The fifth revision (#10)

Author: habedi

.editorconfig

@@ -1,5 +1,3 @@
-# EditorConfig is awesome: https://EditorConfig.org
-
 # Top-most EditorConfig file
 root = true
 
@@ -19,7 +17,7 @@ max_line_length = 100
 # Markdown files
 [*.md]
 max_line_length = 120
-trim_trailing_whitespace = false # Don't remove trailing whitespace in Markdown files
+trim_trailing_whitespace = false
 
 # Bash scripts
 [*.sh]
@@ -29,3 +27,6 @@ indent_size = 2
 [*.{yaml,yml}]
 indent_size = 2
 
+# Python files
+[*.py]
+max_line_length = 100

.github/workflows/benchmarks.yml .github/workflows/benches.yml.github/workflows/benchmarks.yml renamed to .github/workflows/benches.yml

@@ -1,16 +1,16 @@
 name: Run Benchmarks
 
 on:
-  workflow_dispatch: { } # Allow manual execution
+  workflow_dispatch:
 
 jobs:
-  build:
+  benchmarks:
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
         # Define the Rust versions to test against
-        rust-version: [ "stable", "beta" ]
+        rust-version: [ "1.83.0", "stable", "beta" ]
 
     steps:
       - name: Checkout Repository
@@ -24,7 +24,7 @@ jobs:
       - name: Install Dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y make
+          sudo apt-get install -y clang curl pkg-config libssl-dev make
           make install-deps
 
       - name: Run Benchmarks

.github/workflows/lints.yml

@@ -1,10 +1,13 @@
-name: Run Linters
+name: Run Linter Checks
 
 on:
-  workflow_dispatch: { } # Allow manual execution
-  push:
-    tags:
-      - 'v*' # Trigger on version tags
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+
+permissions:
+  contents: read
 
 jobs:
   lint:

.github/workflows/publish.yml

@@ -1,10 +1,13 @@
 name: Publish to Crates.io
 
 on:
-  workflow_dispatch: { } # Allow manual execution
+  workflow_dispatch:
   push:
     tags:
-      - 'v*' # Trigger on version tags
+      - 'v*'
+
+permissions:
+  contents: read
 
 jobs:
 
@@ -33,6 +36,7 @@ jobs:
           CARGO_REGISTRY_TOKEN: ${{ secrets.CARGO_REGISTRY_TOKEN }}
         run: |
           sudo apt-get update
-          sudo apt-get install -y make
+          sudo apt-get install -y clang curl pkg-config libssl-dev make
+          make install-deps
           cargo publish --token $CARGO_REGISTRY_TOKEN
-        continue-on-error: false
+        continue-on-error: false

.github/workflows/publish_py.yml

@@ -0,0 +1,34 @@
+name: Publish PySpart to PyPI
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - 'v*'
+
+permissions:
+  contents: read
+
+jobs:
+  publish_to_pypi:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Set Up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install Dependencies
+        run: |
+          pip install -U pip
+          pip install uv
+          uv sync --all-extras
+
+      - name: Build and Publish Package
+        run: |
+          make wheel-manylinux
+          env PYPI_TOKEN=${{ secrets.PYPI_API_TOKEN }} make publish-py

.github/workflows/tests.yml

@@ -1,17 +1,23 @@
 name: Run Tests
 
 on:
-  workflow_dispatch: { } # Allow manual execution
-  workflow_call: # Make this workflow callable from other workflows
+  workflow_dispatch:
+  workflow_call:
+  pull_request:
+    branches:
+      - main
+
+permissions:
+  contents: read
 
 jobs:
-  build:
+  tests:
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
         # Define the Rust versions to test against
-        rust-version: [ "1.83.0", "1.84.0", "beta", "stable" ]
+        rust-version: [ "1.83.0", "stable", "beta" ]
 
     steps:
       - name: Checkout Repository
@@ -25,7 +31,7 @@ jobs:
       - name: Install Dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y make
+          sudo apt-get install -y clang curl pkg-config libssl-dev make
           make install-deps
 
       - name: Run Tests and Generate Coverage Report

.gitignore

@@ -89,3 +89,6 @@ rtree_2d.dot
 rtree_3d.dot
 src/main.rs
 .benchmarks
+*.log
+*_output.txt
+pyspart/target/

CONTRIBUTING.md

@@ -11,7 +11,7 @@ would like to work on or if it has already been resolved.
 ### Reporting Bugs
 
 1. Open an issue on the [issue tracker](https://github.com/habedi/spart/issues).
-2. Include information such as steps to reproduce, expected/actual behavior, and relevant logs or screenshots.
+2. Include information such as steps to reproduce the bug, expected behavior, and actual behavior.
 
