Fix install docs and trim packaging, hooks and CI config

.github/workflows/python-test.yml

@@ -1,7 +1,10 @@
 # Run tests, linting, and type checking
 name: CI
 
-on: [push, pull_request]
+on:
+  push:
+    branches: [main]
+  pull_request:
 
 jobs:
   test:

.gitignore

@@ -86,14 +86,6 @@ __pypackages__/
 # Cursor
 .cursorrules
 
-# Jupyter Notebooks
-.ipynb_checkpoints
-.virtual_documents/
-
-# Documentation
-# MkDocs
-/site
-
 # OS Specific
 # macOS
 .DS_Store
@@ -105,7 +97,6 @@ Desktop.ini
 
 # Private content
 private/
-notebooks/private/
 *_private/
 *.private.*
 
@@ -128,14 +119,6 @@ temp/
 temporary/
 analysis_temp/
 tmp/
-analysis*.ipynb
-*_analysis.ipynb
-analysis*.html
-*_analysis.html
-
-# Performance analysis results
-dev/perf_results/
-dev/perf_plots/
 
 # Repo root file ignores
 # Ignore certain file types only at the repository root
@@ -145,7 +128,6 @@ dev/perf_plots/
 /*.json
 
 # Allow required config files
-!/mkdocs.yml
 !/.pre-commit-config.yaml
 
 # Project directories to ignore at the repository root

.pre-commit-config.yaml

@@ -6,31 +6,6 @@ repos:
         args: [--fix]
       - id: ruff-format
 
-  - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.401
-    hooks:
-      - id: pyright
-        args: [--project, pyproject.toml]
-        additional_dependencies:
-          [
-            "pyyaml",
-            "pandas",
-            "matplotlib",
-            "nbformat",
-            "nbconvert",
-            "ipykernel",
-            "itables",
-            "rasterio",
-            "pyproj",
-            "geopandas",
-            "shapely",
-            "scikit-learn",
-            "networkx",
-            "contextily",
-            "pandas-stubs",
-            "ngraph>=0.23.1",
-          ]
-
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:

CHANGELOG.md

@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **Workflows**: Use `design_analysis_brief` as the default in both Python and YAML configurations.
 - **Workflows**: Bind built-in demand references to `traffic.matrix_name`.
 - **Failures**: Make the `empty` policy a valid no-failure mode.
+- **Docs**: Install from GitHub; the `topogen` name on PyPI belongs to an unrelated project.
 
 ### Changed
 
@@ -30,12 +31,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **Workflows**: Validate `lib/workflows.yml` with NetGraph before emission; steps use `type` and `demand_set`.
 - **Workflows**: Use `parallelism: auto` in built-in and sample workflows.
 - **Validation**: Construct the full NetGraph scenario to check workflow arguments and failure policies before topology audits.
-- **Internal**: Remove redundant validation and scenario code; shorten comments and documentation.
+- **Internal**: Remove redundant validation and scenario code, the PyPI publish workflow, the pre-commit Pyright hook and benchmark flags.
 
 ### Added
 
 - **Superset**: Add setup, teardown and run commands to install dev dependencies, copy local `.env` files and run checks.
 
+### Removed
+
+- **Dependencies**: Unused `seaborn`, `rich`, `nbformat`, `nbconvert`, `ipykernel`, `itables`, `rasterio` and `scikit-learn` requirements.
+
 ## [0.4.0] - 2026-03-15
 
 ### Changed

Makefile

@@ -1,6 +1,6 @@
 # TopoGen development commands
 
-.PHONY: help venv clean-venv dev install check check-ci lint format test qt build clean check-dist publish-test publish validate info hooks check-python
+.PHONY: help venv clean-venv dev install check check-ci lint format test qt build clean check-dist validate info hooks check-python
 
 .DEFAULT_GOAL := help
 
@@ -33,18 +33,14 @@ help:
 	@echo "  make lint          - Run only linting (non-mutating: ruff + pyright)"
 	@echo "  make format        - Auto-format code with ruff"
 	@echo "  make validate      - Validate YAML configs against schemas"
-	@echo "  make test          - Run tests with coverage (includes slow and benchmark)"
-	@echo "  make qt            - Run quick tests only (excludes slow and benchmark)"
+	@echo "  make test          - Run tests with coverage (includes slow)"
+	@echo "  make qt            - Run quick tests only (excludes slow)"
 	@echo ""
 	@echo "Build & Package:"
 	@echo "  make build         - Build distribution packages"
+	@echo "  make check-dist    - Check distribution metadata with twine"
 	@echo "  make clean         - Clean build artifacts and cache files"
 	@echo ""
-	@echo "Publishing:"
-	@echo "  make check-dist    - Check distribution packages with twine"
-	@echo "  make publish-test  - Publish to Test PyPI"
-	@echo "  make publish       - Publish to PyPI"
-	@echo ""
 	@echo "Utilities:"
 	@echo "  make hooks         - Run pre-commit on all files"
 	@echo "  make check-python  - Check if venv Python matches best available"
@@ -121,12 +117,12 @@ format:
 	@$(RUFF) format .
 
