Add Initial SIST Regression Test Suite

.github/workflows/pr.yaml

@@ -0,0 +1,82 @@
+name: Pull Request CI
+
+on:
+  pull_request:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: pr-ci-${{ github.event.pull_request.number }}
+  cancel-in-progress: true
+
+jobs:
+  regression:
+    name: Regression
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version: "3.14"
+
+      - name: Install testing dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e '.[testing]'
+
+      - name: Run regression tests
+        run: |
+          python -m pytest tests \
+            -m regression \
+            -vv \
+            --durations=20 \
+            --basetemp=.testdata
+
+      - name: Upload regression artefacts on failure
+        if: failure()
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: pr-regression-failure
+          path: .testdata/
+          if-no-files-found: ignore
+          include-hidden-files: true
+          retention-days: 7
+
+  docs:
+    name: Docs
+    runs-on: ubuntu-24.04
+    timeout-minutes: 20
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version: "3.14"
+
+      - name: Install documentation dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r docs/requirements.txt
+
+      - name: Build documentation
+        run: |
+          make -C docs clean
+          make -C docs html SPHINXOPTS="-W --keep-going"
+
+      - name: Upload documentation
+        if: success()
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: docs-html
+          path: docs/build/html/
+          if-no-files-found: error
+          retention-days: 7

.github/workflows/regression-tests.yaml

@@ -0,0 +1,54 @@
+name: Regression Tests
+
+on:
+  push:
+    branches:
+      - main
+  schedule:
+    - cron: "0 8 * * 1"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: sist-regression-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  regression:
+    name: SIST Regression
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version: "3.14"
+
+      - name: Install testing dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e '.[testing]'
+
+      - name: Run regression tests
+        run: |
+          python -m pytest tests \
+            -m regression \
+            -vv \
+            --durations=20 \
+            --basetemp=.testdata
+
+      - name: Upload regression artefacts on failure
+        if: failure()
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: sist-regression-failure
+          path: .testdata/
+          if-no-files-found: ignore
+          include-hidden-files: true
+          retention-days: 7

.gitignore

@@ -1,32 +1,34 @@
 # Default ignored files
 /shelf/
 /workspace.xml
+
 # Editor-based HTTP Client requests
 /httpRequests/
+
 # Datasource local storage ignored files
 /dataSources/
 /dataSources.local.xml
 
 # Prerequisites
 *.d
 
-# Compiled Object files
+# Compiled object files
 *.slo
 *.lo
 *.o
 *.obj
 
-# Precompiled Headers
+# Precompiled headers
 *.gch
 *.pch
 
 # Linker files
 *.ilk
 
-# Debugger Files
+# Debugger files
 *.pdb
 
-# Compiled Dynamic libraries
+# Compiled dynamic libraries
 *.so
 *.dylib
 *.dll
@@ -35,7 +37,7 @@
 *.mod
 *.smod
 
-# Compiled Static libraries
+# Compiled static libraries
 *.lai
 *.la
 *.a
@@ -46,13 +48,27 @@
 *.out
 *.app
 
-# debug information files
+# Debug information files
 *.dwo
 
+# Build directories
+build/
+dist/
+cmake-build-*/
+
 # Sphinx build output
 docs/build/
 docs/source/_autosummary/
 
-# Python cache
+# Python environments, caches, and packaging
+.venv/
+venv/
 __pycache__/
-*.pyc
+*.py[cod]
+.pytest_cache/
+.ruff_cache/
+*.egg-info/
+
+# Regression test artefacts
+.testdata/
+test-results/

docs/source/conf.py

@@ -38,4 +38,4 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
 html_theme = 'furo'
-html_static_path = ['_static']
+# html_static_path = ['_static']

pyproject.toml

@@ -0,0 +1,36 @@
+[build-system]
+requires = ["setuptools>=77,<84"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "SIST"
+version = "0.0.1"
+description = "Stress-Induced Structural Transitions in superhelical DNA."
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = []
+
+maintainers = [
+    { name = "Harry Swift", email = "harry.swift@stfc.ac.uk" },
+]
+
+[project.urls]
+Repository = "https://github.com/CCPBioSim/SIST"
+
+[project.optional-dependencies]
+testing = [
+    "pytest>=9.0,<10.0",
+]
+
+[tool.setuptools]
+# SIST is currently a Perl/C++ application. This metadata manages the Python
+# test harness and its development dependencies; it does not package SIST.
+packages = []
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-ra"
+markers = [
+    "regression: end-to-end regression tests against reference outputs",
+    "slow: long-running tests excluded from the default test suite",
+]