From 794a37ccf3d331a163d5b621acacb60bf7c10113 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Fri, 25 Sep 2026 11:24:10 +0100
Subject: [PATCH 01/13] tests: split test suite into `tests/unit` and
 `tests/regression`

---
 tests/{ => regression}/conftest.py                        | 8 ++++++--
 tests/{ => regression}/data/pbr322.toy.fa                 | 0
 tests/{ => regression}/reference/v1.0.0/README.md         | 0
 .../reference/v1.0.0/competition.inherited.txt            | 0
 .../reference/v1.0.0/competition.rebuilt.txt              | 0
 tests/{ => regression}/reference/v1.0.0/cruciform.txt     | 0
 tests/{ => regression}/reference/v1.0.0/melting.txt       | 0
 tests/{ => regression}/reference/v1.0.0/z-dna.txt         | 0
 tests/{ => regression}/test_cli.py                        | 0
 tests/{ => regression}/test_legacy_entrypoints.py         | 4 ++--
 tests/{ => regression}/test_regression.py                 | 8 +-------
 tests/{ => unit}/test_energetics.py                       | 0
 tests/{ => unit}/test_ir_finder.py                        | 0
 13 files changed, 9 insertions(+), 11 deletions(-)
 rename tests/{ => regression}/conftest.py (93%)
 rename tests/{ => regression}/data/pbr322.toy.fa (100%)
 rename tests/{ => regression}/reference/v1.0.0/README.md (100%)
 rename tests/{ => regression}/reference/v1.0.0/competition.inherited.txt (100%)
 rename tests/{ => regression}/reference/v1.0.0/competition.rebuilt.txt (100%)
 rename tests/{ => regression}/reference/v1.0.0/cruciform.txt (100%)
 rename tests/{ => regression}/reference/v1.0.0/melting.txt (100%)
 rename tests/{ => regression}/reference/v1.0.0/z-dna.txt (100%)
 rename tests/{ => regression}/test_cli.py (100%)
 rename tests/{ => regression}/test_legacy_entrypoints.py (95%)
 rename tests/{ => regression}/test_regression.py (98%)
 rename tests/{ => unit}/test_energetics.py (100%)
 rename tests/{ => unit}/test_ir_finder.py (100%)

diff --git a/tests/conftest.py b/tests/regression/conftest.py
similarity index 93%
rename from tests/conftest.py
rename to tests/regression/conftest.py
index 09632e9..234dff2 100644
--- a/tests/conftest.py
+++ b/tests/regression/conftest.py
@@ -9,7 +9,7 @@
 
 import pytest
 
-REPOSITORY_ROOT = Path(__file__).resolve().parents[1]
+REPOSITORY_ROOT = Path(__file__).resolve().parents[2]
 
 SIST_TRANSITIONS = (
     pytest.param(("melting", "M"), id="melting"),
@@ -136,6 +136,10 @@ def sist_command(
     During conda-build testing, use the installed console script. Otherwise
     run `python -m sist` against the maintained source tree, with its qsidd
     binaries resolved via env vars pointing at a freshly built copy.
+
+    `built_sist_copy` is looked up lazily (rather than taken as a normal
+    fixture parameter) so conda-build testing never triggers it: that build
+    only has `tests/` and `pyproject.toml` available, not the C++ sources.
     """
 
     if os.environ.get("CONDA_BUILD_STATE") == "TEST":
@@ -172,7 +176,7 @@ def run_sist_calculation(
 
     runtime_directory = tmp_path_factory.mktemp(f"sist-{name}")
 
-    source_input = REPOSITORY_ROOT / "tests" / "data" / "pbr322.toy.fa"
+    source_input = Path(__file__).resolve().parent / "data" / "pbr322.toy.fa"
     runtime_input = runtime_directory / "pbr322.toy.fa"
 
