Fix quality

.github/ISSUE_TEMPLATE.md

@@ -8,4 +8,4 @@ Briefly describe the issue you are experiencing (or feature you want to see adde
 * Dropdown menu option
 * File uploaded (if applicable)
 
-_PR template was adopted from [appium](https://github.com/appium/appium/blob/master/.github/ISSUE_TEMPLATE.md)_
+_PR template was adopted from [appium](https://github.com/appium/appium/blob/master/.github/ISSUE_TEMPLATE.md)_

.github/workflows/afids-validator_ci.yml

@@ -119,16 +119,16 @@ jobs:
         run: poetry install --no-interaction --no-root --with dev
 
       - name: isort
-        run: poetry run isort afidsvalidator -c
+        run: poetry run isort afidsvalidator test -c
 
       - name: black
-        run: poetry run black afidsvalidator --check
+        run: poetry run black afidsvalidator test --check
 
       - name: flake8
-        run: poetry run flake8 afidsvalidator
+        run: poetry run flake8 afidsvalidator test
 
       - name: pylint
-        run: poetry run pylint afidsvalidator
+        run: poetry run pylint afidsvalidator test
 
   assign:
     name: Reviewer assignment

.gitignore

@@ -12,4 +12,4 @@ dist/
 *.egg-info
 
 # Workspaces
-afids.code-workspace
+afids.code-workspace

.pre-commit-config.yaml

@@ -1,3 +1,4 @@
+exclude: "^migrations/"
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.3.0
@@ -16,17 +17,7 @@ repos:
     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]
+-   repo: https://github.com/pycqa/flake8
+    rev: 5.0.4
+    hooks:
+    -   id: flake8

afidsvalidator/__init__.py

@@ -7,7 +7,7 @@
 from afidsvalidator.model import db, login_manager
 from afidsvalidator.orcid import orcid_blueprint
 from afidsvalidator.views import validator
-from config import *
+from config import DevelopmentConfig, ProductionConfig, TestingConfig
 
 
 class ConfigException(Exception):
@@ -40,6 +40,7 @@ def __init__(self, message):
 
 
 def create_app():
+    """Create and initialize an app according to the config."""
     app = Flask(__name__)
 
     app.config.from_object(config_settings)

afidsvalidator/model.py

@@ -48,17 +48,37 @@
     ["L olfactory sulcal fundus", "LOSF"],
 ]
 EXPECTED_MAP = dict(zip(EXPECTED_LABELS, EXPECTED_DESCS))
+FCSV_FIELDS = (
+    "id",
+    "x",
+    "y",
+    "z",
+    "ow",
+    "ox",
+    "oy",
+    "oz",
+    "vis",
+    "sel",
+    "lock",
+    "label",
+    "desc",
+    "associatedNodeID",
+)
+
 
 db = SQLAlchemy()
 login_manager = LoginManager()
 
 
 @login_manager.user_loader
 def load_user(user_id):
+    """Get the user with the given ID."""
     return User.query.get(user_id)
 
 
 class User(UserMixin, db.Model):
+    """AFIDs Validator registered user."""
+
     id = db.Column(db.Integer, primary_key=True)
     name = db.Column(db.String, nullable=True)
     oauths = db.relationship("OAuth", backref="user", lazy=True)
@@ -70,12 +90,18 @@ def __repr__(self):
         return f"<email={self.email}>"
 
 
+# pylint: disable-next=too-few-public-methods
 class OAuth(OAuthConsumerMixin, db.Model):
+    """Mapping from ORCID ID to internal user ID."""
+
     user_id = db.Column(db.Integer, db.ForeignKey("user.id"), nullable=False)
     provider_user_id = db.Column(db.String(20), nullable=False)
 
 
-class FiducialPosition(object):
+class FiducialPosition:
+    """A fiducial position, in voxels."""
+
+    # pylint: disable=invalid-name
     def __init__(self, x, y, z):
         self.x = x
         self.y = y
@@ -85,7 +111,7 @@ def __composite_values__(self):
         return self.x, self.y, self.z
 
     def __repr__(self):
-        return "FiducialPosition(x=%r, y=%r, z=%r)" % (self.x, self.y, self.z)
+        return f"FiducialPosition(x={self.x}, y={self.y}, z={self.z})"
 
     def __eq__(self, other):
         return (
@@ -102,9 +128,6 @@ def __ne__(self, other):
 class FiducialSet:
     """Base class for afids."""
 
