The fourth pre-release (#14)

Author: habedi

.editorconfig

@@ -36,4 +36,3 @@ indent_size = 2
 # TOML files
 [*.toml]
 indent_size = 2
-

.github/FUNDING.yml

@@ -0,0 +1 @@
+github: [habedi]

.github/workflows/lint.yml renamed to .github/workflows/lints.yml

@@ -1,10 +1,16 @@
 name: Run Linters
 
 on:
-  workflow_dispatch: { } # Allow manual execution
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
   push:
     tags:
-      - 'v*' # Trigger on version tags
+      - 'v*'
+
+permissions:
+  contents: read
 
 jobs:
   lint:
@@ -17,7 +23,7 @@ jobs:
       - name: Set up Rust
         uses: actions-rust-lang/setup-rust-toolchain@v1
         with:
-          toolchain: stable
+          toolchain: '1.86.0' # Pinned to project's MSRV
 
       - name: Install Dependencies
         run: |

.github/workflows/publish.yml

@@ -1,14 +1,15 @@
 name: Publish to Crates.io
 
 on:
-  workflow_dispatch: { } # Allow manual execution
+  workflow_dispatch:
   push:
     tags:
-      - 'v*' # Trigger on version tags
+      - 'v*'
 
-jobs:
+permissions:
+  contents: read
 
-  # Run tests before publishing and only publish if tests pass
+jobs:
   call_tests:
     uses: ./.github/workflows/tests.yml
 
@@ -35,4 +36,4 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y make
           cargo publish --token $CARGO_REGISTRY_TOKEN
-        continue-on-error: false
+        continue-on-error: false

.github/workflows/publish_py.yml

@@ -1,20 +1,17 @@
 name: Publish to PyPI
 
 on:
-  workflow_dispatch: # Enable manual runs
+  workflow_dispatch:
   push:
     tags:
-      - 'v*' # Trigger on version tags
+      - 'v*'
 
-jobs:
-
-  #  # Run tests before publishing
-  #  call_tests:
-  #    uses: ./.github/workflows/tests_py.yml
+permissions:
+  contents: read
 
+jobs:
   publish_to_pypi:
     runs-on: ubuntu-latest
-    #    needs: call_tests
 
     steps:
       - name: Checkout Repository
@@ -38,4 +35,4 @@ jobs:
       - name: Build and Publish Package
         run: |
           poetry run make wheel-manylinux
-          PYPI_TOKEN=${{ secrets.PYPI_API_TOKEN }} poetry run make publish_py
+          PYPI_TOKEN=${{ secrets.PYPI_API_TOKEN }} poetry run make publish-py

.github/workflows/tests.yml

@@ -1,11 +1,17 @@
 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
   push:
     tags:
-      - 'v*' # Trigger on version tags
+      - 'v*'
+
+permissions:
+  contents: read
 
 jobs:
   build:
@@ -14,7 +20,7 @@ jobs:
     strategy:
       matrix:
         # Define the Rust versions to test against
-        rust-version: [ "1.83.0", "1.84.0", "beta", "stable" ]
+        rust-version: [ "1.86.0", "stable" ]
 
     steps:
       - name: Checkout Repository
@@ -32,7 +38,7 @@ jobs:
           make install-deps
 
       - name: Run Tests and Generate Coverage Report
-        run: make coverage # Generates a coverage report
+        run: make coverage
 
       - name: Upload Coverage Reports to Codecov
         uses: codecov/codecov-action@v5

.gitignore

@@ -73,17 +73,7 @@ tarpaulin-report.html
 # Dependency lock files (uncomment to ignore)
 poetry.lock
 Cargo.lock
-
-# Miscellaneous files and directories to ignore
-# Add any additional file patterns a directory names that should be ignored down here
-.DS_Store
-tmp_*
-temp_*
-output_*
-*.so
-.benchmarks/
-ci.yml
-src/main.rs
+#uv.lock
 
 # Ignore files in the tests/testdata/[graphina-graphs] directory
 tests/testdata/*.txt
@@ -97,3 +87,15 @@ tests/testdata/graphina-graphs/*.txt
 tests/testdata/graphina-graphs/*.csv
 tests/testdata/graphina-graphs/*.json
 tests/testdata/graphina-graphs/*.parquet
+
+# Miscellaneous files and directories to ignore
+# Add any additional file patterns a directory names that should be ignored down here
+.DS_Store
+tmp_*
+temp_*
+output_*
+*.so
+.benchmarks/
+ci.yml
+src/main.rs
+*_output.txt