     shutil.copy2(source_input, runtime_input)
diff --git a/tests/data/pbr322.toy.fa b/tests/regression/data/pbr322.toy.fa
similarity index 100%
rename from tests/data/pbr322.toy.fa
rename to tests/regression/data/pbr322.toy.fa
diff --git a/tests/reference/v1.0.0/README.md b/tests/regression/reference/v1.0.0/README.md
similarity index 100%
rename from tests/reference/v1.0.0/README.md
rename to tests/regression/reference/v1.0.0/README.md
diff --git a/tests/reference/v1.0.0/competition.inherited.txt b/tests/regression/reference/v1.0.0/competition.inherited.txt
similarity index 100%
rename from tests/reference/v1.0.0/competition.inherited.txt
rename to tests/regression/reference/v1.0.0/competition.inherited.txt
diff --git a/tests/reference/v1.0.0/competition.rebuilt.txt b/tests/regression/reference/v1.0.0/competition.rebuilt.txt
similarity index 100%
rename from tests/reference/v1.0.0/competition.rebuilt.txt
rename to tests/regression/reference/v1.0.0/competition.rebuilt.txt
diff --git a/tests/reference/v1.0.0/cruciform.txt b/tests/regression/reference/v1.0.0/cruciform.txt
similarity index 100%
rename from tests/reference/v1.0.0/cruciform.txt
rename to tests/regression/reference/v1.0.0/cruciform.txt
diff --git a/tests/reference/v1.0.0/melting.txt b/tests/regression/reference/v1.0.0/melting.txt
similarity index 100%
rename from tests/reference/v1.0.0/melting.txt
rename to tests/regression/reference/v1.0.0/melting.txt
diff --git a/tests/reference/v1.0.0/z-dna.txt b/tests/regression/reference/v1.0.0/z-dna.txt
similarity index 100%
rename from tests/reference/v1.0.0/z-dna.txt
rename to tests/regression/reference/v1.0.0/z-dna.txt
diff --git a/tests/test_cli.py b/tests/regression/test_cli.py
similarity index 100%
rename from tests/test_cli.py
rename to tests/regression/test_cli.py
diff --git a/tests/test_legacy_entrypoints.py b/tests/regression/test_legacy_entrypoints.py
similarity index 95%
rename from tests/test_legacy_entrypoints.py
rename to tests/regression/test_legacy_entrypoints.py
index 4a9f141..9bbe9c6 100644
--- a/tests/test_legacy_entrypoints.py
+++ b/tests/regression/test_legacy_entrypoints.py
@@ -12,7 +12,6 @@
 from pathlib import Path
 
 import pytest
-from conftest import REPOSITORY_ROOT
 
 pytestmark = pytest.mark.regression
 
@@ -41,7 +40,8 @@ def test_master_pl_alias_matches_sist_output(
 
     runtime_directory = tmp_path_factory.mktemp("master-pl-alias")
     input_path = runtime_directory / "pbr322.toy.fa"
-    shutil.copy2(REPOSITORY_ROOT / "tests" / "data" / "pbr322.toy.fa", input_path)
+    data_path = Path(__file__).resolve().parent / "data" / "pbr322.toy.fa"
+    shutil.copy2(data_path, input_path)
 
     result = subprocess.run(
         ["master.pl", "-f", input_path.name, "-a", "M", "-b", "-p", "-r"],
diff --git a/tests/test_regression.py b/tests/regression/test_regression.py
similarity index 98%
rename from tests/test_regression.py
rename to tests/regression/test_regression.py
index 8ae18da..29d1e0a 100644
--- a/tests/test_regression.py
+++ b/tests/regression/test_regression.py
@@ -11,15 +11,9 @@
 pytestmark = pytest.mark.regression
 
 
-REPOSITORY_ROOT = Path(__file__).resolve().parents[1]
 REFERENCE_VERSION = "v1.0.0"
 
-REFERENCE_DIRECTORY = (
-    REPOSITORY_ROOT
-    / "tests"
-    / "reference"
-    / REFERENCE_VERSION
-)
+REFERENCE_DIRECTORY = Path(__file__).resolve().parent / "reference" / REFERENCE_VERSION
 
 COMPETITION_REFERENCE = (
     REFERENCE_DIRECTORY
diff --git a/tests/test_energetics.py b/tests/unit/test_energetics.py
similarity index 100%
rename from tests/test_energetics.py
rename to tests/unit/test_energetics.py
diff --git a/tests/test_ir_finder.py b/tests/unit/test_ir_finder.py
similarity index 100%
rename from tests/test_ir_finder.py
rename to tests/unit/test_ir_finder.py

From a2ef3414b56af8b059f93c9f98738057822ce661 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Fri, 25 Sep 2026 11:48:19 +0100
Subject: [PATCH 02/13] ci: add daily unit tests, weekly docs build, and
 coverage reporting

