docs: Update installation instructions to recommend uv

.gitattributes

@@ -1 +1 @@
-*.ipynb linguist-language=Python
+*.ipynb linguist-language=Python

.github/workflows/tests.yml

@@ -21,12 +21,29 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Install uv
+      uses: astral-sh/setup-uv@v2
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -e .
         pip install pytest pytest-cov pytest-testmon
 
+    - name: Install prek and ty
+      run: |
+        uv tool install prek ty
+
+    - name: Run prek hooks (ruff + code quality checks)
+      run: |
+        prek install
+        prek install-hooks
+        prek run --all-files
+
+    - name: Run ty type checker
+      run: |
+        ty check
+
     - name: Run tests (optimized with testmon)
       run: |
         pytest umap/tests/ -v --cov=umap --cov-report=xml --testmon

.gitignore

@@ -34,4 +34,9 @@ dist
 # coverage
 .coverage
 .coverage.*
-.coverage.xml
+.coverage.xml
+
+
+# Added by cargo
+
+/target

.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+repos:
+  # Ruff linter with all rules enabled
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.3
+    hooks:
+      - id: ruff-check
+        args: [--fix, --unsafe-fixes]
+        types_or: [python, pyi]
+      - id: ruff-format
+        types_or: [python, pyi]
+
+  # Type checker: ty (Astral's Rust-based type checker) & Skylos
+  - repo: local
+    hooks:
+      - id: ty
+        name: ty type checker
+        entry: ty check umap/
+        language: system
+        types: [python]
+        pass_filenames: false
+        stages: [manual]
+      - id: skylos
+        name: Skylos static analysis
+        entry: python -m skylos.cli .
+        language: system
+        types: [python]
+        pass_filenames: false
+
+  # Standard pre-commit hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+        args: [--maxkb=5000]
+      - id: check-ast
+      - id: check-merge-conflict

AGENTS.md

@@ -0,0 +1,179 @@
+# Agent Development Workflow
+
+This document specifies the workflow for implementing tasks and features in this repository.
+
+## Core Principles
+
+Every task should follow a structured workflow to ensure code quality, traceability, and easy review.
+
+## Workflow
+
+### 1. Create a Fresh Branch
+
+Before starting any task, create a new branch from `master`:
+
+```bash
+git checkout master
+git pull origin master
+git checkout -b <branch-name>
+```
+
+**Branch naming conventions:**
+- Feature: `feat/<description>` (e.g., `feat/add-gpu-support`)
+- Bug fix: `fix/<description>` (e.g., `fix/memory-leak`)
+- Documentation: `docs/<description>` (e.g., `docs/update-installation`)
+- Refactoring: `refactor/<description>` (e.g., `refactor/optimize-metric-computation`)
+- Tests: `test/<description>` (e.g., `test/add-parametric-umap-tests`)
+
+### 2. Implement the Task
+
+Work on the implementation in your branch:
+
+- Write code following the project's conventions
+- Add tests for new functionality
+- Update documentation as needed
+- Run pre-commit hooks to ensure code quality
+- Commit changes with clear, descriptive messages
+
+**Commit Message Guidelines:**
+- Use imperative mood ("add" not "adds", "fix" not "fixes")
+- First line should be concise (50 chars or less)
+- Provide detailed explanation in the body if needed
+- Reference related issues if applicable
+
+Example:
+```bash
+git add .
+git commit -m "Add GPU support for metric computation
+
+- Implement CUDA kernels for distance calculations
+- Add device selection logic
+- Update tests for GPU paths
+"
+```
+
+### 3. Submit a Draft PR
+
+After completing the task, push your branch and create a **draft pull request**:
+
+```bash
+git push -u origin <branch-name>
+gh pr create --draft --title "<title>" --body "<description>"
+```
+
+**Draft PR Requirements:**
+- Clear, descriptive title
+- Summary of changes made
+- List of key implementation details
+- Note any testing performed
+- Flag any known issues or TODOs
+
+Example:
+```markdown
+## Summary
+Implements GPU acceleration for metric computation using CUDA.
+
+## Changes
+- Added CUDA kernels for Euclidean and Cosine distances
+- Implemented device management and memory pooling
+- Added fallback to CPU for unsupported operations
+
+## Testing
+- Unit tests pass on GPU and CPU paths
+- Performance benchmarks show 3.2x speedup on MNIST
+
+## Known Issues
+- Sparse matrix operations not yet GPU-accelerated
+```
+
+### 4. Code Review
+
+The draft PR allows for:
+- Early feedback on approach and design
+- Discussion of implementation details
+- Identification of issues before final submission
+- Iteration based on review comments
+
+When ready for final review, convert the draft to a regular PR or request review.
+
+## Pre-submission Checklist
+
+Before creating a PR, ensure:
+
+- [ ] All tests pass locally
+- [ ] Pre-commit hooks pass
+- [ ] Code follows project conventions
+- [ ] Documentation is updated
+- [ ] Commit messages are clear and descriptive
+- [ ] Branch is up to date with `master`
+- [ ] No unrelated changes are included
+
+## Important Notes
+
+### No Direct Commits to Master
+- **Never commit directly to `master`**
+- All changes must go through the branch → draft PR → review → merge workflow
+
+### Keep Branches Fresh
+- Rebase on `master` if it diverges significantly
+- Keep branch scope focused on a single task
+- Delete branch after merge
+
+### Tests Are Required
+- All new code must have corresponding tests
+- All tests must pass before submitting PR
+- Include both unit and integration tests where appropriate
+
+### Documentation
+- Update README if adding user-facing features
+- Update docstrings for code changes
+- Add migration guides for breaking changes
+
+## Example Workflow
+
+```bash
+# 1. Create a branch
+git checkout -b feat/add-inverse-transform-optimization
+
+# 2. Implement the feature
+# ... write code, tests, docs ...
+
+# 3. Test locally
+pytest umap/tests/ -v
+
+# 4. Commit changes
+git add .
+git commit -m "Optimize inverse transform computation
+
+- Use vectorized operations for faster calculation
+- Add caching for repeated transforms
+- Improve memory efficiency
+"
+
+# 5. Push to remote
+git push -u origin feat/add-inverse-transform-optimization
+
+# 6. Create draft PR
+gh pr create --draft \
+  --title "feat: Optimize inverse transform computation" \
+  --body "
+## Summary
+Implements optimization improvements for inverse_transform method.
+
+## Changes
+- Vectorized operations for 2x speedup
+- Caching layer for repeated queries
+- Reduced memory allocation
+
+## Testing
+- All tests pass
+- Benchmarks show 50% improvement on large datasets
+  "
+```
+
+## Questions?
+
+If you're unsure about any aspect of the workflow:
+1. Check existing PRs for examples
+2. Refer to the project's CLAUDE.md for additional conventions
+3. Open an issue with questions about the process

