Merge branch 'main' of https://github.com/pchlenski/manify

Author: DylanSatow

.github/workflows/test.yml

@@ -12,24 +12,24 @@ jobs:
     strategy:
       fail-fast: false    # don’t stop the matrix if one Python version fails
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11"] # jaxtyping requires >= 3.10; scipy requires < 3.12
 
     steps:
+      # Setup and installation
       - name: Check out code
         uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: "pip"
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          # install manify with test deps
-          pip install -e ".[test]"
-          # install all extras if any, but don’t fail CI if some optional deps are missing
-          pip install -e ".[all]" || echo "Optional extras failed—continuing"
+          pip install -e .
+          pip install -e ".[dev]"
 
       - name: Smoke‑test pip install manify
         run: |
@@ -38,17 +38,29 @@ jobs:
           print("manify version:", getattr(manify, "__version__", "unknown"))
           EOF
 
+      # Code quality checks
+      - name: Check code formatting with Black
+        run: black --check manify/ --line-length 120
+        continue-on-error: true
+
+      - name: Check import ordering with isort
+        run: isort --check-only --profile black manify/ --line-width 120
+        continue-on-error: true
+
+      - name: Run pylint
+        run: pylint manify/
+        continue-on-error: true
+
+      # Type checking
       - 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/__init__.py manify/embedders manify/predictors manify/manifolds
+        run: mypy manify/
         continue-on-error: true
 
+      # Unit testing
       - name: Run unit tests & collect coverage
-        run: |
-          pytest tests --cov=manify --cov-report=xml:coverage.xml
+        run: pytest tests --cov=manify --cov-report=xml:coverage.xml
 
+      # Code coverage
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5
         with:

.gitignore

@@ -11,3 +11,4 @@ notebooks/scratch*
 wandb/
 data/results_wandb/incremental/
 data/results_wandb/*incremental*
+site/

.pylintrc

@@ -0,0 +1,24 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+# # Build documentation in the docs/ directory with Sphinx
+# sphinx:
+#   configuration: docs/source/conf.py
+
+mkdocs:
+  configuration: mkdocs.yml
+
+# Set the OS and Python version
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+# Install dependencies
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements: [docs]

.readthedocs.yaml

@@ -1,5 +1,5 @@
 # Manify: A Python Library for Learning Non-Euclidean Representations
-[![Python Version](https://img.shields.io/badge/python-3.8%2B-blue.svg)](https://www.python.org/downloads/)
+[![Python Version](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/downloads/)
 [![License](https://img.shields.io/github/license/pchlenski/manify)](https://github.com/pchlenski/manify/blob/main/LICENSE)
 [![PyPI version](https://badge.fury.io/py/manify.svg)](https://badge.fury.io/py/manify)
 [![Tests](https://github.com/pchlenski/manify/actions/workflows/test.yml/badge.svg)](https://github.com/pchlenski/manify/actions/workflows/test.yml)

README.md

@@ -6,7 +6,7 @@
 import sys
 from tqdm.notebook import tqdm
 from pathlib import Path
-from manify.utils.dataloaders import load
+from manify.utils.dataloaders_old import load
 from manify.utils.benchmarks import benchmark
 from manify.manifolds import ProductManifold
 from manify.embedders.coordinate_learning import train_coords