---
 .github/workflows/coveralls-main.yaml         | 54 +++++++++++++++++++
 .github/workflows/daily.yaml                  | 38 +++++++++++++
 ...pdate-copyright-years-in-license-file.yaml | 17 ++++++
 .github/workflows/weekly-docs.yaml            | 47 ++++++++++++++++
 .gitignore                                    |  4 ++
 pyproject.toml                                |  1 +
 6 files changed, 161 insertions(+)
 create mode 100644 .github/workflows/coveralls-main.yaml
 create mode 100644 .github/workflows/daily.yaml
 create mode 100644 .github/workflows/update-copyright-years-in-license-file.yaml
 create mode 100644 .github/workflows/weekly-docs.yaml

diff --git a/.github/workflows/coveralls-main.yaml b/.github/workflows/coveralls-main.yaml
new file mode 100644
index 0000000..b9d9ac6
--- /dev/null
+++ b/.github/workflows/coveralls-main.yaml
@@ -0,0 +1,54 @@
+name: Coveralls Main
+
+on:
+  push:
+    branches: [main]
+
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: coveralls-main-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  coveralls:
+    name: Build main coverage baseline
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+
+    permissions:
+      contents: read
+      checks: write
+      statuses: write
+
+    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 coverage
+        run: |
+          python -m pytest tests/unit \
+            --cov sist \
+            --cov-report term-missing \
+            --cov-report xml \
+            -q
+
+      - name: Upload coverage to Coveralls
+        uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          file: coverage.xml
+          fail-on-error: false
diff --git a/.github/workflows/daily.yaml b/.github/workflows/daily.yaml
new file mode 100644
index 0000000..9e8458b
--- /dev/null
+++ b/.github/workflows/daily.yaml
@@ -0,0 +1,38 @@
+name: Daily Unit Tests
+
+on:
+  schedule:
+    - cron: '0 8 * * 1-5'
+  workflow_dispatch:
+
+concurrency:
+  group: daily-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  unit:
+    name: Unit (py${{ matrix.python-version }})
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12", "3.13", "3.14"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install testing dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[testing]
+
+      - name: Run unit tests
+        run: python -m pytest tests/unit
diff --git a/.github/workflows/update-copyright-years-in-license-file.yaml b/.github/workflows/update-copyright-years-in-license-file.yaml
new file mode 100644
index 0000000..a252dd5
--- /dev/null
+++ b/.github/workflows/update-copyright-years-in-license-file.yaml
@@ -0,0 +1,17 @@
+name: Update copyright year(s) in license file
+
+on:
+  schedule:
+    - cron: '0 3 1 1 *' # 03:00 AM on January 1
+  workflow_dispatch:
+
+jobs:
+    update-license-year:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+              with:
+                  fetch-depth: 0
+            - uses: FantasticFiasco/action-update-license-year@f180e962fa988db222d8f03ef4636750312d1b3d # v3
+              with:
+                  token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/weekly-docs.yaml b/.github/workflows/weekly-docs.yaml
new file mode 100644
index 0000000..30d0eda
--- /dev/null
+++ b/.github/workflows/weekly-docs.yaml
@@ -0,0 +1,47 @@
+name: Weekly Docs Build
+
+on:
+  schedule:
+    - cron: '0 8 * * 1'
+  workflow_dispatch:
+
+concurrency:
+  group: weekly-docs-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  docs:
+    name: Docs build (python ${{ matrix.python-version }})
+    runs-on: ubuntu-24.04
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12", "3.13", "3.14"]
+    timeout-minutes: 30
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r docs/requirements.txt
+
+      - name: Build docs (warnings as errors)
+        run: |
+          make -C docs clean
+          make -C docs html SPHINXOPTS="-W --keep-going"
+
+      - name: Upload docs artifacts on failure
+        if: failure()
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: docs-py${{ matrix.python-version }}-failure
+          path: |
+            docs/build/**
diff --git a/.gitignore b/.gitignore
index b855c85..5ae4d20 100644
--- a/.gitignore
+++ b/.gitignore
@@ -75,6 +75,10 @@ __pycache__/
 .ruff_cache/
 *.egg-info/
 
+# Coverage
+.coverage
+coverage.xml
+
 # Regression test artefacts
 .testdata/
 test-results/
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index f2fab85..579aa2e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,6 +41,7 @@ sist = "sist.cli:main"
 [project.optional-dependencies]
 testing = [
     "pytest>=9.0,<10.0",
+    "pytest-cov>=7.0,<8.0",
     "mypy>=1.14,<2.0",
 ]
 

From 1432dc79773d9434ad4bc2956f60f790118eb30a Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Fri, 25 Sep 2026 12:22:07 +0100
Subject: [PATCH 03/13] ci: split pr.yaml into unit/regression jobs and add C++
 coverage reporting