CONTRIBUTING.md

@@ -1,26 +1,26 @@
 # Contributing
 
-Contributions of all kinds are welcome. In particular pull requests are appreciated. 
+Contributions of all kinds are welcome. In particular pull requests are appreciated.
 The authors will endeavour to help walk you through any issues in the pull request
 discussion, so please feel free to open a pull request even if you are new to such things.
 
 ## Issues
 
 The easiest contribution to make is to [file an issue](https://github.com/lmcinnes/umap/issues/new).
-It is beneficial if you check the [FAQ](https://umap-learn.readthedocs.io/en/latest/faq.html), 
+It is beneficial if you check the [FAQ](https://umap.readthedocs.io/en/latest/faq.html),
 and do a cursory search of [existing issues](https://github.com/lmcinnes/umap/issues?utf8=%E2%9C%93&q=is%3Aissue).
-It is also helpful, but not necessary, if you can provide clear instruction for 
+It is also helpful, but not necessary, if you can provide clear instruction for
 how to reproduce a problem. If you have resolved an issue yourself please consider
 contributing to the FAQ to add your problem, and its resolution, so others can
 benefit from your work.
 
 ## Documentation
 
 Contributing to documentation is the easiest way to get started. Providing simple
-clear or helpful documentation for new users is critical. Anything that *you* as 
+clear or helpful documentation for new users is critical. Anything that *you* as
 a new user found hard to understand, or difficult to work out, are excellent places
 to begin. Contributions to more detailed and descriptive error messages is
-especially appreciated. To contribute to the documentation please 
+especially appreciated. To contribute to the documentation please
 [fork the project](https://github.com/lmcinnes/umap/issues#fork-destination-box)
 into your own repository, make changes there, and then submit a pull request.
 
@@ -44,12 +44,12 @@ in the `doc/_build` folder.
 ## Code
 
 Code contributions are always welcome, from simple bug fixes, to new features. To
-contribute code please 
+contribute code please
 [fork the project](https://github.com/lmcinnes/umap/issues#fork-destination-box)
 into your own repository, make changes there, and then submit a pull request. If
 you are fixing a known issue please add the issue number to the PR message. If you
 are fixing a new issue feel free to file an issue and then reference it in the PR.
-You can [browse open issues](https://github.com/lmcinnes/umap/issues), 
+You can [browse open issues](https://github.com/lmcinnes/umap/issues),
 or consult the [project roadmap](https://github.com/lmcinnes/umap/issues/15), for potential code
 contributions. Fixes for issues tagged with 'help wanted' are especially appreciated.