[dependabot]

Updates the requirements on EpiAwareADTools and EpiAwarePackageTools to permit the latest version.
Updates EpiAwareADTools to 0.2.0

Release notes

Sourced from EpiAwareADTools's releases.

v0.2.0

EpiAwareADTools v0.2.0

Diff since v0.1.2

This is a breaking release.

• Fixed logccdf_ad_safe(::Gamma) returning -Inf in the far right tail, where the stock (non-differentiable) logccdf stays finite; the same issue affected SurvivalDistributions.GeneralizedGamma. A new log-space Gamma survival primitive fixes both, with AD rules across every backend.
• Fixed _beta_cdf's continued-fraction evaluator returning NaN for widely disparate shape parameters near the boundary of x, and improved its accuracy by raising the default term count.
• Fixed primal_distribution throwing a MethodError on Truncated and Censored distributions; it now rebuilds them recursively through the public truncated/censored constructors. This also unblocks EpiAware/CensoredDistributions.jl.
• Added fixed_draw and ad_eltype, a reparameterisation-trick helper pair mirroring the existing primal/primal_distribution tape-strip helpers.
• Pointed the release notes docs page at GitHub releases instead of NEWS.md.

Merged pull requests:

• ci(deps): bump the github-actions group with 9 updates (#59) (@​dependabot[bot])
• fix: primal_distribution rebuilds Truncated/Censored via public constructors (#60) (@​seabbs-bot)
• fix: logccdf_ad_safe underflows in the Gamma far right tail (#61) (@​seabbs-bot)
• fix: rescale continued-fraction accumulators to stop beta CDF NaN (#62) (@​seabbs-bot)
• feat: reparameterisation-trick helpers (fixed_draw/ad_eltype) (#63) (@​seabbs-bot)
• docs: point the release notes page at GitHub releases (#64) (@​seabbs-bot)
• chore!: sync with EpiAwarePackageTools main and raise the Julia floor to 1.11 (#69) (@​seabbs-bot)
• ci(deps): bump the github-actions group with 11 updates (#70) (@​dependabot[bot])
• chore(deps): bump the julia-isolated group across 2 directories with 15 updates (#71) (@​dependabot[bot])

Closed issues:

• Widen the AD-safe function family to more continuous families and publish per-family coverage (#36)
• Reparameterisation-trick helpers for differentiating through a stochastic computation (#38)
• _beta_cdf continued fraction overflows to NaN for disparate shapes near the x boundary (#42)
• logccdf_ad_safe loses the far right tail: log1p(-F) underflows where the stock evaluator does not (#47)
• Point the release-notes docs page at GitHub Releases (#53)
• primal_distribution has no method for Truncated (#57)
• primal_distribution(::Truncated) reconstructs via stale 3-float Truncated(...) constructor (MethodError) (#58)

Commits

• c164a87 chore(deps): bump the julia-isolated group across 2 directories with 15 updat...
• 2ce680c ci(deps): bump the github-actions group with 11 updates (#70)
• 1e0bb97 chore!: sync with EpiAwarePackageTools main and raise the Julia floor to 1.11...
• e20662b fix: primal_distribution rebuilds Truncated/Censored via public constructors ...
• f374df0 docs: add tool page and charter row for fixed_draw/ad_eltype (#38)
• 43f3a68 test: cover fixed_draw/ad_eltype across the AD backend matrix (#38)
• 9ff7062 feat: add fixed_draw/ad_eltype reparameterisation-trick pair (#38)
• 53dd4bc test: add failing unit coverage for fixed_draw/ad_eltype (#38)
• 40f1328 docs: drop retired NEWS.md convention from release process page
• f707901 docs: point the release notes page at GitHub releases
• Additional commits viewable in compare view

Updates EpiAwarePackageTools to 0.4.0

Release notes

Sourced from EpiAwarePackageTools's releases.

v0.4.0

EpiAwarePackageTools v0.4.0

Diff since v0.3.0

This is a breaking release.

Release notes (draft)

Breaking

• The formatter is Runic, not JuliaFormatter. .JuliaFormatter.toml is a retired path, so a sync deletes it. The isolated test/formatter environment pins Runic exactly, kept in step with the .pre-commit-config.yaml hook revision.
• docs/pages.jl is now a managed base with extension points, regenerated on every sync. A package adds nav through PACKAGE_TUTORIALS, PACKAGE_SECTIONS, DEVELOPMENT_EXTEND_PAGE and GETTING_STARTED_FAQ in the package-owned docs/docs_config.jl. A bespoke pages.jl without the managed header is preserved and warned about rather than clobbered.
• The AD-backends tutorial is retired. Its content is folded into the AD-comparison benchmark page, which now carries the ad-backends anchor so existing @ref links across the org keep resolving. A sync deletes the page and warns while a package still registers it.