---
 .github/workflows/coveralls-main.yaml         | 95 ++++++++++++++++++-
 .github/workflows/pr.yaml                     | 70 +++++++++++++-
 ...sion-tests.yaml => weekly-regression.yaml} |  5 +-
 .gitignore                                    |  5 +
 README.md                                     |  5 +-
 conda-recipe/run_test.sh                      |  2 +-
 src/trans_compete/Makefile                    |  3 +
 src/trans_three/Makefile                      |  3 +
 8 files changed, 178 insertions(+), 10 deletions(-)
 rename .github/workflows/{regression-tests.yaml => weekly-regression.yaml} (95%)

diff --git a/.github/workflows/coveralls-main.yaml b/.github/workflows/coveralls-main.yaml
index b9d9ac6..e3bf3d2 100644
--- a/.github/workflows/coveralls-main.yaml
+++ b/.github/workflows/coveralls-main.yaml
@@ -14,8 +14,8 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  coveralls:
-    name: Build main coverage baseline
+  python-coverage:
+    name: Build main coverage baseline (Python)
     runs-on: ubuntu-24.04
     timeout-minutes: 30
 
@@ -51,4 +51,95 @@ jobs:
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           file: coverage.xml
+          flag-name: python
+          parallel: true
           fail-on-error: false
+
+  cpp-coverage:
+    name: Build main coverage baseline (C++)
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+
+    permissions:
+      contents: read
+      checks: write
+      statuses: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version: "3.14"
+
+      - name: Setup Conda (for irf only)
+        uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
+        with:
+          miniforge-variant: Miniforge3
+          auto-activate: true
+          activate-environment: base
+          conda-remove-defaults: true
+          channels: conda-forge,bioconda
+          channel-priority: strict
+
+      - name: Install irf
+        shell: bash -l {0}
+        run: |
+          conda install -y \
+            --override-channels \
+            -c bioconda \
+            -c conda-forge \
+            "irf>=3.09,<3.10"
+
+      - name: Install sist and coverage tooling
+        shell: bash -l {0}
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[testing]
+          python -m pip install gcovr
+
+      - name: Build qsidd with coverage instrumentation
+        run: |
+          make -C src/trans_three clean
+          make -C src/trans_three coverage
+          make -C src/trans_compete clean
+          make -C src/trans_compete coverage
+
+      - name: Run regression tests against instrumented binaries
+        shell: bash -l {0}
+        env:
+          CONDA_BUILD_STATE: TEST
+          SIST_TRANS_THREE_BIN: ${{ github.workspace }}/src/trans_three/qsidd
+          SIST_TRANS_COMPETE_BIN: ${{ github.workspace }}/src/trans_compete/qsidd
+        run: python -m pytest tests/regression -vv
+
+      - name: Generate lcov report
+        run: |
+          gcovr --root . \
+            --filter 'src/trans_three/.*' \
+            --filter 'src/trans_compete/.*' \
+            --gcov-ignore-parse-errors=suspicious_hits.warn \
+            --lcov coverage.info
+
+      - name: Upload coverage to Coveralls
+        uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: coverage.info
+          flag-name: cpp
+          parallel: true
+          fail-on-error: false
+
+  finish:
+    name: Close Coveralls build
+    needs: [python-coverage, cpp-coverage]
+    runs-on: ubuntu-24.04
+
+    steps:
+      - name: Close parallel build
+        uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          parallel-finished: true
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 106b2f6..5680da4 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -11,6 +11,33 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  unit:
+    name: Unit (py${{ matrix.python-version }})
+    runs-on: ubuntu-24.04
+    timeout-minutes: 15
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12", "3.13", "3.14"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install testing dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[testing]
+
+      - name: Run unit tests
+        run: python -m pytest tests/unit
+
   regression:
     name: Regression
     runs-on: ubuntu-24.04
@@ -78,4 +105,45 @@ jobs:
           name: docs-html
           path: docs/build/html/
           if-no-files-found: error
-          retention-days: 7
\ No newline at end of file
+          retention-days: 7
+
+  coverage:
+    name: Coverage
+    needs: unit
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+
+    permissions:
+      contents: read
+      checks: write
+      statuses: write
+      pull-requests: write
+
+    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 coverage
+        run: |
+          python -m pytest tests/unit \
+            --cov sist \
+            --cov-report term-missing \
+            --cov-report xml \
+            -q
+
+      - name: Upload coverage to Coveralls
+        uses: coverallsapp/github-action@5cbfd81b66ca5d10c19b062c04de0199c215fb6e
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          file: coverage.xml
+          fail-on-error: false
\ No newline at end of file
diff --git a/.github/workflows/regression-tests.yaml b/.github/workflows/weekly-regression.yaml
similarity index 95%
rename from .github/workflows/regression-tests.yaml
rename to .github/workflows/weekly-regression.yaml
index d046ca2..9d07a6d 100644
--- a/.github/workflows/regression-tests.yaml
+++ b/.github/workflows/weekly-regression.yaml
@@ -1,9 +1,6 @@
-name: Regression Tests
+name: Weekly Regression Tests
 
 on:
-  push:
-    branches:
-      - main
   schedule:
     - cron: "0 8 * * 1"
   workflow_dispatch:
diff --git a/.gitignore b/.gitignore
index 5ae4d20..4753c57 100644
--- a/.gitignore
+++ b/.gitignore
@@ -57,6 +57,11 @@ src/trans_compete/depend
 # Debug information files
 *.dwo
 
