Update NetGraph integration and Superset setup

.gitignore

@@ -50,6 +50,11 @@ tests/*no_publish*
 # -----------------------------------------------------------------------------
 # Virtual environments
 .env
+.env.*
+!.env.example
+!.env.sample
+!.env.template
+!.env.*.example
 .venv
 env/
 venv/
@@ -67,6 +72,9 @@ __pypackages__/
 # Type checkers & linters
 .ruff_cache/
 
+# Superset per-machine lifecycle overrides
+.superset/config.local.json
+
 # -----------------------------------------------------------------------------
 # IDEs & Editors
 # -----------------------------------------------------------------------------

.superset/config.json

@@ -0,0 +1,5 @@
+{
+  "setup": ["bash .superset/workspace.sh setup"],
+  "teardown": ["bash .superset/workspace.sh teardown"],
+  "run": ["bash .superset/workspace.sh check"]
+}

.superset/workspace.sh

@@ -0,0 +1,49 @@
+#!/usr/bin/env bash
+set -euo pipefail
+cd "$(dirname "${BASH_SOURCE[0]}")/.."
+
+mode=${1:-help}
+case "$mode" in
+    setup|check) ;;
+    teardown)
+        # Setup starts no background processes or services.
+        echo 'No workspace services to stop.'
+        exit 0
+        ;;
+    *) echo 'Usage: bash .superset/workspace.sh {setup|check|teardown}'; exit 2 ;;
+esac
+
+unset PYTHONPATH PYTHONHOME
+if [[ "$mode" == setup ]]; then
+    # Copy missing, untracked environment files from the root checkout.
+    root_path=${SUPERSET_ROOT_PATH:-$PWD}
+    [[ -d "$root_path" ]] || { echo "Root checkout not found: $root_path" >&2; exit 1; }
+    shopt -s nullglob
+    for source_file in "$root_path"/.env "$root_path"/.env.*; do
+        [[ -f "$source_file" ]] || continue
+        filename=${source_file##*/}
+        if git -C "$root_path" ls-files --error-unmatch -- "$filename" >/dev/null 2>&1; then
+            continue
+        fi
+        [[ ! -e "$filename" && ! -L "$filename" ]] || continue
+        cp -p "$source_file" "$filename"
+        echo "Copied $filename from root checkout."
+    done
+    shopt -u nullglob
+    git submodule update --init
+    if [[ ! -x venv/bin/python ]]; then
+        make venv
+    fi
+fi
+
+[[ -x venv/bin/python ]] || { echo 'Run bash .superset/workspace.sh setup first.' >&2; exit 1; }
+export VIRTUAL_ENV="$PWD/venv"
+export PATH="$VIRTUAL_ENV/bin:$PATH"
+
+if [[ "$mode" == setup ]]; then
+    python -m pip install -e '.[dev]'
+    python -m pip check
+    python -c 'import netlab, ngraph, netgraph_core, topogen; print("Workspace environment ready")'
+else
+    make check-ci
+fi

CHANGELOG.md

@@ -5,6 +5,42 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+
+### Fixed
+
+- **CLI**: Invoke `ngraph inspect` without the unsupported output option.
+- **CLI**: Return a nonzero exit status when scenario inspection or simulation fails.
+- **BAC**: Keep destinations distinct for flows sharing a source and sum priority classes within each direction.
+- **Sweeps**: Normalize directional BAC by baseline delivery, matching the metrics pipeline.
+- **Plots**: Compute iteration-count and timing medians and interquartile ranges from per-seed data.
+
+### Changed
+
+- **BREAKING**: **Dependencies**: Require NetGraph `>=0.24.0`.
+- **BREAKING**: **Workflows**: Placement inherits the scenario seed; set step `seed` explicitly to keep using `42`.
+- **BREAKING**: **Metrics**: Require a positive integer `occurrence_count` on every failure flow result.
+- **BREAKING**: **Summaries**: Replace operation counters with `iters_fail`, `iters_total`, and `unique_patterns`.
+- **Scenarios**: Generated scenarios, shared templates, and the autoresearch prompt use current NetGraph keys.
+- **Autoresearch**: Prompts distinguish measurements from explanations and flag missing or inconsistent evidence.
+- **Autoresearch**: Load the NetGraph DSL reference from the `.claude/skills` submodule; run `git submodule update --init` to enable it.
+- **Fixtures**: Regenerate scenarios, results, and metrics; see `tests/data/README.md` for numerical changes.
+- **Docs**: Correct command examples, metric definitions, and scenario descriptions.
+- **Internal**: Consolidate metric and provenance helpers, run the TopoGen pipeline checks in the default test suite, and remove unused code, fixtures, and the PyPI publish workflow.
+
+### Added
+
+- **Workspaces**: Superset setup creates an isolated environment and copies missing `.env` files; Run executes `make check-ci`.
+- **Integration**: Add local-source validation and fixture regeneration commands.
+
+### Removed
+
+- **BREAKING**: **MSD**: Remove `base_demands` aliases `source_path`, `sink_path`, and `demand`; use `source`, `target`, and `volume`.
+- **BREAKING**: **MSD**: Read alpha from `msd_baseline.data.alpha_star`; remove `msd` and placement-probe inference.
+- **BREAKING**: **Timing**: Read step duration from `metadata.duration_sec`; remove the `execution_time` alias.
+- **BREAKING**: **Graphs**: Require `edges` in graph results; remove support for the `links` alias.
+- **BREAKING**: **Autoresearch**: Remove the `parameters` alias in hypothesis templates; use `params`.
+
 ## [0.3.0] - 2026-03-26
 
 ### Fixed

Makefile

@@ -1,6 +1,6 @@
 # NetLab Development Makefile
 
-.PHONY: help venv clean-venv dev install check check-ci lint format test qt build clean check-dist publish-test publish info hooks check-python
+.PHONY: help venv clean-venv dev install check check-ci lint format test qt build clean check-dist info hooks check-python
 
 .DEFAULT_GOAL := help
 
@@ -51,8 +51,6 @@ help:
 	@echo "  make build         - Build distribution packages"
 	@echo "  make clean         - Clean build artifacts and cache files"
 	@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 info          - Show project information"
@@ -159,24 +157,6 @@ check-dist:
 		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
-
 info:
 	@echo "📋 NetLab Project Information"
 	@echo "============================="