Added

• ReverseDiff (compiled) joins the managed AD backends, so the matrix, codecov flags, README badge row and scenario seeds all cover seven backends.
• run_selected, a filtered AD scenario/backend runner, so one suspect combination can be checked without the full suite.
• Per-tutorial documentation environments. A heavy tutorial can build against its own environment via TUTORIAL_ENVIRONMENTS, for a dependency that cannot co-resolve with the rest of the docs environment. Dependabot watches each one.
• Agent files are AGENTS.md plus a CLAUDE.md pointer, both linking the standards docs rather than copying them, so there is one copy that cannot drift. The managed block is a single marker line.

Fixed

• An AD backend with no test item no longer reports green. Adding a backend to the kit reached an adopter's CI, badges and coverage flags but not their write-once test seeds, so the new job ran zero tests, passed, and uploaded an empty coverage flag behind a public badge. update now names each unbacked tag, and a tag filter matching nothing is an error.
• Enzyme codecov flags name the Enzyme extension, not the whole ext/ directory. The directory claim charged those jobs for every other extension: measured as -17% on a package with seven.
• The generated Extensions nav entry gets a trailing comma, so a package with [extensions] no longer fails its own formatting check and then reverts on the next sync, looping forever.
• update reports package-owned docs describing a retired standard. A sync converges the managed files and said nothing about the package's own prose, so a contributing guide could keep naming a tool the standard had moved off.
• README prose checks no longer misread markup and abbreviations, and the extension-by-dispatch deviation inventory is published in the standards.
• Assorted infrastructure repairs: the release-nudge seed ref, docs-environment dependency warnings, world-age-guarded docs_config.jl reads, and the ExplicitImports floor.

Internal

• Every .jl template is asserted to reach the Runic sweep, so a template gated on an unswept flag combination cannot go unchecked silently, and a failure names the template rather than a temp path.

Merged pull requests:

• feat(scaffold): ship the org coding standards as a managed CLAUDE.md block (#370) (@​seabbs-bot)
• ci(deps): bump the github-actions group with 10 updates (#383) (@​dependabot[bot])
• ci: migrate the managed standard from JuliaFormatter to Runic (#387) (@​seabbs-bot)
• feat: add run_selected, a filtered AD scenario/backend runner (#389) (@​seabbs-bot)
• feat: add ReverseDiff (compiled) to the managed AD backends (#390) (@​seabbs-bot)
• ci(deps): bump the github-actions group with 9 updates (#392) (@​dependabot[bot])
• feat: add run_selected, a filtered AD scenario/backend runner (#394) (@​seabbs-bot)
• feat: docs/pages.jl becomes a managed base with extension points (#397) (@​seabbs-bot)
• fix: raise the ExplicitImports floor to 1.6 (#401) (@​seabbs-bot)
• fix: strip trailing whitespace from test/scaffold.jl (#402) (@​seabbs-bot)
• docs(standards): publish dispatch deviation inventory; fix(taskfile): thread docs builds (#403) (@​seabbs-bot)
• fix: stop the README prose checks misreading markup and abbreviations (#404) (@​seabbs-bot)
• fix: repin the release-nudge seed ref to a commit that resolves (#405) (@​seabbs-bot)

... (truncated)

Commits

• See full diff in compare view

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[github-actions]

Try this Pull Request!

Option 1: Julia Package Manager

Open Julia and type:

import Pkg
Pkg.activate(temp=true)
Pkg.add(url="https://github.com/EpiAware/ModifiedDistributions.jl", rev="dependabot/julia/julia-e2c8a9b1c7")
using ModifiedDistributions

Option 2: Local Checkout

If you have the repo locally:

git checkout dependabot/julia/julia-e2c8a9b1c7
julia --project=. -e "using Pkg; Pkg.instantiate()"

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

Flag	Coverage Δ
ad-enzyme-forward	40.80% <ø> (+13.66%)	⬆️
ad-enzyme-reverse	40.80% <ø> (+13.66%)	⬆️
ad-forwarddiff	34.74% <ø> (+18.57%)	⬆️
ad-mooncake-forward	34.74% <ø> (+18.57%)	⬆️
ad-mooncake-reverse	34.74% <ø> (+18.57%)	⬆️
ad-reversediff	34.74% <ø> (+18.57%)	⬆️
unit	97.42% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.
see 1 file with indirect coverage changes

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[github-actions]

📖 Documentation preview is ready!

View the docs for this PR at: https://EpiAware.github.io/ModifiedDistributions.jl/previews/PR157/

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[dependabot]

Looks like these dependencies are updatable in another way, so this is no longer needed.