Pre-commit and poetry tasks

.pre-commit-config.yaml

@@ -1,11 +1,32 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v4.3.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
+
+-   repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+    -   id: isort
+
 -   repo: https://github.com/psf/black
-    rev: 21.4b2
+    rev: 22.8.0
     hooks:
     -   id: black
+
+# -   repo: https://github.com/pycqa/flake8
+#     rev: 5.0.4
+#     hooks:
+#     -   id: flake8
+
+# Pylint needs to be installed locally for precommit
+# https://pylint.pycqa.org/en/latest/user_guide/installation/pre-commit-integration.html
+# -   repo: local
+#     hooks:
+#     -   id: pylint
+#         name: pylint
+#         entry: pylint
+#         language: system
+#         types: [python]

README.md

@@ -18,7 +18,7 @@ Anatomical fiducials (AFIDs) is an open framework for evaluating correspondence
 curl -sSL https://install.python-poetry.org | python3 - --version 1.2.0
 ```
 
-For detailed setup instructions, see the documentation (here)[https://python-poetry.org/].
+For detailed setup instructions, see the documentation [here](https://python-poetry.org/).
 
 
 
@@ -30,16 +30,17 @@ _Install via `apt-get` or `snap`_
 1. Git clone the afids-validator repository `git clone https://github.com/afids/afids-validator.git`
 2. Set up python environment via `poetry shell`
 3. Install the required libraries via `poetry install --with dev`
-4. Access the postgres CLI via `sudo su - postgres`
-5. Create a database via postgres `createdb fid_db`
-6. Set password for the created database
+4. Install the pre-commit action via `poetry run poe setup`. This will automatically perform quality tasks for each new commit.
+5. Access the postgres CLI via `sudo su - postgres`
+6. Create a database via postgres `createdb fid_db`
+7. Set password for the created database
     ```
     psql fid_db
     \password
     ```
 8. Update configuration in `.env.template` and rename to `.env` file
-10. `python manage.py db upgrade`
-11. `python manage.py runserver`
+9. `python manage.py db upgrade`
+10. `python manage.py runserver`
 
 If there are no errors, you can test it out locally at http://localhost:5000
 

afidsvalidator/__init__.py

@@ -4,11 +4,10 @@
 
 from flask import Flask
 
-from config import *
-
-from afidsvalidator.views import validator
 from afidsvalidator.model import db, login_manager
 from afidsvalidator.orcid import orcid_blueprint
+from afidsvalidator.views import validator
+from config import *
 
 
 class ConfigException(Exception):

afidsvalidator/model.py

@@ -1,17 +1,16 @@
 """Handle parsing files to internal AFIDs representation."""
 
-import io
 import csv
+import io
 import json
 import math
 import re
 
+from flask_dance.consumer.storage.sqla import OAuthConsumerMixin
+from flask_login import LoginManager, UserMixin
+from flask_sqlalchemy import SQLAlchemy
 from pkg_resources import parse_version
 from sqlalchemy.orm import composite
-from flask_sqlalchemy import SQLAlchemy
-from flask_login import LoginManager, UserMixin
-from flask_dance.consumer.storage.sqla import OAuthConsumerMixin
-
 
 EXPECTED_LABELS = [str(x + 1) for x in range(32)]
 EXPECTED_DESCS = [
@@ -137,7 +136,7 @@ def validate(self):
             True if the Afids set is valid.
         """
         valid = True
-        for label, name in EXPECTED_MAP.items():
+        for _, name in EXPECTED_MAP.items():
             try:
                 valid = valid and math.isfinite(getattr(self, name[-1]).x)
                 valid = valid and math.isfinite(getattr(self, name[-1]).y)

afidsvalidator/orcid.py

@@ -5,7 +5,7 @@
 from flask_login import current_user, login_user
 from sqlalchemy.orm.exc import NoResultFound
 
-from afidsvalidator.model import db, OAuth, User
+from afidsvalidator.model import OAuth, User, db
 
 orcid_blueprint = OAuth2ConsumerBlueprint(
     "orcid",

afidsvalidator/views.py

@@ -3,32 +3,31 @@
 import os
 from datetime import datetime, timezone
 
+import numpy as np
+import wtforms as wtf
 from flask import (
-    render_template,
-    request,
-    jsonify,
     Blueprint,
     current_app,
+    jsonify,
     redirect,
+    render_template,
+    request,
 )
-from flask_login import logout_user, current_user
-import numpy as np
-import wtforms as wtf
+from flask_login import current_user, logout_user
 
 from afidsvalidator.model import (
-    db,
-    csv_to_afids,
-    json_to_afids,
-    InvalidFileError,
     EXPECTED_DESCS,
     HumanFiducialSet,
+    InvalidFileError,
+    csv_to_afids,
+    db,
+    json_to_afids,
 )
 from afidsvalidator.visualizations import (
     generate_3d_scatter,
     generate_histogram,
 )
 
-
 validator = Blueprint("validator", __name__, template_folder="templates")
 
 

afidsvalidator/visualizations.py

@@ -1,6 +1,7 @@
 """Utilities for generating AFIDs-related graphics"""
 
 import plotly.graph_objects as go
+
 from afidsvalidator.model import EXPECTED_DESCS
 
 

pyproject.toml

@@ -31,6 +31,8 @@ poethepoet = "^0.16.2"
 
 [tool.poe.tasks]
 setup = "pre-commit install"
+quality = {shell = "isort afidsvalidator && black afidsvalidator -l 79 && flake8 afidsvalidator && pylint afidsvalidator" }
+test = { shell = "python -m unittest" }
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]