-    def __repr__(self):
-        return "<id {}>".format(self.id)
-
     def serialize(self):
         """Produce a dict of each column."""
         serialized = {}
@@ -115,8 +138,17 @@ def serialize(self):
         return serialized
 
     def add_fiducial(self, desc, points):
-        for d, p in zip(["_x", "_y", "_z"], points):
-            setattr(self, "".join([desc, d]), float(p))
+        """Set a fiducial point's value.
+
+        Parameters
+        ----------
+        desc : str
+            The point's description.
+        points: list[float] or list[str]
+            The x, y, and z values of the point.
+        """
+        for suffix, val in zip(["_x", "_y", "_z"], points):
+            setattr(self, "".join([desc, suffix]), float(val))
         setattr(
             self,
             desc,
@@ -320,6 +352,9 @@ class HumanFiducialSet(FiducialSet, db.Model):
     LOSF_z = db.Column(db.Float(), nullable=False)
     LOSF = composite(FiducialPosition, LOSF_x, LOSF_y, LOSF_z)
 
+    def __repr__(self):
+        return f"<id {self.id}>"
+
 
 class InvalidFileError(Exception):
     """Exception raised when a file to be parsed is invalid.
@@ -404,26 +439,7 @@ def csv_to_afids(in_csv):
             f"Markups fiducial file version {parsed_version} too low"
         )
 
-    # Some fields irrelevant, but know they should be there
-    fields = (
-        "id",
-        "x",
-        "y",
-        "z",
-        "ow",
-        "ox",
-        "oy",
-        "oz",
-        "vis",
-        "sel",
-        "lock",
-        "label",
-        "desc",
-        "associatedNodeID",
-    )
-
-    in_csv = io.StringIO(in_csv)
-    csv_reader = csv.DictReader(in_csv, fields)
+    csv_reader = csv.DictReader(io.StringIO(in_csv), FCSV_FIELDS)
 
     # Read csv file and dump to AFIDs object
     afids = HumanFiducialSet()
@@ -439,7 +455,8 @@ def csv_to_afids(in_csv):
         # Check if label is numerical
         if not row_label.isdigit():
             raise InvalidFileError(
-                f"Row label {row_label} is invalid for fiducial {expected_label}"
+                f"Row label {row_label} is invalid for fiducial "
+                f"{expected_label}"
             )
 
         expected_label += 1

afidsvalidator/orcid.py

@@ -44,8 +44,8 @@ def orcid_logged_in(blueprint, token):
     else:
         user = User(name=token["name"])
         oauth.user = user
-        db.session.add_all([user, oauth])
-        db.session.commit()
+        db.session.add_all([user, oauth])  # pylint: disable=no-member
+        db.session.commit()  # pylint: disable=no-member
         login_user(user)
 
     return False

afidsvalidator/templates/contact.html

@@ -17,4 +17,3 @@
       </div>
     </article>
 {% endblock %}
-

afidsvalidator/templates/db.html

@@ -10,4 +10,3 @@
       </table>
     </section>
 {% endblock %}
-

afidsvalidator/templates/login.html

@@ -19,4 +19,3 @@
       </div>
     </div>
 {% endblock %}
-

afidsvalidator/views.py

@@ -2,6 +2,7 @@
 
 import os
 from datetime import datetime, timezone
+from pathlib import Path
 
 import numpy as np
 import wtforms as wtf
@@ -32,6 +33,7 @@
 
 
 class Average(wtf.Form):
+    # pylint: disable=too-few-public-methods
     """Form for selecting and submitting a file."""
 
