Seperate out Testing Suite into Unit and Regression Testing

.github/workflows/coveralls-main.yaml

@@ -0,0 +1,145 @@
+name: Coveralls Main
+
+on:
+  push:
+    branches: [main]
+
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: coveralls-main-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  python-coverage:
+    name: Build main coverage baseline (Python)
+    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
+          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

.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

.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
+          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

.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 }}

.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/**

.github/workflows/regression-tests.yaml → .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:

.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/
@@ -75,6 +80,10 @@ __pycache__/
 .ruff_cache/
 *.egg-info/
 
+# Coverage
+.coverage
+coverage.xml
+
 # Regression test artefacts
 .testdata/
 test-results/

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) |

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

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",
 ]