 ### Suggesting Features
 

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "spart"
-version = "0.1.4"
+version = "0.2.0"
 description = "A collection of space partitioning tree data structures for Rust"
 repository = "https://github.com/habedi/spart"
 license = "MIT OR Apache-2.0"
@@ -11,6 +11,9 @@ homepage = "https://github.com/habedi/spart"
 documentation = "https://docs.rs/spart"
 categories = ["data-structures", "algorithms"]
 edition = "2021"
+rust-version = "1.83.0"
+
+resolver = "2"
 
 [lib]
 name = "spart"
@@ -20,10 +23,10 @@ path = "src/lib.rs"
 tracing = "0.1.41"
 tracing-subscriber = "0.3.19"
 ordered-float = "5.0.0"
-ctor = "0.4.1"
+ctor = "0.5.0"
 
 [dev-dependencies]
-criterion = { version = "0.5", features = ["html_reports"] }
+criterion = { version = "0.7.0", features = ["html_reports"] }
 
 [[bench]]
 name = "main"
@@ -40,6 +43,22 @@ debug = true
 [profile.test]
 debug = true
 
+[[example]]
+name = "quadtree"
+path = "examples/quadtree.rs"
+
+[[example]]
+name = "octree"
+path = "examples/octree.rs"
+
+[[example]]
+name = "kdtree"
+path = "examples/kdtree.rs"
+
+[[example]]
+name = "rtree"
+path = "examples/rtree.rs"
+
 [package.metadata.rustfmt]
 max_width = 100
 hard_tabs = false

Makefile

@@ -5,14 +5,22 @@ BINARY = :target/release/$(BINARY_NAME)
 PATH := /snap/bin:$(PATH)
 RUST_BACKTRACE := 0
 DEBUG_SPART := 0
+RUST_LOG        := info
+WHEEL_DIR       := dist
+PYSPART_DIR     := pyspart
+PY_DEP_MNGR     := uv
+WHEEL_FILE      := $(shell ls $(PYSPART_DIR)/$(WHEEL_DIR)/pyspart-*.whl 2>/dev/null | head -n 1)
 
 # Default target
 .DEFAULT_GOAL := help
 
 .PHONY: help
-help: ## Show the help message for each target
-	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; \
- 	{printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
+help: ## Show the help messages for all targets
+	@echo "Usage: make <target>"
+	@echo ""
+	@echo "Targets:"
+	@grep -E '^[a-zA-Z_-]+:.*## .*$$' Makefile | \
+	awk 'BEGIN {FS = ":.*## "}; {printf "  \033[36m%-15s\033[0m %s\n", $$1, $$2}'
 
 .PHONY: format
 format: ## Format Rust files
@@ -39,10 +47,28 @@ run: build ## Build and run the binary
 	@echo "Running the $(BINARY) binary..."
 	@DEBUG_SPART=$(DEBUG_SPART) ./$(BINARY)
 
+.PHONY: run-examples
+run-examples: build ## Run the Rust examples
+	@echo "Running Rust examples..."
+	@cargo run --example quadtree
+	@cargo run --example octree
+	@cargo run --example kdtree
+	@cargo run --example rtree
+
+.PHONY: run-py-examples
+run-py-examples: develop-py ## Run the Python examples
+	@echo "Running Python examples..."
+	@$(PY_DEP_MNGR) run python pyspart/examples/quadtree.py
+	@$(PY_DEP_MNGR) run python pyspart/examples/octree.py
+	@$(PY_DEP_MNGR) run python pyspart/examples/kdtree.py
+	@$(PY_DEP_MNGR) run python pyspart/examples/rtree.py
+
 .PHONY: clean
 clean: ## Remove generated and temporary files
 	@echo "Cleaning up..."
 	@cargo clean
+	@rm -rf $(WHEEL_DIR) dist/ $(PYSPART_DIR)/$(WHEEL_DIR)
+	@rm -f $(PYSPART_DIR)/*.so
 
