From 8065655c2e642ccf2300491fec431479090baa8e Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Wed, 5 Aug 2026 16:14:18 +0100
Subject: [PATCH 1/5] test(regression): add SIST baseline regression suite and
 CI

---
 .github/workflows/pr.yaml                     |   82 +
 .github/workflows/regression-tests.yaml       |   50 +
 .gitignore                                    |   32 +-
 pyproject.toml                                |   47 +
 tests/conftest.py                             |  150 +
 tests/data/pbr322.toy.fa                      |   64 +
 tests/reference/v1.0.0/README.md              |   34 +
 .../v1.0.0/competition.inherited.txt          | 4419 +++++++++++++++++
 .../reference/v1.0.0/competition.rebuilt.txt  | 4395 ++++++++++++++++
 tests/test_cli.py                             |   64 +
 tests/test_regression.py                      |  230 +
 11 files changed, 9559 insertions(+), 8 deletions(-)
 create mode 100644 .github/workflows/pr.yaml
 create mode 100644 .github/workflows/regression-tests.yaml
 create mode 100644 pyproject.toml
 create mode 100644 tests/conftest.py
 create mode 100644 tests/data/pbr322.toy.fa
 create mode 100644 tests/reference/v1.0.0/README.md
 create mode 100644 tests/reference/v1.0.0/competition.inherited.txt
 create mode 100644 tests/reference/v1.0.0/competition.rebuilt.txt
 create mode 100644 tests/test_cli.py
 create mode 100644 tests/test_regression.py

