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docs: Document refactored tracing #936

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ns-rse
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@ns-rse ns-rse commented Oct 9, 2024

Adds documentation, written by @MaxGamill-Sheffield, for...

  • Disordered tracing
  • Nodestats
  • Ordered tracing
  • Splining

I squashed the history of all the incremental commits that wrote this documentation but have left the changes I've made recently as individual commits.

Locally the advanced Table of Contentes (toctree) is not rendered, I need to check if this is the case on the GitHub CI rendered pages too though (which this PR should trigger).

NB Ideally this should be merged to maxgamill-sheffield/800-better-tracing before it is merged to main so the documentation and features arrive on main at the same time.

MaxGamill-Sheffield and others added 7 commits October 8, 2024 19:53
- Disordered tracing
- Nodestats
- Ordered tracing
- Splining
As per Markdown linting defined in `.markdownlint-cli2.yaml`

- Wrap lines at 120 characters.
- Fix all other linting errors automatically.
As per [myst docs](https://myst-parser.readthedocs.io/en/latest/syntax/optional.html#auto-generated-header-anchors)
setting the `myst_heading_anchors` sets the maximum depth for auto-generating label "slugs" for section headers.

Helps resolve some, but not all, complaints about internal links.
Myst-Parser complains about the use of Markdown footnotes (e.g. `[^1]`) therefore switch these to alternatives.
@MaxGamill-Sheffield
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MaxGamill-Sheffield commented Oct 9, 2024

@ns-rse you've requested a review, but this is still a draft, so are you happy with the toctrees?

Locally the advanced Table of Contentes (toctree) is not rendered, I need to check if this is the case on the GitHub CI rendered pages too though (which this PR should trigger).

And shall I re-examine the docs to ensure everything is rendered ok? (Also, how do I do this for CI and not local e.g. to see if the equations are loaded correctly?)

@ns-rse
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ns-rse commented Oct 9, 2024

Evening @MaxGamill-Sheffield

Not completely happy with toctrees but for some reason this hasn't triggered the build of the pages on CI which I was hoping for to help me see if its something with my local setup.

Its slightly obfuscated but the commands to replicate what CI does using sphinx-multidocs are in .github/workflows/sphinx_docs_to_gh_pages.yaml.

sphinx-multiversion . _build/html "../*setup*" "../*tests*" "../*.ipynb" ../demo.py ../make_baseline.py ../jupyter_notebook_config.py ../demo_ftrs.py

Weirdly using sphinx-build includes the new toctree but using sphinx-multiversion doesn't (it's essentially a wrapper which checks out each tag and runs sphinx-build on each tagged commit and maind and placing the output under _build/html/<tag|main> so that there are multiple versions of the documentation).

I add reviewers to drafts when creating them (so I don't forget when I hit the "Ready for review") but in this instance will see if making it "Ready for review" triggers the build.

If not and for expedience I will rejig how the advanced docs are linked from the front page.

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Not sure I'm understanding this.

Is the issue that we aren't able to check that they're rendering okay on gh-pages? If so, if we are happy with the contents could we try just pushing to main which would presumably force a build?

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ns-rse commented Oct 14, 2024

we aren't able to check that they're rendering okay on gh-pages?

Correct.

If so, if we are happy with the contents could we try just pushing to main which would presumably force a build?

This would result in the main documentation having documentation which isn't quite yet on that branch.

I'm going to look at this today and may just ditch having an additional toctree in favour of an extra Advanced entry in the existing one and link articles from there (as I can envisage this section growing considerably) but go sidetracked trying to work out why tests are failing on Windows and possible solutions.

The second `.. toctree::` was not being rendered for some reason. Instead a new page `docs/advanced.md` has been created
and serves as an index to the documentation which resides under `advanced/` with sub-headings for each section as I can
envisage this growing as more functionality is added.
@ns-rse ns-rse marked this pull request as ready for review October 15, 2024 13:54
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ns-rse commented Oct 15, 2024

Ready for review, its not triggering the GitHub Action to build the documentation here on GitHub because that is configured to only run on Pull Requests that target the main branch. Once this is merged into maxgamill-sheffield/800-better-tracing it will trigger a build.

I couldn't work out how to get the second .. toctree:: so have instead added a docs/advanced.md which serves as an index for Advanced topics which reside under docs/advanced/. Hopefully over time the pages detailing the inner workings will grow.

@MaxGamill-Sheffield MaxGamill-Sheffield merged commit f476c65 into maxgamill-sheffield/800-better-tracing Oct 15, 2024
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@MaxGamill-Sheffield MaxGamill-Sheffield deleted the maxgamill-sheffield/btr-docs branch October 15, 2024 15:03
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3 participants