Restore validated safety behaviour and prepare v0.1.1

.github/workflows/tests.yml

@@ -0,0 +1,43 @@
+name: Tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
+        python-version:
+          - "3.10"
+          - "3.11"
+          - "3.12"
+          - "3.13"
+          - "3.14"
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install NEXCISION
+        run: python -m pip install .
+
+      - name: Run tests
+        run: python -m unittest discover -s tests -v

.gitignore

@@ -0,0 +1,21 @@
+# Python virtual environments
+.venv/
+venv/
+
+# Python cache files
+__pycache__/
+*.py[cod]
+
+# Python package/build metadata
+*.egg-info/
+build/
+dist/
+
+# Test and coverage artefacts
+.pytest_cache/
+.coverage
+htmlcov/
+
+# Operating-system/editor files
+.DS_Store
+Thumbs.db

CHANGELOG.md

@@ -1,5 +1,14 @@
 # Changelog
 
+## 0.1.1 — 2026-08-10
+
+- Synchronizes the public source with the implementation used in the formal NEXCISION validation.
+- Rejects removal of every matrix row by default; `--allow-empty` permits this only when explicitly requested.
+- Stages all requested outputs before committing them and rolls back partial writes if a multi-output operation fails.
+- Handles invalid UTF-8 NEXUS and region files with controlled errors.
+- Records the `allow_empty` setting in the deterministic JSON provenance report.
+- Adds permanent regression tests for these safety behaviours.
+
 ## 0.1.0 — 2026-07-21
 
 - Initial NEXCISION release.

CITATION.cff

@@ -5,8 +5,8 @@ type: software
 authors:
   - family-names: "White"
     given-names: "Rhys"
-version: 0.1.0
-date-released: 2026-07-21
+version: 0.1.1
+date-released: 2026-08-10
 repository-code: "https://github.com/RhysWhite/nexcision"
 license: MIT
 abstract: >-

README.md

@@ -155,6 +155,9 @@ acceptance rule depends on the supplied mask and analysis. See
 [Workflow integration](docs/workflow-integration.md) for shell and Snakemake
 examples, including a report-gated downstream step.
 
+For a detailed plain-English explanation of how the program works, see the
+[Code walkthrough](docs/code-walkthrough.md).
+
 ## Dimension handling
 
 By default, NEXCISION automatically selects the appropriate NEXUS dimension to update: