Add pre-commit hooks with Ruff and C++ formatting/linting support

.github/workflows/pr.yaml

@@ -81,6 +81,35 @@ jobs:
             --python 3.14 \
             --no-anaconda-upload
 
+  pre-commit:
+    name: Pre-commit
+    needs: unit
+    runs-on: ubuntu-26.04
+    timeout-minutes: 15
+
+    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 pre-commit dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[pre-commit]
+
+      - name: Run pre-commit
+        run: |
+          pre-commit install
+          pre-commit run --all-files || {
+            git status --short
+            git diff
+            exit 1
+          }
+
   docs:
     name: Docs
     needs: unit
@@ -154,4 +183,4 @@ jobs:
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           file: coverage.xml
-          fail-on-error: false
+          fail-on-error: false

.github/workflows/weekly-regression.yaml

@@ -53,4 +53,4 @@ jobs:
             -c conda-forge \
             -c bioconda \
             --python ${{ matrix.python-version }} \
-            --no-anaconda-upload
+            --no-anaconda-upload

.gitignore

@@ -86,4 +86,4 @@ coverage.xml
 
 # Regression test artefacts
 .testdata/
-test-results/
+test-results/

.pre-commit-config.yaml

@@ -0,0 +1,46 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.2
+    hooks:
+      - id: ruff-check
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pocc/pre-commit-hooks
+    rev: v1.3.5
+    hooks:
+      - id: clang-format
+        files: \.(c|cc|cpp|cxx|h|hh|hpp|hxx)$
+      - id: clang-tidy
+        files: \.(c|cc|cpp|cxx)$
+        args: ["-checks=-*,clang-analyzer-*,bugprone-*"]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-merge-conflict
+      - id: check-yaml
+        exclude: ^conda-recipe/meta\.yaml$
+      - id: check-toml
+      - id: check-case-conflict
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/rstcheck/rstcheck
+    rev: v6.2.0
+    hooks:
+      - id: rstcheck
+        name: rstcheck (docstrings only)
+        files: \.py$
+        args: ["--report-level", "warning"]
+
+  - repo: local
+    hooks:
+      - id: sphinx-docs
+        name: sphinx-build (pre-push, warnings as errors)
+        entry: bash -lc 'make -C docs clean && make -C docs html SPHINXOPTS="-W --keep-going"'
+        language: system
+        pass_filenames: false
+        stages: [pre-push]

.readthedocs.yaml

@@ -20,5 +20,3 @@ sphinx:
 python:
    install:
    - requirements: docs/requirements.txt
-
-

CITATION.cff

@@ -72,4 +72,4 @@ keywords:
 
 license: MIT
 version: 1.0.0
-date-released: '2026-09-14'
+date-released: '2026-09-14'

README.md

@@ -1,4 +1,4 @@
-SIST: Stress-Induced Structural Transitions in superhelical DNA 
+SIST: Stress-Induced Structural Transitions in superhelical DNA
 ==============================
 
 | Category       | Badges |
@@ -12,7 +12,7 @@ SIST: Stress-Induced Structural Transitions in superhelical DNA
 
 ## Purpose of SIST
 
-The codes in this repository are for analyzing three types of structural transitions in superhelical DNA molecules of specified base sequences and kilobase lengths.  These are strand separation, BZ transitions and cruciform extrusion.  More types of transitions may be added as their energetics become known.  The statistical mechanical methods and algorithms used in these analyses are described in the papers cited below. 
+The codes in this repository are for analyzing three types of structural transitions in superhelical DNA molecules of specified base sequences and kilobase lengths.  These are strand separation, BZ transitions and cruciform extrusion.  More types of transitions may be added as their energetics become known.  The statistical mechanical methods and algorithms used in these analyses are described in the papers cited below.
 