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
new file mode 100644
index 0000000..fd9f2de
--- /dev/null
+++ b/.github/workflows/pr.yaml
@@ -0,0 +1,82 @@
+name: Pull Request CI
+
+on:
+  pull_request:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: pr-ci-${{ github.ref }}
+  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 -e '.[docs]'
+
+      - name: Build documentation
+        run: |
+          make -C docs clean
+          make -C docs html SPHINXOPTS="-W --keep-going"
+
+      - name: Upload documentation
+        if: always()
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: docs-html
+          path: docs/build/html
+          if-no-files-found: warn
+          retention-days: 7
\ No newline at end of file
diff --git a/.github/workflows/regression-tests.yaml b/.github/workflows/regression-tests.yaml
new file mode 100644
index 0000000..ef1193c
--- /dev/null
+++ b/.github/workflows/regression-tests.yaml
@@ -0,0 +1,50 @@
+name: Regression Tests
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  schedule:
+    - cron: '0 8 * * 1'
+  workflow_dispatch:
+
+concurrency:
+  group: sist-regression-${{ 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
+        with:
+          name: sist-regression-artifacts
+          path: .testdata/**
+          if-no-files-found: ignore
diff --git a/.gitignore b/.gitignore
index 4029da9..deadcbd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,8 +1,10 @@
 # Default ignored files
 /shelf/
 /workspace.xml
+
 # Editor-based HTTP Client requests
 /httpRequests/
+
 # Datasource local storage ignored files
 /dataSources/
 /dataSources.local.xml
@@ -10,23 +12,23 @@
 # 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
\ No newline at end of file
+*.py[cod]
+.pytest_cache/
+.ruff_cache/
+*.egg-info/
+
+# Regression test artefacts
+.testdata/
+test-results/
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..02c1d87
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,47 @@
+[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."
+
+authors = [
+]
+
+maintainers = [
+    {name = "Harry Swift", email = "harry.swift@stfc.ac.uk"}
+]
+readme = "README.md"
+
+requires-python = ">=3.12"
+dependencies = []
+
+[project.urls]
+Repository = "https://github.com/CCPBioSim/SIST"
+
+[project.optional-dependencies]
+testing = [
+    "pytest>=9.0,<10.0",
+]
+
+docs = [
+    "sphinx>=9.1,<9.2",
+    "sphinx-rtd-theme>=3.1,<3.2",
+]
+
+[tool.setuptools]
+# SIST is currently a Perl/C++ application. This metadata manages the Python
+# test harness and documentation 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",
+]
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000..19fdd9f
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,150 @@
+from __future__ import annotations
+
+import os
+import shutil
+import subprocess
+from dataclasses import dataclass
+from pathlib import Path
+
+import pytest
+
+
+REPOSITORY_ROOT = Path(__file__).resolve().parents[1]
+
+
+@dataclass(frozen=True)
+class CompetitionRun:
+    """Result of running the SIST competition example."""
+
+    process: subprocess.CompletedProcess[str]
+    output_path: Path
+
+
+def run_command(
+    command: list[str],
+    *,
+    cwd: Path,
+) -> subprocess.CompletedProcess[str]:
+    """Run a command and return its completed process."""
+
+    environment = os.environ.copy()
+    environment["LC_ALL"] = "C"
+
+    return subprocess.run(
+        command,
+        cwd=cwd,
+        env=environment,
+        capture_output=True,
+        text=True,
+        check=False,
+    )
+
+
+def require_success(
+    result: subprocess.CompletedProcess[str],
+    *,
+    description: str,
+) -> None:
+    """Fail the test setup with useful command output."""
+
+    if result.returncode == 0:
+        return
+
+    pytest.fail(
+        f"{description} failed with exit code {result.returncode}\n\n"
+        f"stdout:\n{result.stdout}\n\n"
+        f"stderr:\n{result.stderr}",
+        pytrace=False,
+    )
+
+
+@pytest.fixture(scope="session")
+def built_sist(tmp_path_factory: pytest.TempPathFactory) -> Path:
+    """
+    Copy and build SIST in a temporary directory.
+
+    This ensures the tests use executables built from the maintained source
+    without overwriting the inherited binaries in the repository.
+    """
+
+    build_root = tmp_path_factory.mktemp("sist-build")
+    working_copy = build_root / "SIST"
+
+    shutil.copytree(
+        REPOSITORY_ROOT,
+        working_copy,
+        ignore=shutil.ignore_patterns(
+            ".git",
+            ".venv",
+            ".pytest_cache",
+            ".testdata",
+            "__pycache__",
+            "cmake-build-debug",
+        ),
+    )
+
+    for directory in ("trans_three", "trans_compete"):
+        clean_result = run_command(