+# gcov/lcov coverage instrumentation and reports
+*.gcno
+*.gcda
+coverage.info
+
 # Build directories
 build/
 dist/
diff --git a/README.md b/README.md
index 651f0b0..217c1b8 100644
--- a/README.md
+++ b/README.md
@@ -3,8 +3,9 @@ SIST: Stress-Induced Structural Transitions in superhelical DNA
 
 | Category       | Badges |
 |----------------|--------|
-| **Build**      | [![PR Checks](https://github.com/CCPBioSim/SIST/actions/workflows/pr.yaml/badge.svg)](https://github.com/CCPBioSim/SIST/actions/workflows/pr.yaml) |
-| **Documentation** | [![Docs - Status](https://app.readthedocs.org/projects/sist/badge/?version=latest)](https://sist.readthedocs.io/en/latest/?badge=latest) |
+| **Build**      | [![PR Checks](https://github.com/CCPBioSim/SIST/actions/workflows/pr.yaml/badge.svg)](https://github.com/CCPBioSim/SIST/actions/workflows/pr.yaml) [![Daily Tests](https://github.com/CCPBioSim/SIST/actions/workflows/daily.yaml/badge.svg)](https://github.com/CCPBioSim/SIST/actions/workflows/daily.yaml) |
+| **Regression** | [![Weekly Regression](https://github.com/CCPBioSim/SIST/actions/workflows/weekly-regression.yaml/badge.svg)](https://github.com/CCPBioSim/SIST/actions/workflows/weekly-regression.yaml) |
+| **Documentation** | [![Weekly Docs](https://github.com/CCPBioSim/SIST/actions/workflows/weekly-docs.yaml/badge.svg)](https://github.com/CCPBioSim/SIST/actions/workflows/weekly-docs.yaml) [![Docs - Status](https://app.readthedocs.org/projects/sist/badge/?version=latest)](https://sist.readthedocs.io/en/latest/?badge=latest) |
 | **Citation**      | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.22753478.svg)](https://doi.org/10.5281/zenodo.22753478) |
 | **Anaconda**       | [![Anaconda.org](https://anaconda.org/CCPBioSim/sist/badges/version.svg)](https://anaconda.org/CCPBioSim/sist/) [![Last Updated](https://anaconda.org/CCPBioSim/sist/badges/latest_release_date.svg)](https://anaconda.org/CCPBioSim/sist) [![Platforms](https://anaconda.org/CCPBioSim/sist/badges/platforms.svg)](https://anaconda.org/CCPBioSim/sist) [![License](https://anaconda.org/CCPBioSim/sist/badges/license.svg)](https://anaconda.org/CCPBioSim/sist) [![Downloads](https://anaconda.org/CCPBioSim/sist/badges/downloads.svg)](https://anaconda.org/CCPBioSim/sist)|
 | **Quality**    | [![Coverage Status](https://coveralls.io/repos/github/CCPBioSim/SIST/badge.svg?branch=main)](https://coveralls.io/github/CCPBioSim/SIST?branch=main) |
diff --git a/conda-recipe/run_test.sh b/conda-recipe/run_test.sh
index 62d6569..8728dc5 100755
--- a/conda-recipe/run_test.sh
+++ b/conda-recipe/run_test.sh
@@ -6,4 +6,4 @@ command -v irf
 command -v python
 command -v pytest
 
-python -m pytest tests -vv
+python -m pytest tests/regression -vv
diff --git a/src/trans_compete/Makefile b/src/trans_compete/Makefile
index 703b15c..93b2108 100644
--- a/src/trans_compete/Makefile
+++ b/src/trans_compete/Makefile
@@ -54,6 +54,9 @@ tar:
 gcc:
 	make $(APP) CC="$(CXX)" CPPFLAGS="-O2 -Wall"
 
+coverage:
+	make $(APP) CC="$(CXX)" CPPFLAGS="-O0 -Wall --coverage -fprofile-abs-path" LDFLAGS="--coverage"
+
 