 <p align="center">
     <img src="docs/source/_static/logos/SIST-logo-white-text.svg#gh-dark-mode-only" alt="SIST logo" width="300"/>

docs/source/_static/examples/one_line.pbr322.toy.fa

@@ -1,2 +1,2 @@
 >one_line.pbr322.toy.fa
-AGTCAGGCACCGTGTATGAAATCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTGTAGGCATAGGCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATATCGTCCATTCCGACAGCATCGCCAGTCACTATGGCGTGCTGCTAGCGCTATATGCGTTGATGCAATTTCTATGCGCACCCGTTCTCGGAGCACTGTCCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACGGAGCCACTATCGACTACGCGATCATGGCGACCACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCACAGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTCATGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGGACTGTTGGGCGCCATCTCCTTGCATGCACCATTCCTTGCGGCGGCGGTGCTCAACGGCCTCAACCTACTACTGGGCTGCTTCCTAATGCAGGAGTCGCATAAGGGAGAGCGTCGACCGATGCCCTTGAGAGCCTTCAACCCAGTCAGCTCCTTCCGGTGGGCGCGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGTCTTGCTGGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGGCATCGGGATGCCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTCGCGCGCGCGCGCGCGCGCAGATGACAAGGATCGCTCGCGGCTCTTACCAGCCTAACTTCGATCACTGGACCGCTGATCGTCACGGCGATTTATGCCGCCTCGGCGAGCACATGGAACGGGTTGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGCGTCGCGGTGCATGGAGCCGGGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGGATTCACCACTCCAAGAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGGCAGAACATATCCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGGTCCTGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTTCCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCAGGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTGGCATTGACCCTGAGTGATTTTTCTCTGGTCCCGCCGCATCCATACCGCCAGTTGTTTACCCTCACAACGTTCCAGTAACCGGGCATGTTCATCATCAGTAACCCGTATCGTGAGCATCCTCTCTCGTTTCATCGGTATCATTACCCCCATGAACAGAAATCCCCCTTACACGGAGGCATCAGTGACCAAACAGGAAAAAACCGCCCTTAACATGGCCCGCTTTATCAGAAGCCAGACATTAACGCTTCTGGAGAAACTCAACGAGCTGGACGCGGATGAACAGGCAGACATCTGTGAATCGCTTCACGACCACGCTGATGAGCTTTACCGCAGCTGCCTCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCGCAGCCATGACCCAGTCACGTAGCGATAGCGGAGTGTATACTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTGCTCAGTGAACCAATTGGCCAACCGGAAGGAAAACCTTCCGGTTGGCCAATTGGTTGAACGAAAACTATCCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAACACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCCCTTTCGTCTTCAAGAA
+AGTCAGGCACCGTGTATGAAATCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTGTAGGCATAGGCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATATCGTCCATTCCGACAGCATCGCCAGTCACTATGGCGTGCTGCTAGCGCTATATGCGTTGATGCAATTTCTATGCGCACCCGTTCTCGGAGCACTGTCCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACGGAGCCACTATCGACTACGCGATCATGGCGACCACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCACAGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTCATGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGGACTGTTGGGCGCCATCTCCTTGCATGCACCATTCCTTGCGGCGGCGGTGCTCAACGGCCTCAACCTACTACTGGGCTGCTTCCTAATGCAGGAGTCGCATAAGGGAGAGCGTCGACCGATGCCCTTGAGAGCCTTCAACCCAGTCAGCTCCTTCCGGTGGGCGCGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGTCTTGCTGGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGGCATCGGGATGCCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTCGCGCGCGCGCGCGCGCGCAGATGACAAGGATCGCTCGCGGCTCTTACCAGCCTAACTTCGATCACTGGACCGCTGATCGTCACGGCGATTTATGCCGCCTCGGCGAGCACATGGAACGGGTTGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGCGTCGCGGTGCATGGAGCCGGGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGGATTCACCACTCCAAGAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGGCAGAACATATCCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGGTCCTGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTTCCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCAGGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTGGCATTGACCCTGAGTGATTTTTCTCTGGTCCCGCCGCATCCATACCGCCAGTTGTTTACCCTCACAACGTTCCAGTAACCGGGCATGTTCATCATCAGTAACCCGTATCGTGAGCATCCTCTCTCGTTTCATCGGTATCATTACCCCCATGAACAGAAATCCCCCTTACACGGAGGCATCAGTGACCAAACAGGAAAAAACCGCCCTTAACATGGCCCGCTTTATCAGAAGCCAGACATTAACGCTTCTGGAGAAACTCAACGAGCTGGACGCGGATGAACAGGCAGACATCTGTGAATCGCTTCACGACCACGCTGATGAGCTTTACCGCAGCTGCCTCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCGCAGCCATGACCCAGTCACGTAGCGATAGCGGAGTGTATACTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTGCTCAGTGAACCAATTGGCCAACCGGAAGGAAAACCTTCCGGTTGGCCAATTGGTTGAACGAAAACTATCCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAACACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCCCTTTCGTCTTCAAGAA

docs/source/_static/examples/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.html