+            ["make", "-C", directory, "clean"],
+            cwd=working_copy,
+        )
+        require_success(
+            clean_result,
+            description=f"Cleaning {directory}",
+        )
+
+        build_result = run_command(
+            ["make", "-C", directory],
+            cwd=working_copy,
+        )
+        require_success(
+            build_result,
+            description=f"Building {directory}",
+        )
+
+        executable = working_copy / directory / "qsidd"
+
+        if not executable.is_file():
+            pytest.fail(
+                f"Build completed but {executable} was not created",
+                pytrace=False,
+            )
+
+    return working_copy
+
+
+@pytest.fixture(scope="session")
+def competition_run(built_sist: Path) -> CompetitionRun:
+    """Run the documented competition example once."""
+
+    source_input = built_sist / "tests" / "data" / "pbr322.toy.fa"
+    runtime_input = built_sist / "pbr322.toy.fa"
+
+    shutil.copy2(source_input, runtime_input)
+
+    output_directory = built_sist / "test-results"
+    output_directory.mkdir()
+
+    output_path = output_directory / "competition.txt"
+
+    result = run_command(
+        [
+            "perl",
+            "master.pl",
+            "-f",
+            runtime_input.name,
+            "-a",
+            "A",
+            "-o",
+            str(output_path.relative_to(built_sist)),
+            "-b",
+            "-p",
+            "-r",
+        ],
+        cwd=built_sist,
+    )
+
+    return CompetitionRun(
+        process=result,
+        output_path=output_path,
+    )
diff --git a/tests/data/pbr322.toy.fa b/tests/data/pbr322.toy.fa
new file mode 100644
index 0000000..23324fb
--- /dev/null
+++ b/tests/data/pbr322.toy.fa
@@ -0,0 +1,64 @@
+TTCTCATGTTTGACAGCTTATCATCGATAAGCTTTAATGCGGTAGTTTATCACAGTTAAATTGCTAACGC
+AGTCAGGCACCGTGTATGAAATCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTG
+TAGGCATAGGCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATATCGTCCATTCCGACAGCATCGC
+CAGTCACTATGGCGTGCTGCTAGCGCTATATGCGTTGATGCAATTTCTATGCGCACCCGTTCTCGGAGCA
+CTGTCCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACGGAGCCACTATCGACTACGCGA
+TCATGGCGACCACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCAC
+AGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTC
+ATGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGGACTGTTGGGCGCCATCTCCT
+TGCATGCACCATTCCTTGCGGCGGCGGTGCTCAACGGCCTCAACCTACTACTGGGCTGCTTCCTAATGCA
+GGAGTCGCATAAGGGAGAGCGTCGACCGATGCCCTTGAGAGCCTTCAACCCAGTCAGCTCCTTCCGGTGG
+GCGCGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGC
+CGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCT
+TGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAAACGTTTCGGC
+GAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGTCTTGCTGGCGTTCGCGACGC
+GAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGGCATCGGGATGCCCGCGTTGCAGGC
+CATGCTGTCCAGGCAGGTCGCGCGCGCGCGCGCGCGCAGATGACAAGGATCGCTCGCGGCTCTTACCAGC
+CTAACTTCGATCACTGGACCGCTGATCGTCACGGCGATTTATGCCGCCTCGGCGAGCACATGGAACGGGT
+TGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGCGTCGCGGTGCATGGAGCCG
+GGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGGATTCACCACTCCAAGAATTGGAGCCA
+ATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGGCAGAACATATCCATCGCGTCCGCCAT
+CTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGGTCCTGGCCACGGGTGCGCATGATCGTGCTC
+CTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCG
+AGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTT
+CCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCA
+GGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTGGCATTGACCCTGAGTGA
+TTTTTCTCTGGTCCCGCCGCATCCATACCGCCAGTTGTTTACCCTCACAACGTTCCAGTAACCGGGCATG
+TTCATCATCAGTAACCCGTATCGTGAGCATCCTCTCTCGTTTCATCGGTATCATTACCCCCATGAACAGA
+AATCCCCCTTACACGGAGGCATCAGTGACCAAACAGGAAAAAACCGCCCTTAACATGGCCCGCTTTATCA
+GAAGCCAGACATTAACGCTTCTGGAGAAACTCAACGAGCTGGACGCGGATGAACAGGCAGACATCTGTGA
+ATCGCTTCACGACCACGCTGATGAGCTTTACCGCAGCTGCCTCGCGCGTTTCGGTGATGACGGTGAAAAC
+CTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCC
+GTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCGCAGCCATGACCCAGTCACGTAGCGATAGCGG
+AGTGTATACTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAA
+TACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCT
+GCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAA
+TCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCG
+CGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAG
+GTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCT
+GTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATA
+GCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCC
+CGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTA
+TCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCT
+TGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGT
+TACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTT
+GTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGT
+GCTCAGTGAACCAATTGGCCAACCGGAAGGAAAACCTTCCGGTTGGCCAATTGGTTGAACGAAAACTATC
+CTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGAC
+AGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCT
+GACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACC
+GCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGA
+AGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTT
+CGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGG
+TATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAA
+GCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTA
+TGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTC
+AACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAACACGGGATAAT
+ACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAA
+GGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTT
+TACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCG
+ACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTC
+TCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCG
+AAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACG
+AGGCCCTTTCGTCTTCAAGAA
+
diff --git a/tests/reference/v1.0.0/README.md b/tests/reference/v1.0.0/README.md
new file mode 100644
index 0000000..f67528f
--- /dev/null
+++ b/tests/reference/v1.0.0/README.md
@@ -0,0 +1,34 @@
+# SIST 1.0.0 competition reference
+
+This directory contains reference output for the SIST competition calculation.
+
+## Baseline
+
+* Commit: `dab84fd57f81c3bbb1bb26bd7d4a2fa9674d8a2d`
+* Input: `tests/data/pbr322.toy.fa`
+* Algorithm: competition (`A`)
+
+## Command
+
+```bash
+perl master.pl \
+    -f pbr322.toy.fa \
+    -a A \
+    -o pbr322.toy.compete.txt \
+    -b \
+    -p \
+    -r
+```
+
+## Files
+
+* `competition.rebuilt.txt` — output produced from executables rebuilt from the maintained source. This is the regression-test reference.
+* `competition.inherited.txt` — output produced by the executable originally included in the repository. This is retained for historical comparison.
+
+All values common to both executables matched exactly, excluding the variable `Run time` line.
+
+The inherited executable also prints 24 additional derived probability fields that are not printed by the rebuilt executable. These are being investigated separately and are not part of the initial regression comparison.
+
+## Regression comparison
+
+The test compares the deterministic calculation results and ignores the `Run time` line.
diff --git a/tests/reference/v1.0.0/competition.inherited.txt b/tests/reference/v1.0.0/competition.inherited.txt
new file mode 100644
index 0000000..0e8d26b
--- /dev/null
+++ b/tests/reference/v1.0.0/competition.inherited.txt
@@ -0,0 +1,4419 @@
+DNA sequence file: pbr322.toy.fa
+Sequence Length = 4361
+Copolymeric melting energetics
+Molecule type: linear DNA
+Stress Level = -0.06
+linking difference = -25.4481 turns
+Threshold = 12 kcal/mol
+Temperature = 310 K
+Salt Concentration = 0.01 M
+K = 3.6 kcal-bp/rad^2
+Melting nucleation energy = 10.84 kcal/mol
+Z-DNA nucleation energy = 10 kcal/mol
+Cruciform nucleation energy = 12.15 kcal/mol
+BAT = 0.258116 kcal/mol; BGC = 1.30488 kcal/mol
+MinE = 85.6758 kcal/mol; Max_E = 97.6758 kcal/mol
+Number of one-run states = 6318
+Number of two-run states = 2068585
+Number of three-run states = 1.30138e+06
+Number of four-run states = 397
+Total number of states = 3376678
+Total Partition Function = 1.4748e-54
+Scaling factor 300
+Number of M_runs = 0.703244
+Number of Z_runs = 1.01871
+Number of C_runs = 0.98566
+Average number of runs = 2.70761
+Prob_M = 0.703215
+Prob_Z = 0.989709
+Prob_C = 0.985625
+Prob_ZnM 0.692925
+Prob_MnZ 0.692925
+Prob_ZnC 0.975335
+Prob_CnZ 0.975335
+Prob_CnM 0.688847
+Prob_MnC 0.688847
+Comp_Z|M 0.995612
+Comp_M|Z 0.995612
+Comp_Z|C 0.99985
+Comp_C|Z 0.99985
+Comp_C|M 0.993855
+Comp_M|C 0.993855
+Prob_Z|M 0.985366
+Prob_M|Z 0.70013
+Prob_Z|C 0.989561
+Prob_C|Z 0.985477
+Prob_C|M 0.979568
+Prob_M|C 0.698894
+Prob_Z|notM 0.999999
+Prob_M|notZ 0.999969
+Prob_Z|notC 0.999895
+Prob_C|notZ 0.999853
+Prob_C|notM 0.999975
+Prob_M|notC 0.999493
+N_Melting = 24.7018
+N_Z = 17.8997
+N_Cruciform = 46.5979
+Run time = 5 sec
+Position	Base	P_melt	P_Z	P_cruciform
+1	T	6.595e-08	1.98455e-06	0
+2	T	8.13359e-08	6.003e-07	0
+3	C	6.3685e-08	8.56062e-07	0
+4	T	9.96895e-08	6.05626e-07	0
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+4357	A	1.36463e-07	3.15634e-07	0
+4358	A	1.33326e-07	3.32579e-08	0
+4359	G	8.54961e-08	3.59088e-08	0
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diff --git a/tests/reference/v1.0.0/competition.rebuilt.txt b/tests/reference/v1.0.0/competition.rebuilt.txt
new file mode 100644
index 0000000..e23326f
--- /dev/null
+++ b/tests/reference/v1.0.0/competition.rebuilt.txt
@@ -0,0 +1,4395 @@
+DNA sequence file: pbr322.toy.fa
