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docs: update ecosystem inventory and syntax pointers#22

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docs: update ecosystem inventory and syntax pointers#22
seabbs-bot wants to merge 7 commits into
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docs/org-site-ecosystem-refresh

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This is entirely from an agent so do not review until I have pinged for review as I will do a first pass

Sam asked for this org-site update after several packages moved:
DistributionsInference.jl became the inference home, ComposedDistributions
gained uncertain(tree, ...)/update(tree, table) and leaf-level
truncated()/censored() support, and a couple of docs links had drifted
from what is actually deployed.

Ecosystem inventory

  • Add DistributionsInference.jl to packages/index.qmd. It has no GitHub
    Pages deployment yet (the Pages API 404s, confirmed just now), so it links
    its GitHub repo rather than a docs subdomain, per the current convention
    for undeployed packages.
  • Refresh LoweredDistributions.jl's description: it undersold current scope
    ("nothing to install yet") when it already lowers a distribution or a
    whole composed event tree onto a phase-type chain or CTMC, across four
    backend extensions.
  • Bump ConvolvedDistributions.jl and EpiAwareADTools.jl from experimental
    to maturing — both are now registered in General (0.2.0 and 0.1.0
    respectively, per ComposedDistributions' own NEWS.md).

Syntax examples

  • The homepage and composed-distributions approach page share one hero code
    block; both now use @uncertain compose(...) with a real uncertain leaf
    (Gamma(Normal(1.2, 0.2), 3.0)) instead of a tree with nothing uncertain
    in it, matching how ComposedDistributions' own README demonstrates it.
  • The approach page's prose now documents uncertain(tree; ...) as the
    promotion verb over an existing tree, the update(tree, table) /
    update(tree, chain) split, and Distributions.jl's own truncated() and
    censored() working as ordinary leaves (correcting a mislabel that
    attributed censored() to CensoredDistributions.jl rather than
    Distributions.jl itself — they are different things).
  • Added LoweredDistributions.jl and DistributionsInference.jl to the
    approach page's "Where next" list, since it already discusses lowering
    and fitting without naming either package.

Link and architecture fixes

  • Two remaining "GitHub Discussions" mentions in faq.qmd and
    get-involved.qmd routed to the forum instead (the earlier fix in fix: route help via the forum, not disabled Discussions #21
    only touched a different page).
  • Three ConvolvedDistributions.jl links pointed at /stable/ paths that are
    not actually deployed — I checked its gh-pages branch directly and it
    only has a dev/ folder (its root index.html redirects to ./dev/,
    unlike CensoredDistributions' which redirects to ./stable/), despite
    ConvolvedDistributions being a registered package. Fixed to /dev/.
  • Conversely, four CensoredDistributions.jl tutorial links pointed at
    /dev/ when /stable/ is what's actually deployed (verified all four
    paths exist under stable/getting-started/tutorials/ on its gh-pages
    branch) — fixed to /stable/.
  • README's description of the site structure was stale
    (packages/_template.qmd and docs.qmd/EPIAWARE_DOCS no longer exist;
    the site now has one filterable packages/index.qmd and one filterable
    tutorials/index.qmd) — updated to match.

No stale "GitHub Discussions" mentions or extension-hosting architecture
claims remain anywhere else on the site (checked with a full-site grep).

All seven changed pages render cleanly with quarto render (rendered
individually rather than the full site, given a memory-tight shared host).

This was opened by a bot. Please ping @seabbs for any questions.

seabbs-bot and others added 7 commits July 18, 2026 18:22
Also refreshes LoweredDistributions.jl's description to its current
phase-type/CTMC lowering scope (it previously undersold it as "nothing
to install yet"), and bumps ConvolvedDistributions.jl and
EpiAwareADTools.jl to the maturing status pill now both are registered
in General.

Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
Demonstrate @Uncertain's natural syntax in the hero example, document
uncertain(tree, ...) as the promotion verb over an existing tree, the
update(tree, table)/update(tree, chain) split, and Distributions.jl's
own truncated()/censored() working as ordinary leaves. Add
LoweredDistributions.jl and DistributionsInference.jl to "Where next",
since the page already discusses lowering and fitting without naming
either package.

Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
Keeps the homepage's code block in step with the identical one on the
composed-distributions approach page (they have always been updated
together), so both now demonstrate the same current syntax rather than
a tree with no uncertain leaves.

Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
faq.qmd and get-involved.qmd still pointed at package GitHub
Discussions, which the earlier help-routing fix (#21) missed since it
only touched a different page. Discussions are disabled ecosystem-wide;
support routes through the epinowcast forum and package issues.

Also points EpiAwarePackageTools.jl's developer.qmd link at /dev/,
matching how every other unreleased package is linked on this site.

Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
CensoredDistributions.jl is released and its GitHub Pages deploys a
stable/ folder (verified against the gh-pages branch directly, all
four tutorial paths present), so these should not point at /dev/.

Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
packages/_template.qmd and docs.qmd/EPIAWARE_DOCS no longer exist
(packages/index.qmd is now the single filterable inventory, and
tutorials/index.qmd the single filterable tutorial listing), but the
README still described the old per-package-page structure.

Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
The brief specifically asked for distribution_params to be shown as
the chain-readback verb; the DistributionsInference bullet named
as_logdensity/as_turing but not the two readback functions.

Co-authored-by: Sam Abbott <contact@samabbott.co.uk>
@seabbs-bot

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Independent QA: MERGE-CLEAN.

A second agent re-verified this PR independently: every syntax claim (the @uncertain macro, uncertain(tree, ...), update(tree, table)/update(tree, chain), distribution_priors/distribution_params, leaf-level truncated()/censored()) was run against a clean checkout of each package's current main, and every doc link was checked against the live gh-pages state rather than assumed from registration status. One adjacent limitation in ComposedDistributions.jl turned up during that check and is being filed separately as a CD issue rather than addressed here, since it's out of scope for the site.

@seabbs — ready for your read whenever convenient. Left as draft per your preference.

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📄 Site preview built

The rendered site for this PR is available as the site-preview artifact on this run. Download it and open _site/index.html to review.

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