-conflict
+
+  - repo: https://github.com/4Catalyzer/fourmat
+    rev: master  # or specify a version
+    hooks:
+      - id: fourmat
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -132,6 +132,13 @@ Some Python code formatters can be useful, but use them with caution. Double che
 * [black](https://github.com/python/black)
 * [yapf](https://github.com/google/yapf/)
 
+### Setup pre-commit
+
+After all above recommendations, we already setup [pre-commit](https://github.com/pre-commit/pre-commit) framework.
+You just need to install it on your local git repo:
+
+      pre-commit install
+
 ### Some useful references
 
 * [**requests** code style](http://python-requests.org//en/latest/dev/contributing/#kenneth-reitz-s-code-style)

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,10 @@
+[tool.black]
+line-length = 99
+target-version = ['py36', 'py37', 'py38', 'py39', 'py310']
+skip-string-normalization = 1
+
+[tool.isort]
+profile = "black"
+combine_as_imports = true
+line_length = 159
+src_paths = ["."]
diff --git a/setup.py b/setup.py
@@ -1,9 +1,8 @@
+import glob
 import os
+from subprocess import CalledProcessError, check_output
 
-import glob
-from subprocess import check_output
-from subprocess import CalledProcessError
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
 setup_path = os.path.dirname(__file__)
 
@@ -47,53 +46,50 @@ def read(fname):
     'singledispatchmethod; python_version < "3.8.0"',
     'dataclasses; python_version < "3.7.0"',
     'PyYAML>=5.1',
-    'orjson>=3.6.1',    # this is a faster json lib support inf/nan and datetime
-                        # v3.6.1 is the last version supports Python 3.6
+    'orjson>=3.6.1',  # this is a faster json lib support inf/nan and datetime
+    # v3.6.1 is the last version supports Python 3.6
 ]
 
 # extra requirements for biothings.web
 web_extra_requires = [
-    'msgpack>=0.6.1',   # support format=msgpack
+    'msgpack>=0.6.1',  # support format=msgpack
     'sentry-sdk>=1.5.3',  # new sentry package
 ]
 
 # extra requirements to run biothings.hub
 hub_requires = [
-    'beautifulsoup4',   # used in dumper.GoogleDriveDumper
-    'aiocron==1.8',     # setup scheduled jobs
-    'aiohttp==3.8.1',   # elasticsearch requires aiohttp>=3,<4
+    'beautifulsoup4',  # used in dumper.GoogleDriveDumper
+    'aiocron==1.8',  # setup scheduled jobs
+    'aiohttp==3.8.1',  # elasticsearch requires aiohttp>=3,<4
     'asyncssh==2.11.0',  # needs libffi-dev installed (apt-get)
     'pymongo>=4.1.0,<5.0',  # support MongoDB 5.0 since v3.12.0
     'psutil',
-    'jsonpointer',      # for utils.jsonpatch
-    'IPython',          # for interactive hub console
+    'jsonpointer',  # for utils.jsonpatch
+    'IPython',  # for interactive hub console
     'multiprocessing_on_dill',  # can replace pickler in concurrent.futures
-    'dill',             # a pickle alternative with extra object type support
-    'pyinotify; sys_platform == "linux"',        # Linux-only; used in utils.hub.PyInotifyHubReloader
-    'prettytable',      # diff report renderer
-    'sockjs-tornado==1.0.7',   # websocket server for HubServer
+    'dill',  # a pickle alternative with extra object type support
+    'pyinotify; sys_platform == "linux"',  # Linux-only; used in utils.hub.PyInotifyHubReloader
+    'prettytable',  # diff report renderer
+    'sockjs-tornado==1.0.7',  # websocket server for HubServer
     'jsonschema>=2.6.0',
-    'pip',              # auto-install requirements from plugins
+    'pip',  # auto-install requirements from plugins
     # 'pandas==1.0.1',    # json with inf/nan and more to come (replaced by orjson below now)
     # 'orjson>=3.5.2',    # this is a faster json lib support inf/nan and datetime
-    'yapf',             # code reformatter, better results than autopep8
-    'requests-aws4auth',    # aws s3 auth requests for autohub
-    'networkx>=2.1,<2.6',            # datatransform
-    'biothings_client>=0.2.6'   # datatransform (api client)
+    'yapf',  # code reformatter, better results than autopep8
+    'requests-aws4auth',  # aws s3 auth requests for autohub
+    'networkx>=2.1,<2.6',  # datatransform
+    'biothings_client>=0.2.6',  # datatransform (api client)
 ]
 
 # extra requirements to develop biothings
 dev_requires = [
     'pytest',
     'pytest-mock',
+    'pre-commit==2.17.0',
 ]
 
 # extra requirements for building docs
-docs_requires = [
-    'sphinx>=2.4.3',
-    'sphinx_rtd_theme>=1.0.0',
-    'sphinx_reredirects>=0.0.1'
-]
+docs_requires = ['sphinx>=2.4.3', 'sphinx_rtd_theme>=1.0.0', 'sphinx_reredirects>=0.0.1']
 
 setup(
     name="biothings",
@@ -133,6 +129,6 @@ def read(fname):
     extras_require={
         'web_extra': web_extra_requires,
         'hub': hub_requires,
-        'dev': web_extra_requires + hub_requires + dev_requires + docs_requires
+        'dev': web_extra_requires + hub_requires + dev_requires + docs_requires,
     },
 )