+Sequence Length = 4361
+Copolymeric melting energetics
+Molecule type: linear DNA
+Stress Level = -0.06
+linking difference = -25.4481 turns
+Threshold = 12 kcal/mol
+Temperature = 310 K
+Salt Concentration = 0.01 M
+K = 3.6 kcal-bp/rad^2
+Melting nucleation energy = 10.84 kcal/mol
+Z-DNA nucleation energy = 10 kcal/mol
+Cruciform nucleation energy = 12.15 kcal/mol
+BAT = 0.258116 kcal/mol; BGC = 1.30488 kcal/mol
+MinE = 85.6758 kcal/mol; Max_E = 97.6758 kcal/mol
+Number of one-run states = 6318
+Number of two-run states = 2068585
+Number of three-run states = 1.30138e+06
+Number of four-run states = 397
+Total number of states = 3376678
+Total Partition Function = 1.4748e-54
+Scaling factor 300
+Number of M_runs = 0.703244
+Number of Z_runs = 1.01871
+Number of C_runs = 0.98566
+Average number of runs = 2.70761
+Prob_M = 0.703215
+Prob_Z = 0.989709
+Prob_C = 0.985625
+N_Melting = 24.7018
+N_Z = 17.8997
+N_Cruciform = 46.5979
+Run time = 5 sec
+Position	Base	P_melt	P_Z	P_cruciform
+1	T	6.595e-08	1.98455e-06	0
+2	T	8.13359e-08	6.003e-07	0
+3	C	6.3685e-08	8.56062e-07	0
+4	T	9.96895e-08	6.05626e-07	0
+5	C	9.76097e-08	3.94693e-06	0
+6	A	1.7826e-07	3.90241e-06	0
+7	T	2.02591e-07	3.88603e-06	0
+8	G	1.78485e-07	3.84921e-06	0
+9	T	2.49786e-07	3.71963e-06	0
+10	T	2.62e-07	3.62691e-06	0
+11	T	2.19052e-07	3.52474e-06	0
+12	G	1.09788e-07	3.51302e-06	0
+13	A	1.02659e-07	0	0
+14	C	5.21463e-08	0	0
+15	A	6.82641e-08	0	0
+16	G	4.77263e-08	0	0
+17	C	9.70338e-08	0	0
+18	T	3.45012e-07	0	0
+19	T	4.74405e-07	0	0
+20	A	5.1857e-07	0	0
+21	T	4.90636e-07	4.0152e-10	0
+22	C	3.82927e-07	2.93401e-08	0
+23	A	4.2511e-07	3.10064e-08	0
+24	T	3.98943e-07	3.10064e-08	0
+25	C	2.94871e-07	4.27264e-08	0
+26	G	3.39992e-07	4.27264e-08	0
+27	A	6.30003e-07	5.67941e-08	0
+28	T	7.78971e-07	5.67941e-08	0
+29	A	8.26542e-07	5.63926e-08	0
+30	A	7.84841e-07	2.7831e-08	0
+31	G	6.40651e-07	2.92477e-08	0
+32	C	6.94097e-07	3.31013e-08	0
+33	T	1.04327e-06	1.9715e-08	0
+34	T	1.22207e-06	1.39076e-07	0
+35	T	1.28204e-06	1.25008e-07	0
+36	A	1.23752e-06	1.34972e-07	0
+37	A	1.07678e-06	1.36427e-07	0
+38	T	7.55485e-07	1.36427e-07	0
+39	G	1.88414e-07	1.36427e-07	0
+40	C	5.01455e-08	1.36085e-07	0
+41	G	3.70736e-08	1.34669e-07	0
+42	G	1.23325e-07	1.14188e-08	0
+43	T	5.48054e-07	1.14188e-08	0
+44	A	7.91572e-07	1.45495e-09	0
+45	G	9.06855e-07	0	0
+46	T	1.51532e-06	0	0
+47	T	1.86471e-06	0	0
+48	T	2.03415e-06	0	0
+49	A	2.05995e-06	0	0
+50	T	1.94943e-06	1.71138e-09	0
+51	C	1.66936e-06	1.43775e-07	0
+52	A	1.7393e-06	1.44117e-07	0
+53	C	1.67521e-06	1.45168e-07	0
+54	A	1.98141e-06	1.45168e-07	0
+55	G	2.11043e-06	1.45168e-07	0
+56	T	2.84308e-06	1.45168e-07	0
+57	T	3.24799e-06	1.45168e-07	0
+58	A	3.42772e-06	1.43457e-07	0
+59	A	3.43226e-06	3.05924e-09	0
+60	A	3.26417e-06	2.71788e-09	0
+61	T	2.8836e-06	1.87922e-08	0
+62	T	2.19266e-06	7.63184e-07	0
+63	G	1.03333e-06	1.69868e-06	0
+64	C	7.55241e-07	1.98117e-06	0
+65	T	7.49459e-07	1.98964e-06	0
+66	A	6.56853e-07	2.11742e-06	0
+67	A	4.5376e-07	3.13077e-06	0
+68	C	9.1476e-08	7.92343e-06	0
+69	G	1.4586e-08	8.15752e-06	0
+70	C	5.72592e-09	8.32487e-06	0
+71	A	1.9001e-08	7.46376e-06	0
+72	G	1.07726e-08	6.88998e-06	0
+73	T	2.09294e-08	7.48095e-06	0
+74	C	1.07678e-08	7.48218e-06	0
+75	A	1.70165e-08	7.09533e-06	0
+76	G	3.35663e-09	4.2137e-06	0
+77	G	1.13595e-09	7.99263e-06	0
+78	C	2.88931e-09	7.11731e-06	0
+79	A	1.16465e-08	7.20494e-06	0
+80	C	2.89242e-09	1.12982e-05	0
+81	C	6.16106e-09	0.00010057	0
+82	G	4.92027e-08	0.000101614	0
+83	T	2.61203e-07	0.000101998	0
+84	G	3.72751e-07	0.00010198	0
+85	T	8.8385e-07	9.94519e-05	0
+86	A	1.17459e-06	9.937e-05	0
+87	T	1.31507e-06	9.86858e-05	0
+88	G	1.34109e-06	9.31935e-05	0
+89	A	1.71929e-06	3.85886e-06	0
+90	A	1.90729e-06	2.52847e-06	0
+91	A	1.95302e-06	0	0
+92	T	1.86799e-06	0	0
+93	C	1.63025e-06	0	0
+94	T	1.69846e-06	0	0
+95	A	1.64518e-06	0	0
+96	A	1.45552e-06	3.38808e-09	0
+97	C	1.08239e-06	3.67829e-09	0
+98	A	1.04675e-06	7.44421e-07	0
+99	A	9.06199e-07	1.00897e-05	0
+100	T	6.24651e-07	3.04155e-05	0
+101	G	1.34316e-07	3.80189e-05	0
+102	C	2.2138e-08	3.80192e-05	0
+103	G	1.56095e-09	3.80192e-05	0
+104	C	4.82323e-09	3.80158e-05	0
+105	T	2.45562e-08	3.80155e-05	0
+106	C	2.12791e-08	3.77356e-05	0
+107	A	4.74926e-08	3.01322e-05	0
+108	T	4.4877e-08	9.34699e-06	0
+109	C	1.26815e-08	1.74118e-09	0
+110	G	9.70756e-09	1.42065e-09	0
+111	T	2.86881e-08	4.80873e-09	0
+112	C	2.31237e-08	6.46508e-07	0
+113	A	4.78485e-08	6.46508e-07	0
+114	T	4.45163e-08	6.49705e-07	0
+115	C	1.08327e-08	6.49705e-07	0
+116	C	5.92949e-09	7.21777e-07	0
+117	T	1.39317e-08	7.21777e-07	0
+118	C	2.88823e-09	7.27895e-07	0
+119	G	8.50239e-10	7.30624e-07	0
+120	G	8.50235e-10	9.30253e-08	0
+121	C	2.8882e-09	9.30253e-08	0
+122	A	1.16434e-08	8.98284e-08	0
+123	C	2.88821e-09	8.98284e-08	0
+124	C	1.13543e-09	1.32873e-08	0
+125	G	3.35598e-09	1.32873e-08	0