.pre-commit-config.yaml

@@ -0,0 +1,40 @@
+default_stages: [ pre-push ]
+fail_fast: false
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+        args: [ --markdown-linebreak-ext=md ]
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: check-merge-conflict
+      - id: check-added-large-files
+      - id: detect-private-key
+      - id: check-yaml
+      - id: check-toml
+      - id: check-json
+      - id: check-docstring-first
+      - id: pretty-format-json
+        args: [ --autofix, --no-sort-keys ]
+
+  - repo: local
+    hooks:
+      - id: format
+        name: Format Code
+        entry: make format
+        language: system
+        pass_filenames: false
+
+      - id: lint
+        name: Check Code Style
+        entry: make lint
+        language: system
+        pass_filenames: false
+
+      - id: test
+        name: Run Tests
+        entry: make nexttest
+        language: system
+        pass_filenames: false

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "graphina"
-version = "0.2.2-alpha"
+version = "0.3.0-a1"
 description = "A graph data science library for Rust"
 repository = "https://github.com/habedi/graphina"
 license = "MIT OR Apache-2.0"
@@ -10,8 +10,8 @@ authors = ["Hassan Abedi <hassan.abedi.t@gmail.com>"]
 homepage = "https://github.com/habedi/graphina"
 documentation = "https://docs.rs/graphina"
 categories = ["data-structures", "algorithms"]
-edition = "2021"
-rust-version = "1.83"
+edition = "2024"
+rust-version = "1.86.0"
 
 resolver = "2"
 
@@ -41,10 +41,10 @@ sprs = "0.11.3"
 ordered-float = "5.0.0"
 rayon = "1.10.0"
 nalgebra = "0.33.2"
-petgraph = { version = "0.7.1", features = ["graphmap", "stable_graph", "matrix_graph", "serde-1", "rayon"] }
+petgraph = { version = "0.8.2", features = ["graphmap", "stable_graph", "matrix_graph", "serde-1", "rayon"] }
 
 [dev-dependencies]
-criterion = { version = "0.5", features = ["html_reports"] }
+criterion = { version = "0.7.0", features = ["html_reports"] }
 
 [[bench]]
 name = "project_benchmarks"

Makefile

@@ -8,9 +8,10 @@ RUST_LOG        := info
 RUST_BACKTRACE  := full
 WHEEL_DIR       := dist
 PYGRAPHINA_DIR  := pygraphina
+PY_DEP_MNGR := uv # Use `uv sync --all-extras` to make the environment
 TEST_DATA_DIR  := tests/testdata
 SHELL           := /bin/bash
-MSRV			:= 1.83
+MSRV          := 1.86
 
 # Find the latest built Python wheel file
 WHEEL_FILE := $(shell ls $(PYGRAPHINA_DIR)/$(WHEEL_DIR)/pygraphina-*.whl 2>/dev/null | head -n 1)
@@ -20,8 +21,8 @@ WHEEL_FILE := $(shell ls $(PYGRAPHINA_DIR)/$(WHEEL_DIR)/pygraphina-*.whl 2>/dev/
 
 .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, $$2}'
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' Makefile | \
+	   awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
 
 ########################################################################################
 ## Rust targets
@@ -74,6 +75,8 @@ install-deps: install-snap ## Install development dependencies
 	@cargo install cargo-tarpaulin
 	@cargo install cargo-audit
 	@cargo install cargo-nextest
+	@sudo apt-get install python3-pip
+	@pip install $(PY_DEP_MNGR)
 
 .PHONY: lint
 lint: format ## Run linters on Rust files
@@ -125,9 +128,9 @@ install-msrv: ## Install the minimum supported Rust version (MSRV) for developme
 run-examples: ## Run all the scripts in the examples directory one by one
 	@echo "Running all example scripts..."
 	@for example in examples/*.rs; do \
-		example_name=$$(basename $$example .rs); \
-		echo "Running example: $$example_name"; \
-		cargo run --example $$example_name; \
+	   example_name=$$(basename $$example .rs); \
+	   echo "Running example: $$example_name"; \
+	   cargo run --example $$example_name; \
 	done
 
 ########################################################################################
@@ -153,14 +156,14 @@ wheel-manylinux: ## Build the manylinux wheel file for PyGraphina (using Zig)
 .PHONY: test-py
 test-py: develop-py ## Run Python tests
 	@echo "Running Python tests..."
-	@poetry run pytest $(PYGRAPHINA_DIR)/tests
+	@$(PY_DEP_MNGR) run pytest
 
 .PHONY: publish-py
 publish-py: wheel-manylinux ## Publish the PyGraphina wheel to PyPI (requires PYPI_TOKEN to be set)
 	@echo "Publishing PyGraphina to PyPI..."
 	@if [ -z "$(WHEEL_FILE)" ]; then \
-		echo "Error: No wheel file found. Please run 'make wheel' first."; \
-		exit 1; \
+	   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)
@@ -169,3 +172,19 @@ publish-py: wheel-manylinux ## Publish the PyGraphina wheel to PyPI (requires PY
 generate-ci: ## Generate CI configuration files (GitHub Actions workflow)
 	@echo "Generating CI configuration files..."
 	@(cd $(PYGRAPHINA_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