@@ -1,9 +1,9 @@
 <HTML><HEAD><TITLE>one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.html</TITLE><BASE TARGET="one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.txt.html"></HEAD><BODY bgcolor="#FBF8BC"><BR><PRE>Inverted Repeats Finder Program written by:</PRE><PRE><CENTER>Gary Benson<BR>Department of Biomathematical Sciences<BR>Mount Sinai School of Medicine<BR>Version 3.05<BR></CENTER>
 Sequence: one_line.pbr322.toy.fa
-Parameters: 2 10 10 80 10 20 10000 100 
+Parameters: 2 10 10 80 10 20 10000 100
 Length:  4291</PRE>
 
-<P><PRE>Tables:   1   
+<P><PRE>Tables:   1
 
 This is table  1  of  1  ( 2 repeats found )
 </PRE><PRE>
@@ -16,7 +16,7 @@
 
 </TABLE>
 
-<P><PRE>Tables:   1   
+<P><PRE>Tables:   1
 </PRE><P>The End!
 
 </BODY></HTML>

docs/source/_static/examples/one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.txt.html

@@ -8,7 +8,7 @@
 Version 3.05
 
 Sequence: one_line.pbr322.toy.fa
-Parameters: 2 10 10 80 10 20 10000 100 
+Parameters: 2 10 10 80 10 20 10000 100
 Length: 4291
 ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23, N:0.00
 
@@ -25,7 +25,7 @@
        2972 >> (LF) TCCGGCAAAC
        3016 << (RF) CGTTTGTTTT
 
-            
+
        2982 >> AAACCACCGCT >> 2992
        3006 << *********** << 2996
 
@@ -60,7 +60,7 @@
        3079 >> (LF) GTGCTCAGTG
        3146 << (RF) CAAAAGCAAG
 
-            
+
        3089 >> AACCAATTGGCCAACCGGAAGG >> 3110
        3136 << ********************** << 3115
 

docs/source/_static/examples/pbr322.toy.fa

@@ -61,4 +61,3 @@ ACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTC
 TCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCG
 AAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACG
 AGGCCCTTTCGTCTTCAAGAA
-

docs/source/citation.rst

@@ -54,4 +54,4 @@ The original SIST documentation listed the following contacts:
 
 * Dina Zhabinskaya - dzhabinskaya@ucdavis.edu
 * Craig Benham - cjbenham@ucdavis.edu
-* Sally Madden - sallymadden@gmail.com
+* Sally Madden - sallymadden@gmail.com

docs/source/conf.py

@@ -6,8 +6,8 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'SIST'
-copyright = '2026, CCPBioSim'
+project = "SIST"
+copyright = "2026, CCPBioSim"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -29,18 +29,17 @@
 napoleon_use_param = False
 napoleon_use_ivar = True
 
-templates_path = ['_templates']
+templates_path = ["_templates"]
 exclude_patterns = []
 
 
-
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'furo'
+html_theme = "furo"
 html_theme_options = {
     "dark_logo": "logos/SIST-logo-white-text.svg",
     "light_logo": "logos/SIST-logo-black-text.svg",
 }
 
-html_static_path = ['_static']
+html_static_path = ["_static"]

docs/source/development.rst

@@ -48,6 +48,36 @@ During a normal source test run, the test fixtures create a temporary copy of
 the repository, build the C++ executables, and run the supported calculations
 from that working copy.
 
