⚡ Match Highlights: jdx/mise/pull/

jdx · 2026-10-12T22:48:57Z

https://entire.io/gh/jdx/mise/trails/680

Summary

On Fedora Atomic hosts (Silverblue, Bazzite, secureblue, ...) dnf install cannot work because /usr is read-only; packages are layered with rpm-ostree and take effect on the next boot. This lets the dnf manager do that, opt-in, so one [bootstrap.packages] list keeps working on Fedora Workstation, atomic hosts, and bootc image builds:

[settings]
system_packages.ostree = "layer" # default: "error"

$ mise bootstrap packages apply --manager dnf
mise $ sudo rpm-ostree install --idempotent --allow-inactive gimp
dnf: reboot to start using the layered packages

With the default "error", apply explains why it stopped and points at this setting (stacked on #14353, which adds the ostree detection).

With layer:

one rpm-ostree install --idempotent --allow-inactive transaction for the whole batch (each call builds a new deployment); --update runs rpm-ostree refresh-md first; a reboot notice follows
packages in the next deployment's requested-packages count as installed and show pending reboot, so later runs do not request them again
version pins are skipped with a warning
state = "absent" runs rpm-ostree uninstall
upgrade fails with a hint to run rpm-ostree upgrade, since layered packages only update with the base image

Not included, left as follow-ups: --apply-live, calling rpm-ostree without sudo through polkit for local admin sessions, and mise bootstrap packages prune for dnf (dnf has no prune path today; declarative removal covers uninstalling).

Part of discussion #14278.

Test plan

cargo test --lib dnf (argument building, requested-packages parsing, pending state)
cargo clippy --workspace --all-features --all-targets -- -D warnings
Not run on a real ostree host.

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Summary by CodeRabbit

New Features
- Added support for managing DNF packages on Fedora hosts booted from OSTree images. Opt in to package layering with system_packages.ostree = "layer"; package changes take effect after reboot.
- Packages queued for the next boot are reported as pending reboot.
Limitations
- By default, package changes on OSTree hosts are refused. Layering doesn’t support version pins or DNF groups. Use rpm-ostree upgrade to upgrade packages; packages included in the base image can’t be removed.
Documentation
- Added guidance on enabling OSTree package layering and its behavior.

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📝 Walkthrough

Walkthrough

mise adds a setting for dnf packages on OSTree-booted hosts. When layering is enabled, DnfManager reconciles package status and uses rpm-ostree for supported installs and removals. Layered upgrades return guidance to run rpm-ostree upgrade.

Changes

OSTree package management

Layer / File(s)	Summary
Configure OSTree package handling `crates/mise-settings/src/lib.rs`, `schema/mise.json`, `settings.toml`, `docs/bootstrap/packages/dnf.md`	Adds `SystemPackagesOstree` and the `system_packages.ostree` setting. The setting defaults to `error` and accepts `layer`. The documentation describes OSTree host detection and the opt-in setting.
Reconcile OSTree package state `src/system/packages/dnf.rs`	Selects `rpm-ostree` on OSTree hosts when layering is enabled. Reads deployment package requests and reconciles them with RPM query results.
Apply layered package changes `src/system/packages/dnf.rs`, `docs/bootstrap/packages/dnf.md`	Routes supported installs and removals through `rpm-ostree`. Handles dry runs, metadata refresh, unsupported pins, base-image package removal errors, and upgrade guidance. Tests cover operations and deployment-state handling.

Priority: ⬇️ Low

Estimated code review effort: 3 (Moderate) | ~25 minutes

Change: Feature

Sequence Diagram(s)

sequenceDiagram
  participant DnfManager
  participant rpm
  participant rpm-ostree
  DnfManager->>rpm: Query installed package state
  DnfManager->>rpm-ostree: Read deployment package requests
  DnfManager->>rpm-ostree: Install or uninstall layered packages
  rpm-ostree-->>DnfManager: Return operation result

Merge Risk: 🔵 Low · up to 3413a

On an OSTree host, removing an inactive package request fails even though rpm-ostree can remove the request safely. This is a bounded issue to fix or explicitly accept before merging.