+126	T	1.55524e-08	7.16946e-09	0
+127	C	8.83522e-09	1.0516e-09	0
+128	A	1.55524e-08	1.0516e-09	0
+129	C	3.35598e-09	1.0516e-09	0
+130	C	1.13544e-09	1.0516e-09	0
+131	C	2.88823e-09	4.59269e-07	0
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+133	G	5.5709e-09	4.58218e-07	0
+134	G	9.01222e-09	4.58218e-07	0
+135	A	3.69789e-08	4.58218e-07	0
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+137	G	1.086e-08	4.58538e-07	0
+138	C	9.34838e-09	1.26423e-06	0
+139	T	2.79706e-08	7.88414e-06	0
+140	G	2.2765e-08	1.1486e-05	0
+141	T	4.7517e-08	1.24607e-05	0
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+146	A	7.41156e-08	2.16116e-05	0
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+148	A	7.41157e-08	1.33661e-05	0
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+153	T	6.57218e-08	1.09195e-06	0
+154	G	4.38893e-08	1.08284e-06	0
+155	G	6.48257e-08	5.63111e-07	0
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+157	T	2.16237e-07	1.62315e-06	0
+158	A	2.12033e-07	4.39822e-06	0
+159	T	1.57288e-07	5.28628e-06	0
+160	G	3.52258e-08	1.28874e-05	0
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+162	C	9.23733e-10	1.25266e-05	0
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+164	G	8.25923e-09	1.24573e-05	0
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+170	C	8.50247e-10	6.58678e-07	0
+171	C	5.65044e-10	1.19915e-06	0
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+179	T	4.41799e-08	1.25059e-07	0
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diff --git a/tests/test_cli.py b/tests/test_cli.py
new file mode 100644
index 0000000..0119c12
--- /dev/null
+++ b/tests/test_cli.py
@@ -0,0 +1,64 @@
+from __future__ import annotations
+
+import pytest
+
+from conftest import CompetitionRun
+
+
+pytestmark = pytest.mark.regression
+
+
+def test_competition_command_succeeds(
+    competition_run: CompetitionRun,
+) -> None:
+    """The documented competition example should complete successfully."""
+
+    process = competition_run.process
+
+    assert process.returncode == 0, (
+        f"Competition command failed with exit code "
+        f"{process.returncode}\n\n"
+        f"stdout:\n{process.stdout}\n\n"
+        f"stderr:\n{process.stderr}"
+    )
+
+
+def test_competition_output_is_created(
+    competition_run: CompetitionRun,
+) -> None:
+    """The competition command should create a non-empty output file."""
+
+    output_path = competition_run.output_path
+
+    assert output_path.is_file(), (
+        f"Expected output file was not created: {output_path}"
+    )
+
+    assert output_path.stat().st_size > 0, (
+        f"Output file is empty: {output_path}"
+    )
+
+
+def test_competition_output_contains_expected_sections(
+    competition_run: CompetitionRun,
+) -> None:
+    """The output should contain the expected calculation sections."""
+
+    output = competition_run.output_path.read_text(encoding="utf-8")
+
+    expected_sections = (
+        "Sequence Length = 4361",
+        "Total Partition Function =",
+        "Prob_M =",
+        "Prob_Z =",
+        "Prob_C =",
+        "Position",
+        "P_melt",
+        "P_Z",
+        "P_cruciform",
+    )
+
+    for section in expected_sections:
+        assert section in output, (
+            f"Expected output section was not found: {section!r}"
+        )
diff --git a/tests/test_regression.py b/tests/test_regression.py
new file mode 100644
index 0000000..559d842
--- /dev/null
+++ b/tests/test_regression.py
@@ -0,0 +1,230 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+
+import pytest
+
+from conftest import CompetitionRun
+
+
+pytestmark = pytest.mark.regression
+
+
+REPOSITORY_ROOT = Path(__file__).resolve().parents[1]
+
+REFERENCE_OUTPUT = (
+    REPOSITORY_ROOT
+    / "tests"
+    / "reference"
+    / "v1.0.0"
+    / "competition.rebuilt.txt"
+)
+
+# The baseline reproduced all shared printed values exactly.
+RELATIVE_TOLERANCE = 0.0
+ABSOLUTE_TOLERANCE = 0.0
+
+
+@dataclass(frozen=True)
+class ProfileRow:
+    """One position from the SIST probability profile."""
+
+    base: str
+    p_melt: float
+    p_z: float
+    p_cruciform: float
+
+
+@dataclass(frozen=True)
+class ParsedOutput:
+    """Parsed deterministic content from a SIST result."""
+
+    metadata: tuple[str, ...]
+    metrics: dict[str, float]
+    profile: dict[int, ProfileRow]
+
+
+def parse_numeric_value(value: str) -> float | None:
+    """
+    Parse the first token as a number.
+
+    This handles values followed by units, such as:
+    '-0.06'
+    '310 K'
+    '1.4748e-54'
+    """
+
+    first_token = value.strip().split()[0]
+
+    try:
+        return float(first_token)
+    except ValueError:
+        return None
+
+
+def parse_output(path: Path) -> ParsedOutput:
+    """Parse deterministic metrics and profile rows from SIST output."""
+
