From 6d7f1e5fd3c55e4f3b39e1c7285f53461351e12f Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Wed, 4 Nov 2026 10:32:59 +0000 Subject: [PATCH 1/3] docs: switch to the shared CCPBioSim Sphinx theme --- docs/requirements.txt | 6 +----- docs/source/conf.py | 21 +++------------------ 2 files changed, 4 insertions(+), 23 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index cbe9f9a..0a91d38 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,7 +1,3 @@ sphinx>=9.2,<9.3 -nbsphinx>=0.9.8,<1.0 -furo>=2025.0,<2026.0 -sphinx_copybutton>=0.5,<1.0 -sphinxcontrib-contentui>=0.2,<1.0 -sphinxcontrib-details-directive>=0.1,<1.0 +ccpbiosim-sphinx-theme>=1.3.4,<2.0 markupsafe>=3.0,<4.0 diff --git a/docs/source/conf.py b/docs/source/conf.py index 8c46a5a..ecbf364 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -13,33 +13,18 @@ # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration extensions = [ - "sphinx.ext.autosummary", - "sphinx.ext.autodoc", "sphinx.ext.mathjax", - "sphinx.ext.viewcode", - "sphinx.ext.napoleon", "sphinx.ext.intersphinx", "sphinx.ext.extlinks", - "nbsphinx", - "sphinx_copybutton", ] -autosummary_generate = True -napoleon_google_docstring = False -napoleon_use_param = False -napoleon_use_ivar = True - 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_options = { - "dark_logo": "logos/SIST-logo-white-text.svg", - "light_logo": "logos/SIST-logo-black-text.svg", -} - +# The shared CCPBioSim theme. +html_theme = "ccpbiosim_sphinx_theme" +html_context = {"github_repo": "SIST"} html_static_path = ["_static"] From 2837c335525f52a2ee1b13cea5d697f4e20378a6 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Wed, 4 Nov 2026 10:33:27 +0000 Subject: [PATCH 2/3] docs: add banner, quick start and selection cards to the home page --- docs/source/index.rst | 94 +++++++++++++++++++++++++++++++++++-------- 1 file changed, 77 insertions(+), 17 deletions(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index 2ac4ff8..fb25961 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,6 +1,16 @@ +:html_theme.sidebar_secondary.remove: + SIST ==== +.. ccpbiosim-hero:: + :logo-light: _static/logos/SIST-logo-black-text.svg + :logo-dark: _static/logos/SIST-logo-white-text.svg + :logo-alt: SIST + :tagline: Stress-Induced Structural Transitions in superhelical DNA + :button: user-guide | Get started + :github: CCPBioSim/SIST + SIST (Stress-Induced Structural Transitions) is a program for analysing stress-induced structural transitions in superhelical DNA with a specified base sequence. @@ -18,31 +28,81 @@ command, and regression testing against reference scientific outputs. Quick start ----------- -Install SIST with Conda: +.. tab-set:: + + .. tab-item:: Install + + Install SIST with Conda: + + .. code-block:: bash + + conda install -c ccpbiosim -c conda-forge -c bioconda sist + + .. tab-item:: Melting + + Run a melting calculation: + + .. code-block:: bash + + sist -a M -f sequence.fa + + .. tab-item:: Competition + + Run a competition calculation and write the result to a file: + + .. code-block:: bash + + sist -a A -f sequence.fa -o results.txt + +Explore the documentation +------------------------- + +.. grid:: 1 2 3 3 + :gutter: 3 + + .. grid-item-card:: ๐Ÿ“– User Guide + :link: user-guide + :link-type: doc + + Calculation modes, options and output. + + .. grid-item-card:: ๐Ÿ“ฆ Installation + :link: installation + :link-type: doc + + Install SIST with Conda or from source. -.. code-block:: bash + .. grid-item-card:: ๐Ÿ”ง Source Usage + :link: source-usage + :link-type: doc - conda install -c ccpbiosim -c conda-forge -c bioconda sist + Run SIST and its parts from a source build. -Run a melting calculation: + .. grid-item-card:: ๐Ÿงฌ Examples + :link: examples + :link-type: doc -.. code-block:: bash + Example inputs and outputs to try. - sist -a M -f sequence.fa + .. grid-item-card:: ๐Ÿงช Development + :link: development + :link-type: doc -Run a competition calculation and write the result to a file: + Building, testing and releasing SIST. -.. code-block:: bash + .. grid-item-card:: ๐Ÿ“ Citation + :link: citation + :link-type: doc - sist -a A -f sequence.fa -o results.txt + How to cite SIST in your work. .. toctree:: :maxdepth: 2 - :caption: Contents - - user-guide - installation - source-usage - examples - development - citation + :hidden: + + User Guide + Installation + Source Usage + Examples + Development + Citation From a162a087e19ab6194d9163b24c627efaa067a520 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Wed, 4 Nov 2026 10:33:59 +0000 Subject: [PATCH 3/3] chore: stop ignoring the old autosummary folder --- .gitignore | 1 - 1 file changed, 1 deletion(-) diff --git a/.gitignore b/.gitignore index 654b986..0f66840 100644 --- a/.gitignore +++ b/.gitignore @@ -69,7 +69,6 @@ cmake-build-*/ # Sphinx build output docs/build/ -docs/source/_autosummary/ # Python environments, caches, and packaging .venv/