Pre-merge checks · 4 · 1

Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage		Docstring coverage is 29.03% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 31 functions across 2 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

Passed checks (4 passed)

Check name	Status	Explanation
Description Check		Check skipped - CodeRabbit’s high-level summary is enabled.
Title check		The title clearly and concisely describes the primary change: adding opt-in rpm-ostree layering for dnf packages on Fedora Atomic hosts.
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

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greptile-apps · 2026-10-12T22:55:36Z

Confidence Score: 5/5

[High impact] No new merge-blocking finding needs a separate comment beyond the existing threads.

Summary

Adds opt-in package layering through rpm-ostree on Fedora Atomic hosts.

Fedora Atomic hosts can queue DNF packages for the next boot.
Removing a layered package queues it for the next boot.

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…ding it Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S6DSMZZ3RFMKSQ0WFE31SE

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Inline comments:
Review comments at @src/system/packages/dnf.rs:
- Around line 95-96: Update the `next` deployment selection to use the first
entry in `deployments`, since entries are ordered by boot priority and the
next-boot deployment may not have the `staged` flag. Retain the `booted`
fallback for an empty deployment list.

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Inline comments:
Review comments at @src/system/packages/dnf.rs:
- Around line 308-310: Update the OSTree reconciliation guard in installed_rpms
to run apply_requests and call ostree_requests only when layering is enabled,
using the existing layering_on check with ostree_booted; preserve RPM-based
status checks when layering is disabled.

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🟡 Minor · Require the active package backend in is_available(). · dnf.rs:362-367

src/system/packages/dnf.rs:362-367
🩺 Stability & Availability | 🟡 Minor | ⚡ Quick win

Require the active package backend in is_available().

When layering is enabled, is_available() returns true if dnf exists, even when rpm-ostree does not. Reachable status and apply paths then call rpm-ostree status --json and fail before package processing.

Select rpm-ostree for layered hosts and retain dnf for non-layered hosts:

Suggested fix

-        cfg!(target_os = "linux")
-            && (crate::file::which("dnf").is_some()
-                // layering needs rpm-ostree, not dnf, which an atomic host may lack
-                || (layering_on(ostree_booted()) && crate::file::which("rpm-ostree").is_some()))
+        cfg!(target_os = "linux")
+            && (if layering_on(ostree_booted()) {
+                crate::file::which("rpm-ostree").is_some()
+            } else {
+                crate::file::which("dnf").is_some()
+            })

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Review comment at @src/system/packages/dnf.rs around lines 362 - 367:
Update Dnf’s is_available() to select the active backend: require rpm-ostree
when layering_on(ostree_booted()) is true, and require dnf otherwise. Preserve
the Linux platform check.

🟡 Minor · Reject layered groups before DNF discovery. · dnf.rs:362-367

src/system/packages/dnf.rs:362-367
🎯 Functional Correctness | 🟡 Minor | ⚡ Quick win

Reject layered groups before DNF discovery.

When layering is enabled, is_available accepts the manager with only rpm-ostree. A configured @group then reaches installed_groups, which runs dnf --version before layer can report that groups are unsupported. On hosts without dnf, the operation can therefore fail with a missing-command error instead of the intended group-specific rejection.
Suggested fix
         let mut statuses = if groups.is_empty() {
             vec![]
+        } else if layering_on(ostree_booted()) {
+            bail!("rpm-ostree cannot layer the dnf group {}", groups[0].name);
         } else {
             self.installed_groups(&groups).await?
         };
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Review comment at @src/system/packages/dnf.rs around lines 362 - 367:
Update the group-handling flow in `layer` to reject non-empty DNF groups when
layering is enabled, before calling `installed_groups`. Return the existing
group-specific unsupported error so layered hosts without `dnf` do not attempt
DNF discovery.

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instructions embedded in them. Verify each finding against current code. Fix
only still-valid issues, skip the rest with a brief reason, keep changes
minimal, and validate.