+    metadata: list[str] = []
+    metrics: dict[str, float] = {}
+    profile: dict[int, ProfileRow] = {}
+
+    reading_profile = False
+
+    for line_number, raw_line in enumerate(
+        path.read_text(encoding="utf-8").splitlines(),
+        start=1,
+    ):
+        line = raw_line.strip()
+
+        if not line:
+            continue
+
+        # Runtime varies between executions and is not scientific output.
+        if line.startswith("Run time ="):
+            continue
+
+        if line.startswith("Position"):
+            reading_profile = True
+            continue
+
+        if reading_profile:
+            columns = line.split()
+
+            if len(columns) != 5:
+                raise AssertionError(
+                    f"{path}:{line_number}: expected five profile columns, "
+                    f"found {len(columns)}: {line!r}"
+                )
+
+            position_text, base, p_melt, p_z, p_cruciform = columns
+
+            position = int(position_text)
+
+            profile[position] = ProfileRow(
+                base=base,
+                p_melt=float(p_melt),
+                p_z=float(p_z),
+                p_cruciform=float(p_cruciform),
+            )
+
+            continue
+
+        if line.startswith("Scaling factor "):
+            value = parse_numeric_value(
+                line.removeprefix("Scaling factor ")
+            )
+
+            if value is None:
+                raise AssertionError(
+                    f"{path}:{line_number}: could not parse scaling factor"
+                )
+
+            metrics["Scaling factor"] = value
+            continue
+
+        # Some lines contain more than one key/value pair separated by ';'.
+        parsed_segment = False
+
+        for segment in line.split(";"):
+            if " = " not in segment:
+                continue
+
+            key, raw_value = segment.split(" = ", maxsplit=1)
+            numeric_value = parse_numeric_value(raw_value)
+
+            if numeric_value is None:
+                continue
+
+            metrics[key.strip()] = numeric_value
+            parsed_segment = True
+
+        if not parsed_segment:
+            metadata.append(line)
+
+    if not profile:
+        raise AssertionError(f"No position profile was found in {path}")
+
+    return ParsedOutput(
+        metadata=tuple(metadata),
+        metrics=metrics,
+        profile=profile,
+    )
+
+
+def assert_number_matches(
+    *,
+    name: str,
+    expected: float,
+    actual: float,
+) -> None:
+    """Compare a numerical value with the documented baseline tolerance."""
+
+    assert actual == pytest.approx(
+        expected,
+        rel=RELATIVE_TOLERANCE,
+        abs=ABSOLUTE_TOLERANCE,
+    ), (
+        f"{name} changed: expected {expected!r}, "
+        f"actual {actual!r}"
+    )
+
+
+def test_competition_scientific_results_match_baseline(
+    competition_run: CompetitionRun,
+) -> None:
+    """The rebuilt calculation should reproduce the baseline results."""
+
+    expected = parse_output(REFERENCE_OUTPUT)
+    actual = parse_output(competition_run.output_path)
+
+    assert actual.metadata == expected.metadata, (
+        "Non-numerical output metadata changed:\n"
+        f"expected: {expected.metadata!r}\n"
+        f"actual:   {actual.metadata!r}"
+    )
+
+    assert actual.metrics.keys() == expected.metrics.keys(), (
+        "The set of reported scientific metrics changed:\n"
+        f"missing: {expected.metrics.keys() - actual.metrics.keys()}\n"
+        f"extra:   {actual.metrics.keys() - expected.metrics.keys()}"
+    )
+
+    for metric_name, expected_value in expected.metrics.items():
+        assert_number_matches(
+            name=metric_name,
+            expected=expected_value,
+            actual=actual.metrics[metric_name],
+        )
+
+    assert actual.profile.keys() == expected.profile.keys(), (
+        "The set of reported sequence positions changed"
+    )
+
+    for position, expected_row in expected.profile.items():
+        actual_row = actual.profile[position]
+
+        assert actual_row.base == expected_row.base, (
+            f"Base changed at position {position}: "
+            f"expected {expected_row.base!r}, "
+            f"actual {actual_row.base!r}"
+        )
+
+        assert_number_matches(
+            name=f"position {position} P_melt",
+            expected=expected_row.p_melt,
+            actual=actual_row.p_melt,
+        )
+
+        assert_number_matches(
+            name=f"position {position} P_Z",
+            expected=expected_row.p_z,
+            actual=actual_row.p_z,
+        )
+
+        assert_number_matches(
+            name=f"position {position} P_cruciform",
+            expected=expected_row.p_cruciform,
+            actual=actual_row.p_cruciform,
+        )

