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DOC: render qrules results with Mermaid - #226

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Sep 9, 2026
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DOC: render qrules results with Mermaid#226
redeboer merged 14 commits into
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dependabot/lock-a509110cae

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📝 Documentation

  • Decay topologies in the notebooks are rendered with Mermaid through qrules.io.asmermaid() and IPython.display.Markdown instead of with Graphviz. Sphinx renders the fenced blocks in the notebook output through sphinxcontrib-mermaid, with myst_fence_as_directive = ["mermaid"].
  • mermaid_init_config and a new docs/_static/mermaid.css keep the diagrams at their natural size instead of stretching them over the page width, and give edge labels a solid background so that edges do not shine through.
  • The main amplitude equation on the front page uses an aligned environment instead of the deprecated eqnarray, which MathJax renders with correct spacing around the alignment points.
  • Hidden input cells in the notebooks carry a code_prompt_show label that says what they contain, and the lineshape cells in the $J/\psi \to K^0_S p \bar{p}$, $\Lambda_c^+ \to p K^- \pi^+$ and $\Xi_b^- \to p K^- K^-$ notebooks show the full lineshape through unfold_definitions() instead of listing each sub-expression by hand.
  • Progress bars and warnings from qrules.transition are muted in the notebooks, so the Sphinx output no longer contains stray logging output.

🖱️ Developer experience

  • Graphviz is no longer needed as a system dependency. It has been removed from .readthedocs.yml, the CI documentation job, .binder/apt.txt, and [tool.compwa.policy], so the documentation can be built without an apt installation step.
  • The notebook dependency group requires qrules>=0.10.12 for qrules.io.asmermaid() instead of the qrules[viz] extra.

Squash commit messages

* DOC: improve notebook renderings in Sphinx
* DX: drop Graphviz as a system dependency
* FIX: replace eqnarray with aligned in amplitude equation
* MAINT: increase minimal QRules version

@dependabot dependabot Bot added the ⬆️ Lock This PR upgrades the lock files label Sep 2, 2026
@redeboer
redeboer marked this pull request as draft September 2, 2026 17:30
@redeboer redeboer changed the title MAINT: bump the lock group with 7 updates DOC: render qrules results with Mermaid Sep 2, 2026
@redeboer redeboer added the 📝 Docs Improvements or additions to documentation label Sep 2, 2026
@redeboer
redeboer marked this pull request as ready for review September 2, 2026 20:11
@redeboer
redeboer self-requested a review September 2, 2026 20:11
dependabot Bot and others added 7 commits September 3, 2026 17:01
Bumps the lock group with 7 updates:

| Package | From | To |
| --- | --- | --- |
| [https://github.com/ComPWA/nbhooks](https://github.com/ComPWA/nbhooks) | `0.0.1` | `0.0.2` |
| [https://github.com/astral-sh/ruff-pre-commit](https://github.com/astral-sh/ruff-pre-commit) | `v0.16.1` | `0.16.5` |
| [https://github.com/tombi-toml/tombi-pre-commit](https://github.com/tombi-toml/tombi-pre-commit) | `v1.2.5` | `1.5.0` |
| [https://github.com/streetsidesoftware/cspell-cli](https://github.com/streetsidesoftware/cspell-cli) | `v10.0.1` | `10.1.0` |
| [https://github.com/editorconfig-checker/editorconfig-checker.python](https://github.com/editorconfig-checker/editorconfig-checker.python) | `3.6.1` | `3.11.1` |
| [https://github.com/astral-sh/ty-pre-commit](https://github.com/astral-sh/ty-pre-commit) | `v0.0.65` | `0.0.75` |
| [https://github.com/astral-sh/uv-pre-commit](https://github.com/astral-sh/uv-pre-commit) | `0.12.0` | `0.12.7` |


