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docs: write real narrative pages, weave guides into the toctree#196

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cailmdaley merged 4 commits into
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chore/docs-narrative-pages
Jun 4, 2026
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docs: write real narrative pages, weave guides into the toctree#196
cailmdaley merged 4 commits into
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chore/docs-narrative-pages

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@cailmdaley cailmdaley commented Jun 4, 2026

What & why

The deployed developer docs read as blank because the four hand-written Sphinx pages (index, about, installation, quickstart) were still the unmodified python-package-template placeholders. The Sphinx machinery is fine — autodoc populates the full API reference, the awesome theme renders, gh-pages deploys. This PR writes real content for the front pages, wires the existing real guides into the navigation, and adds a docs-build CI check.

Docs content

The four template pages, rewritten with grounded content:

  • index — a true landing page: what sp_validation is, the four tasks (shear validation → post-processing → cosmology validation → inference), the pipeline flow chart, where to go next.
  • about — CosmoStat / UNIONS context, the problem the package solves, authors & contributors (from the README), contact, MIT license.
  • installation — container / Apptainer first (recommended), then a uv dev checkout. Removes the false pip install sp_validation PyPI claim (the package is not on PyPI).
  • quickstart — a deliberately light four-stage orientation, each stage linking to its guide. Kept brief pending a broader docs rework.

Navigation & the existing real guides:

  • toc.rst regrouped into Getting Started / User Guide / API Reference / Guidelines.
  • run_validation.md and post_processing.md were stray .md files in no toctree — built by Sphinx but unreachable from the sidebar. They (and the Leakage tutorial, moved out of "API Documentation") now live under User Guide.
  • Added H1 titles to the two header-less guides; fixed post_processing's broken internal cross-reference and two H2→H4 heading jumps in the Leakage tutorial.

Cleanup:

  • contributing.rst: fixed dead github.com/martin.kilbinger/... links → CosmoStat/sp_validation on develop.
  • Removed citing.rst + its placeholder my_ref.bib — nothing substantive to cite yet.

Docs CI

Split the docs build into its own deploy-docs.yml workflow:

  • Builds on every pull request (as a check) and on pushes to develop.
  • Deploys to gh-pages only on develop pushes.
  • Runs inside the published image (which carries the scientific stack autodoc imports) and installs the checked-out package on top via .[docs], so the rendered docs reflect the code under review.
  • The now-redundant deploy-docs job is removed from deploy-image.yml.

Previously the docs only built on develop, so a broken docs build never surfaced on a branch or PR. This PR is itself the first to exercise the new check.

Verification

Built the way CI does — sphinx-apidoc + sphinx-build inside ghcr.io/cosmostat/sp_validation:develop (sphinx 8.2.3, full scientific stack). Build succeeds with zero warnings; the API pages populate with [source] links (autodoc imports all resolve), and the rendered landing page shows real content.

Docs redeploy on merge to develop; please don't merge until reviewed. A broader docs rework is the natural follow-up — this PR stands up the structure.

(Pre-existing docstring RST warnings were fixed separately, straight to develop, in 78b4d17.)

— Claude on behalf of Cail

cailmdaley and others added 4 commits June 4, 2026 19:49
The four hand-written Sphinx pages were still the python-package-template
placeholders, so the deployed docs read as blank even though the API reference
and several real guides were already present. Replace the placeholders with
grounded content and wire the existing guides into the navigation.

- index.rst: a true landing page — what sp_validation is, the four tasks
  (shear validation → post-processing → cosmology validation → inference), the
  pipeline flow chart, and where to go next. Strips the template note and the
  Admonitions/Code-Blocks demo sections.
- about.rst: CosmoStat/UNIONS context, the problem the package solves, authors
  and contributors (from the README), contact, license.
- installation.rst: the real install story — container/Apptainer first
  (recommended), then a uv development checkout. Removes the false
  "pip install sp_validation" PyPI claim.
- quickstart.rst: a light four-stage orientation grounded in the real entry
  points, each stage linking to its guide. Kept deliberately brief pending a
  broader docs rework.
- toc.rst: regroup the sidebar into Getting Started / User Guide / API Reference
  / Guidelines; move the existing run_validation, post_processing and Leakage
  tutorial into the User Guide so they are no longer stray .md files outside any
  toctree.
- run_validation.md / post_processing.md: add an H1 page title so the toctree
  entries render cleanly and the "headings start at H2" warnings clear; fix
  post_processing's broken internal cross-reference with an explicit anchor.
- Leakage_object_Tutorial.md: drop two H2→H4 heading jumps to H3.
- contributing.rst: fix the dead github.com/martin.kilbinger/... links to the
  real CosmoStat/sp_validation repo on the develop branch.
- Remove citing.rst and its placeholder my_ref.bib: there is nothing
  substantive to cite yet, so the stub is dropped rather than shipped.

Verified by building the way CI does (sphinx-apidoc + sphinx-build inside the
sp_validation container): build succeeds with zero content warnings, the API
pages populate with [source] links, and the landing page renders real content.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The docs previously built only inside the deploy-image workflow, gated to
develop — so a broken docs build never surfaced on a branch or PR. Split the
docs into their own workflow that builds on pull requests (as a check) and
deploys to gh-pages only on pushes to develop.

The job runs inside the published image — which already carries the scientific
stack autodoc must import — and installs the checked-out package on top via
.[docs], so the rendered docs reflect the code under review rather than the code
baked into the image. The deploy step is gated to develop pushes; pull requests
build only.

Removes the now-redundant deploy-docs job from deploy-image.yml.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
On a pull request the deploy step is skipped, so the rendered HTML had nowhere
to go. Upload docs/_build as a workflow artifact (docs-html) so it can be
downloaded from the run summary and previewed locally — the practical way to
review the docs on a PR before they ever reach gh-pages.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Apply the writing skill to the four pages authored in this PR (index, about,
installation, quickstart): active voice over passive, real verbs released from
noun phrases, varied sentence rhythm, fewer em-dashes, one sentence per line in
source. No technical facts, commands, paths, or cross-references change.

about.rst drops the essay-style "The problem it solves" section — which opened
with a philosophical claim about catalogue trustworthiness — for a plain,
factual "What it does". quickstart stays deliberately light.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
@cailmdaley cailmdaley merged commit 574f4bf into develop Jun 4, 2026
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@cailmdaley cailmdaley deleted the chore/docs-narrative-pages branch June 4, 2026 19:30
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