 ###################
 # Inference Rules #
diff --git a/src/trans_three/Makefile b/src/trans_three/Makefile
index 06b0afe..1908f1d 100644
--- a/src/trans_three/Makefile
+++ b/src/trans_three/Makefile
@@ -54,6 +54,9 @@ tar:
 gcc:
 	make $(APP) CC="$(CXX)" CPPFLAGS="-O2 -Wall "
 
+coverage:
+	make $(APP) CC="$(CXX)" CPPFLAGS="-O0 -Wall --coverage -fprofile-abs-path" LDFLAGS="--coverage"
+
 
 ###################
 # Inference Rules #

From d2c6e381bf98fb6e6ca4282f901f78bb5acce02d Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Fri, 25 Sep 2026 13:52:16 +0100
Subject: [PATCH 04/13] tests: update comments within `regression/conftest.py`

---
 tests/regression/conftest.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tests/regression/conftest.py b/tests/regression/conftest.py
index 234dff2..d5854a7 100644
--- a/tests/regression/conftest.py
+++ b/tests/regression/conftest.py
@@ -136,10 +136,6 @@ def sist_command(
     During conda-build testing, use the installed console script. Otherwise
     run `python -m sist` against the maintained source tree, with its qsidd
     binaries resolved via env vars pointing at a freshly built copy.
-
-    `built_sist_copy` is looked up lazily (rather than taken as a normal
-    fixture parameter) so conda-build testing never triggers it: that build
-    only has `tests/` and `pyproject.toml` available, not the C++ sources.
     """
 
     if os.environ.get("CONDA_BUILD_STATE") == "TEST":

From 825233eb35246f1638fcac60d4b9912a4b93e462 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Mon, 28 Sep 2026 09:23:26 +0100
Subject: [PATCH 05/13] chore(workflows): update all workflows to use new
 `ubuntu-26.04` images

---
 .github/workflows/coveralls-main.yaml | 6 +++---
 .github/workflows/daily.yaml          | 2 +-
 .github/workflows/pr.yaml             | 4 ++--
 .github/workflows/weekly-docs.yaml    | 2 +-
 .readthedocs.yaml                     | 2 +-
 5 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/coveralls-main.yaml b/.github/workflows/coveralls-main.yaml
index e3bf3d2..3186354 100644
--- a/.github/workflows/coveralls-main.yaml
+++ b/.github/workflows/coveralls-main.yaml
@@ -16,7 +16,7 @@ concurrency:
 jobs:
   python-coverage:
     name: Build main coverage baseline (Python)
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 30
 
     permissions:
@@ -57,7 +57,7 @@ jobs:
 
   cpp-coverage:
     name: Build main coverage baseline (C++)
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 30
 
     permissions:
@@ -135,7 +135,7 @@ jobs:
   finish:
     name: Close Coveralls build
     needs: [python-coverage, cpp-coverage]
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
 
     steps:
       - name: Close parallel build
diff --git a/.github/workflows/daily.yaml b/.github/workflows/daily.yaml
index 9e8458b..01a5343 100644
--- a/.github/workflows/daily.yaml
+++ b/.github/workflows/daily.yaml
@@ -12,7 +12,7 @@ concurrency:
 jobs:
   unit:
     name: Unit (py${{ matrix.python-version }})
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 30
 
     strategy:
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index f0b6054..dbd8407 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -13,7 +13,7 @@ concurrency:
 jobs:
   unit:
     name: Unit (py${{ matrix.python-version }})
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 15
 
     strategy:
@@ -115,7 +115,7 @@ jobs:
   coverage:
     name: Coverage
     needs: unit
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     timeout-minutes: 30
 
     permissions:
diff --git a/.github/workflows/weekly-docs.yaml b/.github/workflows/weekly-docs.yaml
index 30d0eda..9a913b7 100644
--- a/.github/workflows/weekly-docs.yaml
+++ b/.github/workflows/weekly-docs.yaml
@@ -12,7 +12,7 @@ concurrency:
 jobs:
   docs:
     name: Docs build (python ${{ matrix.python-version }})
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     strategy:
       fail-fast: false
       matrix:
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index db69c29..87e396c 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -6,7 +6,7 @@ version: 2
 
 # Set the OS, Python version, and other tools you might need
 build:
-  os: ubuntu-24.04
+  os: ubuntu-26.04
   tools:
     python: "3.13"
 

From 5184f25c9d071ae09dae4a75ec0981434c2e4267 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Mon, 28 Sep 2026 09:37:57 +0100
Subject: [PATCH 06/13] chore(workflows): matrix regression tests across all
 supported python versions