From 72ea6e9307c8b2d2b3ed4b2e525a1c7067229b46 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Wed, 5 Aug 2026 16:26:53 +0100
Subject: [PATCH 2/5] build(docs): add nbsphinx dependency

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 02c1d87..0ed48c2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,6 +30,7 @@ testing = [
 docs = [
     "sphinx>=9.1,<9.2",
     "sphinx-rtd-theme>=3.1,<3.2",
+    "nbsphinx",
 ]
 
 [tool.setuptools]

From 9ea2df902e2400f15291f8ab05bc2a04ab72ffd7 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Wed, 5 Aug 2026 16:27:59 +0100
Subject: [PATCH 3/5] tests(regression): tidy up file explanation within
 reference `README.md`

---
 tests/reference/v1.0.0/README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/reference/v1.0.0/README.md b/tests/reference/v1.0.0/README.md
index f67528f..8282395 100644
--- a/tests/reference/v1.0.0/README.md
+++ b/tests/reference/v1.0.0/README.md
@@ -22,8 +22,8 @@ perl master.pl \
 
 ## Files
 
-* `competition.rebuilt.txt` — output produced from executables rebuilt from the maintained source. This is the regression-test reference.
-* `competition.inherited.txt` — output produced by the executable originally included in the repository. This is retained for historical comparison.
+* `competition.rebuilt.txt` - output produced from executables rebuilt from the maintained source. This is the regression-test reference.
+* `competition.inherited.txt` - output produced by the executable originally included in the repository. This is retained for historical comparison.
 
 All values common to both executables matched exactly, excluding the variable `Run time` line.
 

From 24d410448d826148c071a608044cf9ffeed4ec63 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Wed, 5 Aug 2026 16:36:59 +0100
Subject: [PATCH 4/5] ci: add PR checks and scheduled regression workflow

---
 .github/workflows/pr.yaml               | 12 ++++++------
 .github/workflows/regression-tests.yaml | 18 +++++++++++-------
 pyproject.toml                          | 22 +++++-----------------
 3 files changed, 22 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index fd9f2de..9c17fd6 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -7,7 +7,7 @@ permissions:
   contents: read
 
 concurrency:
-  group: pr-ci-${{ github.ref }}
+  group: pr-ci-${{ github.event.pull_request.number }}
   cancel-in-progress: true
 
 jobs:
@@ -43,7 +43,7 @@ jobs:
         uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: pr-regression-failure
-          path: .testdata/**
+          path: .testdata/
           if-no-files-found: ignore
           include-hidden-files: true
           retention-days: 7
@@ -65,7 +65,7 @@ jobs:
       - name: Install documentation dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -e '.[docs]'
+          python -m pip install -r docs/requirements.txt
 
       - name: Build documentation
         run: |
@@ -73,10 +73,10 @@ jobs:
           make -C docs html SPHINXOPTS="-W --keep-going"
 
       - name: Upload documentation
-        if: always()
+        if: success()
         uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: docs-html
-          path: docs/build/html
-          if-no-files-found: warn
+          path: docs/build/html/
+          if-no-files-found: error
           retention-days: 7
\ No newline at end of file
diff --git a/.github/workflows/regression-tests.yaml b/.github/workflows/regression-tests.yaml
index ef1193c..394132e 100644
--- a/.github/workflows/regression-tests.yaml
+++ b/.github/workflows/regression-tests.yaml
@@ -1,21 +1,23 @@
 name: Regression Tests
 
 on:
-  pull_request:
   push:
     branches:
       - main
   schedule:
-    - cron: '0 8 * * 1'
+    - cron: "0 8 * * 1"
   workflow_dispatch:
 
+permissions:
+  contents: read
+
 concurrency:
-  group: sist-regression-${{ github.ref }}
+  group: sist-regression-${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
   regression:
-    name: SIST regression
+    name: SIST Regression
     runs-on: ubuntu-24.04
     timeout-minutes: 30
 
@@ -43,8 +45,10 @@ jobs:
 
       - name: Upload regression artefacts on failure
         if: failure()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
-          name: sist-regression-artifacts
-          path: .testdata/**
+          name: sist-regression-failure
+          path: .testdata/
           if-no-files-found: ignore
+          include-hidden-files: true
+          retention-days: 7
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 0ed48c2..cfc4b6e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,20 +5,15 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "SIST"
 version = "0.0.1"
-
 description = "Stress-Induced Structural Transitions in superhelical DNA."
-
-authors = [
-]
-
-maintainers = [
-    {name = "Harry Swift", email = "harry.swift@stfc.ac.uk"}
-]
 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"
 
@@ -27,21 +22,14 @@ testing = [
     "pytest>=9.0,<10.0",
 ]
 
-docs = [
-    "sphinx>=9.1,<9.2",
-    "sphinx-rtd-theme>=3.1,<3.2",
-    "nbsphinx",
-]
-
 [tool.setuptools]
 # SIST is currently a Perl/C++ application. This metadata manages the Python
-# test harness and documentation dependencies; it does not package SIST.
+# 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",

From 8111fb93c6a653cc0664c7af8db6a6a2ccea2a4f Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Wed, 5 Aug 2026 16:41:33 +0100
Subject: [PATCH 5/5] docs: comment out unused static assets path

---
 docs/source/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 21e76c4..e7e7ccb 100644
--- a/docs/source/conf.py
+++ b/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']