 test:
-	@echo "🧪 Running tests with coverage (includes slow and benchmark)..."
+	@echo "🧪 Running tests with coverage (includes slow)..."
 	@$(PYTEST)
 
 qt:
-	@echo "⚡ Running quick tests only (excludes slow and benchmark)..."
-	@$(PYTEST) --no-cov -m "not slow and not benchmark"
+	@echo "⚡ Running quick tests only (excludes slow)..."
+	@$(PYTEST) --no-cov -m "not slow"
 
 validate:
 	@echo "📋 Validating TopoGen config YAMLs..."
@@ -149,42 +145,23 @@ build:
 clean:
 	@echo "🧹 Cleaning build artifacts and cache files..."
 	@rm -rf build/ dist/ *.egg-info/ || true
-	@rm -rf .pytest_cache .ruff_cache .mypy_cache htmlcov htmlcov-python .coverage coverage.xml coverage-*.xml .benchmarks .pytest-benchmark || true
+	@rm -rf .pytest_cache .ruff_cache htmlcov .coverage coverage.xml || true
 	@find . -path "./venv" -prune -o -type f -name "*.pyc" -delete 2>/dev/null || true
 	@find . -path "./venv" -prune -o -type d -name "__pycache__" -exec rm -rf {} + 2>/dev/null || true
 	@find . -path "./venv" -prune -o -type f -name "*.pyo" -delete 2>/dev/null || true
 	@find . -path "./venv" -prune -o -type f -name "*~" -delete 2>/dev/null || true
 	@find . -path "./venv" -prune -o -type f -name "*.orig" -delete 2>/dev/null || true
 	@echo "✅ Cleanup complete!"
 
-# Publishing
 check-dist:
-	@echo "🔍 Checking distribution packages..."
+	@echo "🔍 Checking distribution metadata..."
 	@if $(PYTHON) -c "import twine" >/dev/null 2>&1; then \
 		$(PYTHON) -m twine check dist/*; \
 	else \
 		echo "❌ twine not installed. Install dev dependencies with: make dev"; \
 		exit 1; \
 	fi
 
-publish-test:
-	@echo "📦 Publishing to Test PyPI..."
-	@if $(PYTHON) -c "import twine" >/dev/null 2>&1; then \
-		$(PYTHON) -m twine upload --repository testpypi dist/*; \
-	else \
-		echo "❌ twine not installed. Install dev dependencies with: make dev"; \
-		exit 1; \
-	fi
-
-publish:
-	@echo "🚀 Publishing to PyPI..."
-	@if $(PYTHON) -c "import twine" >/dev/null 2>&1; then \
-		$(PYTHON) -m twine upload dist/*; \
-	else \
-		echo "❌ twine not installed. Install dev dependencies with: make dev"; \
-		exit 1; \
-	fi
-
 # Project Information
 info:
 	@echo "📋 TopoGen Project Information"

README.md

@@ -10,10 +10,11 @@ scenarios with site blueprints, hardware, risk groups, traffic, and workflows.
 ## Install
 
 Requires Python 3.11+. Dependencies include `ngraph>=0.23.1` and
-`netgraph-core>=0.10.0`.
+`netgraph-core>=0.10.0`. TopoGen is not on PyPI; the `topogen` package there is
+an unrelated project.
 
 ```bash
-pip install topogen
+pip install git+https://github.com/networmix/TopoGen
 ```
 
 For a source checkout:
@@ -44,8 +45,8 @@ ngraph run output/config_scenario.yml
 ```
 
 `generate` writes `output/config_integrated_graph.json`, a metro-to-metro corridor
-graph. `build` reads it and writes `output/config_scenario.yml`. File prefixes
-come from the config filename.
+graph, and a preview JPEG. `build` reads the graph and writes
+`output/config_scenario.yml`. File prefixes come from the config filename.
 
 `build` checks the schema, NetGraph Scenario construction, topology, and hardware.
 `ngraph run` executes the workflows. Add `--print` to `topogen build` to also print

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "topogen"
 version = "0.4.0"
-description = "A network topology generator."
+description = "Generate NetGraph backbone scenarios from US Census urban areas and TIGER/Line roads."
 readme = "README.md"
 authors = [{ name = "Andrey Golovanov" }]
 license = "MIT"
@@ -27,19 +27,11 @@ dependencies = [
     "numpy",
     "pandas",
     "matplotlib",
-    "seaborn",
-    "rich",
-    "nbformat",
-    "nbconvert",
-    "ipykernel",
-    "itables",
     # Geographic processing
-    "rasterio",
     "pyproj",
     "geopandas",
     "shapely",
     "scipy",
-    "scikit-learn",
     "networkx",
     "contextily",
     # Strict schema validation at runtime
@@ -55,34 +47,33 @@ dev = [
     # testing
     "pytest>=8",
     "pytest-cov",
-    "pytest-benchmark",
-    "pytest-mock",
     "pytest-timeout",
-    # json schema validation for scenarios
-    "jsonschema",
     # style + type checking
     "ruff==0.11.13",
     "pyright==1.1.401",
     # type stubs
     "pandas-stubs",
     # pre-commit hooks
     "pre-commit",
-    # build
+    # build and metadata checks
     "build",
-    # publishing
     "twine",
 ]
 
+[project.urls]
+Repository = "https://github.com/networmix/TopoGen"
+Changelog = "https://github.com/networmix/TopoGen/blob/main/CHANGELOG.md"
+Issues = "https://github.com/networmix/TopoGen/issues"
+
 [project.scripts]
 topogen = "topogen.cli:main"
 
 # Pytest flags
 [tool.pytest.ini_options]
-addopts = "--cov=./topogen --cov-fail-under=50 --cov-report term-missing --benchmark-disable-gc --benchmark-min-rounds=5 --benchmark-warmup=on"
+addopts = "--cov=./topogen --cov-fail-under=50 --cov-report term-missing"
 timeout = 30
 markers = [
     "slow: marks integration tests as slow (deselect with '-m \"not slow\"')",
-    "benchmark: marks tests as performance benchmarks (run with '-m benchmark')",
 ]
 
 # Coverage configuration
@@ -101,7 +92,6 @@ exclude_lines = [
 # Package discovery
 [tool.setuptools.packages.find]
 include = ["topogen*"]
-exclude = ["tests*", "notebooks*", "examples*", "dev*"]
 
 [tool.setuptools.package-data]
 "topogen.schemas" = ["topogen_config.json"]