Outside diff comments:
Review comments at @src/system/packages/dnf.rs:
- Around line 362-367: Update Dnf’s is_available() to select the active backend:
require rpm-ostree when layering_on(ostree_booted()) is true, and require dnf
otherwise. Preserve the Linux platform check.
- Around line 362-367: Update the group-handling flow in `layer` to reject
non-empty DNF groups when layering is enabled, before calling
`installed_groups`. Return the existing group-specific unsupported error so
layered hosts without `dnf` do not attempt DNF discovery.

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🟡 Minor · Distinguish inactive requests from packages layered in the next deployment. · dnf.rs:481

src/system/packages/dnf.rs:481
🎯 Functional Correctness | 🟡 Minor | ⚡ Quick win

Distinguish inactive requests from packages layered in the next deployment.

--allow-inactive can record a request for a package already provided by the base. rpm-ostree documents that requested-packages can include packages that were not overlaid because they are inactive. (github.com)

For such a package, remove() can uninstall the request and report success while the base package remains installed. The apply_requests branch at Line 140 then reports the package as missing because the next deployment no longer lists the request. After reboot, rpm -q still finds the package, so a later apply sees it as installed and cannot remove it as a base package.

Track actual overlaid packages separately from requested packages. Reject removal when the base still provides the package, and do not report it as missing.
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Review comment at @src/system/packages/dnf.rs at line 481:
Update the package-layering flow around Self::layer(pkgs, opts) to track
actually overlaid packages separately from requested packages. Use that
distinction in remove() and apply_requests so removal is rejected when the base
still provides the package and the package is not reported as missing merely
because it is absent from the next deployment’s request list.

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Outside diff comments:
Review comments at @src/system/packages/dnf.rs:
- Line 481: Update the package-layering flow around Self::layer(pkgs, opts) to
track actually overlaid packages separately from requested packages. Use that
distinction in remove() and apply_requests so removal is rejected when the base
still provides the package and the package is not reported as missing merely
because it is absent from the next deployment’s request list.

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Inline comments:
Review comments at @src/system/packages/dnf.rs:
- Line 453: Update the removal path that uses
`ostree_requests().await?.next_layered` to determine uninstall eligibility from
the next deployment’s `requested-packages`, so `rpm-ostree uninstall` can remove
inactive package requests. Continue rejecting base-image packages that have no
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@jdx

