Remove dead notebook/gallery infrastructure from master

[waltsims]

• Delete: generate-notebooks.yml, docs/examples.rst, docs/generate_example_notebooks.py, jupytext.toml, run_examples.py, docs/Makefile
• Remove nbsphinx extension and Colab prolog from docs/conf.py
• Remove nbsphinx and jupytext from docs dependencies
• Remove examples gallery from docs index toctree
• Revert test_pages.yml to simple Sphinx build (no pandoc/notebooks)
• Remove docs/_examples/ from .gitignore

The notebook gallery approach was closed — proper documentation with static images will replace it. Legacy example notebooks untouched.

Greptile Summary

This PR removes all the notebook/gallery infrastructure that was introduced to generate interactive Jupyter notebook documentation from the examples/*.py files. The approach has been abandoned in favour of static-image documentation, so all associated files, CI workflows, Sphinx extensions, and dependencies are cleanly deleted.

• Deleted files: generate-notebooks.yml, run_examples.py, docs/generate_example_notebooks.py, docs/examples.rst, docs/Makefile, Makefile, jupytext.toml
• docs/conf.py: nbsphinx extension and Colab-badge prolog removed
• pyproject.toml: nbsphinx==0.9.7 and jupytext==1.16.6 dropped from the [docs] extra
• test_pages.yml: Simplified — pandoc install and notebook-generation steps removed; dependency installation delegated to the waltsims/pages action via the new pyproject_toml_deps input
• docs/index.rst: examples toctree entry removed alongside the now-deleted examples.rst
• .gitignore: docs/_examples/ rule removed (directory is no longer generated)

No remaining references to the removed infrastructure exist in any build-critical file; the only mentions are in plans/release-strategy.md, a planning document where the historical context is appropriate to retain.

Confidence Score: 5/5

Safe to merge — purely a deletion of dead infrastructure with no impact on library functionality or existing tests.

All changes are deletions or straightforward removals of references. Every deleted file, extension, and dependency has been consistently removed across the workflow, Sphinx config, pyproject.toml, .gitignore, and index. No broken cross-references remain in build-critical files. No remaining findings rise above P2.

.github/workflows/test_pages.yml — uses a branch ref (waltsims/pages@pyproject.toml-support) rather than a pinned commit SHA, which is a pre-existing pattern not introduced by this PR.

Important Files Changed

Filename	Overview
.github/workflows/generate-notebooks.yml	Deleted: CI workflow that auto-converted examples/*.py to notebooks and committed them back to master.
.github/workflows/test_pages.yml	Simplified: removed pandoc install + notebook generation steps; now delegates full dependency installation to the waltsims/pages action via the new pyproject_toml_deps input.
docs/conf.py	Removed nbsphinx extension, nbsphinx_execute setting, and the Colab-badge prolog template; rest of config unchanged.
pyproject.toml	Removed nbsphinx==0.9.7 and jupytext==1.16.6 from [docs] optional dependency group.
docs/index.rst	Removed examples toctree entry; the now-deleted examples.rst is no longer referenced.
docs/generate_example_notebooks.py	Deleted: script that converted examples/.py (percent-format) to docs/_examples/.ipynb for nbsphinx rendering.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    subgraph BEFORE["Before - Removed"]
        A[push to master] --> B[generate-notebooks.yml]
        B --> C[jupytext converts .py to .ipynb]
        C --> D[commit notebooks/ to master]
        E[push any branch] --> F[test_pages.yml - old]
        F --> G[install pandoc]
        G --> H[pip install docs deps]
        H --> I[generate_example_notebooks.py]
        I --> J[nbsphinx renders notebooks]
        J --> K[Sphinx build and deploy]
    end

    subgraph AFTER["After - This PR"]
        L[push any branch] --> M[test_pages.yml - new]
        M --> N[waltsims/pages action with pyproject_toml_deps]
        N --> O[Sphinx build and deploy - static RST/MD only]
    end

    style BEFORE fill:#ffeaea,stroke:#cc0000
    style AFTER fill:#eaffea,stroke:#006600

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Comments Outside Diff (3)

1. run_examples.py

   Stale references to deleted run_examples.py

   run_examples.py is deleted by this PR, but two places still reference it and will break:

   1. Root Makefile line 20 — the run-examples target (and by extension the default all target) calls python run_examples.py directly. Anyone running make run-examples or make all will get a file-not-found error immediately after this merges.

   2. docs/development/development_environment.rst lines 98 & 104 — the development docs show users how to run examples with two explicit invocations of run_examples.py:

      MPLBACKEND=Agg python run_examples.py
      MPLBACKEND=Agg KWAVE_FORCE_CPU=1 python run_examples.py
      

   Both references should be removed or updated to reflect whatever the new recommended way to run examples is (e.g., pointing users at the examples/ directory directly).

2. Makefile, line 20 (link)

   make run-examples now broken — run_examples.py was deleted

   run_examples.py is deleted in this PR, but the root Makefile's run-examples target (and the all target which depends on it) still calls python run_examples.py. Any developer running make run-examples or make all will hit a No such file or directory error immediately.

   This Makefile target should either be removed or updated to invoke the examples via a different mechanism.

3. docs/development/development_environment.rst, line 96-104 (link)

   Docs reference deleted run_examples.py

   The "Running Examples" section shows two commands that both rely on run_examples.py, which is deleted in this PR:

   make run-examples
   # or
   MPLBACKEND=Agg python run_examples.py
   

   and

   MPLBACKEND=Agg KWAVE_FORCE_CPU=1 python run_examples.py
   

   Both will fail with No such file or directory. This section of the developer documentation should be updated or removed to reflect the new approach for running examples.

_{Reviews (3): Last reviewed commit: "Merge master (readme cleanup already mer..." | Re-trigger Greptile}

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 74.40%. Comparing base (3a7ae8f) to head (a4cda49).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #693   +/-   ##
=======================================
  Coverage   74.40%   74.40%           
=======================================
  Files          56       56           
  Lines        8026     8026           
  Branches     1570     1570           
=======================================
  Hits         5972     5972           
  Misses       1437     1437           
  Partials      617      617           

Flag	Coverage Δ
3.10	74.40% <ø> (ø)
3.11	74.40% <ø> (ø)
3.12	74.40% <ø> (ø)
3.13	74.40% <ø> (ø)
macos-latest	74.38% <ø> (ø)
ubuntu-latest	74.38% <ø> (ø)
windows-latest	74.39% <ø> (ø)

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[waltsims]

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