---
 .github/workflows/daily.yaml             | 5 +++--
 .github/workflows/pr.yaml                | 9 ++++++---
 .github/workflows/weekly-regression.yaml | 4 +++-
 conda-recipe/meta.yaml                   | 2 +-
 4 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/daily.yaml b/.github/workflows/daily.yaml
index 01a5343..c1e2da3 100644
--- a/.github/workflows/daily.yaml
+++ b/.github/workflows/daily.yaml
@@ -11,13 +11,14 @@ concurrency:
 
 jobs:
   unit:
-    name: Unit (py${{ matrix.python-version }})
-    runs-on: ubuntu-26.04
+    name: Unit (${{ matrix.os }}, py${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
     timeout-minutes: 30
 
     strategy:
       fail-fast: false
       matrix:
+        os: [ubuntu-26.04, macos-26-intel, macos-26]
         python-version: ["3.12", "3.13", "3.14"]
 
     steps:
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index dbd8407..e859677 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -12,13 +12,14 @@ concurrency:
 
 jobs:
   unit:
-    name: Unit (py${{ matrix.python-version }})
-    runs-on: ubuntu-26.04
+    name: Unit (${{ matrix.os }}, py${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
     timeout-minutes: 15
 
     strategy:
       fail-fast: false
       matrix:
+        os: [ubuntu-26.04, macos-26-intel, macos-26]
         python-version: ["3.12", "3.13", "3.14"]
 
     steps:
@@ -39,13 +40,14 @@ jobs:
         run: python -m pytest tests/unit
 
   regression:
-    name: Regression (${{ matrix.os }})
+    name: Regression (${{ matrix.os }}, py${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
     timeout-minutes: 60
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-26.04, macos-26-intel, macos-26]
+        python-version: ["3.12", "3.13", "3.14"]
 
     steps:
       - name: Checkout
@@ -77,6 +79,7 @@ jobs:
             --override-channels \
             -c conda-forge \
             -c bioconda \
+            --python ${{ matrix.python-version }} \
             --no-anaconda-upload
 
   docs:
diff --git a/.github/workflows/weekly-regression.yaml b/.github/workflows/weekly-regression.yaml
index bcfa4da..a5900cc 100644
--- a/.github/workflows/weekly-regression.yaml
+++ b/.github/workflows/weekly-regression.yaml
@@ -14,13 +14,14 @@ concurrency:
 
 jobs:
   regression:
-    name: SIST Regression (${{ matrix.os }})
+    name: SIST Regression (${{ matrix.os }}, py${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
     timeout-minutes: 30
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-26.04, macos-26-intel, macos-26]
+        python-version: ["3.12", "3.13", "3.14"]
 
     steps:
       - name: Checkout
@@ -51,4 +52,5 @@ jobs:
             --override-channels \
             -c conda-forge \
             -c bioconda \
+            --python ${{ matrix.python-version }} \
             --no-anaconda-upload
\ No newline at end of file
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index c2b1143..6e4fa95 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -29,7 +29,7 @@ requirements:
 
 test:
   requires:
-    - python >=3.14
+    - python >=3.12
     - pytest >=9,<10
 
   source_files:

From d811b37a980960c7b8b70567c65a68bec09cde0a Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Mon, 28 Sep 2026 09:47:27 +0100
Subject: [PATCH 07/13] ci(sist): gate docs job behind unit tests

---
 .github/workflows/pr.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index e859677..23bdb24 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -84,6 +84,7 @@ jobs:
 
   docs:
     name: Docs
+    needs: unit
     runs-on: ubuntu-26.04
     timeout-minutes: 20
 

From 569fb13ff6eb98be66f5ba367dd393afa7b9ada5 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Mon, 28 Sep 2026 09:51:54 +0100
Subject: [PATCH 08/13] ci(sist): limit pr regression to a single python
 version, keep full matrix weekly

---
 .github/workflows/pr.yaml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 23bdb24..41fbb03 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -40,14 +40,13 @@ jobs:
         run: python -m pytest tests/unit
 
   regression:
-    name: Regression (${{ matrix.os }}, py${{ matrix.python-version }})
+    name: Regression (${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     timeout-minutes: 60
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-26.04, macos-26-intel, macos-26]
-        python-version: ["3.12", "3.13", "3.14"]
 
     steps:
       - name: Checkout
@@ -79,7 +78,7 @@ jobs:
             --override-channels \
             -c conda-forge \
             -c bioconda \
-            --python ${{ matrix.python-version }} \
+            --python 3.14 \
             --no-anaconda-upload
 
   docs:

From ef164cf9044b4ca755834e1a560370896008c2f2 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Mon, 28 Sep 2026 09:57:54 +0100
Subject: [PATCH 09/13] chore(workflows): update workflow names for consistency

---
 .github/workflows/pr.yaml                | 4 ++--
 .github/workflows/weekly-regression.yaml | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 41fbb03..815ffeb 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -12,7 +12,7 @@ concurrency:
 
 jobs:
   unit:
-    name: Unit (${{ matrix.os }}, py${{ matrix.python-version }})
+    name: Pytest unit • ${{ matrix.os }}, ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     timeout-minutes: 15
 
@@ -40,7 +40,7 @@ jobs:
         run: python -m pytest tests/unit
 
   regression:
-    name: Regression (${{ matrix.os }})
+    name: Regression • ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     timeout-minutes: 60
     strategy:
diff --git a/.github/workflows/weekly-regression.yaml b/.github/workflows/weekly-regression.yaml
index a5900cc..8d29eda 100644
--- a/.github/workflows/weekly-regression.yaml
+++ b/.github/workflows/weekly-regression.yaml
@@ -14,7 +14,7 @@ concurrency:
 
 jobs:
   regression:
-    name: SIST Regression (${{ matrix.os }}, py${{ matrix.python-version }})
+    name: SIST Regression (${{ matrix.os }}, ${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
     timeout-minutes: 30
     strategy:

From 9ede062ecf6dbac8e9a53dc3184c05a032153f54 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Mon, 28 Sep 2026 10:02:37 +0100
Subject: [PATCH 10/13] chore: remove debug from IRF calculation

---
 src/sist/ir_finder.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/sist/ir_finder.py b/src/sist/ir_finder.py
index 8509d66..236add7 100644
--- a/src/sist/ir_finder.py
+++ b/src/sist/ir_finder.py
@@ -325,7 +325,6 @@ def _score_reports(
                 str(self.IRF_MAX_LENGTH),
                 str(self.IRF_MAX_LOOP),
             ],
-            stdin=subprocess.DEVNULL,
             stdout=subprocess.DEVNULL,
             stderr=subprocess.DEVNULL,
             check=False,

From f6c8692f64092cd0294bd759638d9a75bf263546 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Mon, 28 Sep 2026 10:05:04 +0100
Subject: [PATCH 11/13] chore(workflows): fix typo within
 `.github/workflows/pr.yaml`

---
 .github/workflows/pr.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 815ffeb..18c1957 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -40,7 +40,7 @@ jobs:
         run: python -m pytest tests/unit
 
   regression:
-    name: Regression • ${{ matrix.os }})
+    name: Regression (${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     timeout-minutes: 60
     strategy:

From a3bcfd5d186a34ca61942cbe607ad8c7c417f88a Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Mon, 28 Sep 2026 10:06:32 +0100
Subject: [PATCH 12/13] chore(workflows): update titles within
 `.github/workflows` for clarity

---
 .github/workflows/pr.yaml                | 2 +-
 .github/workflows/weekly-regression.yaml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 18c1957..8467d20 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -12,7 +12,7 @@ concurrency:
 
 jobs:
   unit:
-    name: Pytest unit • ${{ matrix.os }}, ${{ matrix.python-version }}
+    name: Pytest unit • ${{ matrix.os }}, Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     timeout-minutes: 15
 
diff --git a/.github/workflows/weekly-regression.yaml b/.github/workflows/weekly-regression.yaml
index 8d29eda..167870a 100644
--- a/.github/workflows/weekly-regression.yaml
+++ b/.github/workflows/weekly-regression.yaml
@@ -14,7 +14,7 @@ concurrency:
 
 jobs:
   regression:
-    name: SIST Regression (${{ matrix.os }}, ${{ matrix.python-version }})
+    name: SIST Regression (${{ matrix.os }}, Python ${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
     timeout-minutes: 30
     strategy:

From ecde1ece84e267257a81b90b8c6e6887c57f8139 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Mon, 28 Sep 2026 10:24:09 +0100
Subject: [PATCH 13/13] fix(docs): floor `nbsphinx` at `v0.9.8` to avoid sphinx
 version conflict

---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index f6ba0b1..71fd2b5 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,5 +1,5 @@
 sphinx>=9.1,<9.2
-nbsphinx>=0.9,<1.0
+nbsphinx>=0.9.8,<1.0
 furo>=2025.0,<2026.0
 sphinx_copybutton>=0.5,<1.0
 sphinxcontrib-contentui>=0.2,<1.0