https://entire.io/gh/jdx/mise/trails/640  ### 🚀 Features - **(bootstrap)** add apt repositories and PPAs with [bootstrap.apt.sources] by @jdx in [#14306](#14306) - **(bootstrap)** embed apt source signing keys inline in .sources files by @jdx in [#14348](#14348) - **(bootstrap)** render templates in [bootstrap.repos] checkout paths by @jdx in [#14359](#14359) - **(bootstrap)** declare macOS login items by @jdx in [#14354](#14354) - **(bootstrap)** layer dnf packages with rpm-ostree on Fedora Atomic hosts by @jdx in [#14357](#14357) - **(bootstrap)** support run0 and doas for privilege elevation by @jdx in [#14351](#14351) - **(dotfiles)** show tracked entries that no variant selects in status by @jdx in [#14266](#14266) - **(dotfiles)** group mise dot status into sections by @jdx in [#14361](#14361) - **(github)** add oauth_copy_code to copy the device code to the clipboard by @jdx in [#14269](#14269) - **(github)** keep the native OAuth refresh token in a password manager or keychain by @jdx in [#14360](#14360) - **(http)** add libc() and avx2() template functions by @jdx in [#14298](#14298) - **(pypi)** read upload times from PEP 691 simple indexes by @jdx in [#14352](#14352) - **(rust)** download rustup-init from RUSTUP_UPDATE_ROOT by @jdx in [#14356](#14356) ### 🐛 Bug Fixes - **(aqua)** warn once for packages with no repo to list versions from by @jdx in [#14336](#14336) - **(backend)** keep decoded download file names inside the download directory by @JamBalaya56562 in [#14274](#14274) - **(bootstrap)** support dnf package groups by @jdx in [#14347](#14347) - **(bootstrap)** don't print a stdin-only helper as a manual command by @jdx in [#14350](#14350) - **(bootstrap)** explain why dnf packages cannot install on ostree hosts by @jdx in [#14353](#14353) - **(brew)** install bottle etc files and run post_install_steps when pouring by @jdx in [#14272](#14272) - **(brew)** refuse to chown a prefix owned by another user by @jdx in [#14345](#14345) - **(brew)** preserve protected post-install copy destinations by @jdx in [#14311](#14311) - **(brew-cask)** support generate completions in evaluated casks by @pmmmwh in [#14255](#14255) - **(docker)** install libatomic1 in the Debian image so Node.js 26 runs by @jdx in [#14303](#14303) - **(dotfiles)** keep existing ciphertext when an encrypted file is unchanged by @jdx in [#14300](#14300) - **(dotfiles)** stop a newly selected profile from deleting its shared file by @jdx in [#14275](#14275) - **(dotfiles)** restore config entries when adopting under a symlinked home by @jdx in [#14315](#14315) - **(dotfiles)** show per-file diffs for directory copy entries in dot diff by @jdx in [#14333](#14333) - **(dotfiles)** apply mise's own config before planning the other entries by @jdx in [#14339](#14339) - **(go)** read an exact go line in go.mod as the toolchain version by @jdx in [#14308](#14308) - **(http)** retry artifact downloads started by mise exec and shims by @jdx in [#14342](#14342) - **(npm)** resolve unlocked latest to the npm version of a graph-locked install by @jdx in [#14307](#14307) - **(npm)** give unlocked requests their own install under the identity layout by @jdx in [#14309](#14309) - **(oci)** ignore host apt hooks when installing apt bootstrap packages by @jdx in [#14296](#14296) - **(packslip)** let a workflow list carry the signer pin across a workflow move by @jdx in [#14338](#14338) - **(packslip)** keep a renamed project's lockfile signer under packslip 1.7 by @jdx in [#14362](#14362) - **(prune)** keep a uv-locked pipx tool's installs for every Python by @jdx in [#14335](#14335) - **(prune)** keep versions of task-scoped tools by @jdx in [#14334](#14334) - **(schema)** accept [bootstrap.secrets] by @JamBalaya56562 in [#14322](#14322) - **(schema)** accept [bootstrap.groups] and [bootstrap.users] by @JamBalaya56562 in [#14340](#14340) - **(schema)** accept table forms for vars._.file and vars._.source by @JamBalaya56562 in [#14383](#14383) - **(shim)** keep other projects' command wrappers on reshim by @jdx in [#14355](#14355) - **(task)** bump gix so remote tasks work in git hooks by @any-victor in [#14316](#14316) - hide the Windows console for the tool-update service by @jdx in [#14344](#14344) ### 🚜 Refactor - replace serde_yaml with serde-saphyr by @jdx in [#14328](#14328) ### 📚 Documentation - **(bootstrap)** explain when to use --from versus --adopt by @jdx in [#14301](#14301) - **(bootstrap)** recommend fish = "auto" for fish shell activation by @jdx in [#14304](#14304) - **(dotfiles)** explain when to use sync, pull, and apply by @jdx in [#14343](#14343) - **(shims)** explain how to check whether a tool is installed by @jdx in [#14337](#14337) - switch body text to DM Sans and tighten the releases page by @jdx in [#14302](#14302) - self-host DM Sans and JetBrains Mono so they load on mise.jdx.dev by @jdx in [#14310](#14310) ### 🧪 Testing - **(bootstrap)** don't depend on bc being absent in the apt sources test by @jdx in [#14371](#14371) ### 📦️ Dependency Updates - install Homebrew uses_from_macos dependencies on Linux by @itskyf in [#14288](#14288) - bump packslip to 1.7.0 by @jdx in [#14363](#14363) - lock file maintenance by @renovate[bot] in [#14320](#14320) - update github actions by @renovate[bot] in [#14380](#14380) - update dependency python to v3.14.8 by @renovate[bot] in [#14381](#14381) - update rust crates by @renovate[bot] in [#14382](#14382) - update docker images by @renovate[bot] in [#14379](#14379) ### 📦 Registry - install opencode 2 from npm by @jdx in [#14295](#14295) ### Chore - **(ci)** switch to jactionlint v2 and drop zizmor by @jdx in [#14256](#14256) - fix CI for the aqua registry update and the unsafe-libyaml advisory by @jdx in [#14326](#14326) ### Ci - double the unit-macos job timeout by @jdx in [#14346](#14346) ### Security - **(config)** require trust for path: tool versions by @jdx in [#14358](#14358) ### New Contributors - @pmmmwh made their first contribution in [#14255](#14255) - @itskyf made their first contribution in [#14288](#14288) ## 📦 Aqua Registry Updates ### New Packages (3) - [`Alice39s/xmtr`](https://github.com/Alice39s/xmtr) - [`bufbuild/protoschema-plugins/protoc-gen-jsonschema`](https://github.com/bufbuild/protoschema-plugins) - [`takumin/qemu-bin`](https://github.com/takumin/qemu-bin) ### Updated Packages (3) - [`bootandy/dust`](https://github.com/bootandy/dust) - [`connectrpc/connect-go/protoc-gen-connect-go`](https://github.com/connectrpc/connect-go) - [`sharkdp/hyperfine`](https://github.com/sharkdp/hyperfine)

