[edkerk]

Adds guide/workflow.md, a page of Mermaid flowcharts with a MATLAB and a Python tab. Each diagram orders the stages from project set-up to analysis, with the parallel kcat sources, the alternative tuning and relaxation paths and the optional steps. A table lists each stage with the stage it runs after, its functions and its output.

• guide/index.md has a Workflow section with a thumbnail that links to the page.
• Each guide page from Getting started to Enzyme usage and bottlenecks has a closed dropdown "Place in the workflow" with a small diagram of the functions of the page and the neighbouring pages.
• The workflow diagram keeps a minimum width and scrolls sideways in a narrow column. Ctrl or Cmd with the mouse wheel zooms in the page, and each diagram has a full-screen button where the wheel zooms and a drag pans.
• docs/conf.py loads sphinxcontrib.mermaid and requirements.txt lists it. The viewer's browser loads mermaid.js from a CDN.
• The thumbnail docs/_static/workflow-overview.png is a screenshot of the MATLAB diagram.
• A download icon at the top of each tab of the workflow page saves its diagram as a PDF. The PDFs are static files in docs/_static and are rendered again when the diagram changes.
• The Documentation cards on the front page link to the workflow overview and to the page on upgrading a GECKO 3 project, in place of the Guide and API reference cards that the menu already links.
• The header bar, the primary sidebar and the article column are changed in docs/_static/custom.css: a thinner header and sidebar, and a wider article column.

The diagrams were rendered in Chromium without syntax errors. sphinx-build -W passes. The branch is based on docs/gecko4-changes (#26) because the page links to pages added there.

[read-the-docs-community]

Documentation build overview

📚 gecko-docs | 🛠️ Build #35578032 | 📁 Comparing ec38eb7 against latest (46bef52)

  🔍 Preview build  

27 files changed · + 5 added · ± 22 modified

+ Added

• gecko3-upgrade-project.html
• gecko4-kcat-assignment.html
• gecko4-project-format.html
• guide/basic-model-operations.html
• guide/workflow.html

± Modified

• gecko-to-geckopy.html
• gecko3-to-gecko4.html
• index.html
• migrate.html
• api/index.html
• guide/applying-kcats.html
• guide/building-ec-model.html
• guide/data-folder-files.html
• guide/enzyme-usage-and-bottlenecks.html
• guide/gathering-kcats.html
• and 12 more...