+Pre-commit hooks
+----------------
+
+SIST uses **pre-commit hooks** to maintain code quality and consistent style
+across the Python and C++ code.
+
+Install the pre-commit dependencies and enable the hooks:
+
+.. code-block:: bash
+
+   python -m pip install -e '.[pre-commit]'
+   pre-commit install
+
+Our tooling stack:
+
+* **Python linting and formatting** via ``ruff``
+* **C++ formatting and static analysis** via ``clang-format`` and ``clang-tidy``
+* **Basic repository checks** via ``pre-commit-hooks``
+* **Docstring RST validation** via ``rstcheck``
+
+Run the checks manually against the whole repository:
+
+.. code-block:: bash
+
+   pre-commit run --all-files
+
+.. note::
+
+   Pull requests must pass all pre-commit checks before being merged.
+
 Scientific regression baselines
 --------------------------------
 

pyproject.toml

@@ -34,7 +34,7 @@ Repository = "https://github.com/CCPBioSim/SIST"
 [project.scripts]
 sist = "sist.cli:main"
 # Deprecated aliases for scripted workflows that still invoke the old Perl
-# script names directly. 
+# script names directly.
 "master.pl" = "sist.cli:main"
 "IR_finder.pl" = "sist.ir_finder_cli:main"
 
@@ -45,6 +45,15 @@ testing = [
     "mypy>=1.14,<2.0",
 ]
 
+pre-commit = [
+    "pre-commit>=4.5,<5.0",
+    "ruff>=0.16,<0.17",
+    "pylint>=4.0,<5.0",
+    "rstcheck>=6.2,<7.0",
+    "clang-format>=23.0,<24.0",
+    "clang-tidy>=22.0,<23.0",
+]
+
 [tool.setuptools.packages.find]
 where = ["src"]
 include = ["sist*"]

src/trans_compete/G_x.cpp

@@ -22,54 +22,47 @@
 // Construction/Destruction
 //////////////////////////////////////////////////////////////////////
 
-G_x::G_x()
-{
+G_x::G_x() {
 
-	sum_xG = 0.0;
-	sum_xB = 0.0; 
-	ave_Gx = 0.0;
-	px = 0.0;
+  sum_xG = 0.0;
+  sum_xB = 0.0;
+  ave_Gx = 0.0;
+  px = 0.0;
 }
 
-void G_x::reset()
-{
-	sum_xG = 0.0; 
-	sum_xB = 0.0;
-	ave_Gx = 0.0;
-	px = 0.0;
+void G_x::reset() {
+  sum_xG = 0.0;
+  sum_xB = 0.0;
+  ave_Gx = 0.0;
+  px = 0.0;
 }
 
-void G_x::add(double gs, double exponent, double rt, double lastG, double lastB)
-{
-	if(gs == -1.0 && rt == -1.0){
-		sum_xG = sum_xG + lastG;
-		sum_xB = sum_xB + lastB;	
-	}
-	else{
-		sum_xG = sum_xG + gs*exponent + lastG;
-		sum_xB = sum_xB + exponent + lastB;
-	}
+void G_x::add(double gs, double exponent, double rt, double lastG,
+              double lastB) {
+  if (gs == -1.0 && rt == -1.0) {
+    sum_xG = sum_xG + lastG;
+    sum_xB = sum_xB + lastB;
+  } else {
+    sum_xG = sum_xG + gs * exponent + lastG;
+    sum_xB = sum_xB + exponent + lastB;
+  }
 }
 
-//intput: average energy and partition function
-void G_x::calc(double ave_Gs, double ZsumB) 
-{
-	if (ZsumB == 0.0)
-		px = 1.0;
-	else
-        // V: This is the calculation for the probability
-		px = sum_xB / ZsumB;  
-
-	if(sum_xB == 0.0)
-		ave_Gx = INFINITE_Gx;
-	else
-        // V: This is the calculation of the energy required to transition
-		ave_Gx = sum_xG / sum_xB - ave_Gs; 
-}
-
-G_x::~G_x()
-{
+// intput: average energy and partition function
+void G_x::calc(double ave_Gs, double ZsumB) {
+  if (ZsumB == 0.0)
+    px = 1.0;
+  else
+    // V: This is the calculation for the probability
+    px = sum_xB / ZsumB;
 
+  if (sum_xB == 0.0)
+    ave_Gx = INFINITE_Gx;
+  else
+    // V: This is the calculation of the energy required to transition
+    ave_Gx = sum_xG / sum_xB - ave_Gs;
 }
 
+G_x::~G_x() {}
+
 #endif