Updates `https://github.com/ComPWA/nbhooks` from 0.0.1 to 0.0.2
- [Release notes](https://github.com/ComPWA/nbhooks/releases)
- [Commits](ComPWA/nbhooks@0.0.1...0.0.2)

Updates `https://github.com/astral-sh/ruff-pre-commit` from v0.16.1 to 0.16.5
- [Release notes](https://github.com/astral-sh/ruff-pre-commit/releases)
- [Commits](astral-sh/ruff-pre-commit@v0.16.1...v0.16.5)

Updates `https://github.com/tombi-toml/tombi-pre-commit` from v1.2.5 to 1.5.0
- [Release notes](https://github.com/tombi-toml/tombi-pre-commit/releases)
- [Commits](tombi-toml/tombi-pre-commit@v1.2.5...v1.5.0)

Updates `https://github.com/streetsidesoftware/cspell-cli` from v10.0.1 to 10.1.0
- [Release notes](https://github.com/streetsidesoftware/cspell-cli/releases)
- [Changelog](https://github.com/streetsidesoftware/cspell-cli/blob/main/CHANGELOG.md)
- [Commits](streetsidesoftware/cspell-cli@v10.0.1...v10.1.0)

Updates `https://github.com/editorconfig-checker/editorconfig-checker.python` from 3.6.1 to 3.11.1
- [Release notes](https://github.com/editorconfig-checker/editorconfig-checker.python/releases)
- [Commits](editorconfig-checker/editorconfig-checker.python@3.6.1...3.11.1)

Updates `https://github.com/astral-sh/ty-pre-commit` from v0.0.65 to 0.0.75
- [Release notes](https://github.com/astral-sh/ty-pre-commit/releases)
- [Commits](astral-sh/ty-pre-commit@v0.0.65...v0.0.75)

Updates `https://github.com/astral-sh/uv-pre-commit` from 0.12.0 to 0.12.7
- [Release notes](https://github.com/astral-sh/uv-pre-commit/releases)
- [Commits](astral-sh/uv-pre-commit@0.12.0...0.12.7)

---
updated-dependencies:
- dependency-name: https://github.com/ComPWA/nbhooks
  dependency-version: 0.0.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: lock
- dependency-name: https://github.com/astral-sh/ruff-pre-commit
  dependency-version: 0.16.5
  dependency-type: direct:production
  dependency-group: lock
- dependency-name: https://github.com/tombi-toml/tombi-pre-commit
  dependency-version: 1.5.0
  dependency-type: direct:production
  dependency-group: lock
- dependency-name: https://github.com/streetsidesoftware/cspell-cli
  dependency-version: 10.1.0
  dependency-type: direct:production
  dependency-group: lock
- dependency-name: https://github.com/editorconfig-checker/editorconfig-checker.python
  dependency-version: 3.11.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: lock
- dependency-name: https://github.com/astral-sh/ty-pre-commit
  dependency-version: 0.0.75
  dependency-type: direct:production
  dependency-group: lock
- dependency-name: https://github.com/astral-sh/uv-pre-commit
  dependency-version: 0.12.7
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: lock
...

Signed-off-by: dependabot[bot] <support@github.com>
@redeboer
redeboer force-pushed the dependabot/lock-a509110cae branch from 61b2a01 to 7f91f58 Compare September 3, 2026 15:17
@redeboer
redeboer removed this pull request from stack #228 September 9, 2026 16:14
@redeboer redeboer added this to the 0.4.2 milestone Sep 9, 2026
@redeboer redeboer added the 🖱️ DX Improvements to the Developer Experience label Sep 9, 2026
@redeboer
redeboer enabled auto-merge (squash) September 9, 2026 18:10
@redeboer
redeboer merged commit 202adac into main Sep 9, 2026
32 checks passed
@redeboer
redeboer deleted the dependabot/lock-a509110cae branch September 9, 2026 18:16
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Render qrules transitions with Mermaid instead of Graphviz Aligned amplitude equation renders as an error under MathJax 4

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