Numerous CI/CD fixed

Author: pchlenski

.github/workflows/test.yml

@@ -46,7 +46,7 @@ jobs:
       # Code quality checks
       - name: Check code formatting with Black
         run: |
-          black --check manify --line-length 120/
+          black --check manify/ --line-length 120
         continue-on-error: true
 
       - name: Check import ordering with isort
@@ -63,13 +63,13 @@ jobs:
       - name: Check type annotations with MyPy
         run: |
           # only check core modules—skip untyped imports
-          mypy --ignore-missing-imports --no-warn-return-any --follow-imports=skip manify
+          mypy --ignore-missing-imports --no-warn-return-any --follow-imports=skip manify/
         continue-on-error: true
 
       # Unit testing
       - name: Run unit tests & collect coverage
         run: |
-          pytest tests --cov=manify --cov-report=xml:coverage.xml
+          pytest tests --cov=manify --cov-report=xml:coverage.xml --cov-fail-under=80
 
       # Code coverage
       - name: Upload coverage to Codecov

manify/manifolds.py

@@ -11,8 +11,7 @@
 from __future__ import annotations
 
 import warnings
-from typing import (TYPE_CHECKING, Callable, List, Literal, Optional, Tuple,
-                    Union)
+from typing import TYPE_CHECKING, Callable, List, Literal, Optional, Tuple, Union
 
 import geoopt
 import torch

manify/utils/benchmarks.py

@@ -9,8 +9,12 @@
 from sklearn.base import BaseEstimator
 from sklearn.ensemble import RandomForestClassifier, RandomForestRegressor
 from sklearn.linear_model import SGDClassifier, SGDRegressor
-from sklearn.metrics import (accuracy_score, f1_score, mean_squared_error,
-                             root_mean_squared_error)
+from sklearn.metrics import (
+    accuracy_score,
+    f1_score,
+    mean_squared_error,
+    root_mean_squared_error,
+)
 from sklearn.model_selection import train_test_split
 from sklearn.neighbors import KNeighborsClassifier, KNeighborsRegressor
 from sklearn.svm import SVC, SVR

pyproject.toml

@@ -22,7 +22,7 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-    "jaxtyping",
+    "jaxtyping[mypy]",
     "beartype",
     "pytest",
     "mypy",
@@ -81,4 +81,4 @@ packages = ["manify"]
 ignore_missing_imports = true
 
 # Use jaxtyping-specific plugins
-plugins = ["jaxtyping.mypy_plugin"]
+plugins = [ "jaxtyping.mypy_plugin", "beartype.mypy_plugin" ]