 .PHONY: install-snap
 install-snap: ## Install a few dependencies using Snapcraft
@@ -57,8 +83,9 @@ install-deps: install-snap ## Install development dependencies
 	@echo "Installing dependencies..."
 	@rustup component add rustfmt clippy
 	@cargo install cargo-tarpaulin
-	@cargo install cargo-audit
-	@cargo install nextest
+	@cargo install --locked cargo-nextest --version 0.9.97-b.2
+	@sudo apt-get install -y python3-pip
+	@pip install $(PY_DEP_MNGR)
 
 .PHONY: lint
 lint: format ## Run linters on Rust files
@@ -85,12 +112,68 @@ nextest: ## Run tests using nextest
 	@echo "Running tests using nextest..."
 	@DEBUG_SPART=$(DEBUG_SPART) RUST_BACKTRACE=$(RUST_BACKTRACE) cargo nextest run
 
-.PHONY: doc
-doc: format ## Generate the documentation
+.PHONY: docs
+docs: format ## Generate the documentation
 	@echo "Generating documentation..."
 	@cargo doc --no-deps --document-private-items
 
 .PHONY: fix-lint
 fix-lint: ## Fix the linter warnings
 	@echo "Fixing linter warnings..."
 	@cargo clippy --fix --allow-dirty --allow-staged --all-targets --workspace --all-features -- -D warnings
+
+########################################################################################
+## Python targets
+########################################################################################
+
+.PHONY: develop-py
+develop-py: ## Build and install PySpart in the current Python environment
+	@echo "Building and installing PySpart..."
+	# Note: Maturin does not work when CONDA_PREFIX and VIRTUAL_ENV are both set
+	@(cd $(PYSPART_DIR) && unset CONDA_PREFIX && maturin develop)
+
+.PHONY: wheel
+wheel: ## Build the wheel file for PySpart
+	@echo "Building the PySpart wheel..."
+	@(cd $(PYSPART_DIR) && maturin build --release --out $(WHEEL_DIR) --auditwheel check)
+
+.PHONY: wheel-manylinux
+wheel-manylinux: ## Build the manylinux wheel file for PySpart (using Zig)
+	@echo "Building the manylinux PySpart wheel..."
+	@(cd $(PYSPART_DIR) && maturin build --release --out $(WHEEL_DIR) --auditwheel check --zig)
+
+.PHONY: test-py
+test-py: develop-py ## Run Python tests
+	@echo "Running Python tests..."
+	@$(PY_DEP_MNGR) run pytest
+
+.PHONY: publish-py
+publish-py: wheel-manylinux ## Publish the PySpart wheel to PyPI (requires PYPI_TOKEN to be set)
+	@echo "Publishing PySpart to PyPI..."
+	@if [ -z "$(WHEEL_FILE)" ]; then \
+	   echo "Error: No wheel file found. Please run 'make wheel' first."; \
+	   exit 1; \
+	fi
+	@echo "Found wheel file: $(WHEEL_FILE)"
+	@twine upload -u __token__ -p $(PYPI_TOKEN) $(WHEEL_FILE)
+
+.PHONY: generate-ci
+generate-ci: ## Generate CI configuration files (GitHub Actions workflow)
+	@echo "Generating CI configuration files..."
+	@(cd $(PYSPART_DIR) && maturin generate-ci --zig --pytest --platform all -o ../.github/workflows/ci.yml github)
+
+########################################################################################
+## Additional targets
+########################################################################################
+
+.PHONY: setup-hooks
+setup-hooks: ## Install Git hooks (pre-commit and pre-push)
+	@echo "Installing Git hooks..."
+	@pre-commit install --hook-type pre-commit
+	@pre-commit install --hook-type pre-push
+	@pre-commit install-hooks
+
+.PHONY: test-hooks
+test-hooks: ## Test Git hooks on all files
+	@echo "Testing Git hooks..."
+	@pre-commit run --all-files