     filename = wtf.FileField(validators=[wtf.validators.InputRequired()])
@@ -80,6 +82,7 @@ def logout():
 
 
 # Validator
+# pylint: disable=no-member
 @validator.route("/app.html", methods=["GET", "POST"])
 def validate():
     """Present the validator form, or validate an AFIDs set."""
@@ -95,11 +98,6 @@ def validate():
     form_choices = [choice.capitalize() for choice in form_choices]
     form_choices.sort()
 
-    # Get time stamp
-    timestamp = str(
-        datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M:%S %Z")
-    )
-
     if not (request.method == "POST" and request.files):
         return render_template(
             "app.html",
@@ -116,7 +114,7 @@ def validate():
     upload_ext, file_check = allowed_file(upload.filename)
 
     if not (upload and file_check):
-        result = f"Invalid file: extension not allowed ({timestamp})"
+        result = "Invalid file: extension not allowed"
 
         return render_template(
             "app.html",
@@ -135,7 +133,7 @@ def validate():
         else:
             user_afids = json_to_afids(upload.read().decode("utf-8"))
     except InvalidFileError as err:
-        result = f"Invalid file: {err.message} ({timestamp})"
+        result = f"Invalid file: {err.message}"
         return render_template(
             "app.html",
             form=form,
@@ -149,14 +147,10 @@ def validate():
         )
 
     if user_afids.validate():
-        result = f"Valid file ({timestamp})"
+        result = "Valid file"
     else:
-        result = (
-            f"Invalid AFIDs set, please double check your file ({timestamp})"
-        )
+        result = "Invalid AFIDs set, please double check your file"
 
-    fid_species = request.form["fid_species"]
-    fid_species = fid_species.lower()
     fid_template = request.form["fid_template"]
 
     if fid_template == "Validate file structure":
@@ -174,9 +168,14 @@ def validate():
 
     result = f"{result}<br>{fid_template} selected"
     # Need to pull from correct folder when more templates are added
-    template_file_path = f"{current_app.config['AFIDS_DIR']}/{fid_species.lower()}/tpl-{fid_template}_afids.fcsv"
 
-    with open(template_file_path, "r") as template_file:
+    with open(
+        Path(current_app.config["AFIDS_DIR"])
+        / request.form["fid_species"].lower()
+        / f"tpl-{fid_template}_afids.fcsv",
+        "r",
+        encoding="utf-8",
+    ) as template_file:
         template_afids = csv_to_afids(template_file.read())
 
     if request.form.get("db_checkbox"):
@@ -189,22 +188,13 @@ def validate():
         print("DB option unchecked, user data not saved")
 
     for desc in EXPECTED_DESCS:
-        distances.append(
-            "{:.5f}".format(
-                np.linalg.norm(
-                    np.array(
-                        [
-                            getattr(
-                                template_afids, desc[-1]
-                            ).__composite_values__()
-                        ]
-                    )
-                    - np.array(
-                        [getattr(user_afids, desc[-1]).__composite_values__()]
-                    )
-                )
+        distance = np.linalg.norm(
+            np.array(
+                [getattr(template_afids, desc[-1]).__composite_values__()]
             )
+            - np.array([getattr(user_afids, desc[-1]).__composite_values__()])
         )
+        distances.append(f"{distance:.5f}")
         labels.append(desc[-1])
 
     return render_template(
@@ -216,7 +206,9 @@ def validate():
         index=list(range(len(EXPECTED_DESCS))),
         labels=labels,
         distances=distances,
-        timestamp=timestamp,
+        timestamp=str(
+            datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M:%S %Z")
+        ),
         scatter_html=generate_3d_scatter(template_afids, user_afids),
         histogram_html=generate_histogram(template_afids, user_afids),
         current_user=current_user,