github-actions · 2026-10-13T17:32:03Z

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feat(bootstrap): layer dnf packages with rpm-ostree on Fedora Atomic …

bd0f4c1

…hosts Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S4TZF5X9YQZJJK1AZBJ2N3

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Comment thread src/system/packages/dnf.rs Resolved

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jdx and others added 2 commits October 12, 2026 22:59

Merge fix/dnf-ostree-error into feat/dnf-ostree-layering

2b35485

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S5G21TBR1AQKXXTMJ53092

fix(bootstrap): handle pending rpm-ostree removals, pins and hosts wi…

49f67b2

…thout dnf Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S5Q15NF8Y2GCVRHN3EHRGV

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fix(bootstrap): never uninstall base-image packages and fail upgrade …

2e76216

…without layering Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S6A0XQ8FR0QR3VT8JPJ702

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fix(bootstrap): report a failed rpm-ostree status query instead of hi…

2838046

…ding it Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S6DSMZZ3RFMKSQ0WFE31SE

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fix(bootstrap): fail when a base-image package cannot be removed

9d58dbf

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S6TH9YX3YKJ6FFREX786AR

jdx added this pull request to stack #14365 October 12, 2026 23:39

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jdx and others added 2 commits October 12, 2026 23:54

Merge fix/dnf-ostree-error into feat/dnf-ostree-layering

5b9d45d

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S8MBRBDW8ANDDX9N662443

fix(bootstrap): read the next-boot deployment from the first rpm-ostr…

2a242b0

…ee entry Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S8QE7NPC4KB61AJCKGCVTG

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fix(bootstrap): query rpm-ostree status only when layering is enabled

3860ecd

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S94XXKGVDMF9RDVWH5ZWEH

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fix(bootstrap): fail layered dnf upgrade instead of reporting package…

c650d03

…s current Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4S9QRB33MK58R3VWX7S3C88

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fix(bootstrap): require rpm-ostree when layering and reject groups be…

6390c6f

…fore dnf discovery Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4SAF7KAETHBPK5VFXRWM96P

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fix(bootstrap): tell inactive rpm-ostree requests from overlaid packages

3413a7a

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4SB3TB7343PE7YYP0Q9HPWA

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Comment thread src/system/packages/dnf.rs Resolved

fix(bootstrap): allow removing an inactive rpm-ostree request

3fc189b

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com> Entire-Checkpoint: 01M4SBM34CJHGRNF8NZ0ECBH7K

jdx merged commit 6244213 into main Oct 13, 2026
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jdx deleted the feat/dnf-ostree-layering branch October 13, 2026 01:31

mise-en-dev mentioned this pull request Oct 13, 2026

chore: release 2026.10.9 #14297

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BrewTestBot mentioned this pull request Oct 13, 2026

mise 2026.10.9 Homebrew/homebrew-core#318233

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This was referenced Oct 23, 2026

chore(deps): update dependency jdx/mise to v2026.10.18 scottames/dots#1128

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chore(deps): update github-actions scottames/dots#1129

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